delete old javadoc to update

author pvtroshin <pvtroshin@e3abac25-378b-4346-85de-24260fe3988d>

Fri, 12 Aug 2011 13:02:22 +0000 (13:02 +0000)

committer pvtroshin <pvtroshin@e3abac25-378b-4346-85de-24260fe3988d>

Fri, 12 Aug 2011 13:02:22 +0000 (13:02 +0000)
author pvtroshin <pvtroshin@e3abac25-378b-4346-85de-24260fe3988d>
Fri, 12 Aug 2011 13:02:22 +0000 (13:02 +0000)
committer pvtroshin <pvtroshin@e3abac25-378b-4346-85de-24260fe3988d>
Fri, 12 Aug 2011 13:02:22 +0000 (13:02 +0000)
diff --git a/website/full_javadoc/allclasses-frame.html b/website/full_javadoc/allclasses-frame.html

deleted file mode 100644 (file)

index 16054f8..0000000
--- a/website/full_javadoc/allclasses-frame.html
+++ /dev/null
@@ -1,309 +0,0 @@
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-<BR>\r
-<A HREF="compbio/engine/cluster/dundee/_QueueConstraints.html" title="class in compbio.engine.cluster.dundee">_QueueConstraints</A>\r
-<BR>\r
-<A HREF="compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>\r
-<BR>\r
-<A HREF="compbio/engine/local/_TrackingExecutor.html" title="class in compbio.engine.local">_TrackingExecutor</A>\r
-<BR>\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-\r
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-</HTML>\r
diff --git a/website/full_javadoc/compbio/data/_structure/JnetAnnotation.html b/website/full_javadoc/compbio/data/_structure/JnetAnnotation.html

deleted file mode 100644 (file)

index 7afbc88..0000000
--- a/website/full_javadoc/compbio/data/_structure/JnetAnnotation.html
+++ /dev/null
@@ -1,418 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-JnetAnnotation\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="JnetAnnotation";\r
-    }\r
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-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
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-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/JnetAnnotation.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV CLASS&nbsp;\r
-&nbsp;<A HREF="../../../compbio/data/_structure/JpredAnnotation.html" title="enum in compbio.data._structure"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/data/_structure/JnetAnnotation.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="JnetAnnotation.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;<A HREF="#enum_constant_summary">ENUM CONSTANTS</A>&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;<A HREF="#enum_constant_detail">ENUM CONSTANTS</A>&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.data._structure</FONT>\r
-<BR>\r
-Enum JnetAnnotation</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../../resources/inherit.gif" ALT="extended by ">java.lang.Enum&lt;<A HREF="../../../compbio/data/_structure/JnetAnnotation.html" title="enum in compbio.data._structure">JnetAnnotation</A>&gt;\r
-      <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.data._structure.JnetAnnotation</B>\r
-</PRE>\r
-<DL>\r
-<DT><B>All Implemented Interfaces:</B> <DD>java.io.Serializable, java.lang.Comparable&lt;<A HREF="../../../compbio/data/_structure/JnetAnnotation.html" title="enum in compbio.data._structure">JnetAnnotation</A>&gt;</DD>\r
-</DL>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public enum <B>JnetAnnotation</B><DT>extends java.lang.Enum&lt;<A HREF="../../../compbio/data/_structure/JnetAnnotation.html" title="enum in compbio.data._structure">JnetAnnotation</A>&gt;</DL>\r
-</PRE>\r
-\r
-<P>\r
-<HR>\r
-\r
-<P>\r
-<!-- =========== ENUM CONSTANT SUMMARY =========== -->\r
-\r
-<A NAME="enum_constant_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Enum Constant Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/data/_structure/JnetAnnotation.html#JNETCONF">JNETCONF</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/data/_structure/JnetAnnotation.html#JNETHMM">JNETHMM</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/data/_structure/JnetAnnotation.html#jnetpred">jnetpred</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/data/_structure/JnetAnnotation.html#JNETPROPE">JNETPROPE</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/data/_structure/JnetAnnotation.html#JNETPROPH">JNETPROPH</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/data/_structure/JnetAnnotation.html#JNETSOL0">JNETSOL0</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/data/_structure/JnetAnnotation.html#JNETSOL25">JNETSOL25</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/data/_structure/JnetAnnotation.html#JNETSOL5">JNETSOL5</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../compbio/data/_structure/JnetAnnotation.html" title="enum in compbio.data._structure">JnetAnnotation</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/_structure/JnetAnnotation.html#valueOf(java.lang.String)">valueOf</A></B>(java.lang.String&nbsp;name)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Returns the enum constant of this type with the specified name.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../compbio/data/_structure/JnetAnnotation.html" title="enum in compbio.data._structure">JnetAnnotation</A>[]</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/_structure/JnetAnnotation.html#values()">values</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Returns an array containing the constants of this enum type, in
-the order they are declared.</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Enum"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Enum</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>compareTo, equals, getDeclaringClass, hashCode, name, ordinal, toString, valueOf</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>getClass, notify, notifyAll, wait, wait, wait</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ============ ENUM CONSTANT DETAIL =========== -->\r
-\r
-<A NAME="enum_constant_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Enum Constant Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="jnetpred"><!-- --></A><H3>\r
-jnetpred</H3>\r
-<PRE>\r
-public static final <A HREF="../../../compbio/data/_structure/JnetAnnotation.html" title="enum in compbio.data._structure">JnetAnnotation</A> <B>jnetpred</B></PRE>\r
-<DL>\r
-<DL>\r
-</DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="JNETCONF"><!-- --></A><H3>\r
-JNETCONF</H3>\r
-<PRE>\r
-public static final <A HREF="../../../compbio/data/_structure/JnetAnnotation.html" title="enum in compbio.data._structure">JnetAnnotation</A> <B>JNETCONF</B></PRE>\r
-<DL>\r
-<DL>\r
-</DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="JNETSOL25"><!-- --></A><H3>\r
-JNETSOL25</H3>\r
-<PRE>\r
-public static final <A HREF="../../../compbio/data/_structure/JnetAnnotation.html" title="enum in compbio.data._structure">JnetAnnotation</A> <B>JNETSOL25</B></PRE>\r
-<DL>\r
-<DL>\r
-</DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="JNETSOL5"><!-- --></A><H3>\r
-JNETSOL5</H3>\r
-<PRE>\r
-public static final <A HREF="../../../compbio/data/_structure/JnetAnnotation.html" title="enum in compbio.data._structure">JnetAnnotation</A> <B>JNETSOL5</B></PRE>\r
-<DL>\r
-<DL>\r
-</DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="JNETSOL0"><!-- --></A><H3>\r
-JNETSOL0</H3>\r
-<PRE>\r
-public static final <A HREF="../../../compbio/data/_structure/JnetAnnotation.html" title="enum in compbio.data._structure">JnetAnnotation</A> <B>JNETSOL0</B></PRE>\r
-<DL>\r
-<DL>\r
-</DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="JNETHMM"><!-- --></A><H3>\r
-JNETHMM</H3>\r
-<PRE>\r
-public static final <A HREF="../../../compbio/data/_structure/JnetAnnotation.html" title="enum in compbio.data._structure">JnetAnnotation</A> <B>JNETHMM</B></PRE>\r
-<DL>\r
-<DL>\r
-</DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="JNETPROPH"><!-- --></A><H3>\r
-JNETPROPH</H3>\r
-<PRE>\r
-public static final <A HREF="../../../compbio/data/_structure/JnetAnnotation.html" title="enum in compbio.data._structure">JnetAnnotation</A> <B>JNETPROPH</B></PRE>\r
-<DL>\r
-<DL>\r
-</DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="JNETPROPE"><!-- --></A><H3>\r
-JNETPROPE</H3>\r
-<PRE>\r
-public static final <A HREF="../../../compbio/data/_structure/JnetAnnotation.html" title="enum in compbio.data._structure">JnetAnnotation</A> <B>JNETPROPE</B></PRE>\r
-<DL>\r
-<DL>\r
-</DL>\r
-</DL>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
-<A NAME="method_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="values()"><!-- --></A><H3>\r
-values</H3>\r
-<PRE>\r
-public static <A HREF="../../../compbio/data/_structure/JnetAnnotation.html" title="enum in compbio.data._structure">JnetAnnotation</A>[] <B>values</B>()</PRE>\r
-<DL>\r
-<DD>Returns an array containing the constants of this enum type, in
-the order they are declared.  This method may be used to iterate
-over the constants as follows:
-<pre>
-for (JnetAnnotation c : JnetAnnotation.values())
-&nbsp;   System.out.println(c);
-</pre>\r
-<P>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>an array containing the constants of this enum type, in
-the order they are declared</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="valueOf(java.lang.String)"><!-- --></A><H3>\r
-valueOf</H3>\r
-<PRE>\r
-public static <A HREF="../../../compbio/data/_structure/JnetAnnotation.html" title="enum in compbio.data._structure">JnetAnnotation</A> <B>valueOf</B>(java.lang.String&nbsp;name)</PRE>\r
-<DL>\r
-<DD>Returns the enum constant of this type with the specified name.
-The string must match <I>exactly</I> an identifier used to declare an
-enum constant in this type.  (Extraneous whitespace characters are 
-not permitted.)\r
-<P>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>name</CODE> - the name of the enum constant to be returned.\r
-<DT><B>Returns:</B><DD>the enum constant with the specified name\r
-<DT><B>Throws:</B>\r
-<DD><CODE>java.lang.IllegalArgumentException</CODE> - if this enum type has no constant
-with the specified name\r
-<DD><CODE>java.lang.NullPointerException</CODE> - if the argument is null</DL>\r
-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
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-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/JnetAnnotation.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
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-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV CLASS&nbsp;\r
-&nbsp;<A HREF="../../../compbio/data/_structure/JpredAnnotation.html" title="enum in compbio.data._structure"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/data/_structure/JnetAnnotation.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
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-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
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-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
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-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;<A HREF="#enum_constant_summary">ENUM CONSTANTS</A>&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;<A HREF="#enum_constant_detail">ENUM CONSTANTS</A>&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
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-\r
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diff --git a/website/full_javadoc/compbio/data/_structure/JpredAnnotation.html b/website/full_javadoc/compbio/data/_structure/JpredAnnotation.html

deleted file mode 100644 (file)

index d72000f..0000000
--- a/website/full_javadoc/compbio/data/_structure/JpredAnnotation.html
+++ /dev/null
@@ -1,418 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-JpredAnnotation\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
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-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="JpredAnnotation";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/JpredAnnotation.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/data/_structure/JnetAnnotation.html" title="enum in compbio.data._structure"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../compbio/data/_structure/JpredResult.html" title="class in compbio.data._structure"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/data/_structure/JpredAnnotation.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="JpredAnnotation.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
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-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;<A HREF="#enum_constant_summary">ENUM CONSTANTS</A>&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;<A HREF="#enum_constant_detail">ENUM CONSTANTS</A>&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.data._structure</FONT>\r
-<BR>\r
-Enum JpredAnnotation</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../../resources/inherit.gif" ALT="extended by ">java.lang.Enum&lt;<A HREF="../../../compbio/data/_structure/JpredAnnotation.html" title="enum in compbio.data._structure">JpredAnnotation</A>&gt;\r
-      <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.data._structure.JpredAnnotation</B>\r
-</PRE>\r
-<DL>\r
-<DT><B>All Implemented Interfaces:</B> <DD>java.io.Serializable, java.lang.Comparable&lt;<A HREF="../../../compbio/data/_structure/JpredAnnotation.html" title="enum in compbio.data._structure">JpredAnnotation</A>&gt;</DD>\r
-</DL>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public enum <B>JpredAnnotation</B><DT>extends java.lang.Enum&lt;<A HREF="../../../compbio/data/_structure/JpredAnnotation.html" title="enum in compbio.data._structure">JpredAnnotation</A>&gt;</DL>\r
-</PRE>\r
-\r
-<P>\r
-<HR>\r
-\r
-<P>\r
-<!-- =========== ENUM CONSTANT SUMMARY =========== -->\r
-\r
-<A NAME="enum_constant_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Enum Constant Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/data/_structure/JpredAnnotation.html#JNETCONF">JNETCONF</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/data/_structure/JpredAnnotation.html#JNETHMM">JNETHMM</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/data/_structure/JpredAnnotation.html#jnetpred">jnetpred</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/data/_structure/JpredAnnotation.html#JNETPROPE">JNETPROPE</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/data/_structure/JpredAnnotation.html#JNETPROPH">JNETPROPH</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/data/_structure/JpredAnnotation.html#JNETSOL0">JNETSOL0</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/data/_structure/JpredAnnotation.html#JNETSOL25">JNETSOL25</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/data/_structure/JpredAnnotation.html#JNETSOL5">JNETSOL5</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../compbio/data/_structure/JpredAnnotation.html" title="enum in compbio.data._structure">JpredAnnotation</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/_structure/JpredAnnotation.html#valueOf(java.lang.String)">valueOf</A></B>(java.lang.String&nbsp;name)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Returns the enum constant of this type with the specified name.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../compbio/data/_structure/JpredAnnotation.html" title="enum in compbio.data._structure">JpredAnnotation</A>[]</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/_structure/JpredAnnotation.html#values()">values</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Returns an array containing the constants of this enum type, in
-the order they are declared.</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Enum"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Enum</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>compareTo, equals, getDeclaringClass, hashCode, name, ordinal, toString, valueOf</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>getClass, notify, notifyAll, wait, wait, wait</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ============ ENUM CONSTANT DETAIL =========== -->\r
-\r
-<A NAME="enum_constant_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Enum Constant Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="jnetpred"><!-- --></A><H3>\r
-jnetpred</H3>\r
-<PRE>\r
-public static final <A HREF="../../../compbio/data/_structure/JpredAnnotation.html" title="enum in compbio.data._structure">JpredAnnotation</A> <B>jnetpred</B></PRE>\r
-<DL>\r
-<DL>\r
-</DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="JNETCONF"><!-- --></A><H3>\r
-JNETCONF</H3>\r
-<PRE>\r
-public static final <A HREF="../../../compbio/data/_structure/JpredAnnotation.html" title="enum in compbio.data._structure">JpredAnnotation</A> <B>JNETCONF</B></PRE>\r
-<DL>\r
-<DL>\r
-</DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="JNETSOL25"><!-- --></A><H3>\r
-JNETSOL25</H3>\r
-<PRE>\r
-public static final <A HREF="../../../compbio/data/_structure/JpredAnnotation.html" title="enum in compbio.data._structure">JpredAnnotation</A> <B>JNETSOL25</B></PRE>\r
-<DL>\r
-<DL>\r
-</DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="JNETSOL5"><!-- --></A><H3>\r
-JNETSOL5</H3>\r
-<PRE>\r
-public static final <A HREF="../../../compbio/data/_structure/JpredAnnotation.html" title="enum in compbio.data._structure">JpredAnnotation</A> <B>JNETSOL5</B></PRE>\r
-<DL>\r
-<DL>\r
-</DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="JNETSOL0"><!-- --></A><H3>\r
-JNETSOL0</H3>\r
-<PRE>\r
-public static final <A HREF="../../../compbio/data/_structure/JpredAnnotation.html" title="enum in compbio.data._structure">JpredAnnotation</A> <B>JNETSOL0</B></PRE>\r
-<DL>\r
-<DL>\r
-</DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="JNETHMM"><!-- --></A><H3>\r
-JNETHMM</H3>\r
-<PRE>\r
-public static final <A HREF="../../../compbio/data/_structure/JpredAnnotation.html" title="enum in compbio.data._structure">JpredAnnotation</A> <B>JNETHMM</B></PRE>\r
-<DL>\r
-<DL>\r
-</DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="JNETPROPH"><!-- --></A><H3>\r
-JNETPROPH</H3>\r
-<PRE>\r
-public static final <A HREF="../../../compbio/data/_structure/JpredAnnotation.html" title="enum in compbio.data._structure">JpredAnnotation</A> <B>JNETPROPH</B></PRE>\r
-<DL>\r
-<DL>\r
-</DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="JNETPROPE"><!-- --></A><H3>\r
-JNETPROPE</H3>\r
-<PRE>\r
-public static final <A HREF="../../../compbio/data/_structure/JpredAnnotation.html" title="enum in compbio.data._structure">JpredAnnotation</A> <B>JNETPROPE</B></PRE>\r
-<DL>\r
-<DL>\r
-</DL>\r
-</DL>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
-<A NAME="method_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="values()"><!-- --></A><H3>\r
-values</H3>\r
-<PRE>\r
-public static <A HREF="../../../compbio/data/_structure/JpredAnnotation.html" title="enum in compbio.data._structure">JpredAnnotation</A>[] <B>values</B>()</PRE>\r
-<DL>\r
-<DD>Returns an array containing the constants of this enum type, in
-the order they are declared.  This method may be used to iterate
-over the constants as follows:
-<pre>
-for (JpredAnnotation c : JpredAnnotation.values())
-&nbsp;   System.out.println(c);
-</pre>\r
-<P>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>an array containing the constants of this enum type, in
-the order they are declared</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="valueOf(java.lang.String)"><!-- --></A><H3>\r
-valueOf</H3>\r
-<PRE>\r
-public static <A HREF="../../../compbio/data/_structure/JpredAnnotation.html" title="enum in compbio.data._structure">JpredAnnotation</A> <B>valueOf</B>(java.lang.String&nbsp;name)</PRE>\r
-<DL>\r
-<DD>Returns the enum constant of this type with the specified name.
-The string must match <I>exactly</I> an identifier used to declare an
-enum constant in this type.  (Extraneous whitespace characters are 
-not permitted.)\r
-<P>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>name</CODE> - the name of the enum constant to be returned.\r
-<DT><B>Returns:</B><DD>the enum constant with the specified name\r
-<DT><B>Throws:</B>\r
-<DD><CODE>java.lang.IllegalArgumentException</CODE> - if this enum type has no constant
-with the specified name\r
-<DD><CODE>java.lang.NullPointerException</CODE> - if the argument is null</DL>\r
-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/JpredAnnotation.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/data/_structure/JnetAnnotation.html" title="enum in compbio.data._structure"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../compbio/data/_structure/JpredResult.html" title="class in compbio.data._structure"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/data/_structure/JpredAnnotation.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="JpredAnnotation.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;<A HREF="#enum_constant_summary">ENUM CONSTANTS</A>&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;<A HREF="#enum_constant_detail">ENUM CONSTANTS</A>&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/data/_structure/JpredResult.html b/website/full_javadoc/compbio/data/_structure/JpredResult.html

deleted file mode 100644 (file)

index 904c222..0000000
--- a/website/full_javadoc/compbio/data/_structure/JpredResult.html
+++ /dev/null
@@ -1,260 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-JpredResult\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="JpredResult";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/JpredResult.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/data/_structure/JpredAnnotation.html" title="enum in compbio.data._structure"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;NEXT CLASS</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/data/_structure/JpredResult.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="JpredResult.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#methods_inherited_from_class_java.lang.Object">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;METHOD</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.data._structure</FONT>\r
-<BR>\r
-Class JpredResult</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.data._structure.JpredResult</B>\r
-</PRE>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public class <B>JpredResult</B><DT>extends java.lang.Object</DL>\r
-</PRE>\r
-\r
-<P>\r
-Jnet result
- 
- jnetpred:-,H,H,H,H,H,H,H,H,H,H,H,-,-,-,-,-,-,-,-,E,E,E,-,-,-,-,-,-,-,-,-,-,-,
- -,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,H,H,H,H,H,H,H,H,H,H
- ,H,H,-,-,H,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,H,H,H,H,H,-,-,-,-,H,H,H,H,
- -,-,-,-,-,-,-,-,-,-,-,-,H,H,H,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-
- , JNETCONF:7,3,7,9,9,9,9,9,9,9,7,5,2,6,6,3,6,7,5,1,0,5,3,3,6,4,6,6,7,7,7,7,7,
- 7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,6,3,6,8,9,9,9,9,9,9,9
- 7,3,7,7,6,2,4,4,1,5,7,8,7,7,7,7,7,7,7,6,5,3,5,6,6,6,4,0,0,2,1,3,5,7,7,7,7,7,7
- , JNETSOL25:B,B,-,-,-,B,-,B,-,B,B,B,-,-,-,B,-,B,-,-,-,-,-,B,-,B,-,-,-,-,-,-,
- -,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,B,-,-,-,B,-,B,-
- , B,B,B,-,-,-,B,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,B,-,-,B,B,-,-,-,-,B,-,-,B,B,-,-
- ,B,
- JNETSOL5:-,-,-,-,-,-,B,-,-,-,-,-,-,-,-,-,B,B,B,B,-,-,-,B,-,-,-,-,-,-,-,-,-
- ,-,-
- JNETSOL0:-,-,-,-,-,-,B,-,-,B,-,B,-,-,-,-,-,-,-,-,B,-,-,-,-,-,-,-,-,-,-,-,
- -,-,- ,-,-,-,-,-,-,-,-,-,-,-,-,B,-,-,B,-,B,-,-,
- JNETHMM:-,H,H,H,H,H,H,H,H,H,H,
- H,-,-,-,-,-,-,-,-,E,E,E,-,-,-,-,-,-,-,-,-,-,-,-,
- -,-,-,-,-,-,-,-,-,-,-,-,-,-,-
- ,-,-,-,-,-,-,-,-,-,-,-,-,-,H,H,H,H,H,H,H,H,H,H,H,
- JNETPROPH:0.0110,0.1125,0.8552,0.0107
- ,0.6245,0.3614,0.0120,0.8702,0.1238,0.0120
- ,0.0193,0.9284,0.0708,0.0278,0.8703,0.1244
- ,0.1591,0.7399,0.1456,0.2488,0.5824,0.1017,
- JNETPROPE:0.0107,0.6245,0.3614,0.0120
- ,0.8702,0.1238,0.0120,0.9335,0.0656,0.0102
- ,0.9586,0.0465,0.0094,0.9662,0.0433,
- ,0.1525,0.7103,0.1088,0.1181,0.7425,0.1784,\r
-<P>\r
-\r
-<P>\r
-<DL>\r
-<DT><B>Author:</B></DT>\r
-  <DD>pvtroshin</DD>\r
-</DL>\r
-<HR>\r
-\r
-<P>\r
-\r
-<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
-\r
-<A NAME="constructor_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Constructor Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/data/_structure/JpredResult.html#JpredResult()">JpredResult</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
-\r
-<A NAME="constructor_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Constructor Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="JpredResult()"><!-- --></A><H3>\r
-JpredResult</H3>\r
-<PRE>\r
-public <B>JpredResult</B>()</PRE>\r
-<DL>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/JpredResult.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/data/_structure/JpredAnnotation.html" title="enum in compbio.data._structure"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;NEXT CLASS</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/data/_structure/JpredResult.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="JpredResult.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#methods_inherited_from_class_java.lang.Object">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;METHOD</FONT></TD>\r
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-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
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-</HTML>\r
diff --git a/website/full_javadoc/compbio/data/_structure/class-use/JnetAnnotation.html b/website/full_javadoc/compbio/data/_structure/class-use/JnetAnnotation.html

deleted file mode 100644 (file)

index db95c3b..0000000
--- a/website/full_javadoc/compbio/data/_structure/class-use/JnetAnnotation.html
+++ /dev/null
@@ -1,189 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Uses of Class compbio.data._structure.JnetAnnotation\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Uses of Class compbio.data._structure.JnetAnnotation";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../compbio/data/_structure/JnetAnnotation.html" title="enum in compbio.data._structure"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/data/_structure/\class-useJnetAnnotation.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="JnetAnnotation.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-<B>Uses of Class<br>compbio.data._structure.JnetAnnotation</B></H2>\r
-</CENTER>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Packages that use <A HREF="../../../../compbio/data/_structure/JnetAnnotation.html" title="enum in compbio.data._structure">JnetAnnotation</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.data._structure"><B>compbio.data._structure</B></A></TD>\r
-<TD>&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.data._structure"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../../compbio/data/_structure/JnetAnnotation.html" title="enum in compbio.data._structure">JnetAnnotation</A> in <A HREF="../../../../compbio/data/_structure/package-summary.html">compbio.data._structure</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/data/_structure/package-summary.html">compbio.data._structure</A> that return <A HREF="../../../../compbio/data/_structure/JnetAnnotation.html" title="enum in compbio.data._structure">JnetAnnotation</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../../compbio/data/_structure/JnetAnnotation.html" title="enum in compbio.data._structure">JnetAnnotation</A></CODE></FONT></TD>\r
-<TD><CODE><B>JnetAnnotation.</B><B><A HREF="../../../../compbio/data/_structure/JnetAnnotation.html#valueOf(java.lang.String)">valueOf</A></B>(java.lang.String&nbsp;name)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Returns the enum constant of this type with the specified name.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../../compbio/data/_structure/JnetAnnotation.html" title="enum in compbio.data._structure">JnetAnnotation</A>[]</CODE></FONT></TD>\r
-<TD><CODE><B>JnetAnnotation.</B><B><A HREF="../../../../compbio/data/_structure/JnetAnnotation.html#values()">values</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Returns an array containing the constants of this enum type, in
-the order they are declared.</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../compbio/data/_structure/JnetAnnotation.html" title="enum in compbio.data._structure"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/data/_structure/\class-useJnetAnnotation.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="JnetAnnotation.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/data/_structure/class-use/JpredAnnotation.html b/website/full_javadoc/compbio/data/_structure/class-use/JpredAnnotation.html

deleted file mode 100644 (file)

index fcae915..0000000
--- a/website/full_javadoc/compbio/data/_structure/class-use/JpredAnnotation.html
+++ /dev/null
@@ -1,189 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Uses of Class compbio.data._structure.JpredAnnotation\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Uses of Class compbio.data._structure.JpredAnnotation";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../compbio/data/_structure/JpredAnnotation.html" title="enum in compbio.data._structure"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/data/_structure/\class-useJpredAnnotation.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="JpredAnnotation.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-<B>Uses of Class<br>compbio.data._structure.JpredAnnotation</B></H2>\r
-</CENTER>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Packages that use <A HREF="../../../../compbio/data/_structure/JpredAnnotation.html" title="enum in compbio.data._structure">JpredAnnotation</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.data._structure"><B>compbio.data._structure</B></A></TD>\r
-<TD>&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.data._structure"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../../compbio/data/_structure/JpredAnnotation.html" title="enum in compbio.data._structure">JpredAnnotation</A> in <A HREF="../../../../compbio/data/_structure/package-summary.html">compbio.data._structure</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/data/_structure/package-summary.html">compbio.data._structure</A> that return <A HREF="../../../../compbio/data/_structure/JpredAnnotation.html" title="enum in compbio.data._structure">JpredAnnotation</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../../compbio/data/_structure/JpredAnnotation.html" title="enum in compbio.data._structure">JpredAnnotation</A></CODE></FONT></TD>\r
-<TD><CODE><B>JpredAnnotation.</B><B><A HREF="../../../../compbio/data/_structure/JpredAnnotation.html#valueOf(java.lang.String)">valueOf</A></B>(java.lang.String&nbsp;name)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Returns the enum constant of this type with the specified name.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../../compbio/data/_structure/JpredAnnotation.html" title="enum in compbio.data._structure">JpredAnnotation</A>[]</CODE></FONT></TD>\r
-<TD><CODE><B>JpredAnnotation.</B><B><A HREF="../../../../compbio/data/_structure/JpredAnnotation.html#values()">values</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Returns an array containing the constants of this enum type, in
-the order they are declared.</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../compbio/data/_structure/JpredAnnotation.html" title="enum in compbio.data._structure"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/data/_structure/\class-useJpredAnnotation.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="JpredAnnotation.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/data/_structure/class-use/JpredResult.html b/website/full_javadoc/compbio/data/_structure/class-use/JpredResult.html

deleted file mode 100644 (file)

index 8366955..0000000
--- a/website/full_javadoc/compbio/data/_structure/class-use/JpredResult.html
+++ /dev/null
@@ -1,144 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Uses of Class compbio.data._structure.JpredResult\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Uses of Class compbio.data._structure.JpredResult";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../compbio/data/_structure/JpredResult.html" title="class in compbio.data._structure"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/data/_structure/\class-useJpredResult.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="JpredResult.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-<B>Uses of Class<br>compbio.data._structure.JpredResult</B></H2>\r
-</CENTER>\r
-No usage of compbio.data._structure.JpredResult\r
-<P>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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deleted file mode 100644 (file)

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deleted file mode 100644 (file)

index 9f34326..0000000
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- 
- jnetpred:-,H,H,H,H,H,H,H,H,H,H,H,-,-,-,-,-,-,-,-,E,E,E,-,-,-,-,-,-,-,-,-,-,-,
- -,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,H,H,H,H,H,H,H,H,H,H
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- JNETPROPH:0.0110,0.1125,0.8552,0.0107
- ,0.6245,0.3614,0.0120,0.8702,0.1238,0.0120
- ,0.0193,0.9284,0.0708,0.0278,0.8703,0.1244
- ,0.1591,0.7399,0.1456,0.2488,0.5824,0.1017,
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- ,0.9586,0.0465,0.0094,0.9662,0.0433,
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-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
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diff --git a/website/full_javadoc/compbio/data/_structure/package-tree.html b/website/full_javadoc/compbio/data/_structure/package-tree.html

deleted file mode 100644 (file)

index defdc96..0000000
--- a/website/full_javadoc/compbio/data/_structure/package-tree.html
+++ /dev/null
@@ -1,163 +0,0 @@
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-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
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-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
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-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
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-  <A HREF="../../../index.html?compbio/data/_structure/package-tree.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
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-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
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-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
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-\r
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-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-Hierarchy For Package compbio.data._structure\r
-</H2>\r
-</CENTER>\r
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-Class Hierarchy\r
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deleted file mode 100644 (file)

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-  <!--\r
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diff --git a/website/full_javadoc/compbio/data/msa/MsaWS.html b/website/full_javadoc/compbio/data/msa/MsaWS.html

deleted file mode 100644 (file)

index 911f90d..0000000
--- a/website/full_javadoc/compbio/data/msa/MsaWS.html
+++ /dev/null
@@ -1,567 +0,0 @@
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-<!--NewPage-->\r
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-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
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-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
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-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
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-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="MsaWS";\r
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-  <A HREF="../../../index.html?compbio/data/msa/MsaWS.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
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-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
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-\r
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-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;CONSTR&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;CONSTR&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
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-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
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-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.data.msa</FONT>\r
-<BR>\r
-Interface MsaWS&lt;T&gt;</H2>\r
-<DL>\r
-<DT><DT><B>Type Parameters:</B><DD><CODE>T</CODE> - executable type / web service type</DL>\r
-<DL>\r
-<DT><B>All Known Implementing Classes:</B> <DD><A HREF="../../../compbio/ws/server/ClustalWS.html" title="class in compbio.ws.server">ClustalWS</A>, <A HREF="../../../compbio/ws/server/MafftWS.html" title="class in compbio.ws.server">MafftWS</A>, <A HREF="../../../compbio/ws/server/MuscleWS.html" title="class in compbio.ws.server">MuscleWS</A>, <A HREF="../../../compbio/ws/server/ProbconsWS.html" title="class in compbio.ws.server">ProbconsWS</A>, <A HREF="../../../compbio/ws/server/TcoffeeWS.html" title="class in compbio.ws.server">TcoffeeWS</A></DD>\r
-</DL>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public interface <B>MsaWS&lt;T&gt;</B></DL>\r
-</PRE>\r
-\r
-<P>\r
-Multiple Sequence Alignment (MSA) Web Services Interface\r
-<P>\r
-\r
-<P>\r
-<DL>\r
-<DT><B>Author:</B></DT>\r
-  <DD>pvtroshin\r
- \r
-         Date September 2009</DD>\r
-</DL>\r
-<HR>\r
-\r
-<P>\r
-\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
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-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/msa/MsaWS.html#align(java.util.List)">align</A></B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Align a list of sequences with default settings.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/msa/MsaWS.html#cancelJob(java.lang.String)">cancelJob</A></B>(java.lang.String&nbsp;jobId)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Stop running job but leave its output untouched</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/msa/MsaWS.html#customAlign(java.util.List, java.util.List)">customAlign</A></B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-            java.util.List&lt;<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../compbio/data/msa/MsaWS.html" title="type parameter in MsaWS">T</A>&gt;&gt;&nbsp;options)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Align a list of sequences with options.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/msa/MsaWS.html#getJobStatus(java.lang.String)">getJobStatus</A></B>(java.lang.String&nbsp;jobId)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Return the status of the job.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;<A HREF="../../../compbio/data/msa/MsaWS.html" title="type parameter in MsaWS">T</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/msa/MsaWS.html#getLimit(java.lang.String)">getLimit</A></B>(java.lang.String&nbsp;presetName)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Get a Limit for a preset.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;<A HREF="../../../compbio/data/msa/MsaWS.html" title="type parameter in MsaWS">T</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/msa/MsaWS.html#getLimits()">getLimits</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;List Limits supported by a web service.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>&lt;<A HREF="../../../compbio/data/msa/MsaWS.html" title="type parameter in MsaWS">T</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/msa/MsaWS.html#getPresets()">getPresets</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Get presets supported by a web service</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/msa/MsaWS.html#getResult(java.lang.String)">getResult</A></B>(java.lang.String&nbsp;jobId)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Return the result of the job.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&lt;<A HREF="../../../compbio/data/msa/MsaWS.html" title="type parameter in MsaWS">T</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/msa/MsaWS.html#getRunnerOptions()">getRunnerOptions</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Get options supported by a web service</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/msa/MsaWS.html#presetAlign(java.util.List, compbio.metadata.Preset)">presetAlign</A></B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-            <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>&lt;<A HREF="../../../compbio/data/msa/MsaWS.html" title="type parameter in MsaWS">T</A>&gt;&nbsp;preset)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Align a list of sequences with preset.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/msa/MsaWS.html#pullExecStatistics(java.lang.String, long)">pullExecStatistics</A></B>(java.lang.String&nbsp;jobId,\r
-                   long&nbsp;position)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Reads 1kb chunk from the statistics file which is specific to a given web\r
- service from the position.</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
-<A NAME="method_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="align(java.util.List)"><!-- --></A><H3>\r
-align</H3>\r
-<PRE>\r
-java.lang.String <B>align</B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences)\r
-                       throws <A HREF="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A>,\r
-                              <A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A>,\r
-                              <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></PRE>\r
-<DL>\r
-<DD>Align a list of sequences with default settings.\r
- \r
- Any dataset containing a greater number of sequences or the average\r
- length of the sequences are greater then defined in the default Limit\r
- will not be accepted for an alignment operation and\r
- JobSubmissionException will be thrown.\r
-<P>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>sequences</CODE> - List of FastaSequence objects. The programme does not perform\r
-            any sequence validity checks. Nor does it checks whether the\r
-            sequences names are unique. It is responsibility of the caller\r
-            to validate this information\r
-<DT><B>Returns:</B><DD>jobId - unique identifier for the job\r
-<DT><B>Throws:</B>\r
-<DD><CODE>JobSubmissionException.</CODE> - This\r
-             exception is thrown when the job could not be submitted due\r
-             to the following reasons: 1) The number of sequences in the\r
-             submission or their average length is greater then defined by\r
-             the default Limit. 2) Any problems on the server side e.g. it\r
-             is misconfigured or malfunction, is reported via this\r
-             exception. In the first case the information on the limit\r
-             could be obtained from an exception.\r
-<DD><CODE>java.security.InvalidParameterException</CODE> - thrown if input list of fasta sequence is null or empty\r
-<DD><CODE><A HREF="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A></CODE> - thrown if server OS does not support native executables for a\r
-             given web service, e.g. JABAWS is deployed on Windows and Mafft\r
-             service is called\r
-<DD><CODE><A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A></CODE> - is throw if the input sequences number or average length\r
-             exceeds what is defined by the limit\r
-<DD><CODE><A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></CODE></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="customAlign(java.util.List, java.util.List)"><!-- --></A><H3>\r
-customAlign</H3>\r
-<PRE>\r
-java.lang.String <B>customAlign</B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-                             java.util.List&lt;<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../compbio/data/msa/MsaWS.html" title="type parameter in MsaWS">T</A>&gt;&gt;&nbsp;options)\r
-                             throws <A HREF="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A>,\r
-                                    <A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A>,\r
-                                    <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A>,\r
-                                    <A HREF="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></PRE>\r
-<DL>\r
-<DD>Align a list of sequences with options.\r
-<P>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>sequences</CODE> - List of FastaSequence objects. The programme does not perform\r
-            any sequence validity checks. Nor does it checks whether the\r
-            sequences names are unique. It is responsibility of the caller\r
-            to validate this information<DD><CODE>options</CODE> - A list of Options\r
-<DT><B>Returns:</B><DD>jobId - unique identifier for the job\r
-<DT><B>Throws:</B>\r
-<DD><CODE>JobSubmissionException.</CODE> - This\r
-             exception is thrown when the job could not be submitted due\r
-             to the following reasons: 1) The number of sequences in the\r
-             submission or their average length is greater then defined by\r
-             the default Limit. 2) Any problems on the server side e.g. it\r
-             is misconfigured or malfunction, is reported via this\r
-             exception. In the first case the information on the limit\r
-             could be obtained from an exception.\r
-<DD><CODE><A HREF="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></CODE> - is throws when 1) One of the Options provided is not\r
-             supported, 2) The value of the option is defined outside the\r
-             boundaries. In both cases exception object contain the\r
-             information on the violating Option.\r
-<DD><CODE>java.security.InvalidParameterException</CODE> - thrown if input list of fasta sequence is null or empty\r
-<DD><CODE><A HREF="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A></CODE> - thrown if server OS does not support native executables for a\r
-             given web service, e.g. JABAWS is deployed on Windows and Mafft\r
-             service is called\r
-<DD><CODE><A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A></CODE> - is throw if the input sequences number or average length\r
-             exceeds what is defined by the limit\r
-<DD><CODE><A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></CODE><DT><B>See Also:</B><DD><A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata"><CODE>Default Limit is used to decide whether the calculation will be\r
-      permitted or denied</CODE></A></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="presetAlign(java.util.List, compbio.metadata.Preset)"><!-- --></A><H3>\r
-presetAlign</H3>\r
-<PRE>\r
-java.lang.String <B>presetAlign</B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-                             <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>&lt;<A HREF="../../../compbio/data/msa/MsaWS.html" title="type parameter in MsaWS">T</A>&gt;&nbsp;preset)\r
-                             throws <A HREF="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A>,\r
-                                    <A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A>,\r
-                                    <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A>,\r
-                                    <A HREF="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></PRE>\r
-<DL>\r
-<DD>Align a list of sequences with preset. @see Preset\r
- \r
- Limit for a presetName is used whether the calculation will be permitted\r
- or denied. If no Limit was defined for a presetName, than default limit\r
- is used.\r
-<P>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>sequences</CODE> - List of FastaSequence objects. The programme does not perform\r
-            any sequence validity checks. Nor does it checks whether the\r
-            sequences names are unique. It is responsibility of the caller\r
-            to validate this information<DD><CODE>preset</CODE> - A list of Options\r
-<DT><B>Returns:</B><DD>String - jobId - unique identifier for the job\r
-<DT><B>Throws:</B>\r
-<DD><CODE>JobSubmissionException.</CODE> - This\r
-             exception is thrown when the job could not be submitted due\r
-             to the following reasons: 1) The number of sequences in the\r
-             submission or their average length is greater then defined by\r
-             the default Limit. 2) Any problems on the server side e.g. it\r
-             is misconfigured or malfunction, is reported via this\r
-             exception. In the first case the information on the limit\r
-             could be obtained from an exception.\r
-<DD><CODE><A HREF="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></CODE> - is throws when 1) One of the Options provided is not\r
-             supported, 2) The value of the option is defined outside the\r
-             boundaries. In both cases exception object contain the\r
-             information on the violating Option.\r
-<DD><CODE>java.security.InvalidParameterException</CODE> - thrown if input list of fasta sequence is null or empty\r
-<DD><CODE><A HREF="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A></CODE> - thrown if server OS does not support native executables for a\r
-             given web service, e.g. JABAWS is deployed on Windows and Mafft\r
-             service is called\r
-<DD><CODE><A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A></CODE> - is throw if the input sequences number or average length\r
-             exceeds what is defined by the limit\r
-<DD><CODE><A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></CODE></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getResult(java.lang.String)"><!-- --></A><H3>\r
-getResult</H3>\r
-<PRE>\r
-<A HREF="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A> <B>getResult</B>(java.lang.String&nbsp;jobId)\r
-                    throws <A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></PRE>\r
-<DL>\r
-<DD>Return the result of the job.\r
-<P>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>jobId</CODE> - a unique job identifier\r
-<DT><B>Returns:</B><DD>Alignment\r
-<DT><B>Throws:</B>\r
-<DD><CODE><A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></CODE> - this exception is throw if the job execution was not\r
-             successful or the result of the execution could not be found.\r
-             (e.g. removed). Exception could also be thrown is dues to the\r
-             lower level problems on the server i.e. IOException,\r
-             FileNotFoundException problems as well as\r
-             UnknownFileFormatException.\r
-<DD><CODE>java.security.InvalidParameterException</CODE> - thrown if jobId is empty or cannot be recognised e.g. in\r
-             invalid format</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="cancelJob(java.lang.String)"><!-- --></A><H3>\r
-cancelJob</H3>\r
-<PRE>\r
-boolean <B>cancelJob</B>(java.lang.String&nbsp;jobId)</PRE>\r
-<DL>\r
-<DD>Stop running job but leave its output untouched\r
-<P>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>true if job was cancelled successfully, false otherwise\r
-<DT><B>Throws:</B>\r
-<DD><CODE>java.security.InvalidParameterException</CODE> - thrown if jobId is empty or cannot be recognised e.g. in\r
-             invalid format</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getJobStatus(java.lang.String)"><!-- --></A><H3>\r
-getJobStatus</H3>\r
-<PRE>\r
-<A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A> <B>getJobStatus</B>(java.lang.String&nbsp;jobId)</PRE>\r
-<DL>\r
-<DD>Return the status of the job. @see JobStatus\r
-<P>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>jobId</CODE> - - unique job identifier\r
-<DT><B>Returns:</B><DD>JobStatus - status of the job\r
-<DT><B>Throws:</B>\r
-<DD><CODE>java.security.InvalidParameterException</CODE> - thrown if jobId is empty or cannot be recognised e.g. in\r
-             invalid format</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="pullExecStatistics(java.lang.String, long)"><!-- --></A><H3>\r
-pullExecStatistics</H3>\r
-<PRE>\r
-<A HREF="../../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A> <B>pullExecStatistics</B>(java.lang.String&nbsp;jobId,\r
-                               long&nbsp;position)</PRE>\r
-<DL>\r
-<DD>Reads 1kb chunk from the statistics file which is specific to a given web\r
- service from the position. If in time of a request less then 1kb data is\r
- available from the position to the end of the file, then it returns all\r
- the data available from the position to the end of the file.\r
-<P>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>jobId</CODE> - - unique job identifier<DD><CODE>position</CODE> - - next position within the file to read\r
-<DT><B>Returns:</B><DD>ChunkHolder - @see ChunkHolder which contains a chuink of data\r
-         and a next position within the file from which no data has been\r
-         read\r
-<DT><B>Throws:</B>\r
-<DD><CODE>java.security.InvalidParameterException</CODE> - thrown if jobId is empty or cannot be recognised e.g. in\r
-             invalid format and also if the position value is negative</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getRunnerOptions()"><!-- --></A><H3>\r
-getRunnerOptions</H3>\r
-<PRE>\r
-<A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&lt;<A HREF="../../../compbio/data/msa/MsaWS.html" title="type parameter in MsaWS">T</A>&gt; <B>getRunnerOptions</B>()</PRE>\r
-<DL>\r
-<DD>Get options supported by a web service\r
-<P>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>RunnerConfig the list of options and parameters supported by a\r
-         web service.</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getPresets()"><!-- --></A><H3>\r
-getPresets</H3>\r
-<PRE>\r
-<A HREF="../../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>&lt;<A HREF="../../../compbio/data/msa/MsaWS.html" title="type parameter in MsaWS">T</A>&gt; <B>getPresets</B>()</PRE>\r
-<DL>\r
-<DD>Get presets supported by a web service\r
-<P>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>PresetManager the object contains information about presets\r
-         supported by a web service</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getLimit(java.lang.String)"><!-- --></A><H3>\r
-getLimit</H3>\r
-<PRE>\r
-<A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;<A HREF="../../../compbio/data/msa/MsaWS.html" title="type parameter in MsaWS">T</A>&gt; <B>getLimit</B>(java.lang.String&nbsp;presetName)</PRE>\r
-<DL>\r
-<DD>Get a Limit for a preset.\r
-<P>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>presetName</CODE> - the name of the preset. if no name is provided, then the\r
-            default preset is returned. If no limit for a particular\r
-            preset is defined then the default preset is returned\r
-<DT><B>Returns:</B><DD>Limit</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getLimits()"><!-- --></A><H3>\r
-getLimits</H3>\r
-<PRE>\r
-<A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;<A HREF="../../../compbio/data/msa/MsaWS.html" title="type parameter in MsaWS">T</A>&gt; <B>getLimits</B>()</PRE>\r
-<DL>\r
-<DD>List Limits supported by a web service.\r
-<P>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>presetName</CODE> - the name of the preset. if no name is provided, then the\r
-            default preset is returned. If no limit for a particular\r
-            preset is defined then the default preset is returned\r
-<DT><B>Returns:</B><DD>LimitManager</DL>\r
-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/MsaWS.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV CLASS&nbsp;\r
-&nbsp;NEXT CLASS</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/data/msa/MsaWS.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="MsaWS.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;CONSTR&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;CONSTR&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/data/msa/class-use/MsaWS.html b/website/full_javadoc/compbio/data/msa/class-use/MsaWS.html

deleted file mode 100644 (file)

index 30ccaec..0000000
--- a/website/full_javadoc/compbio/data/msa/class-use/MsaWS.html
+++ /dev/null
@@ -1,249 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Uses of Interface compbio.data.msa.MsaWS\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Uses of Interface compbio.data.msa.MsaWS";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/data/msa/\class-useMsaWS.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="MsaWS.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-<B>Uses of Interface<br>compbio.data.msa.MsaWS</B></H2>\r
-</CENTER>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Packages that use <A HREF="../../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.ws.client"><B>compbio.ws.client</B></A></TD>\r
-<TD>&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.ws.server"><B>compbio.ws.server</B></A></TD>\r
-<TD>&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.ws.client"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A> in <A HREF="../../../../compbio/ws/client/package-summary.html">compbio.ws.client</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/ws/client/package-summary.html">compbio.ws.client</A> that return <A HREF="../../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
-<TR ALIGN="right" VALIGN="">\r
-<TD NOWRAP><FONT SIZE="-1">\r
-<CODE>&lt;T&gt; <A HREF="../../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>&lt;T&gt;</CODE></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-</CODE></FONT></TD>\r
-<TD><CODE><B>Jws2Client.</B><B><A HREF="../../../../compbio/ws/client/Jws2Client.html#connect(java.lang.String, compbio.ws.client.Jws2Client.Services)">connect</A></B>(java.lang.String&nbsp;host,\r
-        <A HREF="../../../../compbio/ws/client/Jws2Client.Services.html" title="enum in compbio.ws.client">Jws2Client.Services</A>&nbsp;service)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Connects to a web service by the host and the service name</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.ws.server"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A> in <A HREF="../../../../compbio/ws/server/package-summary.html">compbio.ws.server</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Classes in <A HREF="../../../../compbio/ws/server/package-summary.html">compbio.ws.server</A> that implement <A HREF="../../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;class</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/ws/server/ClustalWS.html" title="class in compbio.ws.server">ClustalWS</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;class</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/ws/server/MafftWS.html" title="class in compbio.ws.server">MafftWS</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;class</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/ws/server/MuscleWS.html" title="class in compbio.ws.server">MuscleWS</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;class</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/ws/server/ProbconsWS.html" title="class in compbio.ws.server">ProbconsWS</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;class</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/ws/server/TcoffeeWS.html" title="class in compbio.ws.server">TcoffeeWS</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/data/msa/\class-useMsaWS.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="MsaWS.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/data/msa/jaxws/Align.html b/website/full_javadoc/compbio/data/msa/jaxws/Align.html

deleted file mode 100644 (file)

index b4181e3..0000000
--- a/website/full_javadoc/compbio/data/msa/jaxws/Align.html
+++ /dev/null
@@ -1,272 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Align\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Align";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/Align.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV CLASS&nbsp;\r
-&nbsp;<A HREF="../../../../compbio/data/msa/jaxws/AlignResponse.html" title="class in compbio.data.msa.jaxws"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/data/msa/jaxws/Align.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="Align.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.data.msa.jaxws</FONT>\r
-<BR>\r
-Class Align</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../../../resources/inherit.gif" ALT="extended by "><B>compbio.data.msa.jaxws.Align</B>\r
-</PRE>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public class <B>Align</B><DT>extends java.lang.Object</DL>\r
-</PRE>\r
-\r
-<P>\r
-<HR>\r
-\r
-<P>\r
-\r
-<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
-\r
-<A NAME="constructor_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Constructor Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../../compbio/data/msa/jaxws/Align.html#Align()">Align</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/data/msa/jaxws/Align.html#getFastaSequences()">getFastaSequences</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/data/msa/jaxws/Align.html#setFastaSequences(java.util.List)">setFastaSequences</A></B>(java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;fastaSequences)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
-\r
-<A NAME="constructor_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Constructor Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="Align()"><!-- --></A><H3>\r
-Align</H3>\r
-<PRE>\r
-public <B>Align</B>()</PRE>\r
-<DL>\r
-</DL>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
-<A NAME="method_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="getFastaSequences()"><!-- --></A><H3>\r
-getFastaSequences</H3>\r
-<PRE>\r
-public java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt; <B>getFastaSequences</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>returns List<FastaSequence></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="setFastaSequences(java.util.List)"><!-- --></A><H3>\r
-setFastaSequences</H3>\r
-<PRE>\r
-public void <B>setFastaSequences</B>(java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;fastaSequences)</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>fastaSequences</CODE> - the value for the fastaSequences property</DL>\r
-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/Align.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV CLASS&nbsp;\r
-&nbsp;<A HREF="../../../../compbio/data/msa/jaxws/AlignResponse.html" title="class in compbio.data.msa.jaxws"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/data/msa/jaxws/Align.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="Align.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/data/msa/jaxws/AlignResponse.html b/website/full_javadoc/compbio/data/msa/jaxws/AlignResponse.html

deleted file mode 100644 (file)

index 1a50071..0000000
--- a/website/full_javadoc/compbio/data/msa/jaxws/AlignResponse.html
+++ /dev/null
@@ -1,272 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-AlignResponse\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="AlignResponse";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/AlignResponse.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../../compbio/data/msa/jaxws/Align.html" title="class in compbio.data.msa.jaxws"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../../compbio/data/msa/jaxws/CancelJob.html" title="class in compbio.data.msa.jaxws"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/data/msa/jaxws/AlignResponse.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="AlignResponse.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.data.msa.jaxws</FONT>\r
-<BR>\r
-Class AlignResponse</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../../../resources/inherit.gif" ALT="extended by "><B>compbio.data.msa.jaxws.AlignResponse</B>\r
-</PRE>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public class <B>AlignResponse</B><DT>extends java.lang.Object</DL>\r
-</PRE>\r
-\r
-<P>\r
-<HR>\r
-\r
-<P>\r
-\r
-<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
-\r
-<A NAME="constructor_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Constructor Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../../compbio/data/msa/jaxws/AlignResponse.html#AlignResponse()">AlignResponse</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/data/msa/jaxws/AlignResponse.html#getReturn()">getReturn</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/data/msa/jaxws/AlignResponse.html#setReturn(java.lang.String)">setReturn</A></B>(java.lang.String&nbsp;_return)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
-\r
-<A NAME="constructor_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Constructor Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="AlignResponse()"><!-- --></A><H3>\r
-AlignResponse</H3>\r
-<PRE>\r
-public <B>AlignResponse</B>()</PRE>\r
-<DL>\r
-</DL>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
-<A NAME="method_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="getReturn()"><!-- --></A><H3>\r
-getReturn</H3>\r
-<PRE>\r
-public java.lang.String <B>getReturn</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>returns String</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="setReturn(java.lang.String)"><!-- --></A><H3>\r
-setReturn</H3>\r
-<PRE>\r
-public void <B>setReturn</B>(java.lang.String&nbsp;_return)</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>_return</CODE> - the value for the _return property</DL>\r
-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/AlignResponse.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../../compbio/data/msa/jaxws/Align.html" title="class in compbio.data.msa.jaxws"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../../compbio/data/msa/jaxws/CancelJob.html" title="class in compbio.data.msa.jaxws"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/data/msa/jaxws/AlignResponse.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="AlignResponse.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/data/msa/jaxws/CancelJob.html b/website/full_javadoc/compbio/data/msa/jaxws/CancelJob.html

deleted file mode 100644 (file)

index e858d81..0000000
--- a/website/full_javadoc/compbio/data/msa/jaxws/CancelJob.html
+++ /dev/null
@@ -1,272 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-CancelJob\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="CancelJob";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/CancelJob.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../../compbio/data/msa/jaxws/AlignResponse.html" title="class in compbio.data.msa.jaxws"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../../compbio/data/msa/jaxws/CancelJobResponse.html" title="class in compbio.data.msa.jaxws"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/data/msa/jaxws/CancelJob.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="CancelJob.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.data.msa.jaxws</FONT>\r
-<BR>\r
-Class CancelJob</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../../../resources/inherit.gif" ALT="extended by "><B>compbio.data.msa.jaxws.CancelJob</B>\r
-</PRE>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public class <B>CancelJob</B><DT>extends java.lang.Object</DL>\r
-</PRE>\r
-\r
-<P>\r
-<HR>\r
-\r
-<P>\r
-\r
-<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
-\r
-<A NAME="constructor_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Constructor Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../../compbio/data/msa/jaxws/CancelJob.html#CancelJob()">CancelJob</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/data/msa/jaxws/CancelJob.html#getJobId()">getJobId</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/data/msa/jaxws/CancelJob.html#setJobId(java.lang.String)">setJobId</A></B>(java.lang.String&nbsp;jobId)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
-\r
-<A NAME="constructor_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Constructor Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="CancelJob()"><!-- --></A><H3>\r
-CancelJob</H3>\r
-<PRE>\r
-public <B>CancelJob</B>()</PRE>\r
-<DL>\r
-</DL>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
-<A NAME="method_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="getJobId()"><!-- --></A><H3>\r
-getJobId</H3>\r
-<PRE>\r
-public java.lang.String <B>getJobId</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>returns String</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="setJobId(java.lang.String)"><!-- --></A><H3>\r
-setJobId</H3>\r
-<PRE>\r
-public void <B>setJobId</B>(java.lang.String&nbsp;jobId)</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>jobId</CODE> - the value for the jobId property</DL>\r
-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/CancelJob.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../../compbio/data/msa/jaxws/AlignResponse.html" title="class in compbio.data.msa.jaxws"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../../compbio/data/msa/jaxws/CancelJobResponse.html" title="class in compbio.data.msa.jaxws"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/data/msa/jaxws/CancelJob.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="CancelJob.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/data/msa/jaxws/CancelJobResponse.html b/website/full_javadoc/compbio/data/msa/jaxws/CancelJobResponse.html

deleted file mode 100644 (file)

index 69785d5..0000000
--- a/website/full_javadoc/compbio/data/msa/jaxws/CancelJobResponse.html
+++ /dev/null
@@ -1,272 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-CancelJobResponse\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
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-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
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-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="CancelJobResponse";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
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-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../../compbio/data/msa/jaxws/CancelJob.html" title="class in compbio.data.msa.jaxws"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../../compbio/data/msa/jaxws/CustomAlign.html" title="class in compbio.data.msa.jaxws"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/data/msa/jaxws/CancelJobResponse.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="CancelJobResponse.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
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-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
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-\r
-\r
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-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
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-\r
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-<H2>\r
-<FONT SIZE="-1">\r
-compbio.data.msa.jaxws</FONT>\r
-<BR>\r
-Class CancelJobResponse</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../../../resources/inherit.gif" ALT="extended by "><B>compbio.data.msa.jaxws.CancelJobResponse</B>\r
-</PRE>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public class <B>CancelJobResponse</B><DT>extends java.lang.Object</DL>\r
-</PRE>\r
-\r
-<P>\r
-<HR>\r
-\r
-<P>\r
-\r
-<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
-\r
-<A NAME="constructor_summary"><!-- --></A>\r
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-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Constructor Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../../compbio/data/msa/jaxws/CancelJobResponse.html#CancelJobResponse()">CancelJobResponse</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
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-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
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-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/data/msa/jaxws/CancelJobResponse.html#isReturn()">isReturn</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/data/msa/jaxws/CancelJobResponse.html#setReturn(boolean)">setReturn</A></B>(boolean&nbsp;_return)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
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-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
-\r
-<A NAME="constructor_detail"><!-- --></A>\r
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-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Constructor Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="CancelJobResponse()"><!-- --></A><H3>\r
-CancelJobResponse</H3>\r
-<PRE>\r
-public <B>CancelJobResponse</B>()</PRE>\r
-<DL>\r
-</DL>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
-<A NAME="method_detail"><!-- --></A>\r
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-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="isReturn()"><!-- --></A><H3>\r
-isReturn</H3>\r
-<PRE>\r
-public boolean <B>isReturn</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>returns boolean</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="setReturn(boolean)"><!-- --></A><H3>\r
-setReturn</H3>\r
-<PRE>\r
-public void <B>setReturn</B>(boolean&nbsp;_return)</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>_return</CODE> - the value for the _return property</DL>\r
-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/CancelJobResponse.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../../compbio/data/msa/jaxws/CancelJob.html" title="class in compbio.data.msa.jaxws"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../../compbio/data/msa/jaxws/CustomAlign.html" title="class in compbio.data.msa.jaxws"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/data/msa/jaxws/CancelJobResponse.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="CancelJobResponse.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
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-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
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-<HR>\r
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diff --git a/website/full_javadoc/compbio/data/msa/jaxws/CustomAlign.html b/website/full_javadoc/compbio/data/msa/jaxws/CustomAlign.html

deleted file mode 100644 (file)

index 838e512..0000000
--- a/website/full_javadoc/compbio/data/msa/jaxws/CustomAlign.html
+++ /dev/null
@@ -1,311 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-CustomAlign\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="CustomAlign";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/CustomAlign.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
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-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../../compbio/data/msa/jaxws/CancelJobResponse.html" title="class in compbio.data.msa.jaxws"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../../compbio/data/msa/jaxws/CustomAlignResponse.html" title="class in compbio.data.msa.jaxws"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/data/msa/jaxws/CustomAlign.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="CustomAlign.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
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-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
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-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
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-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.data.msa.jaxws</FONT>\r
-<BR>\r
-Class CustomAlign</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../../../resources/inherit.gif" ALT="extended by "><B>compbio.data.msa.jaxws.CustomAlign</B>\r
-</PRE>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public class <B>CustomAlign</B><DT>extends java.lang.Object</DL>\r
-</PRE>\r
-\r
-<P>\r
-<HR>\r
-\r
-<P>\r
-\r
-<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
-\r
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-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Constructor Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../../compbio/data/msa/jaxws/CustomAlign.html#CustomAlign()">CustomAlign</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
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-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/data/msa/jaxws/CustomAlign.html#getFastaSequences()">getFastaSequences</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.util.List&lt;<A HREF="../../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/data/msa/jaxws/CustomAlign.html#getOptions()">getOptions</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/data/msa/jaxws/CustomAlign.html#setFastaSequences(java.util.List)">setFastaSequences</A></B>(java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;fastaSequences)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/data/msa/jaxws/CustomAlign.html#setOptions(java.util.List)">setOptions</A></B>(java.util.List&lt;<A HREF="../../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&gt;&nbsp;options)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
-\r
-<A NAME="constructor_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Constructor Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="CustomAlign()"><!-- --></A><H3>\r
-CustomAlign</H3>\r
-<PRE>\r
-public <B>CustomAlign</B>()</PRE>\r
-<DL>\r
-</DL>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
-<A NAME="method_detail"><!-- --></A>\r
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-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="getFastaSequences()"><!-- --></A><H3>\r
-getFastaSequences</H3>\r
-<PRE>\r
-public java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt; <B>getFastaSequences</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>returns List<FastaSequence></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="setFastaSequences(java.util.List)"><!-- --></A><H3>\r
-setFastaSequences</H3>\r
-<PRE>\r
-public void <B>setFastaSequences</B>(java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;fastaSequences)</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>fastaSequences</CODE> - the value for the fastaSequences property</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getOptions()"><!-- --></A><H3>\r
-getOptions</H3>\r
-<PRE>\r
-public java.util.List&lt;<A HREF="../../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&gt; <B>getOptions</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>returns List<Option></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="setOptions(java.util.List)"><!-- --></A><H3>\r
-setOptions</H3>\r
-<PRE>\r
-public void <B>setOptions</B>(java.util.List&lt;<A HREF="../../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&gt;&nbsp;options)</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>options</CODE> - the value for the options property</DL>\r
-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/CustomAlign.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../../compbio/data/msa/jaxws/CancelJobResponse.html" title="class in compbio.data.msa.jaxws"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../../compbio/data/msa/jaxws/CustomAlignResponse.html" title="class in compbio.data.msa.jaxws"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/data/msa/jaxws/CustomAlign.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="CustomAlign.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/data/msa/jaxws/CustomAlignResponse.html b/website/full_javadoc/compbio/data/msa/jaxws/CustomAlignResponse.html

deleted file mode 100644 (file)

index a7d5cfe..0000000
--- a/website/full_javadoc/compbio/data/msa/jaxws/CustomAlignResponse.html
+++ /dev/null
@@ -1,272 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-CustomAlignResponse\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="CustomAlignResponse";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/CustomAlignResponse.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../../compbio/data/msa/jaxws/CustomAlign.html" title="class in compbio.data.msa.jaxws"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../../compbio/data/msa/jaxws/GetJobStatus.html" title="class in compbio.data.msa.jaxws"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/data/msa/jaxws/CustomAlignResponse.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="CustomAlignResponse.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.data.msa.jaxws</FONT>\r
-<BR>\r
-Class CustomAlignResponse</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../../../resources/inherit.gif" ALT="extended by "><B>compbio.data.msa.jaxws.CustomAlignResponse</B>\r
-</PRE>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public class <B>CustomAlignResponse</B><DT>extends java.lang.Object</DL>\r
-</PRE>\r
-\r
-<P>\r
-<HR>\r
-\r
-<P>\r
-\r
-<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
-\r
-<A NAME="constructor_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Constructor Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../../compbio/data/msa/jaxws/CustomAlignResponse.html#CustomAlignResponse()">CustomAlignResponse</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
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-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/data/msa/jaxws/CustomAlignResponse.html#getReturn()">getReturn</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/data/msa/jaxws/CustomAlignResponse.html#setReturn(java.lang.String)">setReturn</A></B>(java.lang.String&nbsp;_return)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
-\r
-<A NAME="constructor_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Constructor Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="CustomAlignResponse()"><!-- --></A><H3>\r
-CustomAlignResponse</H3>\r
-<PRE>\r
-public <B>CustomAlignResponse</B>()</PRE>\r
-<DL>\r
-</DL>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
-<A NAME="method_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="getReturn()"><!-- --></A><H3>\r
-getReturn</H3>\r
-<PRE>\r
-public java.lang.String <B>getReturn</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>returns String</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="setReturn(java.lang.String)"><!-- --></A><H3>\r
-setReturn</H3>\r
-<PRE>\r
-public void <B>setReturn</B>(java.lang.String&nbsp;_return)</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>_return</CODE> - the value for the _return property</DL>\r
-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
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-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/CustomAlignResponse.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
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-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../../compbio/data/msa/jaxws/CustomAlign.html" title="class in compbio.data.msa.jaxws"><B>PREV CLASS</B></A>&nbsp;\r
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diff --git a/website/full_javadoc/compbio/data/msa/jaxws/GetJobStatus.html b/website/full_javadoc/compbio/data/msa/jaxws/GetJobStatus.html

deleted file mode 100644 (file)

index e4f1719..0000000
--- a/website/full_javadoc/compbio/data/msa/jaxws/GetJobStatus.html
+++ /dev/null
@@ -1,272 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
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-</TITLE>\r
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-    if (location.href.indexOf('is-external=true') == -1) {\r
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-    }\r
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-<FONT SIZE="-1">\r
-compbio.data.msa.jaxws</FONT>\r
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-Class GetJobStatus</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../../../resources/inherit.gif" ALT="extended by "><B>compbio.data.msa.jaxws.GetJobStatus</B>\r
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-<DT><PRE>public class <B>GetJobStatus</B><DT>extends java.lang.Object</DL>\r
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-<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
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-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../../compbio/data/msa/jaxws/GetJobStatus.html#GetJobStatus()">GetJobStatus</A></B>()</CODE>\r
-\r
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-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
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-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/data/msa/jaxws/GetJobStatus.html#getJobId()">getJobId</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
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-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/data/msa/jaxws/GetJobStatus.html#setJobId(java.lang.String)">setJobId</A></B>(java.lang.String&nbsp;jobId)</CODE>\r
-\r
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-<B>Constructor Detail</B></FONT></TH>\r
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-</TABLE>\r
-\r
-<A NAME="GetJobStatus()"><!-- --></A><H3>\r
-GetJobStatus</H3>\r
-<PRE>\r
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-<DL>\r
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-<!-- ============ METHOD DETAIL ========== -->\r
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-\r
-<A NAME="getJobId()"><!-- --></A><H3>\r
-getJobId</H3>\r
-<PRE>\r
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-setJobId</H3>\r
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-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
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-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
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-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
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-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
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-\r
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diff --git a/website/full_javadoc/compbio/data/msa/jaxws/GetJobStatusResponse.html b/website/full_javadoc/compbio/data/msa/jaxws/GetJobStatusResponse.html

deleted file mode 100644 (file)

index 401d145..0000000
--- a/website/full_javadoc/compbio/data/msa/jaxws/GetJobStatusResponse.html
+++ /dev/null
@@ -1,272 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
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-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
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-\r
-<SCRIPT type="text/javascript">\r
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-    if (location.href.indexOf('is-external=true') == -1) {\r
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-java.lang.Object\r
-  <IMG SRC="../../../../resources/inherit.gif" ALT="extended by "><B>compbio.data.msa.jaxws.GetJobStatusResponse</B>\r
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-\r
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-\r
-<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
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-<B>Constructor Summary</B></FONT></TH>\r
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-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../../compbio/data/msa/jaxws/GetJobStatusResponse.html#GetJobStatusResponse()">GetJobStatusResponse</A></B>()</CODE>\r
-\r
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-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
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-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
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-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/data/msa/jaxws/GetJobStatusResponse.html#getReturn()">getReturn</A></B>()</CODE>\r
-\r
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-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/data/msa/jaxws/GetJobStatusResponse.html#setReturn(compbio.metadata.JobStatus)">setReturn</A></B>(<A HREF="../../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A>&nbsp;_return)</CODE>\r
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-<B>Constructor Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="GetJobStatusResponse()"><!-- --></A><H3>\r
-GetJobStatusResponse</H3>\r
-<PRE>\r
-public <B>GetJobStatusResponse</B>()</PRE>\r
-<DL>\r
-</DL>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
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-<B>Method Detail</B></FONT></TH>\r
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-<DT><B>Parameters:</B><DD><CODE>_return</CODE> - the value for the _return property</DL>\r
-</DD>\r
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-<!-- ========= END OF CLASS DATA ========= -->\r
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-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
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-&nbsp;<A HREF="../../../../compbio/data/msa/jaxws/GetLimit.html" title="class in compbio.data.msa.jaxws"><B>NEXT CLASS</B></A></FONT></TD>\r
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diff --git a/website/full_javadoc/compbio/data/msa/jaxws/GetLimit.html b/website/full_javadoc/compbio/data/msa/jaxws/GetLimit.html

deleted file mode 100644 (file)

index 3433200..0000000
--- a/website/full_javadoc/compbio/data/msa/jaxws/GetLimit.html
+++ /dev/null
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-<HEAD>\r
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-</EM>\r
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-&nbsp;<A HREF="../../../../compbio/data/msa/jaxws/GetLimitResponse.html" title="class in compbio.data.msa.jaxws"><B>NEXT CLASS</B></A></FONT></TD>\r
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-compbio.data.msa.jaxws</FONT>\r
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-Class GetLimit</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../../../resources/inherit.gif" ALT="extended by "><B>compbio.data.msa.jaxws.GetLimit</B>\r
-</PRE>\r
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-</PRE>\r
-\r
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-<HR>\r
-\r
-<P>\r
-\r
-<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
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-<B>Constructor Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../../compbio/data/msa/jaxws/GetLimit.html#GetLimit()">GetLimit</A></B>()</CODE>\r
-\r
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-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
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-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/data/msa/jaxws/GetLimit.html#getPresetName()">getPresetName</A></B>()</CODE>\r
-\r
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-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
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-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/data/msa/jaxws/GetLimit.html#setPresetName(java.lang.String)">setPresetName</A></B>(java.lang.String&nbsp;presetName)</CODE>\r
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-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
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-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>\r
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-<B>Constructor Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="GetLimit()"><!-- --></A><H3>\r
-GetLimit</H3>\r
-<PRE>\r
-public <B>GetLimit</B>()</PRE>\r
-<DL>\r
-</DL>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
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-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
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-getPresetName</H3>\r
-<PRE>\r
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-<DL>\r
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-<DT><B>Parameters:</B><DD><CODE>presetName</CODE> - the value for the presetName property</DL>\r
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-<!-- ========= END OF CLASS DATA ========= -->\r
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-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
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-&nbsp;<A HREF="../../../../compbio/data/msa/jaxws/GetLimitResponse.html" title="class in compbio.data.msa.jaxws"><B>NEXT CLASS</B></A></FONT></TD>\r
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-</TR>\r
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-\r
-<HR>\r
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diff --git a/website/full_javadoc/compbio/data/msa/jaxws/GetLimitResponse.html b/website/full_javadoc/compbio/data/msa/jaxws/GetLimitResponse.html

deleted file mode 100644 (file)

index 5def54c..0000000
--- a/website/full_javadoc/compbio/data/msa/jaxws/GetLimitResponse.html
+++ /dev/null
@@ -1,272 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-GetLimitResponse\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
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-\r
-<SCRIPT type="text/javascript">\r
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-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
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-    }\r
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-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
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-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
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-<TR>\r
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-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/GetLimitResponse.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
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-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
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-&nbsp;<A HREF="../../../../compbio/data/msa/jaxws/GetLimits.html" title="class in compbio.data.msa.jaxws"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
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-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
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-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
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-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
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-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.data.msa.jaxws</FONT>\r
-<BR>\r
-Class GetLimitResponse</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../../../resources/inherit.gif" ALT="extended by "><B>compbio.data.msa.jaxws.GetLimitResponse</B>\r
-</PRE>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public class <B>GetLimitResponse</B><DT>extends java.lang.Object</DL>\r
-</PRE>\r
-\r
-<P>\r
-<HR>\r
-\r
-<P>\r
-\r
-<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
-\r
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-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Constructor Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../../compbio/data/msa/jaxws/GetLimitResponse.html#GetLimitResponse()">GetLimitResponse</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
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-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
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-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/data/msa/jaxws/GetLimitResponse.html#getReturn()">getReturn</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/data/msa/jaxws/GetLimitResponse.html#setReturn(compbio.metadata.Limit)">setReturn</A></B>(<A HREF="../../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&nbsp;_return)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
-\r
-<A NAME="constructor_detail"><!-- --></A>\r
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-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Constructor Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="GetLimitResponse()"><!-- --></A><H3>\r
-GetLimitResponse</H3>\r
-<PRE>\r
-public <B>GetLimitResponse</B>()</PRE>\r
-<DL>\r
-</DL>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
-<A NAME="method_detail"><!-- --></A>\r
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-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="getReturn()"><!-- --></A><H3>\r
-getReturn</H3>\r
-<PRE>\r
-public <A HREF="../../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A> <B>getReturn</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>returns Limit</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="setReturn(compbio.metadata.Limit)"><!-- --></A><H3>\r
-setReturn</H3>\r
-<PRE>\r
-public void <B>setReturn</B>(<A HREF="../../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&nbsp;_return)</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>_return</CODE> - the value for the _return property</DL>\r
-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
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-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/GetLimitResponse.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
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-  </TR>\r
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-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../../compbio/data/msa/jaxws/GetLimit.html" title="class in compbio.data.msa.jaxws"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../../compbio/data/msa/jaxws/GetLimits.html" title="class in compbio.data.msa.jaxws"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/data/msa/jaxws/GetLimitResponse.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="GetLimitResponse.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
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-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
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diff --git a/website/full_javadoc/compbio/data/msa/jaxws/GetLimits.html b/website/full_javadoc/compbio/data/msa/jaxws/GetLimits.html

deleted file mode 100644 (file)

index aa83b59..0000000
--- a/website/full_javadoc/compbio/data/msa/jaxws/GetLimits.html
+++ /dev/null
@@ -1,224 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-GetLimits\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="GetLimits";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
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-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/GetLimits.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
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-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../../compbio/data/msa/jaxws/GetLimitResponse.html" title="class in compbio.data.msa.jaxws"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../../compbio/data/msa/jaxws/GetLimitsResponse.html" title="class in compbio.data.msa.jaxws"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/data/msa/jaxws/GetLimits.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="GetLimits.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
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-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
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-\r
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-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#methods_inherited_from_class_java.lang.Object">METHOD</A></FONT></TD>\r
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-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
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-compbio.data.msa.jaxws</FONT>\r
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-Class GetLimits</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../../../resources/inherit.gif" ALT="extended by "><B>compbio.data.msa.jaxws.GetLimits</B>\r
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-<DT><PRE>public class <B>GetLimits</B><DT>extends java.lang.Object</DL>\r
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-\r
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-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../../compbio/data/msa/jaxws/GetLimits.html#GetLimits()">GetLimits</A></B>()</CODE>\r
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-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>\r
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-\r
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-<B>Constructor Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="GetLimits()"><!-- --></A><H3>\r
-GetLimits</H3>\r
-<PRE>\r
-public <B>GetLimits</B>()</PRE>\r
-<DL>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
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diff --git a/website/full_javadoc/compbio/data/msa/jaxws/GetLimitsResponse.html b/website/full_javadoc/compbio/data/msa/jaxws/GetLimitsResponse.html

deleted file mode 100644 (file)

index 04d2e7a..0000000
--- a/website/full_javadoc/compbio/data/msa/jaxws/GetLimitsResponse.html
+++ /dev/null
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-compbio.data.msa.jaxws</FONT>\r
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-Class GetLimitsResponse</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../../../resources/inherit.gif" ALT="extended by "><B>compbio.data.msa.jaxws.GetLimitsResponse</B>\r
-</PRE>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public class <B>GetLimitsResponse</B><DT>extends java.lang.Object</DL>\r
-</PRE>\r
-\r
-<P>\r
-<HR>\r
-\r
-<P>\r
-\r
-<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
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-<B>Constructor Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../../compbio/data/msa/jaxws/GetLimitsResponse.html#GetLimitsResponse()">GetLimitsResponse</A></B>()</CODE>\r
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-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A></CODE></FONT></TD>\r
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-</TR>\r
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-<B>Constructor Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
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-GetLimitsResponse</H3>\r
-<PRE>\r
-public <B>GetLimitsResponse</B>()</PRE>\r
-<DL>\r
-</DL>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
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-getReturn</H3>\r
-<PRE>\r
-public <A HREF="../../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A> <B>getReturn</B>()</PRE>\r
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-<PRE>\r
-public void <B>setReturn</B>(<A HREF="../../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&nbsp;_return)</PRE>\r
-<DL>\r
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-<DT><B>Parameters:</B><DD><CODE>_return</CODE> - the value for the _return property</DL>\r
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-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
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-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
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-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
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-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
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-</EM>\r
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-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../../compbio/data/msa/jaxws/GetLimits.html" title="class in compbio.data.msa.jaxws"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../../compbio/data/msa/jaxws/GetPresets.html" title="class in compbio.data.msa.jaxws"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
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-&nbsp;<A HREF="GetLimitsResponse.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
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-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/data/msa/jaxws/GetPresets.html b/website/full_javadoc/compbio/data/msa/jaxws/GetPresets.html

deleted file mode 100644 (file)

index a9ea45a..0000000
--- a/website/full_javadoc/compbio/data/msa/jaxws/GetPresets.html
+++ /dev/null
@@ -1,224 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-GetPresets\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="GetPresets";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
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-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/GetPresets.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../../compbio/data/msa/jaxws/GetLimitsResponse.html" title="class in compbio.data.msa.jaxws"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../../compbio/data/msa/jaxws/GetPresetsResponse.html" title="class in compbio.data.msa.jaxws"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/data/msa/jaxws/GetPresets.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="GetPresets.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#methods_inherited_from_class_java.lang.Object">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;METHOD</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.data.msa.jaxws</FONT>\r
-<BR>\r
-Class GetPresets</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../../../resources/inherit.gif" ALT="extended by "><B>compbio.data.msa.jaxws.GetPresets</B>\r
-</PRE>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public class <B>GetPresets</B><DT>extends java.lang.Object</DL>\r
-</PRE>\r
-\r
-<P>\r
-<HR>\r
-\r
-<P>\r
-\r
-<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
-\r
-<A NAME="constructor_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Constructor Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../../compbio/data/msa/jaxws/GetPresets.html#GetPresets()">GetPresets</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
-\r
-<A NAME="constructor_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Constructor Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="GetPresets()"><!-- --></A><H3>\r
-GetPresets</H3>\r
-<PRE>\r
-public <B>GetPresets</B>()</PRE>\r
-<DL>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/GetPresets.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../../compbio/data/msa/jaxws/GetLimitsResponse.html" title="class in compbio.data.msa.jaxws"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../../compbio/data/msa/jaxws/GetPresetsResponse.html" title="class in compbio.data.msa.jaxws"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/data/msa/jaxws/GetPresets.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="GetPresets.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#methods_inherited_from_class_java.lang.Object">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;METHOD</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/data/msa/jaxws/GetPresetsResponse.html b/website/full_javadoc/compbio/data/msa/jaxws/GetPresetsResponse.html

deleted file mode 100644 (file)

index f5f62bb..0000000
--- a/website/full_javadoc/compbio/data/msa/jaxws/GetPresetsResponse.html
+++ /dev/null
@@ -1,272 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-GetPresetsResponse\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="GetPresetsResponse";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/GetPresetsResponse.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../../compbio/data/msa/jaxws/GetPresets.html" title="class in compbio.data.msa.jaxws"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../../compbio/data/msa/jaxws/GetProgress.html" title="class in compbio.data.msa.jaxws"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/data/msa/jaxws/GetPresetsResponse.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="GetPresetsResponse.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.data.msa.jaxws</FONT>\r
-<BR>\r
-Class GetPresetsResponse</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../../../resources/inherit.gif" ALT="extended by "><B>compbio.data.msa.jaxws.GetPresetsResponse</B>\r
-</PRE>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public class <B>GetPresetsResponse</B><DT>extends java.lang.Object</DL>\r
-</PRE>\r
-\r
-<P>\r
-<HR>\r
-\r
-<P>\r
-\r
-<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
-\r
-<A NAME="constructor_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Constructor Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../../compbio/data/msa/jaxws/GetPresetsResponse.html#GetPresetsResponse()">GetPresetsResponse</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/data/msa/jaxws/GetPresetsResponse.html#getReturn()">getReturn</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/data/msa/jaxws/GetPresetsResponse.html#setReturn(compbio.metadata.PresetManager)">setReturn</A></B>(<A HREF="../../../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>&nbsp;_return)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
-\r
-<A NAME="constructor_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Constructor Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="GetPresetsResponse()"><!-- --></A><H3>\r
-GetPresetsResponse</H3>\r
-<PRE>\r
-public <B>GetPresetsResponse</B>()</PRE>\r
-<DL>\r
-</DL>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
-<A NAME="method_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="getReturn()"><!-- --></A><H3>\r
-getReturn</H3>\r
-<PRE>\r
-public <A HREF="../../../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A> <B>getReturn</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>returns PresetManager</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="setReturn(compbio.metadata.PresetManager)"><!-- --></A><H3>\r
-setReturn</H3>\r
-<PRE>\r
-public void <B>setReturn</B>(<A HREF="../../../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>&nbsp;_return)</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>_return</CODE> - the value for the _return property</DL>\r
-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/GetPresetsResponse.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../../compbio/data/msa/jaxws/GetPresets.html" title="class in compbio.data.msa.jaxws"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../../compbio/data/msa/jaxws/GetProgress.html" title="class in compbio.data.msa.jaxws"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/data/msa/jaxws/GetPresetsResponse.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="GetPresetsResponse.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/data/msa/jaxws/GetProgress.html b/website/full_javadoc/compbio/data/msa/jaxws/GetProgress.html

deleted file mode 100644 (file)

index 97f3af9..0000000
--- a/website/full_javadoc/compbio/data/msa/jaxws/GetProgress.html
+++ /dev/null
@@ -1,272 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-GetProgress\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="GetProgress";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/GetProgress.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../../compbio/data/msa/jaxws/GetPresetsResponse.html" title="class in compbio.data.msa.jaxws"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../../compbio/data/msa/jaxws/GetProgressResponse.html" title="class in compbio.data.msa.jaxws"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/data/msa/jaxws/GetProgress.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="GetProgress.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.data.msa.jaxws</FONT>\r
-<BR>\r
-Class GetProgress</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../../../resources/inherit.gif" ALT="extended by "><B>compbio.data.msa.jaxws.GetProgress</B>\r
-</PRE>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public class <B>GetProgress</B><DT>extends java.lang.Object</DL>\r
-</PRE>\r
-\r
-<P>\r
-<HR>\r
-\r
-<P>\r
-\r
-<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
-\r
-<A NAME="constructor_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Constructor Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../../compbio/data/msa/jaxws/GetProgress.html#GetProgress()">GetProgress</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/data/msa/jaxws/GetProgress.html#getJobId()">getJobId</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/data/msa/jaxws/GetProgress.html#setJobId(java.lang.String)">setJobId</A></B>(java.lang.String&nbsp;jobId)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
-\r
-<A NAME="constructor_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Constructor Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="GetProgress()"><!-- --></A><H3>\r
-GetProgress</H3>\r
-<PRE>\r
-public <B>GetProgress</B>()</PRE>\r
-<DL>\r
-</DL>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
-<A NAME="method_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="getJobId()"><!-- --></A><H3>\r
-getJobId</H3>\r
-<PRE>\r
-public java.lang.String <B>getJobId</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>returns String</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="setJobId(java.lang.String)"><!-- --></A><H3>\r
-setJobId</H3>\r
-<PRE>\r
-public void <B>setJobId</B>(java.lang.String&nbsp;jobId)</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>jobId</CODE> - the value for the jobId property</DL>\r
-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/GetProgress.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../../compbio/data/msa/jaxws/GetPresetsResponse.html" title="class in compbio.data.msa.jaxws"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../../compbio/data/msa/jaxws/GetProgressResponse.html" title="class in compbio.data.msa.jaxws"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/data/msa/jaxws/GetProgress.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="GetProgress.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/data/msa/jaxws/GetProgressResponse.html b/website/full_javadoc/compbio/data/msa/jaxws/GetProgressResponse.html

deleted file mode 100644 (file)

index 0f30084..0000000
--- a/website/full_javadoc/compbio/data/msa/jaxws/GetProgressResponse.html
+++ /dev/null
@@ -1,272 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-GetProgressResponse\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="GetProgressResponse";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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-<FONT SIZE="-1">\r
-compbio.data.msa.jaxws</FONT>\r
-<BR>\r
-Class GetProgressResponse</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../../../resources/inherit.gif" ALT="extended by "><B>compbio.data.msa.jaxws.GetProgressResponse</B>\r
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-\r
-<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
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-<B>Constructor Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../../compbio/data/msa/jaxws/GetProgressResponse.html#GetProgressResponse()">GetProgressResponse</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
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-<B>Method Summary</B></FONT></TH>\r
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-\r
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-<CODE>&nbsp;void</CODE></FONT></TD>\r
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-\r
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-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
-\r
-<A NAME="constructor_detail"><!-- --></A>\r
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-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Constructor Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="GetProgressResponse()"><!-- --></A><H3>\r
-GetProgressResponse</H3>\r
-<PRE>\r
-public <B>GetProgressResponse</B>()</PRE>\r
-<DL>\r
-</DL>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
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-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="getReturn()"><!-- --></A><H3>\r
-getReturn</H3>\r
-<PRE>\r
-public byte <B>getReturn</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>returns byte</DL>\r
-</DD>\r
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-<HR>\r
-\r
-<A NAME="setReturn(byte)"><!-- --></A><H3>\r
-setReturn</H3>\r
-<PRE>\r
-public void <B>setReturn</B>(byte&nbsp;_return)</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>_return</CODE> - the value for the _return property</DL>\r
-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
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-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
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-&nbsp;<A HREF="../../../../compbio/data/msa/jaxws/GetProgress.html" title="class in compbio.data.msa.jaxws"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../../compbio/data/msa/jaxws/GetResult.html" title="class in compbio.data.msa.jaxws"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
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-&nbsp;<SCRIPT type="text/javascript">\r
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diff --git a/website/full_javadoc/compbio/data/msa/jaxws/GetResult.html b/website/full_javadoc/compbio/data/msa/jaxws/GetResult.html

deleted file mode 100644 (file)

index c4e3b36..0000000
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+++ /dev/null
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-<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
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-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>\r
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-<B>Constructor Detail</B></FONT></TH>\r
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-</TABLE>\r
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-GetResult</H3>\r
-<PRE>\r
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-<B>Method Detail</B></FONT></TH>\r
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-\r
-<A NAME="getJobId()"><!-- --></A><H3>\r
-getJobId</H3>\r
-<PRE>\r
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-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>returns String</DL>\r
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-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
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-\r
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-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
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-&nbsp;<A HREF="../../../../compbio/data/msa/jaxws/GetProgressResponse.html" title="class in compbio.data.msa.jaxws"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../../compbio/data/msa/jaxws/GetResultResponse.html" title="class in compbio.data.msa.jaxws"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
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diff --git a/website/full_javadoc/compbio/data/msa/jaxws/GetResultResponse.html b/website/full_javadoc/compbio/data/msa/jaxws/GetResultResponse.html

deleted file mode 100644 (file)

index e5da690..0000000
--- a/website/full_javadoc/compbio/data/msa/jaxws/GetResultResponse.html
+++ /dev/null
@@ -1,272 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-GetResultResponse\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
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-\r
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-function windowTitle()\r
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-    }\r
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-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
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-&nbsp;<A HREF="../../../../compbio/data/msa/jaxws/GetRunnerOptions.html" title="class in compbio.data.msa.jaxws"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
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-  <!--\r
-  if(window==top) {\r
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-  }\r
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-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
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-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
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-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.data.msa.jaxws</FONT>\r
-<BR>\r
-Class GetResultResponse</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../../../resources/inherit.gif" ALT="extended by "><B>compbio.data.msa.jaxws.GetResultResponse</B>\r
-</PRE>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public class <B>GetResultResponse</B><DT>extends java.lang.Object</DL>\r
-</PRE>\r
-\r
-<P>\r
-<HR>\r
-\r
-<P>\r
-\r
-<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
-\r
-<A NAME="constructor_summary"><!-- --></A>\r
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-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Constructor Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../../compbio/data/msa/jaxws/GetResultResponse.html#GetResultResponse()">GetResultResponse</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
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-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/data/msa/jaxws/GetResultResponse.html#getReturn()">getReturn</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/data/msa/jaxws/GetResultResponse.html#setReturn(compbio.data.sequence.Alignment)">setReturn</A></B>(<A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A>&nbsp;_return)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
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-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>\r
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-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
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-<B>Constructor Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="GetResultResponse()"><!-- --></A><H3>\r
-GetResultResponse</H3>\r
-<PRE>\r
-public <B>GetResultResponse</B>()</PRE>\r
-<DL>\r
-</DL>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
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-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
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-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="getReturn()"><!-- --></A><H3>\r
-getReturn</H3>\r
-<PRE>\r
-public <A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A> <B>getReturn</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>returns Alignment</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="setReturn(compbio.data.sequence.Alignment)"><!-- --></A><H3>\r
-setReturn</H3>\r
-<PRE>\r
-public void <B>setReturn</B>(<A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A>&nbsp;_return)</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>_return</CODE> - the value for the _return property</DL>\r
-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/GetResultResponse.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../../compbio/data/msa/jaxws/GetResult.html" title="class in compbio.data.msa.jaxws"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../../compbio/data/msa/jaxws/GetRunnerOptions.html" title="class in compbio.data.msa.jaxws"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/data/msa/jaxws/GetResultResponse.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="GetResultResponse.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
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-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
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diff --git a/website/full_javadoc/compbio/data/msa/jaxws/GetRunnerOptions.html b/website/full_javadoc/compbio/data/msa/jaxws/GetRunnerOptions.html

deleted file mode 100644 (file)

index e3125c6..0000000
--- a/website/full_javadoc/compbio/data/msa/jaxws/GetRunnerOptions.html
+++ /dev/null
@@ -1,224 +0,0 @@
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-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
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-GetRunnerOptions\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="GetRunnerOptions";\r
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-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
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-Class GetRunnerOptions</H2>\r
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-java.lang.Object\r
-  <IMG SRC="../../../../resources/inherit.gif" ALT="extended by "><B>compbio.data.msa.jaxws.GetRunnerOptions</B>\r
-</PRE>\r
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-<DL>\r
-<DT><PRE>public class <B>GetRunnerOptions</B><DT>extends java.lang.Object</DL>\r
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-\r
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-\r
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-<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
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-<B>Constructor Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../../compbio/data/msa/jaxws/GetRunnerOptions.html#GetRunnerOptions()">GetRunnerOptions</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
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-<B>Constructor Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="GetRunnerOptions()"><!-- --></A><H3>\r
-GetRunnerOptions</H3>\r
-<PRE>\r
-public <B>GetRunnerOptions</B>()</PRE>\r
-<DL>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
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-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
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diff --git a/website/full_javadoc/compbio/data/msa/jaxws/GetRunnerOptionsResponse.html b/website/full_javadoc/compbio/data/msa/jaxws/GetRunnerOptionsResponse.html

deleted file mode 100644 (file)

index ddc4c44..0000000
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+++ /dev/null
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-Class GetRunnerOptionsResponse</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../../../resources/inherit.gif" ALT="extended by "><B>compbio.data.msa.jaxws.GetRunnerOptionsResponse</B>\r
-</PRE>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public class <B>GetRunnerOptionsResponse</B><DT>extends java.lang.Object</DL>\r
-</PRE>\r
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-<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
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-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../../compbio/data/msa/jaxws/GetRunnerOptionsResponse.html#GetRunnerOptionsResponse()">GetRunnerOptionsResponse</A></B>()</CODE>\r
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-GetRunnerOptionsResponse</H3>\r
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-<DL>\r
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diff --git a/website/full_javadoc/compbio/data/msa/jaxws/JobExecutionExceptionBean.html b/website/full_javadoc/compbio/data/msa/jaxws/JobExecutionExceptionBean.html

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diff --git a/website/full_javadoc/compbio/data/msa/jaxws/JobSubmissionExceptionBean.html b/website/full_javadoc/compbio/data/msa/jaxws/JobSubmissionExceptionBean.html

deleted file mode 100644 (file)

index 53f43dd..0000000
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-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
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-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/data/msa/jaxws/LimitExceededExceptionBean.html#setNumberOfSequencesAllowed(int)">setNumberOfSequencesAllowed</A></B>(int&nbsp;numberOfSequencesAllowed)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/data/msa/jaxws/LimitExceededExceptionBean.html#setSequenceLenghtActual(int)">setSequenceLenghtActual</A></B>(int&nbsp;sequenceLenghtActual)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/data/msa/jaxws/LimitExceededExceptionBean.html#setSequenceLenghtAllowed(int)">setSequenceLenghtAllowed</A></B>(int&nbsp;sequenceLenghtAllowed)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
-\r
-<A NAME="constructor_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Constructor Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="LimitExceededExceptionBean()"><!-- --></A><H3>\r
-LimitExceededExceptionBean</H3>\r
-<PRE>\r
-public <B>LimitExceededExceptionBean</B>()</PRE>\r
-<DL>\r
-</DL>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
-<A NAME="method_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="getActualNumberofSequences()"><!-- --></A><H3>\r
-getActualNumberofSequences</H3>\r
-<PRE>\r
-public int <B>getActualNumberofSequences</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>returns int</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="setActualNumberofSequences(int)"><!-- --></A><H3>\r
-setActualNumberofSequences</H3>\r
-<PRE>\r
-public void <B>setActualNumberofSequences</B>(int&nbsp;actualNumberofSequences)</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>actualNumberofSequences</CODE> - the value for the actualNumberofSequences property</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getMessage()"><!-- --></A><H3>\r
-getMessage</H3>\r
-<PRE>\r
-public java.lang.String <B>getMessage</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>returns String</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="setMessage(java.lang.String)"><!-- --></A><H3>\r
-setMessage</H3>\r
-<PRE>\r
-public void <B>setMessage</B>(java.lang.String&nbsp;message)</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>message</CODE> - the value for the message property</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getNumberOfSequencesAllowed()"><!-- --></A><H3>\r
-getNumberOfSequencesAllowed</H3>\r
-<PRE>\r
-public int <B>getNumberOfSequencesAllowed</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>returns int</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="setNumberOfSequencesAllowed(int)"><!-- --></A><H3>\r
-setNumberOfSequencesAllowed</H3>\r
-<PRE>\r
-public void <B>setNumberOfSequencesAllowed</B>(int&nbsp;numberOfSequencesAllowed)</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>numberOfSequencesAllowed</CODE> - the value for the numberOfSequencesAllowed property</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getSequenceLenghtActual()"><!-- --></A><H3>\r
-getSequenceLenghtActual</H3>\r
-<PRE>\r
-public int <B>getSequenceLenghtActual</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>returns int</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="setSequenceLenghtActual(int)"><!-- --></A><H3>\r
-setSequenceLenghtActual</H3>\r
-<PRE>\r
-public void <B>setSequenceLenghtActual</B>(int&nbsp;sequenceLenghtActual)</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>sequenceLenghtActual</CODE> - the value for the sequenceLenghtActual property</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getSequenceLenghtAllowed()"><!-- --></A><H3>\r
-getSequenceLenghtAllowed</H3>\r
-<PRE>\r
-public int <B>getSequenceLenghtAllowed</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>returns int</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="setSequenceLenghtAllowed(int)"><!-- --></A><H3>\r
-setSequenceLenghtAllowed</H3>\r
-<PRE>\r
-public void <B>setSequenceLenghtAllowed</B>(int&nbsp;sequenceLenghtAllowed)</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>sequenceLenghtAllowed</CODE> - the value for the sequenceLenghtAllowed property</DL>\r
-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/LimitExceededExceptionBean.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../../compbio/data/msa/jaxws/JobSubmissionExceptionBean.html" title="class in compbio.data.msa.jaxws"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../../compbio/data/msa/jaxws/PresetAlign.html" title="class in compbio.data.msa.jaxws"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/data/msa/jaxws/LimitExceededExceptionBean.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="LimitExceededExceptionBean.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
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-\r
-\r
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-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
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-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
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diff --git a/website/full_javadoc/compbio/data/msa/jaxws/PresetAlign.html b/website/full_javadoc/compbio/data/msa/jaxws/PresetAlign.html

deleted file mode 100644 (file)

index 57cf5af..0000000
--- a/website/full_javadoc/compbio/data/msa/jaxws/PresetAlign.html
+++ /dev/null
@@ -1,311 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-PresetAlign\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="PresetAlign";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/PresetAlign.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../../compbio/data/msa/jaxws/LimitExceededExceptionBean.html" title="class in compbio.data.msa.jaxws"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../../compbio/data/msa/jaxws/PresetAlignResponse.html" title="class in compbio.data.msa.jaxws"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/data/msa/jaxws/PresetAlign.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="PresetAlign.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.data.msa.jaxws</FONT>\r
-<BR>\r
-Class PresetAlign</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../../../resources/inherit.gif" ALT="extended by "><B>compbio.data.msa.jaxws.PresetAlign</B>\r
-</PRE>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public class <B>PresetAlign</B><DT>extends java.lang.Object</DL>\r
-</PRE>\r
-\r
-<P>\r
-<HR>\r
-\r
-<P>\r
-\r
-<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
-\r
-<A NAME="constructor_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Constructor Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../../compbio/data/msa/jaxws/PresetAlign.html#PresetAlign()">PresetAlign</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/data/msa/jaxws/PresetAlign.html#getFastaSequences()">getFastaSequences</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/data/msa/jaxws/PresetAlign.html#getPreset()">getPreset</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/data/msa/jaxws/PresetAlign.html#setFastaSequences(java.util.List)">setFastaSequences</A></B>(java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;fastaSequences)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/data/msa/jaxws/PresetAlign.html#setPreset(compbio.metadata.Preset)">setPreset</A></B>(<A HREF="../../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>&nbsp;preset)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
-\r
-<A NAME="constructor_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Constructor Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="PresetAlign()"><!-- --></A><H3>\r
-PresetAlign</H3>\r
-<PRE>\r
-public <B>PresetAlign</B>()</PRE>\r
-<DL>\r
-</DL>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
-<A NAME="method_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="getFastaSequences()"><!-- --></A><H3>\r
-getFastaSequences</H3>\r
-<PRE>\r
-public java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt; <B>getFastaSequences</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>returns List<FastaSequence></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="setFastaSequences(java.util.List)"><!-- --></A><H3>\r
-setFastaSequences</H3>\r
-<PRE>\r
-public void <B>setFastaSequences</B>(java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;fastaSequences)</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>fastaSequences</CODE> - the value for the fastaSequences property</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getPreset()"><!-- --></A><H3>\r
-getPreset</H3>\r
-<PRE>\r
-public <A HREF="../../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A> <B>getPreset</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>returns Preset</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="setPreset(compbio.metadata.Preset)"><!-- --></A><H3>\r
-setPreset</H3>\r
-<PRE>\r
-public void <B>setPreset</B>(<A HREF="../../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>&nbsp;preset)</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>preset</CODE> - the value for the preset property</DL>\r
-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/PresetAlign.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../../compbio/data/msa/jaxws/LimitExceededExceptionBean.html" title="class in compbio.data.msa.jaxws"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../../compbio/data/msa/jaxws/PresetAlignResponse.html" title="class in compbio.data.msa.jaxws"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/data/msa/jaxws/PresetAlign.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="PresetAlign.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/data/msa/jaxws/PresetAlignResponse.html b/website/full_javadoc/compbio/data/msa/jaxws/PresetAlignResponse.html

deleted file mode 100644 (file)

index 318712e..0000000
--- a/website/full_javadoc/compbio/data/msa/jaxws/PresetAlignResponse.html
+++ /dev/null
@@ -1,272 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-PresetAlignResponse\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="PresetAlignResponse";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/PresetAlignResponse.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../../compbio/data/msa/jaxws/PresetAlign.html" title="class in compbio.data.msa.jaxws"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../../compbio/data/msa/jaxws/PullExecStatistics.html" title="class in compbio.data.msa.jaxws"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/data/msa/jaxws/PresetAlignResponse.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="PresetAlignResponse.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.data.msa.jaxws</FONT>\r
-<BR>\r
-Class PresetAlignResponse</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../../../resources/inherit.gif" ALT="extended by "><B>compbio.data.msa.jaxws.PresetAlignResponse</B>\r
-</PRE>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public class <B>PresetAlignResponse</B><DT>extends java.lang.Object</DL>\r
-</PRE>\r
-\r
-<P>\r
-<HR>\r
-\r
-<P>\r
-\r
-<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
-\r
-<A NAME="constructor_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Constructor Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../../compbio/data/msa/jaxws/PresetAlignResponse.html#PresetAlignResponse()">PresetAlignResponse</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/data/msa/jaxws/PresetAlignResponse.html#getReturn()">getReturn</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/data/msa/jaxws/PresetAlignResponse.html#setReturn(java.lang.String)">setReturn</A></B>(java.lang.String&nbsp;_return)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
-\r
-<A NAME="constructor_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Constructor Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="PresetAlignResponse()"><!-- --></A><H3>\r
-PresetAlignResponse</H3>\r
-<PRE>\r
-public <B>PresetAlignResponse</B>()</PRE>\r
-<DL>\r
-</DL>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
-<A NAME="method_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="getReturn()"><!-- --></A><H3>\r
-getReturn</H3>\r
-<PRE>\r
-public java.lang.String <B>getReturn</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>returns String</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="setReturn(java.lang.String)"><!-- --></A><H3>\r
-setReturn</H3>\r
-<PRE>\r
-public void <B>setReturn</B>(java.lang.String&nbsp;_return)</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>_return</CODE> - the value for the _return property</DL>\r
-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/PresetAlignResponse.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../../compbio/data/msa/jaxws/PresetAlign.html" title="class in compbio.data.msa.jaxws"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../../compbio/data/msa/jaxws/PullExecStatistics.html" title="class in compbio.data.msa.jaxws"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/data/msa/jaxws/PresetAlignResponse.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="PresetAlignResponse.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/data/msa/jaxws/PullExecStatistics.html b/website/full_javadoc/compbio/data/msa/jaxws/PullExecStatistics.html

deleted file mode 100644 (file)

index 1ab6ead..0000000
--- a/website/full_javadoc/compbio/data/msa/jaxws/PullExecStatistics.html
+++ /dev/null
@@ -1,311 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-PullExecStatistics\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
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-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="PullExecStatistics";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
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-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/PullExecStatistics.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
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-&nbsp;<A HREF="../../../../compbio/data/msa/jaxws/PullExecStatisticsResponse.html" title="class in compbio.data.msa.jaxws"><B>NEXT CLASS</B></A></FONT></TD>\r
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-  <!--\r
-  if(window==top) {\r
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-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.data.msa.jaxws</FONT>\r
-<BR>\r
-Class PullExecStatistics</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../../../resources/inherit.gif" ALT="extended by "><B>compbio.data.msa.jaxws.PullExecStatistics</B>\r
-</PRE>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public class <B>PullExecStatistics</B><DT>extends java.lang.Object</DL>\r
-</PRE>\r
-\r
-<P>\r
-<HR>\r
-\r
-<P>\r
-\r
-<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
-\r
-<A NAME="constructor_summary"><!-- --></A>\r
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-<B>Constructor Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../../compbio/data/msa/jaxws/PullExecStatistics.html#PullExecStatistics()">PullExecStatistics</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
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-<B>Method Summary</B></FONT></TH>\r
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-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/data/msa/jaxws/PullExecStatistics.html#getJobId()">getJobId</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;long</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/data/msa/jaxws/PullExecStatistics.html#getPosition()">getPosition</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/data/msa/jaxws/PullExecStatistics.html#setJobId(java.lang.String)">setJobId</A></B>(java.lang.String&nbsp;jobId)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/data/msa/jaxws/PullExecStatistics.html#setPosition(long)">setPosition</A></B>(long&nbsp;position)</CODE>\r
-\r
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-<B>Constructor Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="PullExecStatistics()"><!-- --></A><H3>\r
-PullExecStatistics</H3>\r
-<PRE>\r
-public <B>PullExecStatistics</B>()</PRE>\r
-<DL>\r
-</DL>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
-<A NAME="method_detail"><!-- --></A>\r
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-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="getJobId()"><!-- --></A><H3>\r
-getJobId</H3>\r
-<PRE>\r
-public java.lang.String <B>getJobId</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>returns String</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="setJobId(java.lang.String)"><!-- --></A><H3>\r
-setJobId</H3>\r
-<PRE>\r
-public void <B>setJobId</B>(java.lang.String&nbsp;jobId)</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>jobId</CODE> - the value for the jobId property</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getPosition()"><!-- --></A><H3>\r
-getPosition</H3>\r
-<PRE>\r
-public long <B>getPosition</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>returns long</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
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-setPosition</H3>\r
-<PRE>\r
-public void <B>setPosition</B>(long&nbsp;position)</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>position</CODE> - the value for the position property</DL>\r
-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
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-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
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-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
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diff --git a/website/full_javadoc/compbio/data/msa/jaxws/PullExecStatisticsResponse.html b/website/full_javadoc/compbio/data/msa/jaxws/PullExecStatisticsResponse.html

deleted file mode 100644 (file)

index a5658d1..0000000
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-Class PullExecStatisticsResponse</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../../../resources/inherit.gif" ALT="extended by "><B>compbio.data.msa.jaxws.PullExecStatisticsResponse</B>\r
-</PRE>\r
-<HR>\r
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-<DT><PRE>public class <B>PullExecStatisticsResponse</B><DT>extends java.lang.Object</DL>\r
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-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
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-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/data/msa/jaxws/PullExecStatisticsResponse.html#getReturn()">getReturn</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/data/msa/jaxws/PullExecStatisticsResponse.html#setReturn(compbio.metadata.ChunkHolder)">setReturn</A></B>(<A HREF="../../../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A>&nbsp;_return)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
-\r
-<A NAME="constructor_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Constructor Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="PullExecStatisticsResponse()"><!-- --></A><H3>\r
-PullExecStatisticsResponse</H3>\r
-<PRE>\r
-public <B>PullExecStatisticsResponse</B>()</PRE>\r
-<DL>\r
-</DL>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
-<A NAME="method_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="getReturn()"><!-- --></A><H3>\r
-getReturn</H3>\r
-<PRE>\r
-public <A HREF="../../../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A> <B>getReturn</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>returns ChunkHolder</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="setReturn(compbio.metadata.ChunkHolder)"><!-- --></A><H3>\r
-setReturn</H3>\r
-<PRE>\r
-public void <B>setReturn</B>(<A HREF="../../../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A>&nbsp;_return)</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>_return</CODE> - the value for the _return property</DL>\r
-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/PullExecStatisticsResponse.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
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-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
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-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../../compbio/data/msa/jaxws/PullExecStatistics.html" title="class in compbio.data.msa.jaxws"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../../compbio/data/msa/jaxws/PullFile.html" title="class in compbio.data.msa.jaxws"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/data/msa/jaxws/PullExecStatisticsResponse.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="PullExecStatisticsResponse.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/data/msa/jaxws/PullFile.html b/website/full_javadoc/compbio/data/msa/jaxws/PullFile.html

deleted file mode 100644 (file)

index ff92d78..0000000
--- a/website/full_javadoc/compbio/data/msa/jaxws/PullFile.html
+++ /dev/null
@@ -1,311 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-PullFile\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="PullFile";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/PullFile.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../../compbio/data/msa/jaxws/PullExecStatisticsResponse.html" title="class in compbio.data.msa.jaxws"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../../compbio/data/msa/jaxws/PullFileResponse.html" title="class in compbio.data.msa.jaxws"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/data/msa/jaxws/PullFile.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="PullFile.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.data.msa.jaxws</FONT>\r
-<BR>\r
-Class PullFile</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../../../resources/inherit.gif" ALT="extended by "><B>compbio.data.msa.jaxws.PullFile</B>\r
-</PRE>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public class <B>PullFile</B><DT>extends java.lang.Object</DL>\r
-</PRE>\r
-\r
-<P>\r
-<HR>\r
-\r
-<P>\r
-\r
-<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
-\r
-<A NAME="constructor_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Constructor Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../../compbio/data/msa/jaxws/PullFile.html#PullFile()">PullFile</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
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-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/data/msa/jaxws/PullFile.html#getJobId()">getJobId</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;long</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/data/msa/jaxws/PullFile.html#getPosition()">getPosition</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/data/msa/jaxws/PullFile.html#setJobId(java.lang.String)">setJobId</A></B>(java.lang.String&nbsp;jobId)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/data/msa/jaxws/PullFile.html#setPosition(long)">setPosition</A></B>(long&nbsp;position)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
-\r
-<A NAME="constructor_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Constructor Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="PullFile()"><!-- --></A><H3>\r
-PullFile</H3>\r
-<PRE>\r
-public <B>PullFile</B>()</PRE>\r
-<DL>\r
-</DL>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
-<A NAME="method_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="getJobId()"><!-- --></A><H3>\r
-getJobId</H3>\r
-<PRE>\r
-public java.lang.String <B>getJobId</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>returns String</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="setJobId(java.lang.String)"><!-- --></A><H3>\r
-setJobId</H3>\r
-<PRE>\r
-public void <B>setJobId</B>(java.lang.String&nbsp;jobId)</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>jobId</CODE> - the value for the jobId property</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getPosition()"><!-- --></A><H3>\r
-getPosition</H3>\r
-<PRE>\r
-public long <B>getPosition</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>returns long</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="setPosition(long)"><!-- --></A><H3>\r
-setPosition</H3>\r
-<PRE>\r
-public void <B>setPosition</B>(long&nbsp;position)</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>position</CODE> - the value for the position property</DL>\r
-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/PullFile.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
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-&nbsp;<A HREF="../../../../compbio/data/msa/jaxws/PullExecStatisticsResponse.html" title="class in compbio.data.msa.jaxws"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../../compbio/data/msa/jaxws/PullFileResponse.html" title="class in compbio.data.msa.jaxws"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/data/msa/jaxws/PullFile.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="PullFile.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
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-\r
-\r
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-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
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-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
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diff --git a/website/full_javadoc/compbio/data/msa/jaxws/PullFileResponse.html b/website/full_javadoc/compbio/data/msa/jaxws/PullFileResponse.html

deleted file mode 100644 (file)

index 966917b..0000000
--- a/website/full_javadoc/compbio/data/msa/jaxws/PullFileResponse.html
+++ /dev/null
@@ -1,272 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-PullFileResponse\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="PullFileResponse";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
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-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/PullFileResponse.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
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-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../../compbio/data/msa/jaxws/PullFile.html" title="class in compbio.data.msa.jaxws"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../../compbio/data/msa/jaxws/ResultNotAvailableExceptionBean.html" title="class in compbio.data.msa.jaxws"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/data/msa/jaxws/PullFileResponse.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="PullFileResponse.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
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-\r
-\r
-</FONT></TD>\r
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-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.data.msa.jaxws</FONT>\r
-<BR>\r
-Class PullFileResponse</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../../../resources/inherit.gif" ALT="extended by "><B>compbio.data.msa.jaxws.PullFileResponse</B>\r
-</PRE>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public class <B>PullFileResponse</B><DT>extends java.lang.Object</DL>\r
-</PRE>\r
-\r
-<P>\r
-<HR>\r
-\r
-<P>\r
-\r
-<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
-\r
-<A NAME="constructor_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Constructor Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../../compbio/data/msa/jaxws/PullFileResponse.html#PullFileResponse()">PullFileResponse</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/data/msa/jaxws/PullFileResponse.html#getReturn()">getReturn</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/data/msa/jaxws/PullFileResponse.html#setReturn(compbio.metadata.ChunkHolder)">setReturn</A></B>(<A HREF="../../../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A>&nbsp;_return)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
-\r
-<A NAME="constructor_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Constructor Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="PullFileResponse()"><!-- --></A><H3>\r
-PullFileResponse</H3>\r
-<PRE>\r
-public <B>PullFileResponse</B>()</PRE>\r
-<DL>\r
-</DL>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
-<A NAME="method_detail"><!-- --></A>\r
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-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="getReturn()"><!-- --></A><H3>\r
-getReturn</H3>\r
-<PRE>\r
-public <A HREF="../../../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A> <B>getReturn</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>returns ChunkHolder</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="setReturn(compbio.metadata.ChunkHolder)"><!-- --></A><H3>\r
-setReturn</H3>\r
-<PRE>\r
-public void <B>setReturn</B>(<A HREF="../../../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A>&nbsp;_return)</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>_return</CODE> - the value for the _return property</DL>\r
-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
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-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/PullFileResponse.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../../compbio/data/msa/jaxws/PullFile.html" title="class in compbio.data.msa.jaxws"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../../compbio/data/msa/jaxws/ResultNotAvailableExceptionBean.html" title="class in compbio.data.msa.jaxws"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/data/msa/jaxws/PullFileResponse.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="PullFileResponse.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/data/msa/jaxws/ResultNotAvailableExceptionBean.html b/website/full_javadoc/compbio/data/msa/jaxws/ResultNotAvailableExceptionBean.html

deleted file mode 100644 (file)

index 9f89492..0000000
--- a/website/full_javadoc/compbio/data/msa/jaxws/ResultNotAvailableExceptionBean.html
+++ /dev/null
@@ -1,278 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-ResultNotAvailableExceptionBean\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="ResultNotAvailableExceptionBean";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
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-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/ResultNotAvailableExceptionBean.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../../compbio/data/msa/jaxws/PullFileResponse.html" title="class in compbio.data.msa.jaxws"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../../compbio/data/msa/jaxws/UnsupportedRuntimeExceptionBean.html" title="class in compbio.data.msa.jaxws"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/data/msa/jaxws/ResultNotAvailableExceptionBean.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="ResultNotAvailableExceptionBean.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
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diff --git a/website/full_javadoc/compbio/data/msa/jaxws/WrongParameterExceptionBean.html b/website/full_javadoc/compbio/data/msa/jaxws/WrongParameterExceptionBean.html

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diff --git a/website/full_javadoc/compbio/data/msa/jaxws/class-use/Align.html b/website/full_javadoc/compbio/data/msa/jaxws/class-use/Align.html

deleted file mode 100644 (file)

index 63a3520..0000000
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deleted file mode 100644 (file)

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deleted file mode 100644 (file)

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deleted file mode 100644 (file)

index 6aa2d31..0000000
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deleted file mode 100644 (file)

index 772c60a..0000000
--- a/website/full_javadoc/compbio/data/msa/jaxws/class-use/CustomAlign.html
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-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
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-<!-- ========= END OF TOP NAVBAR ========= -->\r
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-<B>Uses of Class<br>compbio.data.msa.jaxws.CustomAlign</B></H2>\r
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deleted file mode 100644 (file)

index f7e6474..0000000
--- a/website/full_javadoc/compbio/data/msa/jaxws/class-use/CustomAlignResponse.html
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deleted file mode 100644 (file)

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deleted file mode 100644 (file)

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deleted file mode 100644 (file)

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deleted file mode 100644 (file)

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deleted file mode 100644 (file)

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deleted file mode 100644 (file)

index e71130c..0000000
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deleted file mode 100644 (file)

index 5778f27..0000000
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deleted file mode 100644 (file)

index 1301129..0000000
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deleted file mode 100644 (file)

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deleted file mode 100644 (file)

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deleted file mode 100644 (file)

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deleted file mode 100644 (file)

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deleted file mode 100644 (file)

index 7052726..0000000
--- a/website/full_javadoc/compbio/data/msa/jaxws/class-use/UnsupportedRuntimeExceptionBean.html
+++ /dev/null
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deleted file mode 100644 (file)

index 3a1887a..0000000
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-    if (location.href.indexOf('is-external=true') == -1) {\r
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deleted file mode 100644 (file)

index 1ad4c67..0000000
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deleted file mode 100644 (file)

index d6430f0..0000000
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diff --git a/website/full_javadoc/compbio/data/msa/package-summary.html b/website/full_javadoc/compbio/data/msa/package-summary.html

deleted file mode 100644 (file)

index 3cb53ac..0000000
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diff --git a/website/full_javadoc/compbio/data/msa/package-tree.html b/website/full_javadoc/compbio/data/msa/package-tree.html

deleted file mode 100644 (file)

index 5c3f09e..0000000
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diff --git a/website/full_javadoc/compbio/data/msa/package-use.html b/website/full_javadoc/compbio/data/msa/package-use.html

deleted file mode 100644 (file)

index 1d034e0..0000000
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-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.ws.client"><B>compbio.ws.client</B></A></TD>\r
-<TD>&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.ws.server"><B>compbio.ws.server</B></A></TD>\r
-<TD>&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.ws.client"><!-- --></A>\r
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-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../../compbio/data/msa/class-use/MsaWS.html#compbio.ws.client"><B>MsaWS</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Multiple Sequence Alignment (MSA) Web Services Interface</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.ws.server"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
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-Classes in <A HREF="../../../compbio/data/msa/package-summary.html">compbio.data.msa</A> used by <A HREF="../../../compbio/ws/server/package-summary.html">compbio.ws.server</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../../compbio/data/msa/class-use/MsaWS.html#compbio.ws.server"><B>MsaWS</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Multiple Sequence Alignment (MSA) Web Services Interface</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<HR>\r
-\r
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-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
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-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
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-</TABLE>\r
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-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
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-&nbsp;NEXT</FONT></TD>\r
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-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
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-<A NAME="skip-navbar_bottom"></A>\r
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diff --git a/website/full_javadoc/compbio/data/sequence/Alignment.html b/website/full_javadoc/compbio/data/sequence/Alignment.html

deleted file mode 100644 (file)

index 8cad073..0000000
--- a/website/full_javadoc/compbio/data/sequence/Alignment.html
+++ /dev/null
@@ -1,381 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:49 GMT 2010 -->\r
-<TITLE>\r
-Alignment\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Alignment";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/Alignment.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
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-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV CLASS&nbsp;\r
-&nbsp;<A HREF="../../../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/data/sequence/Alignment.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="Alignment.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
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-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.data.sequence</FONT>\r
-<BR>\r
-Class Alignment</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.data.sequence.Alignment</B>\r
-</PRE>\r
-<HR>\r
-<DL>\r
-<DT><PRE><FONT SIZE="-1">@Immutable\r
-</FONT>public final class <B>Alignment</B><DT>extends java.lang.Object</DL>\r
-</PRE>\r
-\r
-<P>\r
-Multiple sequence alignment.
- 
- Does not give any guarantees on the content of individual FastaSequece
- records. That is it does not guarantee that the neither the names of
- sequences or the sequences themselves are unique.\r
-<P>\r
-\r
-<P>\r
-<DL>\r
-<DT><B>Author:</B></DT>\r
-  <DD>pvtroshin
- 
-         Date September 2009</DD>\r
-<DT><B>See Also:</B><DD><A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence"><CODE>FastaSequence</CODE></A>, \r
-<A HREF="../../../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence"><CODE>AlignmentMetadata</CODE></A></DL>\r
-<HR>\r
-\r
-<P>\r
-\r
-<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
-\r
-<A NAME="constructor_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Constructor Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/Alignment.html#Alignment(java.util.List, compbio.data.sequence.AlignmentMetadata)">Alignment</A></B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-          <A HREF="../../../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence">AlignmentMetadata</A>&nbsp;metadata)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/Alignment.html#Alignment(java.util.List, compbio.data.sequence.Program, char)">Alignment</A></B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-          <A HREF="../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A>&nbsp;program,\r
-          char&nbsp;gapchar)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/Alignment.html#equals(java.lang.Object)">equals</A></B>(java.lang.Object&nbsp;obj)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Please note that this implementation does not take the order of sequences
- into account!</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence">AlignmentMetadata</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/Alignment.html#getMetadata()">getMetadata</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/Alignment.html#getSequences()">getSequences</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;int</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/Alignment.html#getSize()">getSize</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/Alignment.html#toString()">toString</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>getClass, hashCode, notify, notifyAll, wait, wait, wait</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
-\r
-<A NAME="constructor_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Constructor Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="Alignment(java.util.List, compbio.data.sequence.Program, char)"><!-- --></A><H3>\r
-Alignment</H3>\r
-<PRE>\r
-public <B>Alignment</B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-                 <A HREF="../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A>&nbsp;program,\r
-                 char&nbsp;gapchar)</PRE>\r
-<DL>\r
-<DL>\r
-<DT><B>Parameters:</B><DD><CODE>sequences</CODE> - <DD><CODE>program</CODE> - <DD><CODE>gapchar</CODE> - </DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="Alignment(java.util.List, compbio.data.sequence.AlignmentMetadata)"><!-- --></A><H3>\r
-Alignment</H3>\r
-<PRE>\r
-public <B>Alignment</B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-                 <A HREF="../../../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence">AlignmentMetadata</A>&nbsp;metadata)</PRE>\r
-<DL>\r
-<DL>\r
-<DT><B>Parameters:</B><DD><CODE>sequences</CODE> - <DD><CODE>metadata</CODE> - </DL>\r
-</DL>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
-<A NAME="method_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="getSequences()"><!-- --></A><H3>\r
-getSequences</H3>\r
-<PRE>\r
-public java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt; <B>getSequences</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>list of FastaSequence records</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getSize()"><!-- --></A><H3>\r
-getSize</H3>\r
-<PRE>\r
-public int <B>getSize</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>a number of sequence in the alignment</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getMetadata()"><!-- --></A><H3>\r
-getMetadata</H3>\r
-<PRE>\r
-public <A HREF="../../../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence">AlignmentMetadata</A> <B>getMetadata</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>AlignmentMetadata object</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="toString()"><!-- --></A><H3>\r
-toString</H3>\r
-<PRE>\r
-public java.lang.String <B>toString</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Overrides:</B><DD><CODE>toString</CODE> in class <CODE>java.lang.Object</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="equals(java.lang.Object)"><!-- --></A><H3>\r
-equals</H3>\r
-<PRE>\r
-public boolean <B>equals</B>(java.lang.Object&nbsp;obj)</PRE>\r
-<DL>\r
-<DD>Please note that this implementation does not take the order of sequences
- into account!\r
-<P>\r
-<DD><DL>\r
-<DT><B>Overrides:</B><DD><CODE>equals</CODE> in class <CODE>java.lang.Object</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/Alignment.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV CLASS&nbsp;\r
-&nbsp;<A HREF="../../../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/data/sequence/Alignment.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="Alignment.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/data/sequence/AlignmentMetadata.html b/website/full_javadoc/compbio/data/sequence/AlignmentMetadata.html

deleted file mode 100644 (file)

index 6650404..0000000
--- a/website/full_javadoc/compbio/data/sequence/AlignmentMetadata.html
+++ /dev/null
@@ -1,329 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:49 GMT 2010 -->\r
-<TITLE>\r
-AlignmentMetadata\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="AlignmentMetadata";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/AlignmentMetadata.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/data/sequence/AlignmentMetadata.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="AlignmentMetadata.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.data.sequence</FONT>\r
-<BR>\r
-Class AlignmentMetadata</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.data.sequence.AlignmentMetadata</B>\r
-</PRE>\r
-<HR>\r
-<DL>\r
-<DT><PRE><FONT SIZE="-1">@Immutable\r
-</FONT>public class <B>AlignmentMetadata</B><DT>extends java.lang.Object</DL>\r
-</PRE>\r
-\r
-<P>\r
-Alignment metadata e.g. method/program being used to generate the alignment
- and its parameters\r
-<P>\r
-\r
-<P>\r
-<DL>\r
-<DT><B>Author:</B></DT>\r
-  <DD>pvtroshin
- 
-         Date September 2009</DD>\r
-</DL>\r
-<HR>\r
-\r
-<P>\r
-\r
-<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
-\r
-<A NAME="constructor_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Constructor Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/AlignmentMetadata.html#AlignmentMetadata(compbio.data.sequence.Program, char)">AlignmentMetadata</A></B>(<A HREF="../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A>&nbsp;program,\r
-                  char&nbsp;gapchar)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/AlignmentMetadata.html#equals(java.lang.Object)">equals</A></B>(java.lang.Object&nbsp;obj)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;char</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/AlignmentMetadata.html#getGapchar()">getGapchar</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/AlignmentMetadata.html#getProgram()">getProgram</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;int</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/AlignmentMetadata.html#hashCode()">hashCode</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>getClass, notify, notifyAll, toString, wait, wait, wait</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
-\r
-<A NAME="constructor_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Constructor Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="AlignmentMetadata(compbio.data.sequence.Program, char)"><!-- --></A><H3>\r
-AlignmentMetadata</H3>\r
-<PRE>\r
-public <B>AlignmentMetadata</B>(<A HREF="../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A>&nbsp;program,\r
-                         char&nbsp;gapchar)</PRE>\r
-<DL>\r
-</DL>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
-<A NAME="method_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="getProgram()"><!-- --></A><H3>\r
-getProgram</H3>\r
-<PRE>\r
-public <A HREF="../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A> <B>getProgram</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getGapchar()"><!-- --></A><H3>\r
-getGapchar</H3>\r
-<PRE>\r
-public char <B>getGapchar</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="equals(java.lang.Object)"><!-- --></A><H3>\r
-equals</H3>\r
-<PRE>\r
-public boolean <B>equals</B>(java.lang.Object&nbsp;obj)</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Overrides:</B><DD><CODE>equals</CODE> in class <CODE>java.lang.Object</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="hashCode()"><!-- --></A><H3>\r
-hashCode</H3>\r
-<PRE>\r
-public int <B>hashCode</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Overrides:</B><DD><CODE>hashCode</CODE> in class <CODE>java.lang.Object</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/AlignmentMetadata.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
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diff --git a/website/full_javadoc/compbio/data/sequence/ClustalAlignmentUtil.html b/website/full_javadoc/compbio/data/sequence/ClustalAlignmentUtil.html

deleted file mode 100644 (file)

index c7fb25a..0000000
--- a/website/full_javadoc/compbio/data/sequence/ClustalAlignmentUtil.html
+++ /dev/null
@@ -1,385 +0,0 @@
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-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:49 GMT 2010 -->\r
-<TITLE>\r
-ClustalAlignmentUtil\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
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-    if (location.href.indexOf('is-external=true') == -1) {\r
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-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;<A HREF="#field_detail">FIELD</A>&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
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-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.data.sequence</FONT>\r
-<BR>\r
-Class ClustalAlignmentUtil</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.data.sequence.ClustalAlignmentUtil</B>\r
-</PRE>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public final class <B>ClustalAlignmentUtil</B><DT>extends java.lang.Object</DL>\r
-</PRE>\r
-\r
-<P>\r
-Tools to read and write clustal formated files\r
-<P>\r
-\r
-<P>\r
-<DL>\r
-<DT><B>Author:</B></DT>\r
-  <DD>Petr Troshin based on jimp class
- 
-         Date September 2009</DD>\r
-</DL>\r
-<HR>\r
-\r
-<P>\r
-<!-- =========== FIELD SUMMARY =========== -->\r
-\r
-<A NAME="field_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Field Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;char</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/ClustalAlignmentUtil.html#gapchar">gapchar</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Dash char to be used as gap char in the alignments</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
-\r
-<A NAME="constructor_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Constructor Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/ClustalAlignmentUtil.html#ClustalAlignmentUtil()">ClustalAlignmentUtil</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/ClustalAlignmentUtil.html#isValidClustalFile(java.io.InputStream)">isValidClustalFile</A></B>(java.io.InputStream&nbsp;input)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/ClustalAlignmentUtil.html#readClustalFile(java.io.File)">readClustalFile</A></B>(java.io.File&nbsp;file)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/ClustalAlignmentUtil.html#readClustalFile(java.io.InputStream)">readClustalFile</A></B>(java.io.InputStream&nbsp;instream)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Read Clustal formatted alignment.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/ClustalAlignmentUtil.html#writeClustalAlignment(java.io.OutputStream, compbio.data.sequence.Alignment)">writeClustalAlignment</A></B>(java.io.OutputStream&nbsp;outStream,\r
-                      <A HREF="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A>&nbsp;alignment)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Write Clustal formatted alignment Limitations: does not record the
- consensus.</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ============ FIELD DETAIL =========== -->\r
-\r
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-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Field Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="gapchar"><!-- --></A><H3>\r
-gapchar</H3>\r
-<PRE>\r
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-<DL>\r
-<DD>Dash char to be used as gap char in the alignments\r
-<P>\r
-<DL>\r
-<DT><B>See Also:</B><DD><A HREF="../../../constant-values.html#compbio.data.sequence.ClustalAlignmentUtil.gapchar">Constant Field Values</A></DL>\r
-</DL>\r
-\r
-<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
-\r
-<A NAME="constructor_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Constructor Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="ClustalAlignmentUtil()"><!-- --></A><H3>\r
-ClustalAlignmentUtil</H3>\r
-<PRE>\r
-public <B>ClustalAlignmentUtil</B>()</PRE>\r
-<DL>\r
-</DL>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
-<A NAME="method_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="readClustalFile(java.io.InputStream)"><!-- --></A><H3>\r
-readClustalFile</H3>\r
-<PRE>\r
-public static <A HREF="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A> <B>readClustalFile</B>(java.io.InputStream&nbsp;instream)\r
-                                 throws java.io.IOException,\r
-                                        <A HREF="../../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</A></PRE>\r
-<DL>\r
-<DD>Read Clustal formatted alignment. Limitations: Does not read consensus
- 
- Sequence names as well as the sequences are not guaranteed to be unique!\r
-<P>\r
-<DD><DL>\r
-\r
-<DT><B>Throws:</B>\r
-<DD><CODE>{@link</CODE> - IOException}\r
-<DD><CODE>{@link</CODE> - UnknownFileFormatException}\r
-<DD><CODE>java.io.IOException</CODE>\r
-<DD><CODE><A HREF="../../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</A></CODE></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="isValidClustalFile(java.io.InputStream)"><!-- --></A><H3>\r
-isValidClustalFile</H3>\r
-<PRE>\r
-public static boolean <B>isValidClustalFile</B>(java.io.InputStream&nbsp;input)</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>input</CODE> - \r
-<DT><B>Returns:</B><DD>true if the file is recognised as Clustal formatted alignment,
-         false otherwise</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="writeClustalAlignment(java.io.OutputStream, compbio.data.sequence.Alignment)"><!-- --></A><H3>\r
-writeClustalAlignment</H3>\r
-<PRE>\r
-public static void <B>writeClustalAlignment</B>(java.io.OutputStream&nbsp;outStream,\r
-                                         <A HREF="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A>&nbsp;alignment)\r
-                                  throws java.io.IOException</PRE>\r
-<DL>\r
-<DD>Write Clustal formatted alignment Limitations: does not record the
- consensus. Potential bug - records 60 chars length alignment where
- Clustal would have recorded 50 chars.\r
-<P>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>outStream</CODE> - <DD><CODE>alignment</CODE> - \r
-<DT><B>Throws:</B>\r
-<DD><CODE>java.io.IOException</CODE></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="readClustalFile(java.io.File)"><!-- --></A><H3>\r
-readClustalFile</H3>\r
-<PRE>\r
-public static <A HREF="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A> <B>readClustalFile</B>(java.io.File&nbsp;file)\r
-                                 throws <A HREF="../../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</A>,\r
-                                        java.io.IOException</PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Throws:</B>\r
-<DD><CODE><A HREF="../../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</A></CODE>\r
-<DD><CODE>java.io.IOException</CODE></DL>\r
-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
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-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
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-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
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-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/ClustalAlignmentUtil.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
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-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence"><B>PREV CLASS</B></A>&nbsp;\r
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-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;<A HREF="#field_summary">FIELD</A>&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;<A HREF="#field_detail">FIELD</A>&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
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diff --git a/website/full_javadoc/compbio/data/sequence/FastaSequence.html b/website/full_javadoc/compbio/data/sequence/FastaSequence.html

deleted file mode 100644 (file)

index 07a1dcf..0000000
--- a/website/full_javadoc/compbio/data/sequence/FastaSequence.html
+++ /dev/null
@@ -1,448 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:49 GMT 2010 -->\r
-<TITLE>\r
-FastaSequence\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="FastaSequence";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
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-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/FastaSequence.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
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-</TD>\r
-</TR>\r
-\r
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-&nbsp;<A HREF="../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/data/sequence/FastaSequence.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="FastaSequence.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
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-</SCRIPT>\r
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-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
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-\r
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-<TR>\r
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-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.data.sequence</FONT>\r
-<BR>\r
-Class FastaSequence</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.data.sequence.FastaSequence</B>\r
-</PRE>\r
-<HR>\r
-<DL>\r
-<DT><PRE><FONT SIZE="-1">@Immutable\r
-</FONT>public class <B>FastaSequence</B><DT>extends java.lang.Object</DL>\r
-</PRE>\r
-\r
-<P>\r
-A FASTA formatted sequence. Please note that this class does not make any
- assumptions as to what sequence it store e.g. it could be nucleotide, protein
- or even gapped alignment sequence! The only guarantee it makes is that the
- sequence does not contain white space characters e.g. spaces, new lines etc\r
-<P>\r
-\r
-<P>\r
-<DL>\r
-<DT><B>Author:</B></DT>\r
-  <DD>pvtroshin
- 
-         Date September 2009</DD>\r
-</DL>\r
-<HR>\r
-\r
-<P>\r
-\r
-<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
-\r
-<A NAME="constructor_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Constructor Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/FastaSequence.html#FastaSequence(java.lang.String, java.lang.String)">FastaSequence</A></B>(java.lang.String&nbsp;id,\r
-              java.lang.String&nbsp;sequence)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Upon construction the any whitespace characters are removed from the
- sequence</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;int</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/FastaSequence.html#countMatchesInSequence(java.lang.String, java.lang.String)">countMatchesInSequence</A></B>(java.lang.String&nbsp;theString,\r
-                       java.lang.String&nbsp;theRegExp)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/FastaSequence.html#equals(java.lang.Object)">equals</A></B>(java.lang.Object&nbsp;obj)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/FastaSequence.html#getFormatedSequence(int)">getFormatedSequence</A></B>(int&nbsp;width)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Format sequence per width letter in one string.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/FastaSequence.html#getFormattedFasta()">getFormattedFasta</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/FastaSequence.html#getId()">getId</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Gets the value of id</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;int</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/FastaSequence.html#getLength()">getLength</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/FastaSequence.html#getOnelineFasta()">getOnelineFasta</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/FastaSequence.html#getSequence()">getSequence</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Gets the value of sequence</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/FastaSequence.html#toString()">toString</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Same as oneLineFasta</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>getClass, hashCode, notify, notifyAll, wait, wait, wait</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
-\r
-<A NAME="constructor_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Constructor Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="FastaSequence(java.lang.String, java.lang.String)"><!-- --></A><H3>\r
-FastaSequence</H3>\r
-<PRE>\r
-public <B>FastaSequence</B>(java.lang.String&nbsp;id,\r
-                     java.lang.String&nbsp;sequence)</PRE>\r
-<DL>\r
-<DD>Upon construction the any whitespace characters are removed from the
- sequence\r
-<P>\r
-<DL>\r
-<DT><B>Parameters:</B><DD><CODE>id</CODE> - <DD><CODE>sequence</CODE> - </DL>\r
-</DL>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
-<A NAME="method_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="getId()"><!-- --></A><H3>\r
-getId</H3>\r
-<PRE>\r
-public java.lang.String <B>getId</B>()</PRE>\r
-<DL>\r
-<DD>Gets the value of id\r
-<P>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>the value of id</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getSequence()"><!-- --></A><H3>\r
-getSequence</H3>\r
-<PRE>\r
-public java.lang.String <B>getSequence</B>()</PRE>\r
-<DL>\r
-<DD>Gets the value of sequence\r
-<P>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>the value of sequence</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="countMatchesInSequence(java.lang.String, java.lang.String)"><!-- --></A><H3>\r
-countMatchesInSequence</H3>\r
-<PRE>\r
-public static int <B>countMatchesInSequence</B>(java.lang.String&nbsp;theString,\r
-                                         java.lang.String&nbsp;theRegExp)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getFormattedFasta()"><!-- --></A><H3>\r
-getFormattedFasta</H3>\r
-<PRE>\r
-public java.lang.String <B>getFormattedFasta</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getOnelineFasta()"><!-- --></A><H3>\r
-getOnelineFasta</H3>\r
-<PRE>\r
-public java.lang.String <B>getOnelineFasta</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>one line name, next line sequence, no matter what the sequence
-         length is</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getFormatedSequence(int)"><!-- --></A><H3>\r
-getFormatedSequence</H3>\r
-<PRE>\r
-public java.lang.String <B>getFormatedSequence</B>(int&nbsp;width)</PRE>\r
-<DL>\r
-<DD>Format sequence per width letter in one string. Without spaces.\r
-<P>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>multiple line formated sequence, one line width letters length</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getLength()"><!-- --></A><H3>\r
-getLength</H3>\r
-<PRE>\r
-public int <B>getLength</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>sequence length</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="toString()"><!-- --></A><H3>\r
-toString</H3>\r
-<PRE>\r
-public java.lang.String <B>toString</B>()</PRE>\r
-<DL>\r
-<DD>Same as oneLineFasta\r
-<P>\r
-<DD><DL>\r
-<DT><B>Overrides:</B><DD><CODE>toString</CODE> in class <CODE>java.lang.Object</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="equals(java.lang.Object)"><!-- --></A><H3>\r
-equals</H3>\r
-<PRE>\r
-public boolean <B>equals</B>(java.lang.Object&nbsp;obj)</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Overrides:</B><DD><CODE>equals</CODE> in class <CODE>java.lang.Object</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/FastaSequence.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
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-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/data/sequence/FastaSequence.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
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-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
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-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/data/sequence/Program.html b/website/full_javadoc/compbio/data/sequence/Program.html

deleted file mode 100644 (file)

index 4c68bca..0000000
--- a/website/full_javadoc/compbio/data/sequence/Program.html
+++ /dev/null
@@ -1,388 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:49 GMT 2010 -->\r
-<TITLE>\r
-Program\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Program";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/Program.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/data/sequence/Program.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="Program.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;<A HREF="#enum_constant_summary">ENUM CONSTANTS</A>&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;<A HREF="#enum_constant_detail">ENUM CONSTANTS</A>&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.data.sequence</FONT>\r
-<BR>\r
-Enum Program</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../../resources/inherit.gif" ALT="extended by ">java.lang.Enum&lt;<A HREF="../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A>&gt;\r
-      <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.data.sequence.Program</B>\r
-</PRE>\r
-<DL>\r
-<DT><B>All Implemented Interfaces:</B> <DD>java.io.Serializable, java.lang.Comparable&lt;<A HREF="../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A>&gt;</DD>\r
-</DL>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public enum <B>Program</B><DT>extends java.lang.Enum&lt;<A HREF="../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A>&gt;</DL>\r
-</PRE>\r
-\r
-<P>\r
-Programmes that can produce alignments\r
-<P>\r
-\r
-<P>\r
-<DL>\r
-<DT><B>Author:</B></DT>\r
-  <DD>pvtroshin</DD>\r
-</DL>\r
-<HR>\r
-\r
-<P>\r
-<!-- =========== ENUM CONSTANT SUMMARY =========== -->\r
-\r
-<A NAME="enum_constant_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Enum Constant Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/Program.html#CLUSTAL">CLUSTAL</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;ClustalW</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/Program.html#MAFFT">MAFFT</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Mafft</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/Program.html#MUSCLE">MUSCLE</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Muscle</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/Program.html#Probcons">Probcons</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Probcons</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/Program.html#Tcoffee">Tcoffee</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Tcoffee</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/Program.html#valueOf(java.lang.String)">valueOf</A></B>(java.lang.String&nbsp;name)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Returns the enum constant of this type with the specified name.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A>[]</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/Program.html#values()">values</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Returns an array containing the constants of this enum type, in
-the order they are declared.</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Enum"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Enum</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>compareTo, equals, getDeclaringClass, hashCode, name, ordinal, toString, valueOf</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>getClass, notify, notifyAll, wait, wait, wait</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ============ ENUM CONSTANT DETAIL =========== -->\r
-\r
-<A NAME="enum_constant_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Enum Constant Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="CLUSTAL"><!-- --></A><H3>\r
-CLUSTAL</H3>\r
-<PRE>\r
-public static final <A HREF="../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A> <B>CLUSTAL</B></PRE>\r
-<DL>\r
-<DD>ClustalW\r
-<P>\r
-<DL>\r
-</DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="MAFFT"><!-- --></A><H3>\r
-MAFFT</H3>\r
-<PRE>\r
-public static final <A HREF="../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A> <B>MAFFT</B></PRE>\r
-<DL>\r
-<DD>Mafft\r
-<P>\r
-<DL>\r
-</DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="MUSCLE"><!-- --></A><H3>\r
-MUSCLE</H3>\r
-<PRE>\r
-public static final <A HREF="../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A> <B>MUSCLE</B></PRE>\r
-<DL>\r
-<DD>Muscle\r
-<P>\r
-<DL>\r
-</DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="Tcoffee"><!-- --></A><H3>\r
-Tcoffee</H3>\r
-<PRE>\r
-public static final <A HREF="../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A> <B>Tcoffee</B></PRE>\r
-<DL>\r
-<DD>Tcoffee\r
-<P>\r
-<DL>\r
-</DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="Probcons"><!-- --></A><H3>\r
-Probcons</H3>\r
-<PRE>\r
-public static final <A HREF="../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A> <B>Probcons</B></PRE>\r
-<DL>\r
-<DD>Probcons\r
-<P>\r
-<DL>\r
-</DL>\r
-</DL>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
-<A NAME="method_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="values()"><!-- --></A><H3>\r
-values</H3>\r
-<PRE>\r
-public static <A HREF="../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A>[] <B>values</B>()</PRE>\r
-<DL>\r
-<DD>Returns an array containing the constants of this enum type, in
-the order they are declared.  This method may be used to iterate
-over the constants as follows:
-<pre>
-for (Program c : Program.values())
-&nbsp;   System.out.println(c);
-</pre>\r
-<P>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>an array containing the constants of this enum type, in
-the order they are declared</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="valueOf(java.lang.String)"><!-- --></A><H3>\r
-valueOf</H3>\r
-<PRE>\r
-public static <A HREF="../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A> <B>valueOf</B>(java.lang.String&nbsp;name)</PRE>\r
-<DL>\r
-<DD>Returns the enum constant of this type with the specified name.
-The string must match <I>exactly</I> an identifier used to declare an
-enum constant in this type.  (Extraneous whitespace characters are 
-not permitted.)\r
-<P>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>name</CODE> - the name of the enum constant to be returned.\r
-<DT><B>Returns:</B><DD>the enum constant with the specified name\r
-<DT><B>Throws:</B>\r
-<DD><CODE>java.lang.IllegalArgumentException</CODE> - if this enum type has no constant
-with the specified name\r
-<DD><CODE>java.lang.NullPointerException</CODE> - if the argument is null</DL>\r
-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/Program.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/data/sequence/Program.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="Program.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;<A HREF="#enum_constant_summary">ENUM CONSTANTS</A>&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;<A HREF="#enum_constant_detail">ENUM CONSTANTS</A>&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/data/sequence/SequenceUtil.html b/website/full_javadoc/compbio/data/sequence/SequenceUtil.html

deleted file mode 100644 (file)

index a7bdf1a..0000000
--- a/website/full_javadoc/compbio/data/sequence/SequenceUtil.html
+++ /dev/null
@@ -1,624 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:49 GMT 2010 -->\r
-<TITLE>\r
-SequenceUtil\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="SequenceUtil";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
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-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;<A HREF="#field_summary">FIELD</A>&nbsp;|&nbsp;CONSTR&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;<A HREF="#field_detail">FIELD</A>&nbsp;|&nbsp;CONSTR&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
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-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
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-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.data.sequence</FONT>\r
-<BR>\r
-Class SequenceUtil</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.data.sequence.SequenceUtil</B>\r
-</PRE>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public final class <B>SequenceUtil</B><DT>extends java.lang.Object</DL>\r
-</PRE>\r
-\r
-<P>\r
-Utility class for operations on sequences\r
-<P>\r
-\r
-<P>\r
-<DL>\r
-<DT><B>Author:</B></DT>\r
-  <DD>pvtroshin
- 
-         Date September 2009</DD>\r
-</DL>\r
-<HR>\r
-\r
-<P>\r
-<!-- =========== FIELD SUMMARY =========== -->\r
-\r
-<A NAME="field_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Field Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;java.util.regex.Pattern</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#AA">AA</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Valid Amino acids</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;java.util.regex.Pattern</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#AMBIGUOUS_AA">AMBIGUOUS_AA</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Same as AA pattern but with two additional letters - XU</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;java.util.regex.Pattern</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#AMBIGUOUS_NUCLEOTIDE">AMBIGUOUS_NUCLEOTIDE</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Ambiguous nucleotide</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;java.util.regex.Pattern</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#DIGIT">DIGIT</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;A digit</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;java.util.regex.Pattern</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#NON_AA">NON_AA</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;inversion of AA pattern</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;java.util.regex.Pattern</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#NON_NUCLEOTIDE">NON_NUCLEOTIDE</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Non nucleotide</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;java.util.regex.Pattern</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#NONWORD">NONWORD</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Non word</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;java.util.regex.Pattern</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#NUCLEOTIDE">NUCLEOTIDE</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Nucleotides a, t, g, c, u</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;java.util.regex.Pattern</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#WHITE_SPACE">WHITE_SPACE</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;A whitespace character: [\t\n\x0B\f\r]</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#cleanSequence(java.lang.String)">cleanSequence</A></B>(java.lang.String&nbsp;sequence)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Removes all whitespace chars in the sequence string</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#deepCleanSequence(java.lang.String)">deepCleanSequence</A></B>(java.lang.String&nbsp;sequence)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Removes all special characters and digits as well as whitespace chars
- from the sequence</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#isAmbiguosProtein(java.lang.String)">isAmbiguosProtein</A></B>(java.lang.String&nbsp;sequence)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Check whether the sequence confirms to amboguous protein sequence</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#isNonAmbNucleotideSequence(java.lang.String)">isNonAmbNucleotideSequence</A></B>(java.lang.String&nbsp;sequence)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Ambiguous DNA chars : AGTCRYMKSWHBVDN // differs from protein in only one
- (!) - B char</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#isNucleotideSequence(compbio.data.sequence.FastaSequence)">isNucleotideSequence</A></B>(<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&nbsp;s)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#isProteinSequence(java.lang.String)">isProteinSequence</A></B>(java.lang.String&nbsp;sequence)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#readFasta(java.io.InputStream)">readFasta</A></B>(java.io.InputStream&nbsp;inStream)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Reads fasta sequences from inStream into the list of FastaSequence
- objects</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#writeFasta(java.io.OutputStream, java.util.List)">writeFasta</A></B>(java.io.OutputStream&nbsp;os,\r
-           java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Writes FastaSequence in the file, each sequence will take one line only</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#writeFasta(java.io.OutputStream, java.util.List, int)">writeFasta</A></B>(java.io.OutputStream&nbsp;outstream,\r
-           java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-           int&nbsp;width)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Writes list of FastaSequeces into the outstream formatting the sequence
- so that it contains width chars on each line</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ============ FIELD DETAIL =========== -->\r
-\r
-<A NAME="field_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Field Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="WHITE_SPACE"><!-- --></A><H3>\r
-WHITE_SPACE</H3>\r
-<PRE>\r
-public static final java.util.regex.Pattern <B>WHITE_SPACE</B></PRE>\r
-<DL>\r
-<DD>A whitespace character: [\t\n\x0B\f\r]\r
-<P>\r
-<DL>\r
-</DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="DIGIT"><!-- --></A><H3>\r
-DIGIT</H3>\r
-<PRE>\r
-public static final java.util.regex.Pattern <B>DIGIT</B></PRE>\r
-<DL>\r
-<DD>A digit\r
-<P>\r
-<DL>\r
-</DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="NONWORD"><!-- --></A><H3>\r
-NONWORD</H3>\r
-<PRE>\r
-public static final java.util.regex.Pattern <B>NONWORD</B></PRE>\r
-<DL>\r
-<DD>Non word\r
-<P>\r
-<DL>\r
-</DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="AA"><!-- --></A><H3>\r
-AA</H3>\r
-<PRE>\r
-public static final java.util.regex.Pattern <B>AA</B></PRE>\r
-<DL>\r
-<DD>Valid Amino acids\r
-<P>\r
-<DL>\r
-</DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="NON_AA"><!-- --></A><H3>\r
-NON_AA</H3>\r
-<PRE>\r
-public static final java.util.regex.Pattern <B>NON_AA</B></PRE>\r
-<DL>\r
-<DD>inversion of AA pattern\r
-<P>\r
-<DL>\r
-</DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="AMBIGUOUS_AA"><!-- --></A><H3>\r
-AMBIGUOUS_AA</H3>\r
-<PRE>\r
-public static final java.util.regex.Pattern <B>AMBIGUOUS_AA</B></PRE>\r
-<DL>\r
-<DD>Same as AA pattern but with two additional letters - XU\r
-<P>\r
-<DL>\r
-</DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="NUCLEOTIDE"><!-- --></A><H3>\r
-NUCLEOTIDE</H3>\r
-<PRE>\r
-public static final java.util.regex.Pattern <B>NUCLEOTIDE</B></PRE>\r
-<DL>\r
-<DD>Nucleotides a, t, g, c, u\r
-<P>\r
-<DL>\r
-</DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="AMBIGUOUS_NUCLEOTIDE"><!-- --></A><H3>\r
-AMBIGUOUS_NUCLEOTIDE</H3>\r
-<PRE>\r
-public static final java.util.regex.Pattern <B>AMBIGUOUS_NUCLEOTIDE</B></PRE>\r
-<DL>\r
-<DD>Ambiguous nucleotide\r
-<P>\r
-<DL>\r
-</DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="NON_NUCLEOTIDE"><!-- --></A><H3>\r
-NON_NUCLEOTIDE</H3>\r
-<PRE>\r
-public static final java.util.regex.Pattern <B>NON_NUCLEOTIDE</B></PRE>\r
-<DL>\r
-<DD>Non nucleotide\r
-<P>\r
-<DL>\r
-</DL>\r
-</DL>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
-<A NAME="method_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="isNucleotideSequence(compbio.data.sequence.FastaSequence)"><!-- --></A><H3>\r
-isNucleotideSequence</H3>\r
-<PRE>\r
-public static boolean <B>isNucleotideSequence</B>(<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&nbsp;s)</PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>true is the sequence contains only letters a,c, t, g, u</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="isNonAmbNucleotideSequence(java.lang.String)"><!-- --></A><H3>\r
-isNonAmbNucleotideSequence</H3>\r
-<PRE>\r
-public static boolean <B>isNonAmbNucleotideSequence</B>(java.lang.String&nbsp;sequence)</PRE>\r
-<DL>\r
-<DD>Ambiguous DNA chars : AGTCRYMKSWHBVDN // differs from protein in only one
- (!) - B char\r
-<P>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="cleanSequence(java.lang.String)"><!-- --></A><H3>\r
-cleanSequence</H3>\r
-<PRE>\r
-public static java.lang.String <B>cleanSequence</B>(java.lang.String&nbsp;sequence)</PRE>\r
-<DL>\r
-<DD>Removes all whitespace chars in the sequence string\r
-<P>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>sequence</CODE> - \r
-<DT><B>Returns:</B><DD>cleaned up sequence</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="deepCleanSequence(java.lang.String)"><!-- --></A><H3>\r
-deepCleanSequence</H3>\r
-<PRE>\r
-public static java.lang.String <B>deepCleanSequence</B>(java.lang.String&nbsp;sequence)</PRE>\r
-<DL>\r
-<DD>Removes all special characters and digits as well as whitespace chars
- from the sequence\r
-<P>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>sequence</CODE> - \r
-<DT><B>Returns:</B><DD>cleaned up sequence</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="isProteinSequence(java.lang.String)"><!-- --></A><H3>\r
-isProteinSequence</H3>\r
-<PRE>\r
-public static boolean <B>isProteinSequence</B>(java.lang.String&nbsp;sequence)</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>sequence</CODE> - \r
-<DT><B>Returns:</B><DD>true is the sequence is a protein sequence, false overwise</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="isAmbiguosProtein(java.lang.String)"><!-- --></A><H3>\r
-isAmbiguosProtein</H3>\r
-<PRE>\r
-public static boolean <B>isAmbiguosProtein</B>(java.lang.String&nbsp;sequence)</PRE>\r
-<DL>\r
-<DD>Check whether the sequence confirms to amboguous protein sequence\r
-<P>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>sequence</CODE> - \r
-<DT><B>Returns:</B><DD>return true only if the sequence if ambiguous protein sequence
-         Return false otherwise. e.g. if the sequence is non-ambiguous
-         protein or DNA</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="writeFasta(java.io.OutputStream, java.util.List, int)"><!-- --></A><H3>\r
-writeFasta</H3>\r
-<PRE>\r
-public static void <B>writeFasta</B>(java.io.OutputStream&nbsp;outstream,\r
-                              java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-                              int&nbsp;width)\r
-                       throws java.io.IOException</PRE>\r
-<DL>\r
-<DD>Writes list of FastaSequeces into the outstream formatting the sequence
- so that it contains width chars on each line\r
-<P>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>outstream</CODE> - <DD><CODE>sequences</CODE> - <DD><CODE>width</CODE> - - the maximum number of characters to write in one line\r
-<DT><B>Throws:</B>\r
-<DD><CODE>java.io.IOException</CODE></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="readFasta(java.io.InputStream)"><!-- --></A><H3>\r
-readFasta</H3>\r
-<PRE>\r
-public static java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt; <B>readFasta</B>(java.io.InputStream&nbsp;inStream)\r
-                                               throws java.io.IOException</PRE>\r
-<DL>\r
-<DD>Reads fasta sequences from inStream into the list of FastaSequence
- objects\r
-<P>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>inStream</CODE> - from\r
-<DT><B>Returns:</B><DD>list of FastaSequence objects\r
-<DT><B>Throws:</B>\r
-<DD><CODE>java.io.IOException</CODE></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="writeFasta(java.io.OutputStream, java.util.List)"><!-- --></A><H3>\r
-writeFasta</H3>\r
-<PRE>\r
-public static void <B>writeFasta</B>(java.io.OutputStream&nbsp;os,\r
-                              java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences)\r
-                       throws java.io.IOException</PRE>\r
-<DL>\r
-<DD>Writes FastaSequence in the file, each sequence will take one line only\r
-<P>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>os</CODE> - <DD><CODE>sequences</CODE> - \r
-<DT><B>Throws:</B>\r
-<DD><CODE>java.io.IOException</CODE></DL>\r
-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/SequenceUtil.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/data/sequence/SequenceUtil.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="SequenceUtil.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;<A HREF="#field_summary">FIELD</A>&nbsp;|&nbsp;CONSTR&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;<A HREF="#field_detail">FIELD</A>&nbsp;|&nbsp;CONSTR&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/data/sequence/UnknownFileFormatException.html b/website/full_javadoc/compbio/data/sequence/UnknownFileFormatException.html

deleted file mode 100644 (file)

index d45a4ea..0000000
--- a/website/full_javadoc/compbio/data/sequence/UnknownFileFormatException.html
+++ /dev/null
@@ -1,300 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:49 GMT 2010 -->\r
-<TITLE>\r
-UnknownFileFormatException\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="UnknownFileFormatException";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/UnknownFileFormatException.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;NEXT CLASS</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/data/sequence/UnknownFileFormatException.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="UnknownFileFormatException.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#methods_inherited_from_class_java.lang.Throwable">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;METHOD</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.data.sequence</FONT>\r
-<BR>\r
-Class UnknownFileFormatException</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../../resources/inherit.gif" ALT="extended by ">java.lang.Throwable\r
-      <IMG SRC="../../../resources/inherit.gif" ALT="extended by ">java.lang.Exception\r
-          <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.data.sequence.UnknownFileFormatException</B>\r
-</PRE>\r
-<DL>\r
-<DT><B>All Implemented Interfaces:</B> <DD>java.io.Serializable</DD>\r
-</DL>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public class <B>UnknownFileFormatException</B><DT>extends java.lang.Exception</DL>\r
-</PRE>\r
-\r
-<P>\r
-<DL>\r
-<DT><B>See Also:</B><DD><A HREF="../../../serialized-form.html#compbio.data.sequence.UnknownFileFormatException">Serialized Form</A></DL>\r
-<HR>\r
-\r
-<P>\r
-\r
-<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
-\r
-<A NAME="constructor_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Constructor Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/UnknownFileFormatException.html#UnknownFileFormatException()">UnknownFileFormatException</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/UnknownFileFormatException.html#UnknownFileFormatException(java.io.File, java.lang.Throwable)">UnknownFileFormatException</A></B>(java.io.File&nbsp;file,\r
-                           java.lang.Throwable&nbsp;cause)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/UnknownFileFormatException.html#UnknownFileFormatException(java.lang.String)">UnknownFileFormatException</A></B>(java.lang.String&nbsp;message)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/UnknownFileFormatException.html#UnknownFileFormatException(java.lang.String, java.lang.Throwable)">UnknownFileFormatException</A></B>(java.lang.String&nbsp;message,\r
-                           java.lang.Throwable&nbsp;cause)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/UnknownFileFormatException.html#UnknownFileFormatException(java.lang.Throwable)">UnknownFileFormatException</A></B>(java.lang.Throwable&nbsp;cause)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Throwable"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Throwable</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>fillInStackTrace, getCause, getLocalizedMessage, getMessage, getStackTrace, initCause, printStackTrace, printStackTrace, printStackTrace, setStackTrace, toString</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>equals, getClass, hashCode, notify, notifyAll, wait, wait, wait</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
-\r
-<A NAME="constructor_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Constructor Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="UnknownFileFormatException()"><!-- --></A><H3>\r
-UnknownFileFormatException</H3>\r
-<PRE>\r
-public <B>UnknownFileFormatException</B>()</PRE>\r
-<DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="UnknownFileFormatException(java.io.File, java.lang.Throwable)"><!-- --></A><H3>\r
-UnknownFileFormatException</H3>\r
-<PRE>\r
-public <B>UnknownFileFormatException</B>(java.io.File&nbsp;file,\r
-                                  java.lang.Throwable&nbsp;cause)</PRE>\r
-<DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="UnknownFileFormatException(java.lang.String, java.lang.Throwable)"><!-- --></A><H3>\r
-UnknownFileFormatException</H3>\r
-<PRE>\r
-public <B>UnknownFileFormatException</B>(java.lang.String&nbsp;message,\r
-                                  java.lang.Throwable&nbsp;cause)</PRE>\r
-<DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="UnknownFileFormatException(java.lang.String)"><!-- --></A><H3>\r
-UnknownFileFormatException</H3>\r
-<PRE>\r
-public <B>UnknownFileFormatException</B>(java.lang.String&nbsp;message)</PRE>\r
-<DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="UnknownFileFormatException(java.lang.Throwable)"><!-- --></A><H3>\r
-UnknownFileFormatException</H3>\r
-<PRE>\r
-public <B>UnknownFileFormatException</B>(java.lang.Throwable&nbsp;cause)</PRE>\r
-<DL>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/UnknownFileFormatException.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;NEXT CLASS</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/data/sequence/UnknownFileFormatException.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="UnknownFileFormatException.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
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-\r
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-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#methods_inherited_from_class_java.lang.Throwable">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;METHOD</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
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-<HR>\r
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-</HTML>\r
diff --git a/website/full_javadoc/compbio/data/sequence/class-use/Alignment.html b/website/full_javadoc/compbio/data/sequence/class-use/Alignment.html

deleted file mode 100644 (file)

index af197d7..0000000
--- a/website/full_javadoc/compbio/data/sequence/class-use/Alignment.html
+++ /dev/null
@@ -1,433 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Uses of Class compbio.data.sequence.Alignment\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Uses of Class compbio.data.sequence.Alignment";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/data/sequence/\class-useAlignment.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="Alignment.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-<B>Uses of Class<br>compbio.data.sequence.Alignment</B></H2>\r
-</CENTER>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Packages that use <A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.data.msa"><B>compbio.data.msa</B></A></TD>\r
-<TD>&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.data.msa.jaxws"><B>compbio.data.msa.jaxws</B></A></TD>\r
-<TD>&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.data.sequence"><B>compbio.data.sequence</B></A></TD>\r
-<TD>A data model for multiple sequence alignment web services 
- Classes in this package have no dependencies to other sources in the project.&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.runner"><B>compbio.runner</B></A></TD>\r
-<TD>Utilities commonly used by all runners.&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.runner.msa"><B>compbio.runner.msa</B></A></TD>\r
-<TD>Wrappers for native executables for multiple sequence alignment (msa)&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.ws.server"><B>compbio.ws.server</B></A></TD>\r
-<TD>&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.data.msa"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A> in <A HREF="../../../../compbio/data/msa/package-summary.html">compbio.data.msa</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/data/msa/package-summary.html">compbio.data.msa</A> that return <A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
-<TD><CODE><B>MsaWS.</B><B><A HREF="../../../../compbio/data/msa/MsaWS.html#getResult(java.lang.String)">getResult</A></B>(java.lang.String&nbsp;jobId)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Return the result of the job.</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.data.msa.jaxws"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A> in <A HREF="../../../../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A> that return <A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
-<TD><CODE><B>GetResultResponse.</B><B><A HREF="../../../../compbio/data/msa/jaxws/GetResultResponse.html#getReturn()">getReturn</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A> with parameters of type <A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B>GetResultResponse.</B><B><A HREF="../../../../compbio/data/msa/jaxws/GetResultResponse.html#setReturn(compbio.data.sequence.Alignment)">setReturn</A></B>(<A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A>&nbsp;_return)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.data.sequence"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A> in <A HREF="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A> that return <A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
-<TD><CODE><B>ClustalAlignmentUtil.</B><B><A HREF="../../../../compbio/data/sequence/ClustalAlignmentUtil.html#readClustalFile(java.io.File)">readClustalFile</A></B>(java.io.File&nbsp;file)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
-<TD><CODE><B>ClustalAlignmentUtil.</B><B><A HREF="../../../../compbio/data/sequence/ClustalAlignmentUtil.html#readClustalFile(java.io.InputStream)">readClustalFile</A></B>(java.io.InputStream&nbsp;instream)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Read Clustal formatted alignment.</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A> with parameters of type <A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B>ClustalAlignmentUtil.</B><B><A HREF="../../../../compbio/data/sequence/ClustalAlignmentUtil.html#writeClustalAlignment(java.io.OutputStream, compbio.data.sequence.Alignment)">writeClustalAlignment</A></B>(java.io.OutputStream&nbsp;outStream,\r
-                      <A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A>&nbsp;alignment)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Write Clustal formatted alignment Limitations: does not record the
- consensus.</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.runner"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A> in <A HREF="../../../../compbio/runner/package-summary.html">compbio.runner</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/runner/package-summary.html">compbio.runner</A> that return <A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
-<TD><CODE><B>Util.</B><B><A HREF="../../../../compbio/runner/Util.html#readClustalFile(java.lang.String, java.lang.String)">readClustalFile</A></B>(java.lang.String&nbsp;workDirectory,\r
-                java.lang.String&nbsp;clustFile)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.runner.msa"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A> in <A HREF="../../../../compbio/runner/msa/package-summary.html">compbio.runner.msa</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/runner/msa/package-summary.html">compbio.runner.msa</A> that return <A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
-<TD><CODE><B>Tcoffee.</B><B><A HREF="../../../../compbio/runner/msa/Tcoffee.html#getResults(java.lang.String)">getResults</A></B>(java.lang.String&nbsp;workDirectory)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
-<TD><CODE><B>ClustalW.</B><B><A HREF="../../../../compbio/runner/msa/ClustalW.html#getResults(java.lang.String)">getResults</A></B>(java.lang.String&nbsp;workDirectory)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
-<TD><CODE><B>Probcons.</B><B><A HREF="../../../../compbio/runner/msa/Probcons.html#getResults(java.lang.String)">getResults</A></B>(java.lang.String&nbsp;workDirectory)</CODE>\r
-\r
-<BR>\r
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-<CODE>&nbsp;<A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
-<TD><CODE><B>Muscle.</B><B><A HREF="../../../../compbio/runner/msa/Muscle.html#getResults(java.lang.String)">getResults</A></B>(java.lang.String&nbsp;workDirectory)</CODE>\r
-\r
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-<CODE>&nbsp;<A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
-<TD><CODE><B>Mafft.</B><B><A HREF="../../../../compbio/runner/msa/Mafft.html#getResults(java.lang.String)">getResults</A></B>(java.lang.String&nbsp;workDirectory)</CODE>\r
-\r
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-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
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-</TR>\r
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-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/ws/server/package-summary.html">compbio.ws.server</A> that return <A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></FONT></TH>\r
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-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
-<TD><CODE><B>TcoffeeWS.</B><B><A HREF="../../../../compbio/ws/server/TcoffeeWS.html#getResult(java.lang.String)">getResult</A></B>(java.lang.String&nbsp;jobId)</CODE>\r
-\r
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-<CODE>&nbsp;<A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
-<TD><CODE><B>ProbconsWS.</B><B><A HREF="../../../../compbio/ws/server/ProbconsWS.html#getResult(java.lang.String)">getResult</A></B>(java.lang.String&nbsp;jobId)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
-<TD><CODE><B>MuscleWS.</B><B><A HREF="../../../../compbio/ws/server/MuscleWS.html#getResult(java.lang.String)">getResult</A></B>(java.lang.String&nbsp;jobId)</CODE>\r
-\r
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-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
-<TD><CODE><B>MafftWS.</B><B><A HREF="../../../../compbio/ws/server/MafftWS.html#getResult(java.lang.String)">getResult</A></B>(java.lang.String&nbsp;jobId)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
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-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
-<TD><CODE><B>ClustalWS.</B><B><A HREF="../../../../compbio/ws/server/ClustalWS.html#getResult(java.lang.String)">getResult</A></B>(java.lang.String&nbsp;jobId)</CODE>\r
-\r
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-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
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-  }\r
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-</SCRIPT>\r
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-\r
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-\r
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diff --git a/website/full_javadoc/compbio/data/sequence/class-use/AlignmentMetadata.html b/website/full_javadoc/compbio/data/sequence/class-use/AlignmentMetadata.html

deleted file mode 100644 (file)

index efa449b..0000000
--- a/website/full_javadoc/compbio/data/sequence/class-use/AlignmentMetadata.html
+++ /dev/null
@@ -1,196 +0,0 @@
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-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Uses of Class compbio.data.sequence.AlignmentMetadata\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
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-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
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-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
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-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
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-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
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-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/data/sequence/\class-useAlignmentMetadata.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
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-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
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-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-<B>Uses of Class<br>compbio.data.sequence.AlignmentMetadata</B></H2>\r
-</CENTER>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Packages that use <A HREF="../../../../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence">AlignmentMetadata</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.data.sequence"><B>compbio.data.sequence</B></A></TD>\r
-<TD>A data model for multiple sequence alignment web services 
- Classes in this package have no dependencies to other sources in the project.&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.data.sequence"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence">AlignmentMetadata</A> in <A HREF="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
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-<P>\r
-\r
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-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A> that return <A HREF="../../../../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence">AlignmentMetadata</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence">AlignmentMetadata</A></CODE></FONT></TD>\r
-<TD><CODE><B>Alignment.</B><B><A HREF="../../../../compbio/data/sequence/Alignment.html#getMetadata()">getMetadata</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Constructors in <A HREF="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A> with parameters of type <A HREF="../../../../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence">AlignmentMetadata</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../../compbio/data/sequence/Alignment.html#Alignment(java.util.List, compbio.data.sequence.AlignmentMetadata)">Alignment</A></B>(java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-          <A HREF="../../../../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence">AlignmentMetadata</A>&nbsp;metadata)</CODE>\r
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-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
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-\r
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-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
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diff --git a/website/full_javadoc/compbio/data/sequence/class-use/ClustalAlignmentUtil.html b/website/full_javadoc/compbio/data/sequence/class-use/ClustalAlignmentUtil.html

deleted file mode 100644 (file)

index 6a07291..0000000
--- a/website/full_javadoc/compbio/data/sequence/class-use/ClustalAlignmentUtil.html
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-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
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-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
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-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
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-    if (location.href.indexOf('is-external=true') == -1) {\r
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-</HEAD>\r
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-<BODY BGCOLOR="white" onload="windowTitle();">\r
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-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
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-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
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-&nbsp;NEXT</FONT></TD>\r
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-  }\r
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-No usage of compbio.data.sequence.ClustalAlignmentUtil\r
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-\r
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-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
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diff --git a/website/full_javadoc/compbio/data/sequence/class-use/FastaSequence.html b/website/full_javadoc/compbio/data/sequence/class-use/FastaSequence.html

deleted file mode 100644 (file)

index cbc8cd7..0000000
--- a/website/full_javadoc/compbio/data/sequence/class-use/FastaSequence.html
+++ /dev/null
@@ -1,718 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Uses of Class compbio.data.sequence.FastaSequence\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Uses of Class compbio.data.sequence.FastaSequence";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
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-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
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-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/data/sequence/\class-useFastaSequence.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="FastaSequence.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
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-\r
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-</FONT></TD>\r
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-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-<B>Uses of Class<br>compbio.data.sequence.FastaSequence</B></H2>\r
-</CENTER>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Packages that use <A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.data.msa"><B>compbio.data.msa</B></A></TD>\r
-<TD>&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.data.msa.jaxws"><B>compbio.data.msa.jaxws</B></A></TD>\r
-<TD>&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.data.sequence"><B>compbio.data.sequence</B></A></TD>\r
-<TD>A data model for multiple sequence alignment web services 
- Classes in this package have no dependencies to other sources in the project.&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.engine"><B>compbio.engine</B></A></TD>\r
-<TD>&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.metadata"><B>compbio.metadata</B></A></TD>\r
-<TD>A meta-data model for multiple sequence alignment web services 
- Classes in this package have no dependencies to other sources in the project.&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.pipeline._jpred"><B>compbio.pipeline._jpred</B></A></TD>\r
-<TD>&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.runner"><B>compbio.runner</B></A></TD>\r
-<TD>Utilities commonly used by all runners.&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.ws.server"><B>compbio.ws.server</B></A></TD>\r
-<TD>&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.data.msa"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A> in <A HREF="../../../../compbio/data/msa/package-summary.html">compbio.data.msa</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Method parameters in <A HREF="../../../../compbio/data/msa/package-summary.html">compbio.data.msa</A> with type arguments of type <A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B>MsaWS.</B><B><A HREF="../../../../compbio/data/msa/MsaWS.html#align(java.util.List)">align</A></B>(java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Align a list of sequences with default settings.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B>MsaWS.</B><B><A HREF="../../../../compbio/data/msa/MsaWS.html#customAlign(java.util.List, java.util.List)">customAlign</A></B>(java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-            java.util.List&lt;<A HREF="../../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../../compbio/data/msa/MsaWS.html" title="type parameter in MsaWS">T</A>&gt;&gt;&nbsp;options)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Align a list of sequences with options.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B>MsaWS.</B><B><A HREF="../../../../compbio/data/msa/MsaWS.html#presetAlign(java.util.List, compbio.metadata.Preset)">presetAlign</A></B>(java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-            <A HREF="../../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>&lt;<A HREF="../../../../compbio/data/msa/MsaWS.html" title="type parameter in MsaWS">T</A>&gt;&nbsp;preset)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Align a list of sequences with preset.</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.data.msa.jaxws"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A> in <A HREF="../../../../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A> that return types with arguments of type <A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>PresetAlign.</B><B><A HREF="../../../../compbio/data/msa/jaxws/PresetAlign.html#getFastaSequences()">getFastaSequences</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>CustomAlign.</B><B><A HREF="../../../../compbio/data/msa/jaxws/CustomAlign.html#getFastaSequences()">getFastaSequences</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>Align.</B><B><A HREF="../../../../compbio/data/msa/jaxws/Align.html#getFastaSequences()">getFastaSequences</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Method parameters in <A HREF="../../../../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A> with type arguments of type <A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B>PresetAlign.</B><B><A HREF="../../../../compbio/data/msa/jaxws/PresetAlign.html#setFastaSequences(java.util.List)">setFastaSequences</A></B>(java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;fastaSequences)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B>CustomAlign.</B><B><A HREF="../../../../compbio/data/msa/jaxws/CustomAlign.html#setFastaSequences(java.util.List)">setFastaSequences</A></B>(java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;fastaSequences)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B>Align.</B><B><A HREF="../../../../compbio/data/msa/jaxws/Align.html#setFastaSequences(java.util.List)">setFastaSequences</A></B>(java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;fastaSequences)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.data.sequence"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A> in <A HREF="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A> that return types with arguments of type <A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>Alignment.</B><B><A HREF="../../../../compbio/data/sequence/Alignment.html#getSequences()">getSequences</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>SequenceUtil.</B><B><A HREF="../../../../compbio/data/sequence/SequenceUtil.html#readFasta(java.io.InputStream)">readFasta</A></B>(java.io.InputStream&nbsp;inStream)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Reads fasta sequences from inStream into the list of FastaSequence
- objects</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A> with parameters of type <A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;boolean</CODE></FONT></TD>\r
-<TD><CODE><B>SequenceUtil.</B><B><A HREF="../../../../compbio/data/sequence/SequenceUtil.html#isNucleotideSequence(compbio.data.sequence.FastaSequence)">isNucleotideSequence</A></B>(<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&nbsp;s)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Method parameters in <A HREF="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A> with type arguments of type <A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B>SequenceUtil.</B><B><A HREF="../../../../compbio/data/sequence/SequenceUtil.html#writeFasta(java.io.OutputStream, java.util.List)">writeFasta</A></B>(java.io.OutputStream&nbsp;os,\r
-           java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Writes FastaSequence in the file, each sequence will take one line only</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B>SequenceUtil.</B><B><A HREF="../../../../compbio/data/sequence/SequenceUtil.html#writeFasta(java.io.OutputStream, java.util.List, int)">writeFasta</A></B>(java.io.OutputStream&nbsp;outstream,\r
-           java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-           int&nbsp;width)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Writes list of FastaSequeces into the outstream formatting the sequence
- so that it contains width chars on each line</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Constructor parameters in <A HREF="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A> with type arguments of type <A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../../compbio/data/sequence/Alignment.html#Alignment(java.util.List, compbio.data.sequence.AlignmentMetadata)">Alignment</A></B>(java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-          <A HREF="../../../../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence">AlignmentMetadata</A>&nbsp;metadata)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../../compbio/data/sequence/Alignment.html#Alignment(java.util.List, compbio.data.sequence.Program, char)">Alignment</A></B>(java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-          <A HREF="../../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A>&nbsp;program,\r
-          char&nbsp;gapchar)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.engine"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A> in <A HREF="../../../../compbio/engine/package-summary.html">compbio.engine</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Method parameters in <A HREF="../../../../compbio/engine/package-summary.html">compbio.engine</A> with type arguments of type <A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
-<TR ALIGN="right" VALIGN="">\r
-<TD NOWRAP><FONT SIZE="-1">\r
-<CODE>&lt;T&gt; <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;T&gt;</CODE></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-</CODE></FONT></TD>\r
-<TD><CODE><B>Configurator.</B><B><A HREF="../../../../compbio/engine/Configurator.html#configureExecutable(compbio.engine.client.Executable, java.util.List)">configureExecutable</A></B>(<A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;T&gt;&nbsp;executable,\r
-                    java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;dataSet)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
-<TR ALIGN="right" VALIGN="">\r
-<TD NOWRAP><FONT SIZE="-1">\r
-<CODE>&lt;T,V&gt; <A HREF="../../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A></CODE></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-</CODE></FONT></TD>\r
-<TD><CODE><B>LoadBalancer.</B><B><A HREF="../../../../compbio/engine/LoadBalancer.html#getEngine(compbio.engine.client.Executable, java.util.List)">getEngine</A></B>(<A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;V&gt;&nbsp;executable,\r
-          java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;dataSet)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.metadata"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A> in <A HREF="../../../../compbio/metadata/package-summary.html">compbio.metadata</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Method parameters in <A HREF="../../../../compbio/metadata/package-summary.html">compbio.metadata</A> with type arguments of type <A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;int</CODE></FONT></TD>\r
-<TD><CODE><B>Limit.</B><B><A HREF="../../../../compbio/metadata/Limit.html#getAvgSequenceLength(java.util.List)">getAvgSequenceLength</A></B>(java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;data)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Calculates an average sequence length of the dataset</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;boolean</CODE></FONT></TD>\r
-<TD><CODE><B>Limit.</B><B><A HREF="../../../../compbio/metadata/Limit.html#isExceeded(java.util.List)">isExceeded</A></B>(java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;data)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Checks if the number of sequences or their average length in the dataset
- exceeds limits the values defined by this Limit</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A></CODE></FONT></TD>\r
-<TD><CODE><B>LimitExceededException.</B><B><A HREF="../../../../compbio/metadata/LimitExceededException.html#newLimitExceeded(compbio.metadata.Limit, java.util.List)">newLimitExceeded</A></B>(<A HREF="../../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;?&gt;&nbsp;limit,\r
-                 java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;seqs)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.pipeline._jpred"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A> in <A HREF="../../../../compbio/pipeline/_jpred/package-summary.html">compbio.pipeline._jpred</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Constructor parameters in <A HREF="../../../../compbio/pipeline/_jpred/package-summary.html">compbio.pipeline._jpred</A> with type arguments of type <A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../../compbio/pipeline/_jpred/Pairwise.html#Pairwise(java.util.List)">Pairwise</A></B>(java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.runner"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A> in <A HREF="../../../../compbio/runner/package-summary.html">compbio.runner</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Method parameters in <A HREF="../../../../compbio/runner/package-summary.html">compbio.runner</A> with type arguments of type <A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B>Util.</B><B><A HREF="../../../../compbio/runner/Util.html#writeInput(java.util.List, compbio.engine.client.ConfiguredExecutable)">writeInput</A></B>(java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-           <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;exec)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.ws.server"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A> in <A HREF="../../../../compbio/ws/server/package-summary.html">compbio.ws.server</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Method parameters in <A HREF="../../../../compbio/ws/server/package-summary.html">compbio.ws.server</A> with type arguments of type <A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B>TcoffeeWS.</B><B><A HREF="../../../../compbio/ws/server/TcoffeeWS.html#align(java.util.List)">align</A></B>(java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B>ProbconsWS.</B><B><A HREF="../../../../compbio/ws/server/ProbconsWS.html#align(java.util.List)">align</A></B>(java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B>MuscleWS.</B><B><A HREF="../../../../compbio/ws/server/MuscleWS.html#align(java.util.List)">align</A></B>(java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B>MafftWS.</B><B><A HREF="../../../../compbio/ws/server/MafftWS.html#align(java.util.List)">align</A></B>(java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B>ClustalWS.</B><B><A HREF="../../../../compbio/ws/server/ClustalWS.html#align(java.util.List)">align</A></B>(java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
-<TR ALIGN="right" VALIGN="">\r
-<TD NOWRAP><FONT SIZE="-1">\r
-<CODE>&lt;T&gt; java.lang.String</CODE></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-</CODE></FONT></TD>\r
-<TD><CODE><B>WSUtil.</B><B><A HREF="../../../../compbio/ws/server/WSUtil.html#align(java.util.List, compbio.engine.client.ConfiguredExecutable, org.apache.log4j.Logger, javax.xml.ws.WebServiceContext, java.lang.String, compbio.metadata.Limit)">align</A></B>(java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-      <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;T&gt;&nbsp;confExec,\r
-      org.apache.log4j.Logger&nbsp;statLog,\r
-      javax.xml.ws.WebServiceContext&nbsp;wsContext,\r
-      java.lang.String&nbsp;callingMethod,\r
-      <A HREF="../../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;T&gt;&nbsp;limit)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B>ClustalWS.</B><B><A HREF="../../../../compbio/ws/server/ClustalWS.html#customAlign(java.util.List, java.util.List)">customAlign</A></B>(java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-            java.util.List&lt;<A HREF="../../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>&gt;&gt;&nbsp;options)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B>MafftWS.</B><B><A HREF="../../../../compbio/ws/server/MafftWS.html#customAlign(java.util.List, java.util.List)">customAlign</A></B>(java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-            java.util.List&lt;<A HREF="../../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>&gt;&gt;&nbsp;options)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B>MuscleWS.</B><B><A HREF="../../../../compbio/ws/server/MuscleWS.html#customAlign(java.util.List, java.util.List)">customAlign</A></B>(java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-            java.util.List&lt;<A HREF="../../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>&gt;&gt;&nbsp;options)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B>ProbconsWS.</B><B><A HREF="../../../../compbio/ws/server/ProbconsWS.html#customAlign(java.util.List, java.util.List)">customAlign</A></B>(java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-            java.util.List&lt;<A HREF="../../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>&gt;&gt;&nbsp;options)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B>TcoffeeWS.</B><B><A HREF="../../../../compbio/ws/server/TcoffeeWS.html#customAlign(java.util.List, java.util.List)">customAlign</A></B>(java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-            java.util.List&lt;<A HREF="../../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>&gt;&gt;&nbsp;options)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B>ClustalWS.</B><B><A HREF="../../../../compbio/ws/server/ClustalWS.html#presetAlign(java.util.List, compbio.metadata.Preset)">presetAlign</A></B>(java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-            <A HREF="../../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>&lt;<A HREF="../../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>&gt;&nbsp;preset)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B>MafftWS.</B><B><A HREF="../../../../compbio/ws/server/MafftWS.html#presetAlign(java.util.List, compbio.metadata.Preset)">presetAlign</A></B>(java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-            <A HREF="../../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>&lt;<A HREF="../../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>&gt;&nbsp;preset)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B>MuscleWS.</B><B><A HREF="../../../../compbio/ws/server/MuscleWS.html#presetAlign(java.util.List, compbio.metadata.Preset)">presetAlign</A></B>(java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-            <A HREF="../../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>&lt;<A HREF="../../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>&gt;&nbsp;preset)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B>ProbconsWS.</B><B><A HREF="../../../../compbio/ws/server/ProbconsWS.html#presetAlign(java.util.List, compbio.metadata.Preset)">presetAlign</A></B>(java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-            <A HREF="../../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>&lt;<A HREF="../../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>&gt;&nbsp;preset)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B>TcoffeeWS.</B><B><A HREF="../../../../compbio/ws/server/TcoffeeWS.html#presetAlign(java.util.List, compbio.metadata.Preset)">presetAlign</A></B>(java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-            <A HREF="../../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>&lt;<A HREF="../../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>&gt;&nbsp;preset)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B>WSUtil.</B><B><A HREF="../../../../compbio/ws/server/WSUtil.html#validateFastaInput(java.util.List)">validateFastaInput</A></B>(java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/data/sequence/\class-useFastaSequence.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="FastaSequence.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/data/sequence/class-use/Program.html b/website/full_javadoc/compbio/data/sequence/class-use/Program.html

deleted file mode 100644 (file)

index bfc36ba..0000000
--- a/website/full_javadoc/compbio/data/sequence/class-use/Program.html
+++ /dev/null
@@ -1,221 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Uses of Class compbio.data.sequence.Program\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Uses of Class compbio.data.sequence.Program";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/data/sequence/\class-useProgram.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="Program.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-<B>Uses of Class<br>compbio.data.sequence.Program</B></H2>\r
-</CENTER>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Packages that use <A HREF="../../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.data.sequence"><B>compbio.data.sequence</B></A></TD>\r
-<TD>A data model for multiple sequence alignment web services 
- Classes in this package have no dependencies to other sources in the project.&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.data.sequence"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A> in <A HREF="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A> that return <A HREF="../../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A></CODE></FONT></TD>\r
-<TD><CODE><B>AlignmentMetadata.</B><B><A HREF="../../../../compbio/data/sequence/AlignmentMetadata.html#getProgram()">getProgram</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A></CODE></FONT></TD>\r
-<TD><CODE><B>Program.</B><B><A HREF="../../../../compbio/data/sequence/Program.html#valueOf(java.lang.String)">valueOf</A></B>(java.lang.String&nbsp;name)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Returns the enum constant of this type with the specified name.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A>[]</CODE></FONT></TD>\r
-<TD><CODE><B>Program.</B><B><A HREF="../../../../compbio/data/sequence/Program.html#values()">values</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Returns an array containing the constants of this enum type, in
-the order they are declared.</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Constructors in <A HREF="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A> with parameters of type <A HREF="../../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../../compbio/data/sequence/Alignment.html#Alignment(java.util.List, compbio.data.sequence.Program, char)">Alignment</A></B>(java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-          <A HREF="../../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A>&nbsp;program,\r
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-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../../compbio/data/sequence/AlignmentMetadata.html#AlignmentMetadata(compbio.data.sequence.Program, char)">AlignmentMetadata</A></B>(<A HREF="../../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A>&nbsp;program,\r
-                  char&nbsp;gapchar)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
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-  </TR>\r
-</TABLE>\r
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-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
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-&nbsp;NEXT</FONT></TD>\r
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-  <A HREF="../../../../index.html?compbio/data/sequence/\class-useProgram.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
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-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
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-</SCRIPT>\r
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diff --git a/website/full_javadoc/compbio/data/sequence/class-use/SequenceUtil.html b/website/full_javadoc/compbio/data/sequence/class-use/SequenceUtil.html

deleted file mode 100644 (file)

index 03ed214..0000000
--- a/website/full_javadoc/compbio/data/sequence/class-use/SequenceUtil.html
+++ /dev/null
@@ -1,144 +0,0 @@
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-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Uses of Class compbio.data.sequence.SequenceUtil\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Uses of Class compbio.data.sequence.SequenceUtil";\r
-    }\r
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-<NOSCRIPT>\r
-</NOSCRIPT>\r
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-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
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-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
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-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
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-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/data/sequence/\class-useSequenceUtil.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="SequenceUtil.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-<B>Uses of Class<br>compbio.data.sequence.SequenceUtil</B></H2>\r
-</CENTER>\r
-No usage of compbio.data.sequence.SequenceUtil\r
-<P>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
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-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
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-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
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-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/data/sequence/\class-useSequenceUtil.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="SequenceUtil.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
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diff --git a/website/full_javadoc/compbio/data/sequence/class-use/UnknownFileFormatException.html b/website/full_javadoc/compbio/data/sequence/class-use/UnknownFileFormatException.html

deleted file mode 100644 (file)

index a24599c..0000000
--- a/website/full_javadoc/compbio/data/sequence/class-use/UnknownFileFormatException.html
+++ /dev/null
@@ -1,219 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Uses of Class compbio.data.sequence.UnknownFileFormatException\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Uses of Class compbio.data.sequence.UnknownFileFormatException";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
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-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/data/sequence/\class-useUnknownFileFormatException.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
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-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
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-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
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-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
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-<CENTER>\r
-<H2>\r
-<B>Uses of Class<br>compbio.data.sequence.UnknownFileFormatException</B></H2>\r
-</CENTER>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Packages that use <A HREF="../../../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.data.sequence"><B>compbio.data.sequence</B></A></TD>\r
-<TD>A data model for multiple sequence alignment web services 
- Classes in this package have no dependencies to other sources in the project.&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.runner"><B>compbio.runner</B></A></TD>\r
-<TD>Utilities commonly used by all runners.&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.data.sequence"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</A> in <A HREF="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A> that throw <A HREF="../../../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
-<TD><CODE><B>ClustalAlignmentUtil.</B><B><A HREF="../../../../compbio/data/sequence/ClustalAlignmentUtil.html#readClustalFile(java.io.File)">readClustalFile</A></B>(java.io.File&nbsp;file)</CODE>\r
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-\r
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-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Read Clustal formatted alignment.</TD>\r
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-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/runner/package-summary.html">compbio.runner</A> that throw <A HREF="../../../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</A></FONT></TH>\r
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-<CODE>static&nbsp;<A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
-<TD><CODE><B>Util.</B><B><A HREF="../../../../compbio/runner/Util.html#readClustalFile(java.lang.String, java.lang.String)">readClustalFile</A></B>(java.lang.String&nbsp;workDirectory,\r
-                java.lang.String&nbsp;clustFile)</CODE>\r
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deleted file mode 100644 (file)

index a4e673c..0000000
--- a/website/full_javadoc/compbio/data/sequence/package-frame.html
+++ /dev/null
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diff --git a/website/full_javadoc/compbio/data/sequence/package-summary.html b/website/full_javadoc/compbio/data/sequence/package-summary.html

deleted file mode 100644 (file)

index 04cec6a..0000000
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-  <!--\r
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-<H2>\r
-Package compbio.data.sequence\r
-</H2>\r
-A data model for multiple sequence alignment web services 
- Classes in this package have no dependencies to other sources in the project.\r
-<P>\r
-<B>See:</B>\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<A HREF="#package_description"><B>Description</B></A>\r
-<P>\r
-\r
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-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Class Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></B></TD>\r
-<TD>Multiple sequence alignment.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence">AlignmentMetadata</A></B></TD>\r
-<TD>Alignment metadata e.g.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../../compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence">ClustalAlignmentUtil</A></B></TD>\r
-<TD>Tools to read and write clustal formated files</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A></B></TD>\r
-<TD>A FASTA formatted sequence.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A></B></TD>\r
-<TD>Utility class for operations on sequences</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Enum Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A></B></TD>\r
-<TD>Programmes that can produce alignments</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Exception Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</A></B></TD>\r
-<TD>&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-\r
-<P>\r
-<A NAME="package_description"><!-- --></A><H2>\r
-Package compbio.data.sequence Description\r
-</H2>\r
-\r
-<P>\r
-A data model for multiple sequence alignment web services 
- Classes in this package have no dependencies to other sources in the project. 
- They form a base layer of Jalview Web Services v2.\r
-<P>\r
-\r
-<P>\r
-<DL>\r
-<DT><B>Author:</B></DT>\r
-  <DD>Petr Troshin 
- 
-        Date January 2010</DD>\r
-</DL>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
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-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
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-</TR>\r
-\r
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-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/data/msa/jaxws/package-summary.html"><B>PREV PACKAGE</B></A>&nbsp;\r
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-&nbsp;<SCRIPT type="text/javascript">\r
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diff --git a/website/full_javadoc/compbio/data/sequence/package-tree.html b/website/full_javadoc/compbio/data/sequence/package-tree.html

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-<B>Uses of Package<br>compbio.data.sequence</B></H2>\r
-</CENTER>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
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-Packages that use <A HREF="../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.data.msa"><B>compbio.data.msa</B></A></TD>\r
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-<TD><A HREF="#compbio.data.msa.jaxws"><B>compbio.data.msa.jaxws</B></A></TD>\r
-<TD>&nbsp;&nbsp;</TD>\r
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-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.data.sequence"><B>compbio.data.sequence</B></A></TD>\r
-<TD>A data model for multiple sequence alignment web services 
- Classes in this package have no dependencies to other sources in the project.&nbsp;</TD>\r
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-<TD><A HREF="#compbio.engine"><B>compbio.engine</B></A></TD>\r
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-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.metadata"><B>compbio.metadata</B></A></TD>\r
-<TD>A meta-data model for multiple sequence alignment web services 
- Classes in this package have no dependencies to other sources in the project.&nbsp;</TD>\r
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-<TD><A HREF="#compbio.runner"><B>compbio.runner</B></A></TD>\r
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-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.runner.msa"><B>compbio.runner.msa</B></A></TD>\r
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-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.ws.server"><B>compbio.ws.server</B></A></TD>\r
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-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../../compbio/data/sequence/class-use/Alignment.html#compbio.data.msa"><B>Alignment</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Multiple sequence alignment.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../../compbio/data/sequence/class-use/FastaSequence.html#compbio.data.msa"><B>FastaSequence</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;A FASTA formatted sequence.</TD>\r
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-\r
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-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Multiple sequence alignment.</TD>\r
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-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Multiple sequence alignment.</TD>\r
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-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
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-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../../compbio/data/sequence/class-use/FastaSequence.html#compbio.metadata"><B>FastaSequence</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;A FASTA formatted sequence.</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
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-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;A FASTA formatted sequence.</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.runner"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
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-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../../compbio/data/sequence/class-use/Alignment.html#compbio.runner"><B>Alignment</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Multiple sequence alignment.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../../compbio/data/sequence/class-use/FastaSequence.html#compbio.runner"><B>FastaSequence</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;A FASTA formatted sequence.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../../compbio/data/sequence/class-use/UnknownFileFormatException.html#compbio.runner"><B>UnknownFileFormatException</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
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-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
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-Classes in <A HREF="../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A> used by <A HREF="../../../compbio/runner/msa/package-summary.html">compbio.runner.msa</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../../compbio/data/sequence/class-use/Alignment.html#compbio.runner.msa"><B>Alignment</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Multiple sequence alignment.</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.ws.server"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
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-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Classes in <A HREF="../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A> used by <A HREF="../../../compbio/ws/server/package-summary.html">compbio.ws.server</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../../compbio/data/sequence/class-use/Alignment.html#compbio.ws.server"><B>Alignment</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Multiple sequence alignment.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../../compbio/data/sequence/class-use/FastaSequence.html#compbio.ws.server"><B>FastaSequence</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;A FASTA formatted sequence.</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<HR>\r
-\r
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-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
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diff --git a/website/full_javadoc/compbio/engine/AsyncExecutor.html b/website/full_javadoc/compbio/engine/AsyncExecutor.html

deleted file mode 100644 (file)

index b5f9af4..0000000
--- a/website/full_javadoc/compbio/engine/AsyncExecutor.html
+++ /dev/null
@@ -1,344 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:49 GMT 2010 -->\r
-<TITLE>\r
-AsyncExecutor\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="AsyncExecutor";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
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-\r
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-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
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-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/AsyncExecutor.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
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-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
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-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV CLASS&nbsp;\r
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-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;CONSTR&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;CONSTR&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
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-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
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-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.engine</FONT>\r
-<BR>\r
-Interface AsyncExecutor</H2>\r
-<DL>\r
-<DT><B>All Known Implementing Classes:</B> <DD><A HREF="../../compbio/engine/cluster/drmaa/AsyncJobRunner.html" title="class in compbio.engine.cluster.drmaa">AsyncJobRunner</A>, <A HREF="../../compbio/engine/local/AsyncLocalRunner.html" title="class in compbio.engine.local">AsyncLocalRunner</A></DD>\r
-</DL>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public interface <B>AsyncExecutor</B></DL>\r
-</PRE>\r
-\r
-<P>\r
-An asynchronous executor engine, capable of running, cancelling, 
- obtaining results calculated by a native executable wrapper in Executable interface. 
- Implementation agnostic. Executables can be run either locally to the JVM or on the cluster.\r
-<P>\r
-\r
-<P>\r
-<DL>\r
-<DT><B>Author:</B></DT>\r
-  <DD>pvtroshin
-                Date October 2009</DD>\r
-</DL>\r
-<HR>\r
-\r
-<P>\r
-\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/engine/AsyncExecutor.html#cancelJob(java.lang.String)">cancelJob</A></B>(java.lang.String&nbsp;jobId)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Stop running job.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/engine/AsyncExecutor.html#cleanup(java.lang.String)">cleanup</A></B>(java.lang.String&nbsp;jobId)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Remove all files and a job directory for a jobid.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/engine/AsyncExecutor.html#getJobStatus(java.lang.String)">getJobStatus</A></B>(java.lang.String&nbsp;jobId)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Query the status of the job</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/engine/AsyncExecutor.html#getResults(java.lang.String)">getResults</A></B>(java.lang.String&nbsp;jobId)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Retrieve the results of the job.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/engine/AsyncExecutor.html#getWorkDirectory(java.lang.String)">getWorkDirectory</A></B>(java.lang.String&nbsp;jobId)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/engine/AsyncExecutor.html#submitJob(compbio.engine.client.ConfiguredExecutable)">submitJob</A></B>(<A HREF="../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;executable)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Submits job for the execution
- Immediate execution is not guaranteed, this method puts the job in the queue.</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
-<A NAME="method_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="submitJob(compbio.engine.client.ConfiguredExecutable)"><!-- --></A><H3>\r
-submitJob</H3>\r
-<PRE>\r
-java.lang.String <B>submitJob</B>(<A HREF="../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;executable)\r
-                           throws <A HREF="../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></PRE>\r
-<DL>\r
-<DD>Submits job for the execution
- Immediate execution is not guaranteed, this method puts the job in the queue. 
- All it guarantees that the job will be eventually executed. 
- The start of execution will depend on the number of jobs in the queue.\r
-<P>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>unique job identifier\r
-<DT><B>Throws:</B>\r
-<DD><CODE><A HREF="../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></CODE> - if submission fails. This usually happens due to the problem on a server side.</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getResults(java.lang.String)"><!-- --></A><H3>\r
-getResults</H3>\r
-<PRE>\r
-<A HREF="../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt; <B>getResults</B>(java.lang.String&nbsp;jobId)\r
-                                   throws <A HREF="../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></PRE>\r
-<DL>\r
-<DD>Retrieve the results of the job. Please not that current implementations of this method 
- blocks if the task is running until the end of the calculation.\r
-<P>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>jobId</CODE> - job identifier obtained at the job submission\r
-<DT><B>Returns:</B><DD>ConfiguredExecutable object from which result can be obtained\r
-<DT><B>Throws:</B>\r
-<DD><CODE><A HREF="../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></CODE> - if the result is not available for whatever reason. 
- Could be due to execution failure, or due to the results being removed from the server at 
- the time of request.</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getWorkDirectory(java.lang.String)"><!-- --></A><H3>\r
-getWorkDirectory</H3>\r
-<PRE>\r
-java.lang.String <B>getWorkDirectory</B>(java.lang.String&nbsp;jobId)</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>jobId</CODE> - unique job identifier\r
-<DT><B>Returns:</B><DD>task working directory</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="cleanup(java.lang.String)"><!-- --></A><H3>\r
-cleanup</H3>\r
-<PRE>\r
-boolean <B>cleanup</B>(java.lang.String&nbsp;jobId)</PRE>\r
-<DL>\r
-<DD>Remove all files and a job directory for a jobid.\r
-<P>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>jobId</CODE> - \r
-<DT><B>Returns:</B><DD>true if job directory was successfully removed, false otherwise.</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="cancelJob(java.lang.String)"><!-- --></A><H3>\r
-cancelJob</H3>\r
-<PRE>\r
-boolean <B>cancelJob</B>(java.lang.String&nbsp;jobId)</PRE>\r
-<DL>\r
-<DD>Stop running job. Please not that this method does not guarantee to remove the job directory and files in it.\r
-<P>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>true if job was cancelled successfully, false otherwise</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getJobStatus(java.lang.String)"><!-- --></A><H3>\r
-getJobStatus</H3>\r
-<PRE>\r
-<A HREF="../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A> <B>getJobStatus</B>(java.lang.String&nbsp;jobId)</PRE>\r
-<DL>\r
-<DD>Query the status of the job\r
-<P>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>String</CODE> - jobId - unique job identifier\r
-<DT><B>Returns:</B><DD>The JobStatus object representing the status of the job<DT><B>See Also:</B><DD><A HREF="../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata"><CODE>JobStatus</CODE></A></DL>\r
-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/AsyncExecutor.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV CLASS&nbsp;\r
-&nbsp;<A HREF="../../compbio/engine/Cleaner.html" title="class in compbio.engine"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../index.html?compbio/engine/AsyncExecutor.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="AsyncExecutor.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;CONSTR&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;CONSTR&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/engine/Cleaner.html b/website/full_javadoc/compbio/engine/Cleaner.html

deleted file mode 100644 (file)

index f5a3e89..0000000
--- a/website/full_javadoc/compbio/engine/Cleaner.html
+++ /dev/null
@@ -1,278 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:49 GMT 2010 -->\r
-<TITLE>\r
-Cleaner\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Cleaner";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/Cleaner.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../compbio/engine/ClusterJobId.html" title="class in compbio.engine"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../index.html?compbio/engine/Cleaner.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="Cleaner.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.engine</FONT>\r
-<BR>\r
-Class Cleaner</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../resources/inherit.gif" ALT="extended by "><B>compbio.engine.Cleaner</B>\r
-</PRE>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public class <B>Cleaner</B><DT>extends java.lang.Object</DL>\r
-</PRE>\r
-\r
-<P>\r
-<HR>\r
-\r
-<P>\r
-\r
-<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
-\r
-<A NAME="constructor_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Constructor Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../compbio/engine/Cleaner.html#Cleaner()">Cleaner</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/engine/Cleaner.html#deleteAllFiles(java.lang.String)">deleteAllFiles</A></B>(java.lang.String&nbsp;directory)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/engine/Cleaner.html#deleteFiles(compbio.engine.client.ConfiguredExecutable)">deleteFiles</A></B>(<A HREF="../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;exec)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;This method returns true if all files specified by List files were
- successfully removed or there was no files to remove (files list was
- empty)</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
-\r
-<A NAME="constructor_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Constructor Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="Cleaner()"><!-- --></A><H3>\r
-Cleaner</H3>\r
-<PRE>\r
-public <B>Cleaner</B>()</PRE>\r
-<DL>\r
-</DL>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
-<A NAME="method_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="deleteFiles(compbio.engine.client.ConfiguredExecutable)"><!-- --></A><H3>\r
-deleteFiles</H3>\r
-<PRE>\r
-public static boolean <B>deleteFiles</B>(<A HREF="../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;exec)</PRE>\r
-<DL>\r
-<DD>This method returns true if all files specified by List files were
- successfully removed or there was no files to remove (files list was
- empty)\r
-<P>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>workDirectory</CODE> - <DD><CODE>files</CODE> - \r
-<DT><B>Returns:</B><DD></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="deleteAllFiles(java.lang.String)"><!-- --></A><H3>\r
-deleteAllFiles</H3>\r
-<PRE>\r
-public static boolean <B>deleteAllFiles</B>(java.lang.String&nbsp;directory)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/Cleaner.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../compbio/engine/ClusterJobId.html" title="class in compbio.engine"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../index.html?compbio/engine/Cleaner.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="Cleaner.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/engine/ClusterJobId.html b/website/full_javadoc/compbio/engine/ClusterJobId.html

deleted file mode 100644 (file)

index cedced1..0000000
--- a/website/full_javadoc/compbio/engine/ClusterJobId.html
+++ /dev/null
@@ -1,297 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:49 GMT 2010 -->\r
-<TITLE>\r
-ClusterJobId\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="ClusterJobId";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
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diff --git a/website/full_javadoc/compbio/engine/Configurator.html b/website/full_javadoc/compbio/engine/Configurator.html

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index 61bbed4..0000000
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-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
-\r
-<A NAME="constructor_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Constructor Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../compbio/engine/Configurator.html#Configurator()">Configurator</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
-<TR ALIGN="right" VALIGN="">\r
-<TD NOWRAP><FONT SIZE="-1">\r
-<CODE>&lt;T&gt; <A HREF="../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;T&gt;</CODE></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/engine/Configurator.html#configureExecutable(compbio.engine.client.Executable)">configureExecutable</A></B>(<A HREF="../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;T&gt;&nbsp;executable)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
-<TR ALIGN="right" VALIGN="">\r
-<TD NOWRAP><FONT SIZE="-1">\r
-<CODE>&lt;T&gt; <A HREF="../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;T&gt;</CODE></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/engine/Configurator.html#configureExecutable(compbio.engine.client.Executable, compbio.engine.client.Executable.ExecProvider)">configureExecutable</A></B>(<A HREF="../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;T&gt;&nbsp;executable,\r
-                    <A HREF="../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
-<TR ALIGN="right" VALIGN="">\r
-<TD NOWRAP><FONT SIZE="-1">\r
-<CODE>&lt;T&gt; <A HREF="../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;T&gt;</CODE></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/engine/Configurator.html#configureExecutable(compbio.engine.client.Executable, java.util.List)">configureExecutable</A></B>(<A HREF="../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;T&gt;&nbsp;executable,\r
-                    java.util.List&lt;<A HREF="../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;dataSet)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine">AsyncExecutor</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/engine/Configurator.html#getAsyncEngine(compbio.engine.client.ConfiguredExecutable)">getAsyncEngine</A></B>(<A HREF="../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;executable)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine">AsyncExecutor</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/engine/Configurator.html#getAsyncEngine(compbio.engine.client.ConfiguredExecutable, compbio.engine.client.Executable.ExecProvider)">getAsyncEngine</A></B>(<A HREF="../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;executable,\r
-               <A HREF="../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine">AsyncExecutor</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/engine/Configurator.html#getAsyncEngine(java.lang.String)">getAsyncEngine</A></B>(java.lang.String&nbsp;taskId)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../compbio/engine/SyncExecutor.html" title="interface in compbio.engine">SyncExecutor</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/engine/Configurator.html#getSyncEngine(compbio.engine.client.ConfiguredExecutable)">getSyncEngine</A></B>(<A HREF="../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;executable)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../compbio/engine/SyncExecutor.html" title="interface in compbio.engine">SyncExecutor</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/engine/Configurator.html#getSyncEngine(compbio.engine.client.ConfiguredExecutable, compbio.engine.client.Executable.ExecProvider)">getSyncEngine</A></B>(<A HREF="../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;executable,\r
-              <A HREF="../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/engine/Configurator.html#getWorkDirectory(java.lang.String)">getWorkDirectory</A></B>(java.lang.String&nbsp;taskId)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ============ FIELD DETAIL =========== -->\r
-\r
-<A NAME="field_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Field Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="IS_LOCAL_ENGINE_ENABLED"><!-- --></A><H3>\r
-IS_LOCAL_ENGINE_ENABLED</H3>\r
-<PRE>\r
-public static final boolean <B>IS_LOCAL_ENGINE_ENABLED</B></PRE>\r
-<DL>\r
-<DL>\r
-</DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="IS_CLUSTER_ENGINE_ENABLED"><!-- --></A><H3>\r
-IS_CLUSTER_ENGINE_ENABLED</H3>\r
-<PRE>\r
-public static final boolean <B>IS_CLUSTER_ENGINE_ENABLED</B></PRE>\r
-<DL>\r
-<DL>\r
-</DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="LOCAL_WORK_DIRECTORY"><!-- --></A><H3>\r
-LOCAL_WORK_DIRECTORY</H3>\r
-<PRE>\r
-public static final java.lang.String <B>LOCAL_WORK_DIRECTORY</B></PRE>\r
-<DL>\r
-<DL>\r
-</DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="CLUSTER_WORK_DIRECTORY"><!-- --></A><H3>\r
-CLUSTER_WORK_DIRECTORY</H3>\r
-<PRE>\r
-public static final java.lang.String <B>CLUSTER_WORK_DIRECTORY</B></PRE>\r
-<DL>\r
-<DL>\r
-</DL>\r
-</DL>\r
-\r
-<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
-\r
-<A NAME="constructor_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Constructor Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="Configurator()"><!-- --></A><H3>\r
-Configurator</H3>\r
-<PRE>\r
-public <B>Configurator</B>()</PRE>\r
-<DL>\r
-</DL>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
-<A NAME="method_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="configureExecutable(compbio.engine.client.Executable)"><!-- --></A><H3>\r
-configureExecutable</H3>\r
-<PRE>\r
-public static &lt;T&gt; <A HREF="../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;T&gt; <B>configureExecutable</B>(<A HREF="../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;T&gt;&nbsp;executable)\r
-                                                   throws <A HREF="../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Throws:</B>\r
-<DD><CODE><A HREF="../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></CODE></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="configureExecutable(compbio.engine.client.Executable, java.util.List)"><!-- --></A><H3>\r
-configureExecutable</H3>\r
-<PRE>\r
-public static &lt;T&gt; <A HREF="../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;T&gt; <B>configureExecutable</B>(<A HREF="../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;T&gt;&nbsp;executable,\r
-                                                              java.util.List&lt;<A HREF="../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;dataSet)\r
-                                                   throws <A HREF="../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Throws:</B>\r
-<DD><CODE><A HREF="../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></CODE></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="configureExecutable(compbio.engine.client.Executable, compbio.engine.client.Executable.ExecProvider)"><!-- --></A><H3>\r
-configureExecutable</H3>\r
-<PRE>\r
-public static &lt;T&gt; <A HREF="../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;T&gt; <B>configureExecutable</B>(<A HREF="../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;T&gt;&nbsp;executable,\r
-                                                              <A HREF="../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider)\r
-                                                   throws <A HREF="../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Throws:</B>\r
-<DD><CODE><A HREF="../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></CODE></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getAsyncEngine(compbio.engine.client.ConfiguredExecutable, compbio.engine.client.Executable.ExecProvider)"><!-- --></A><H3>\r
-getAsyncEngine</H3>\r
-<PRE>\r
-public static <A HREF="../../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine">AsyncExecutor</A> <B>getAsyncEngine</B>(<A HREF="../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;executable,\r
-                                           <A HREF="../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getSyncEngine(compbio.engine.client.ConfiguredExecutable, compbio.engine.client.Executable.ExecProvider)"><!-- --></A><H3>\r
-getSyncEngine</H3>\r
-<PRE>\r
-public static <A HREF="../../compbio/engine/SyncExecutor.html" title="interface in compbio.engine">SyncExecutor</A> <B>getSyncEngine</B>(<A HREF="../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;executable,\r
-                                         <A HREF="../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider)\r
-                                  throws <A HREF="../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Throws:</B>\r
-<DD><CODE><A HREF="../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></CODE></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getAsyncEngine(compbio.engine.client.ConfiguredExecutable)"><!-- --></A><H3>\r
-getAsyncEngine</H3>\r
-<PRE>\r
-public static <A HREF="../../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine">AsyncExecutor</A> <B>getAsyncEngine</B>(<A HREF="../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;executable)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getAsyncEngine(java.lang.String)"><!-- --></A><H3>\r
-getAsyncEngine</H3>\r
-<PRE>\r
-public static <A HREF="../../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine">AsyncExecutor</A> <B>getAsyncEngine</B>(java.lang.String&nbsp;taskId)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getSyncEngine(compbio.engine.client.ConfiguredExecutable)"><!-- --></A><H3>\r
-getSyncEngine</H3>\r
-<PRE>\r
-public static <A HREF="../../compbio/engine/SyncExecutor.html" title="interface in compbio.engine">SyncExecutor</A> <B>getSyncEngine</B>(<A HREF="../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;executable)\r
-                                  throws <A HREF="../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Throws:</B>\r
-<DD><CODE><A HREF="../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></CODE></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getWorkDirectory(java.lang.String)"><!-- --></A><H3>\r
-getWorkDirectory</H3>\r
-<PRE>\r
-public static java.lang.String <B>getWorkDirectory</B>(java.lang.String&nbsp;taskId)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/Configurator.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
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-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../compbio/engine/ClusterJobId.html" title="class in compbio.engine"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../compbio/engine/FilePuller.html" title="class in compbio.engine"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../index.html?compbio/engine/Configurator.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="Configurator.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;<A HREF="#field_summary">FIELD</A>&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;<A HREF="#field_detail">FIELD</A>&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/engine/FilePuller.html b/website/full_javadoc/compbio/engine/FilePuller.html

deleted file mode 100644 (file)

index 5a017ae..0000000
--- a/website/full_javadoc/compbio/engine/FilePuller.html
+++ /dev/null
@@ -1,551 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:49 GMT 2010 -->\r
-<TITLE>\r
-FilePuller\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="FilePuller";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/FilePuller.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../compbio/engine/Configurator.html" title="class in compbio.engine"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../compbio/engine/Job.html" title="class in compbio.engine"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../index.html?compbio/engine/FilePuller.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="FilePuller.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;CONSTR&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;CONSTR&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.engine</FONT>\r
-<BR>\r
-Class FilePuller</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../resources/inherit.gif" ALT="extended by "><B>compbio.engine.FilePuller</B>\r
-</PRE>\r
-<DL>\r
-<DT><B>All Implemented Interfaces:</B> <DD>java.lang.Comparable&lt;java.util.concurrent.Delayed&gt;, java.util.concurrent.Delayed</DD>\r
-</DL>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public class <B>FilePuller</B><DT>extends java.lang.Object<DT>implements java.util.concurrent.Delayed</DL>\r
-</PRE>\r
-\r
-<P>\r
-<HR>\r
-\r
-<P>\r
-\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;int</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/engine/FilePuller.html#compareTo(java.util.concurrent.Delayed)">compareTo</A></B>(java.util.concurrent.Delayed&nbsp;o)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/engine/FilePuller.html#disconnect()">disconnect</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/engine/FilePuller.html#equals(java.lang.Object)">equals</A></B>(java.lang.Object&nbsp;obj)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;long</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/engine/FilePuller.html#getDelay(java.util.concurrent.TimeUnit)">getDelay</A></B>(java.util.concurrent.TimeUnit&nbsp;unit)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/engine/FilePuller.html#getFile()">getFile</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;byte</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/engine/FilePuller.html#getProgress()">getProgress</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;int</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/engine/FilePuller.html#hashCode()">hashCode</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/engine/FilePuller.html#hasMoreData()">hasMoreData</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/engine/FilePuller.html#initPull()">initPull</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/engine/FilePuller.html#isFileCreated()">isFileCreated</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../compbio/engine/FilePuller.html" title="class in compbio.engine">FilePuller</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/engine/FilePuller.html#newFilePuller(java.lang.String, int)">newFilePuller</A></B>(java.lang.String&nbsp;file,\r
-              int&nbsp;chunkSize)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../compbio/engine/FilePuller.html" title="class in compbio.engine">FilePuller</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/engine/FilePuller.html#newProgressPuller(java.lang.String)">newProgressPuller</A></B>(java.lang.String&nbsp;file)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Progress Puller is designed to read 3 characters from the beginning of
- the file, nothing more.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/engine/FilePuller.html#pull(long)">pull</A></B>(long&nbsp;position)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/engine/FilePuller.html#toString()">toString</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/engine/FilePuller.html#waitForFile(long)">waitForFile</A></B>(long&nbsp;maxWaitSeconds)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>getClass, notify, notifyAll, wait, wait, wait</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
-<A NAME="method_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="newFilePuller(java.lang.String, int)"><!-- --></A><H3>\r
-newFilePuller</H3>\r
-<PRE>\r
-public static <A HREF="../../compbio/engine/FilePuller.html" title="class in compbio.engine">FilePuller</A> <B>newFilePuller</B>(java.lang.String&nbsp;file,\r
-                                       int&nbsp;chunkSize)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="newProgressPuller(java.lang.String)"><!-- --></A><H3>\r
-newProgressPuller</H3>\r
-<PRE>\r
-public static <A HREF="../../compbio/engine/FilePuller.html" title="class in compbio.engine">FilePuller</A> <B>newProgressPuller</B>(java.lang.String&nbsp;file)</PRE>\r
-<DL>\r
-<DD>Progress Puller is designed to read 3 characters from the beginning of
- the file, nothing more. Intended to be used in conjunction with a tool
- which output progress as a percent value from 0 to 100. In any cases
- progress could not be more than the largest byte value 255.\r
-<P>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>file</CODE> - \r
-<DT><B>Returns:</B><DD></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="pull(long)"><!-- --></A><H3>\r
-pull</H3>\r
-<PRE>\r
-public <A HREF="../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A> <B>pull</B>(long&nbsp;position)\r
-                 throws java.io.IOException</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-<DD><DL>\r
-\r
-<DT><B>Throws:</B>\r
-<DD><CODE>java.io.IOException</CODE></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="initPull()"><!-- --></A><H3>\r
-initPull</H3>\r
-<PRE>\r
-public void <B>initPull</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getFile()"><!-- --></A><H3>\r
-getFile</H3>\r
-<PRE>\r
-public java.lang.String <B>getFile</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="isFileCreated()"><!-- --></A><H3>\r
-isFileCreated</H3>\r
-<PRE>\r
-public boolean <B>isFileCreated</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="waitForFile(long)"><!-- --></A><H3>\r
-waitForFile</H3>\r
-<PRE>\r
-public void <B>waitForFile</B>(long&nbsp;maxWaitSeconds)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="hasMoreData()"><!-- --></A><H3>\r
-hasMoreData</H3>\r
-<PRE>\r
-public boolean <B>hasMoreData</B>()\r
-                    throws java.io.IOException</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-<DD><DL>\r
-\r
-<DT><B>Throws:</B>\r
-<DD><CODE>java.io.IOException</CODE></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="compareTo(java.util.concurrent.Delayed)"><!-- --></A><H3>\r
-compareTo</H3>\r
-<PRE>\r
-public int <B>compareTo</B>(java.util.concurrent.Delayed&nbsp;o)</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE>compareTo</CODE> in interface <CODE>java.lang.Comparable&lt;java.util.concurrent.Delayed&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getDelay(java.util.concurrent.TimeUnit)"><!-- --></A><H3>\r
-getDelay</H3>\r
-<PRE>\r
-public long <B>getDelay</B>(java.util.concurrent.TimeUnit&nbsp;unit)</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE>getDelay</CODE> in interface <CODE>java.util.concurrent.Delayed</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="disconnect()"><!-- --></A><H3>\r
-disconnect</H3>\r
-<PRE>\r
-public void <B>disconnect</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="toString()"><!-- --></A><H3>\r
-toString</H3>\r
-<PRE>\r
-public java.lang.String <B>toString</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Overrides:</B><DD><CODE>toString</CODE> in class <CODE>java.lang.Object</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="equals(java.lang.Object)"><!-- --></A><H3>\r
-equals</H3>\r
-<PRE>\r
-public boolean <B>equals</B>(java.lang.Object&nbsp;obj)</PRE>\r
-<DL>\r
-<DD><DL>\r
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-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="hashCode()"><!-- --></A><H3>\r
-hashCode</H3>\r
-<PRE>\r
-public int <B>hashCode</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Overrides:</B><DD><CODE>hashCode</CODE> in class <CODE>java.lang.Object</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
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-<HR>\r
-\r
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-getProgress</H3>\r
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-                 throws java.io.IOException</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-<DD><DL>\r
-\r
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-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
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-<TR>\r
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-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/FilePuller.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../compbio/engine/Configurator.html" title="class in compbio.engine"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../compbio/engine/Job.html" title="class in compbio.engine"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../index.html?compbio/engine/FilePuller.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="FilePuller.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>\r
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-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;CONSTR&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;CONSTR&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/engine/Job.html b/website/full_javadoc/compbio/engine/Job.html

deleted file mode 100644 (file)

index dc4790d..0000000
--- a/website/full_javadoc/compbio/engine/Job.html
+++ /dev/null
@@ -1,403 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:49 GMT 2010 -->\r
-<TITLE>\r
-Job\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Job";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/Job.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../compbio/engine/FilePuller.html" title="class in compbio.engine"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../compbio/engine/LoadBalancer.html" title="class in compbio.engine"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../index.html?compbio/engine/Job.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="Job.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.engine</FONT>\r
-<BR>\r
-Class Job</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../resources/inherit.gif" ALT="extended by "><B>compbio.engine.Job</B>\r
-</PRE>\r
-<HR>\r
-<DL>\r
-<DT><PRE><FONT SIZE="-1">@Immutable\r
-</FONT>public final class <B>Job</B><DT>extends java.lang.Object</DL>\r
-</PRE>\r
-\r
-<P>\r
-<HR>\r
-\r
-<P>\r
-\r
-<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
-\r
-<A NAME="constructor_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Constructor Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../compbio/engine/Job.html#Job(java.lang.String, java.lang.String, compbio.engine.client.ConfiguredExecutable)">Job</A></B>(java.lang.String&nbsp;taskId,\r
-    java.lang.String&nbsp;jobId,\r
-    <A HREF="../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;cexecutable)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/engine/Job.html#equals(java.lang.Object)">equals</A></B>(java.lang.Object&nbsp;obj)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../compbio/engine/Job.html" title="class in compbio.engine">Job</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/engine/Job.html#getByJobId(java.lang.String, java.util.List)">getByJobId</A></B>(java.lang.String&nbsp;jobId,\r
-           java.util.List&lt;<A HREF="../../compbio/engine/Job.html" title="class in compbio.engine">Job</A>&gt;&nbsp;jobs)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../compbio/engine/Job.html" title="class in compbio.engine">Job</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/engine/Job.html#getByTaskId(java.lang.String, java.util.List)">getByTaskId</A></B>(java.lang.String&nbsp;taskId,\r
-            java.util.List&lt;<A HREF="../../compbio/engine/Job.html" title="class in compbio.engine">Job</A>&gt;&nbsp;jobs)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/engine/Job.html#getConfExecutable()">getConfExecutable</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../compbio/engine/ClusterJobId.html" title="class in compbio.engine">ClusterJobId</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/engine/Job.html#getJobId()">getJobId</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/engine/Job.html#getTaskId()">getTaskId</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;int</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/engine/Job.html#hashCode()">hashCode</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/engine/Job.html#toString()">toString</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>getClass, notify, notifyAll, wait, wait, wait</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
-\r
-<A NAME="constructor_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Constructor Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="Job(java.lang.String, java.lang.String, compbio.engine.client.ConfiguredExecutable)"><!-- --></A><H3>\r
-Job</H3>\r
-<PRE>\r
-public <B>Job</B>(java.lang.String&nbsp;taskId,\r
-           java.lang.String&nbsp;jobId,\r
-           <A HREF="../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;cexecutable)</PRE>\r
-<DL>\r
-</DL>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
-<A NAME="method_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="getJobId()"><!-- --></A><H3>\r
-getJobId</H3>\r
-<PRE>\r
-public <A HREF="../../compbio/engine/ClusterJobId.html" title="class in compbio.engine">ClusterJobId</A> <B>getJobId</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getTaskId()"><!-- --></A><H3>\r
-getTaskId</H3>\r
-<PRE>\r
-public java.lang.String <B>getTaskId</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getConfExecutable()"><!-- --></A><H3>\r
-getConfExecutable</H3>\r
-<PRE>\r
-public <A HREF="../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt; <B>getConfExecutable</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="hashCode()"><!-- --></A><H3>\r
-hashCode</H3>\r
-<PRE>\r
-public int <B>hashCode</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Overrides:</B><DD><CODE>hashCode</CODE> in class <CODE>java.lang.Object</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="equals(java.lang.Object)"><!-- --></A><H3>\r
-equals</H3>\r
-<PRE>\r
-public boolean <B>equals</B>(java.lang.Object&nbsp;obj)</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Overrides:</B><DD><CODE>equals</CODE> in class <CODE>java.lang.Object</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="toString()"><!-- --></A><H3>\r
-toString</H3>\r
-<PRE>\r
-public java.lang.String <B>toString</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Overrides:</B><DD><CODE>toString</CODE> in class <CODE>java.lang.Object</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getByTaskId(java.lang.String, java.util.List)"><!-- --></A><H3>\r
-getByTaskId</H3>\r
-<PRE>\r
-public static <A HREF="../../compbio/engine/Job.html" title="class in compbio.engine">Job</A> <B>getByTaskId</B>(java.lang.String&nbsp;taskId,\r
-                              java.util.List&lt;<A HREF="../../compbio/engine/Job.html" title="class in compbio.engine">Job</A>&gt;&nbsp;jobs)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getByJobId(java.lang.String, java.util.List)"><!-- --></A><H3>\r
-getByJobId</H3>\r
-<PRE>\r
-public static <A HREF="../../compbio/engine/Job.html" title="class in compbio.engine">Job</A> <B>getByJobId</B>(java.lang.String&nbsp;jobId,\r
-                             java.util.List&lt;<A HREF="../../compbio/engine/Job.html" title="class in compbio.engine">Job</A>&gt;&nbsp;jobs)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/Job.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../compbio/engine/FilePuller.html" title="class in compbio.engine"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../compbio/engine/LoadBalancer.html" title="class in compbio.engine"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../index.html?compbio/engine/Job.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="Job.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/engine/LoadBalancer.html b/website/full_javadoc/compbio/engine/LoadBalancer.html

deleted file mode 100644 (file)

index eb3b1d9..0000000
--- a/website/full_javadoc/compbio/engine/LoadBalancer.html
+++ /dev/null
@@ -1,247 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:49 GMT 2010 -->\r
-<TITLE>\r
-LoadBalancer\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="LoadBalancer";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/LoadBalancer.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../compbio/engine/Job.html" title="class in compbio.engine"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../compbio/engine/ProgressGetter.html" title="class in compbio.engine"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../index.html?compbio/engine/LoadBalancer.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="LoadBalancer.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;CONSTR&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;CONSTR&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.engine</FONT>\r
-<BR>\r
-Class LoadBalancer</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../resources/inherit.gif" ALT="extended by "><B>compbio.engine.LoadBalancer</B>\r
-</PRE>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public class <B>LoadBalancer</B><DT>extends java.lang.Object</DL>\r
-</PRE>\r
-\r
-<P>\r
-<HR>\r
-\r
-<P>\r
-\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/engine/LoadBalancer.html#getEngine(compbio.engine.client.Executable)">getEngine</A></B>(<A HREF="../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;?&gt;&nbsp;executable)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
-<TR ALIGN="right" VALIGN="">\r
-<TD NOWRAP><FONT SIZE="-1">\r
-<CODE>&lt;T,V&gt; <A HREF="../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A></CODE></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/engine/LoadBalancer.html#getEngine(compbio.engine.client.Executable, java.util.List)">getEngine</A></B>(<A HREF="../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;V&gt;&nbsp;executable,\r
-          java.util.List&lt;<A HREF="../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;dataSet)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
-<A NAME="method_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="getEngine(compbio.engine.client.Executable)"><!-- --></A><H3>\r
-getEngine</H3>\r
-<PRE>\r
-public static <A HREF="../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A> <B>getEngine</B>(<A HREF="../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;?&gt;&nbsp;executable)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getEngine(compbio.engine.client.Executable, java.util.List)"><!-- --></A><H3>\r
-getEngine</H3>\r
-<PRE>\r
-public static &lt;T,V&gt; <A HREF="../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A> <B>getEngine</B>(<A HREF="../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;V&gt;&nbsp;executable,\r
-                                                      java.util.List&lt;<A HREF="../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;dataSet)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/LoadBalancer.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../compbio/engine/Job.html" title="class in compbio.engine"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../compbio/engine/ProgressGetter.html" title="class in compbio.engine"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../index.html?compbio/engine/LoadBalancer.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="LoadBalancer.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;CONSTR&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;CONSTR&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/engine/ProgressGetter.html b/website/full_javadoc/compbio/engine/ProgressGetter.html

deleted file mode 100644 (file)

index 93c4cd3..0000000
--- a/website/full_javadoc/compbio/engine/ProgressGetter.html
+++ /dev/null
@@ -1,273 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:49 GMT 2010 -->\r
-<TITLE>\r
-ProgressGetter\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="ProgressGetter";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/ProgressGetter.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../compbio/engine/LoadBalancer.html" title="class in compbio.engine"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../compbio/engine/PulledFileCache.html" title="class in compbio.engine"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../index.html?compbio/engine/ProgressGetter.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="ProgressGetter.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.engine</FONT>\r
-<BR>\r
-Class ProgressGetter</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../resources/inherit.gif" ALT="extended by "><B>compbio.engine.ProgressGetter</B>\r
-</PRE>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public class <B>ProgressGetter</B><DT>extends java.lang.Object</DL>\r
-</PRE>\r
-\r
-<P>\r
-<HR>\r
-\r
-<P>\r
-\r
-<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
-\r
-<A NAME="constructor_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Constructor Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../compbio/engine/ProgressGetter.html#ProgressGetter()">ProgressGetter</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;byte</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/engine/ProgressGetter.html#getProgress(java.lang.String)">getProgress</A></B>(java.lang.String&nbsp;progressFile)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/engine/ProgressGetter.html#pull(java.lang.String, long)">pull</A></B>(java.lang.String&nbsp;file,\r
-     long&nbsp;position)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
-\r
-<A NAME="constructor_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Constructor Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="ProgressGetter()"><!-- --></A><H3>\r
-ProgressGetter</H3>\r
-<PRE>\r
-public <B>ProgressGetter</B>()</PRE>\r
-<DL>\r
-</DL>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
-<A NAME="method_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="pull(java.lang.String, long)"><!-- --></A><H3>\r
-pull</H3>\r
-<PRE>\r
-public static final <A HREF="../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A> <B>pull</B>(java.lang.String&nbsp;file,\r
-                                     long&nbsp;position)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getProgress(java.lang.String)"><!-- --></A><H3>\r
-getProgress</H3>\r
-<PRE>\r
-public static final byte <B>getProgress</B>(java.lang.String&nbsp;progressFile)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/ProgressGetter.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../compbio/engine/LoadBalancer.html" title="class in compbio.engine"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../compbio/engine/PulledFileCache.html" title="class in compbio.engine"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../index.html?compbio/engine/ProgressGetter.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="ProgressGetter.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/engine/PulledFileCache.html b/website/full_javadoc/compbio/engine/PulledFileCache.html

deleted file mode 100644 (file)

index 0d11dcf..0000000
--- a/website/full_javadoc/compbio/engine/PulledFileCache.html
+++ /dev/null
@@ -1,275 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:49 GMT 2010 -->\r
-<TITLE>\r
-PulledFileCache\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="PulledFileCache";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/PulledFileCache.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../compbio/engine/ProgressGetter.html" title="class in compbio.engine"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../compbio/engine/SubmissionManager.html" title="class in compbio.engine"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../index.html?compbio/engine/PulledFileCache.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="PulledFileCache.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.engine</FONT>\r
-<BR>\r
-Class PulledFileCache</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../resources/inherit.gif" ALT="extended by "><B>compbio.engine.PulledFileCache</B>\r
-</PRE>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public final class <B>PulledFileCache</B><DT>extends java.lang.Object</DL>\r
-</PRE>\r
-\r
-<P>\r
-<HR>\r
-\r
-<P>\r
-\r
-<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
-\r
-<A NAME="constructor_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Constructor Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../compbio/engine/PulledFileCache.html#PulledFileCache()">PulledFileCache</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../compbio/engine/FilePuller.html" title="class in compbio.engine">FilePuller</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/engine/PulledFileCache.html#get(java.lang.String)">get</A></B>(java.lang.String&nbsp;fileName)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/engine/PulledFileCache.html#put(compbio.engine.FilePuller)">put</A></B>(<A HREF="../../compbio/engine/FilePuller.html" title="class in compbio.engine">FilePuller</A>&nbsp;fpuller)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;This method allows duplicates to be added.</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
-\r
-<A NAME="constructor_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Constructor Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="PulledFileCache()"><!-- --></A><H3>\r
-PulledFileCache</H3>\r
-<PRE>\r
-public <B>PulledFileCache</B>()</PRE>\r
-<DL>\r
-</DL>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
-<A NAME="method_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="get(java.lang.String)"><!-- --></A><H3>\r
-get</H3>\r
-<PRE>\r
-public static <A HREF="../../compbio/engine/FilePuller.html" title="class in compbio.engine">FilePuller</A> <B>get</B>(java.lang.String&nbsp;fileName)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="put(compbio.engine.FilePuller)"><!-- --></A><H3>\r
-put</H3>\r
-<PRE>\r
-public static boolean <B>put</B>(<A HREF="../../compbio/engine/FilePuller.html" title="class in compbio.engine">FilePuller</A>&nbsp;fpuller)</PRE>\r
-<DL>\r
-<DD>This method allows duplicates to be added. This is a responsibility of
- the called to ensure this will not happen!\r
-<P>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>fpuller</CODE> - \r
-<DT><B>Returns:</B><DD></DL>\r
-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
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-\r
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-&nbsp;<A HREF="../../compbio/engine/ProgressGetter.html" title="class in compbio.engine"><B>PREV CLASS</B></A>&nbsp;\r
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diff --git a/website/full_javadoc/compbio/engine/SubmissionManager.html b/website/full_javadoc/compbio/engine/SubmissionManager.html

deleted file mode 100644 (file)

index 9a83cd7..0000000
--- a/website/full_javadoc/compbio/engine/SubmissionManager.html
+++ /dev/null
@@ -1,286 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:49 GMT 2010 -->\r
-<TITLE>\r
-SubmissionManager\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
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-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="SubmissionManager";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
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-\r
-\r
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-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../compbio/engine/PulledFileCache.html" title="class in compbio.engine"><B>PREV CLASS</B></A>&nbsp;\r
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-  <A HREF="../../index.html?compbio/engine/SubmissionManager.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
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-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
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-\r
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-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;CONSTR&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
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-\r
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-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.engine</FONT>\r
-<BR>\r
-Class SubmissionManager</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../resources/inherit.gif" ALT="extended by "><B>compbio.engine.SubmissionManager</B>\r
-</PRE>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public class <B>SubmissionManager</B><DT>extends java.lang.Object</DL>\r
-</PRE>\r
-\r
-<P>\r
-Submit jobs for execution\r
-<P>\r
-\r
-<P>\r
-<DL>\r
-<DT><B>Author:</B></DT>\r
-  <DD>pvtroshin</DD>\r
-</DL>\r
-<HR>\r
-\r
-<P>\r
-\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
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-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/engine/SubmissionManager.html#addTask(compbio.engine.client.ConfiguredExecutable, java.util.concurrent.Future)">addTask</A></B>(<A HREF="../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;executable,\r
-        java.util.concurrent.Future&lt;<A HREF="../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&gt;&nbsp;future)</CODE>\r
-\r
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-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;java.util.concurrent.Future&lt;<A HREF="../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/engine/SubmissionManager.html#getTask(java.lang.String)">getTask</A></B>(java.lang.String&nbsp;taskId)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/engine/SubmissionManager.html#removeTask(compbio.engine.client.ConfiguredExecutable)">removeTask</A></B>(<A HREF="../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;executable)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;void</CODE></FONT></TD>\r
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-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
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-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
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-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>\r
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-\r
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-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="addTask(compbio.engine.client.ConfiguredExecutable, java.util.concurrent.Future)"><!-- --></A><H3>\r
-addTask</H3>\r
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-public static void <B>addTask</B>(<A HREF="../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;executable,\r
-                           java.util.concurrent.Future&lt;<A HREF="../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&gt;&nbsp;future)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getTask(java.lang.String)"><!-- --></A><H3>\r
-getTask</H3>\r
-<PRE>\r
-public static java.util.concurrent.Future&lt;<A HREF="../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&gt; <B>getTask</B>(java.lang.String&nbsp;taskId)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="removeTask(compbio.engine.client.ConfiguredExecutable)"><!-- --></A><H3>\r
-removeTask</H3>\r
-<PRE>\r
-public static void <B>removeTask</B>(<A HREF="../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;executable)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="removeTask(java.lang.String)"><!-- --></A><H3>\r
-removeTask</H3>\r
-<PRE>\r
-public static void <B>removeTask</B>(java.lang.String&nbsp;key)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
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-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/SubmissionManager.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
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-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../compbio/engine/PulledFileCache.html" title="class in compbio.engine"><B>PREV CLASS</B></A>&nbsp;\r
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-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
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-  <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>\r
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-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
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-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;CONSTR&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
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diff --git a/website/full_javadoc/compbio/engine/SyncExecutor.html b/website/full_javadoc/compbio/engine/SyncExecutor.html

deleted file mode 100644 (file)

index ac2be71..0000000
--- a/website/full_javadoc/compbio/engine/SyncExecutor.html
+++ /dev/null
@@ -1,337 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:49 GMT 2010 -->\r
-<TITLE>\r
-SyncExecutor\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="SyncExecutor";\r
-    }\r
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-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
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-\r
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-<FONT SIZE="-1">\r
-compbio.engine</FONT>\r
-<BR>\r
-Interface SyncExecutor</H2>\r
-<DL>\r
-<DT><B>All Known Implementing Classes:</B> <DD><A HREF="../../compbio/engine/cluster/drmaa/JobRunner.html" title="class in compbio.engine.cluster.drmaa">JobRunner</A>, <A HREF="../../compbio/engine/local/LocalRunner.html" title="class in compbio.engine.local">LocalRunner</A></DD>\r
-</DL>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public interface <B>SyncExecutor</B></DL>\r
-</PRE>\r
-\r
-<P>\r
-Synchronous executor, is an engine to run the Executable synchronously.\r
-<P>\r
-\r
-<P>\r
-<DL>\r
-<DT><B>Author:</B></DT>\r
-  <DD>pvtroshin
-                Date October 2009</DD>\r
-</DL>\r
-<HR>\r
-\r
-<P>\r
-\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
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-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/engine/SyncExecutor.html#cancelJob()">cancelJob</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Stops running job.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/engine/SyncExecutor.html#cleanup()">cleanup</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Clean up after the job</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/engine/SyncExecutor.html#executeJob()">executeJob</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Execute the job</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/engine/SyncExecutor.html#getJobStatus()">getJobStatus</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Query the status of the job by its id.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/engine/SyncExecutor.html#getWorkDirectory()">getWorkDirectory</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/engine/SyncExecutor.html#waitForResult()">waitForResult</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Call to this method block for as long as it is required for an executable to finish its job.</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
-<A NAME="method_detail"><!-- --></A>\r
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-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
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-<B>Method Detail</B></FONT></TH>\r
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-\r
-<A NAME="executeJob()"><!-- --></A><H3>\r
-executeJob</H3>\r
-<PRE>\r
-void <B>executeJob</B>()\r
-                throws <A HREF="../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></PRE>\r
-<DL>\r
-<DD>Execute the job\r
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-<DD><DL>\r
-\r
-<DT><B>Throws:</B>\r
-<DD><CODE><A HREF="../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></CODE> - if submission fails</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="cleanup()"><!-- --></A><H3>\r
-cleanup</H3>\r
-<PRE>\r
-boolean <B>cleanup</B>()</PRE>\r
-<DL>\r
-<DD>Clean up after the job\r
-<P>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>true if all the files created by this job have been removed successfully, false otherwise</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="waitForResult()"><!-- --></A><H3>\r
-waitForResult</H3>\r
-<PRE>\r
-<A HREF="../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt; <B>waitForResult</B>()\r
-                                      throws <A HREF="../../compbio/metadata/JobExecutionException.html" title="class in compbio.metadata">JobExecutionException</A></PRE>\r
-<DL>\r
-<DD>Call to this method block for as long as it is required for an executable to finish its job. 
- If the calculation has been completed already, the this method returns results immediately. 
- This could return the result directly, but that would be type unsafe\r
-<P>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>object from wich the result can be obtained\r
-<DT><B>Throws:</B>\r
-<DD><CODE><A HREF="../../compbio/metadata/JobExecutionException.html" title="class in compbio.metadata">JobExecutionException</A></CODE></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getWorkDirectory()"><!-- --></A><H3>\r
-getWorkDirectory</H3>\r
-<PRE>\r
-java.lang.String <B>getWorkDirectory</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>working directory if the task</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="cancelJob()"><!-- --></A><H3>\r
-cancelJob</H3>\r
-<PRE>\r
-boolean <B>cancelJob</B>()</PRE>\r
-<DL>\r
-<DD>Stops running job. 
- Clean up is not performed.\r
-<P>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>true if job was cancelled successfully, false otherwise</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getJobStatus()"><!-- --></A><H3>\r
-getJobStatus</H3>\r
-<PRE>\r
-<A HREF="../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A> <B>getJobStatus</B>()</PRE>\r
-<DL>\r
-<DD>Query the status of the job by its id.\r
-<P>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>- JobStatus</DL>\r
-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
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-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
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diff --git a/website/full_javadoc/compbio/engine/class-use/AsyncExecutor.html b/website/full_javadoc/compbio/engine/class-use/AsyncExecutor.html

deleted file mode 100644 (file)

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--- a/website/full_javadoc/compbio/engine/class-use/AsyncExecutor.html
+++ /dev/null
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-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
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-Uses of Interface compbio.engine.AsyncExecutor\r
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-<B>Uses of Interface<br>compbio.engine.AsyncExecutor</B></H2>\r
-</CENTER>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Packages that use <A HREF="../../../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine">AsyncExecutor</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.engine"><B>compbio.engine</B></A></TD>\r
-<TD>&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.engine.cluster.drmaa"><B>compbio.engine.cluster.drmaa</B></A></TD>\r
-<TD>An cluster engine classes responsible for execution of Executables on the clusters.&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.engine.local"><B>compbio.engine.local</B></A></TD>\r
-<TD>An local engine classes responsible for execution of Executables on the local computer 
- (the same machine as JVM running these classes).&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.ws.server"><B>compbio.ws.server</B></A></TD>\r
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-Uses of <A HREF="../../../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine">AsyncExecutor</A> in <A HREF="../../../compbio/engine/package-summary.html">compbio.engine</A></FONT></TH>\r
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-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/engine/package-summary.html">compbio.engine</A> that return <A HREF="../../../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine">AsyncExecutor</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine">AsyncExecutor</A></CODE></FONT></TD>\r
-<TD><CODE><B>Configurator.</B><B><A HREF="../../../compbio/engine/Configurator.html#getAsyncEngine(compbio.engine.client.ConfiguredExecutable)">getAsyncEngine</A></B>(<A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;executable)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine">AsyncExecutor</A></CODE></FONT></TD>\r
-<TD><CODE><B>Configurator.</B><B><A HREF="../../../compbio/engine/Configurator.html#getAsyncEngine(compbio.engine.client.ConfiguredExecutable, compbio.engine.client.Executable.ExecProvider)">getAsyncEngine</A></B>(<A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;executable,\r
-               <A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine">AsyncExecutor</A></CODE></FONT></TD>\r
-<TD><CODE><B>Configurator.</B><B><A HREF="../../../compbio/engine/Configurator.html#getAsyncEngine(java.lang.String)">getAsyncEngine</A></B>(java.lang.String&nbsp;taskId)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.engine.cluster.drmaa"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine">AsyncExecutor</A> in <A HREF="../../../compbio/engine/cluster/drmaa/package-summary.html">compbio.engine.cluster.drmaa</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Classes in <A HREF="../../../compbio/engine/cluster/drmaa/package-summary.html">compbio.engine.cluster.drmaa</A> that implement <A HREF="../../../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine">AsyncExecutor</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;class</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/cluster/drmaa/AsyncJobRunner.html" title="class in compbio.engine.cluster.drmaa">AsyncJobRunner</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Single cluster job runner class</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.engine.local"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine">AsyncExecutor</A> in <A HREF="../../../compbio/engine/local/package-summary.html">compbio.engine.local</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Classes in <A HREF="../../../compbio/engine/local/package-summary.html">compbio.engine.local</A> that implement <A HREF="../../../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine">AsyncExecutor</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;class</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/local/AsyncLocalRunner.html" title="class in compbio.engine.local">AsyncLocalRunner</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.ws.server"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine">AsyncExecutor</A> in <A HREF="../../../compbio/ws/server/package-summary.html">compbio.ws.server</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/ws/server/package-summary.html">compbio.ws.server</A> that return <A HREF="../../../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine">AsyncExecutor</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine">AsyncExecutor</A></CODE></FONT></TD>\r
-<TD><CODE><B>WSUtil.</B><B><A HREF="../../../compbio/ws/server/WSUtil.html#getEngine(compbio.engine.client.ConfiguredExecutable)">getEngine</A></B>(<A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;confClustal)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/engine/\class-useAsyncExecutor.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="AsyncExecutor.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/engine/class-use/Cleaner.html b/website/full_javadoc/compbio/engine/class-use/Cleaner.html

deleted file mode 100644 (file)

index 2817a0e..0000000
--- a/website/full_javadoc/compbio/engine/class-use/Cleaner.html
+++ /dev/null
@@ -1,144 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Uses of Class compbio.engine.Cleaner\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Uses of Class compbio.engine.Cleaner";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../compbio/engine/Cleaner.html" title="class in compbio.engine"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/engine/\class-useCleaner.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="Cleaner.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-<B>Uses of Class<br>compbio.engine.Cleaner</B></H2>\r
-</CENTER>\r
-No usage of compbio.engine.Cleaner\r
-<P>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../compbio/engine/Cleaner.html" title="class in compbio.engine"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/engine/\class-useCleaner.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="Cleaner.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/engine/class-use/ClusterJobId.html b/website/full_javadoc/compbio/engine/class-use/ClusterJobId.html

deleted file mode 100644 (file)

index b2ba6dc..0000000
--- a/website/full_javadoc/compbio/engine/class-use/ClusterJobId.html
+++ /dev/null
@@ -1,227 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Uses of Class compbio.engine.ClusterJobId\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Uses of Class compbio.engine.ClusterJobId";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../compbio/engine/ClusterJobId.html" title="class in compbio.engine"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/engine/\class-useClusterJobId.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="ClusterJobId.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-<B>Uses of Class<br>compbio.engine.ClusterJobId</B></H2>\r
-</CENTER>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Packages that use <A HREF="../../../compbio/engine/ClusterJobId.html" title="class in compbio.engine">ClusterJobId</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.engine"><B>compbio.engine</B></A></TD>\r
-<TD>&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.engine.cluster.drmaa"><B>compbio.engine.cluster.drmaa</B></A></TD>\r
-<TD>An cluster engine classes responsible for execution of Executables on the clusters.&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.engine"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../compbio/engine/ClusterJobId.html" title="class in compbio.engine">ClusterJobId</A> in <A HREF="../../../compbio/engine/package-summary.html">compbio.engine</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/engine/package-summary.html">compbio.engine</A> that return <A HREF="../../../compbio/engine/ClusterJobId.html" title="class in compbio.engine">ClusterJobId</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/engine/ClusterJobId.html" title="class in compbio.engine">ClusterJobId</A></CODE></FONT></TD>\r
-<TD><CODE><B>Job.</B><B><A HREF="../../../compbio/engine/Job.html#getJobId()">getJobId</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.engine.cluster.drmaa"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../compbio/engine/ClusterJobId.html" title="class in compbio.engine">ClusterJobId</A> in <A HREF="../../../compbio/engine/cluster/drmaa/package-summary.html">compbio.engine.cluster.drmaa</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/engine/cluster/drmaa/package-summary.html">compbio.engine.cluster.drmaa</A> that return <A HREF="../../../compbio/engine/ClusterJobId.html" title="class in compbio.engine">ClusterJobId</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../compbio/engine/ClusterJobId.html" title="class in compbio.engine">ClusterJobId</A></CODE></FONT></TD>\r
-<TD><CODE><B>ClusterSession.</B><B><A HREF="../../../compbio/engine/cluster/drmaa/ClusterSession.html#getClusterJobId(java.lang.String)">getClusterJobId</A></B>(java.lang.String&nbsp;taskId)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/engine/cluster/drmaa/package-summary.html">compbio.engine.cluster.drmaa</A> with parameters of type <A HREF="../../../compbio/engine/ClusterJobId.html" title="class in compbio.engine">ClusterJobId</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;int</CODE></FONT></TD>\r
-<TD><CODE><B>ClusterSession.</B><B><A HREF="../../../compbio/engine/cluster/drmaa/ClusterSession.html#getJobStatus(compbio.engine.ClusterJobId)">getJobStatus</A></B>(<A HREF="../../../compbio/engine/ClusterJobId.html" title="class in compbio.engine">ClusterJobId</A>&nbsp;jobId)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Apparently completed jobs cannot be found! If this happened most likely
- that the job is not running any more and Most likely it has been
- cancelled, finished or failed.</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../compbio/engine/ClusterJobId.html" title="class in compbio.engine"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/engine/\class-useClusterJobId.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="ClusterJobId.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/engine/class-use/Configurator.html b/website/full_javadoc/compbio/engine/class-use/Configurator.html

deleted file mode 100644 (file)

index 40b9770..0000000
--- a/website/full_javadoc/compbio/engine/class-use/Configurator.html
+++ /dev/null
@@ -1,144 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Uses of Class compbio.engine.Configurator\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Uses of Class compbio.engine.Configurator";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../compbio/engine/Configurator.html" title="class in compbio.engine"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/engine/\class-useConfigurator.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="Configurator.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-<B>Uses of Class<br>compbio.engine.Configurator</B></H2>\r
-</CENTER>\r
-No usage of compbio.engine.Configurator\r
-<P>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../compbio/engine/Configurator.html" title="class in compbio.engine"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/engine/\class-useConfigurator.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="Configurator.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/engine/class-use/FilePuller.html b/website/full_javadoc/compbio/engine/class-use/FilePuller.html

deleted file mode 100644 (file)

index c27be52..0000000
--- a/website/full_javadoc/compbio/engine/class-use/FilePuller.html
+++ /dev/null
@@ -1,214 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Uses of Class compbio.engine.FilePuller\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Uses of Class compbio.engine.FilePuller";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../compbio/engine/FilePuller.html" title="class in compbio.engine"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/engine/\class-useFilePuller.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="FilePuller.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-<B>Uses of Class<br>compbio.engine.FilePuller</B></H2>\r
-</CENTER>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Packages that use <A HREF="../../../compbio/engine/FilePuller.html" title="class in compbio.engine">FilePuller</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.engine"><B>compbio.engine</B></A></TD>\r
-<TD>&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.engine"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../compbio/engine/FilePuller.html" title="class in compbio.engine">FilePuller</A> in <A HREF="../../../compbio/engine/package-summary.html">compbio.engine</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/engine/package-summary.html">compbio.engine</A> that return <A HREF="../../../compbio/engine/FilePuller.html" title="class in compbio.engine">FilePuller</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../compbio/engine/FilePuller.html" title="class in compbio.engine">FilePuller</A></CODE></FONT></TD>\r
-<TD><CODE><B>PulledFileCache.</B><B><A HREF="../../../compbio/engine/PulledFileCache.html#get(java.lang.String)">get</A></B>(java.lang.String&nbsp;fileName)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../compbio/engine/FilePuller.html" title="class in compbio.engine">FilePuller</A></CODE></FONT></TD>\r
-<TD><CODE><B>FilePuller.</B><B><A HREF="../../../compbio/engine/FilePuller.html#newFilePuller(java.lang.String, int)">newFilePuller</A></B>(java.lang.String&nbsp;file,\r
-              int&nbsp;chunkSize)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../compbio/engine/FilePuller.html" title="class in compbio.engine">FilePuller</A></CODE></FONT></TD>\r
-<TD><CODE><B>FilePuller.</B><B><A HREF="../../../compbio/engine/FilePuller.html#newProgressPuller(java.lang.String)">newProgressPuller</A></B>(java.lang.String&nbsp;file)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Progress Puller is designed to read 3 characters from the beginning of
- the file, nothing more.</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/engine/package-summary.html">compbio.engine</A> with parameters of type <A HREF="../../../compbio/engine/FilePuller.html" title="class in compbio.engine">FilePuller</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;boolean</CODE></FONT></TD>\r
-<TD><CODE><B>PulledFileCache.</B><B><A HREF="../../../compbio/engine/PulledFileCache.html#put(compbio.engine.FilePuller)">put</A></B>(<A HREF="../../../compbio/engine/FilePuller.html" title="class in compbio.engine">FilePuller</A>&nbsp;fpuller)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;This method allows duplicates to be added.</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../compbio/engine/FilePuller.html" title="class in compbio.engine"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/engine/\class-useFilePuller.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="FilePuller.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/engine/class-use/Job.html b/website/full_javadoc/compbio/engine/class-use/Job.html

deleted file mode 100644 (file)

index def898e..0000000
--- a/website/full_javadoc/compbio/engine/class-use/Job.html
+++ /dev/null
@@ -1,216 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Uses of Class compbio.engine.Job\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Uses of Class compbio.engine.Job";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../compbio/engine/Job.html" title="class in compbio.engine"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/engine/\class-useJob.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="Job.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-<B>Uses of Class<br>compbio.engine.Job</B></H2>\r
-</CENTER>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Packages that use <A HREF="../../../compbio/engine/Job.html" title="class in compbio.engine">Job</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.engine"><B>compbio.engine</B></A></TD>\r
-<TD>&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.engine"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../compbio/engine/Job.html" title="class in compbio.engine">Job</A> in <A HREF="../../../compbio/engine/package-summary.html">compbio.engine</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/engine/package-summary.html">compbio.engine</A> that return <A HREF="../../../compbio/engine/Job.html" title="class in compbio.engine">Job</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../compbio/engine/Job.html" title="class in compbio.engine">Job</A></CODE></FONT></TD>\r
-<TD><CODE><B>Job.</B><B><A HREF="../../../compbio/engine/Job.html#getByJobId(java.lang.String, java.util.List)">getByJobId</A></B>(java.lang.String&nbsp;jobId,\r
-           java.util.List&lt;<A HREF="../../../compbio/engine/Job.html" title="class in compbio.engine">Job</A>&gt;&nbsp;jobs)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../compbio/engine/Job.html" title="class in compbio.engine">Job</A></CODE></FONT></TD>\r
-<TD><CODE><B>Job.</B><B><A HREF="../../../compbio/engine/Job.html#getByTaskId(java.lang.String, java.util.List)">getByTaskId</A></B>(java.lang.String&nbsp;taskId,\r
-            java.util.List&lt;<A HREF="../../../compbio/engine/Job.html" title="class in compbio.engine">Job</A>&gt;&nbsp;jobs)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Method parameters in <A HREF="../../../compbio/engine/package-summary.html">compbio.engine</A> with type arguments of type <A HREF="../../../compbio/engine/Job.html" title="class in compbio.engine">Job</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../compbio/engine/Job.html" title="class in compbio.engine">Job</A></CODE></FONT></TD>\r
-<TD><CODE><B>Job.</B><B><A HREF="../../../compbio/engine/Job.html#getByJobId(java.lang.String, java.util.List)">getByJobId</A></B>(java.lang.String&nbsp;jobId,\r
-           java.util.List&lt;<A HREF="../../../compbio/engine/Job.html" title="class in compbio.engine">Job</A>&gt;&nbsp;jobs)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../compbio/engine/Job.html" title="class in compbio.engine">Job</A></CODE></FONT></TD>\r
-<TD><CODE><B>Job.</B><B><A HREF="../../../compbio/engine/Job.html#getByTaskId(java.lang.String, java.util.List)">getByTaskId</A></B>(java.lang.String&nbsp;taskId,\r
-            java.util.List&lt;<A HREF="../../../compbio/engine/Job.html" title="class in compbio.engine">Job</A>&gt;&nbsp;jobs)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../compbio/engine/Job.html" title="class in compbio.engine"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/engine/\class-useJob.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="Job.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/engine/class-use/LoadBalancer.html b/website/full_javadoc/compbio/engine/class-use/LoadBalancer.html

deleted file mode 100644 (file)

index 233f48a..0000000
--- a/website/full_javadoc/compbio/engine/class-use/LoadBalancer.html
+++ /dev/null
@@ -1,144 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Uses of Class compbio.engine.LoadBalancer\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Uses of Class compbio.engine.LoadBalancer";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../compbio/engine/LoadBalancer.html" title="class in compbio.engine"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/engine/\class-useLoadBalancer.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="LoadBalancer.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-<B>Uses of Class<br>compbio.engine.LoadBalancer</B></H2>\r
-</CENTER>\r
-No usage of compbio.engine.LoadBalancer\r
-<P>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../compbio/engine/LoadBalancer.html" title="class in compbio.engine"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/engine/\class-useLoadBalancer.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="LoadBalancer.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/engine/class-use/ProgressGetter.html b/website/full_javadoc/compbio/engine/class-use/ProgressGetter.html

deleted file mode 100644 (file)

index 7841509..0000000
--- a/website/full_javadoc/compbio/engine/class-use/ProgressGetter.html
+++ /dev/null
@@ -1,144 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Uses of Class compbio.engine.ProgressGetter\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Uses of Class compbio.engine.ProgressGetter";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../compbio/engine/ProgressGetter.html" title="class in compbio.engine"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/engine/\class-useProgressGetter.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="ProgressGetter.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-<B>Uses of Class<br>compbio.engine.ProgressGetter</B></H2>\r
-</CENTER>\r
-No usage of compbio.engine.ProgressGetter\r
-<P>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../compbio/engine/ProgressGetter.html" title="class in compbio.engine"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/engine/\class-useProgressGetter.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="ProgressGetter.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/engine/class-use/PulledFileCache.html b/website/full_javadoc/compbio/engine/class-use/PulledFileCache.html

deleted file mode 100644 (file)

index 2454b33..0000000
--- a/website/full_javadoc/compbio/engine/class-use/PulledFileCache.html
+++ /dev/null
@@ -1,144 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Uses of Class compbio.engine.PulledFileCache\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Uses of Class compbio.engine.PulledFileCache";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../compbio/engine/PulledFileCache.html" title="class in compbio.engine"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/engine/\class-usePulledFileCache.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="PulledFileCache.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-<B>Uses of Class<br>compbio.engine.PulledFileCache</B></H2>\r
-</CENTER>\r
-No usage of compbio.engine.PulledFileCache\r
-<P>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../compbio/engine/PulledFileCache.html" title="class in compbio.engine"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/engine/\class-usePulledFileCache.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="PulledFileCache.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/engine/class-use/SubmissionManager.html b/website/full_javadoc/compbio/engine/class-use/SubmissionManager.html

deleted file mode 100644 (file)

index 557e5c0..0000000
--- a/website/full_javadoc/compbio/engine/class-use/SubmissionManager.html
+++ /dev/null
@@ -1,144 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Uses of Class compbio.engine.SubmissionManager\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Uses of Class compbio.engine.SubmissionManager";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../compbio/engine/SubmissionManager.html" title="class in compbio.engine"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/engine/\class-useSubmissionManager.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="SubmissionManager.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-<B>Uses of Class<br>compbio.engine.SubmissionManager</B></H2>\r
-</CENTER>\r
-No usage of compbio.engine.SubmissionManager\r
-<P>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../compbio/engine/SubmissionManager.html" title="class in compbio.engine"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/engine/\class-useSubmissionManager.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="SubmissionManager.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/engine/class-use/SyncExecutor.html b/website/full_javadoc/compbio/engine/class-use/SyncExecutor.html

deleted file mode 100644 (file)

index 5bb0963..0000000
--- a/website/full_javadoc/compbio/engine/class-use/SyncExecutor.html
+++ /dev/null
@@ -1,248 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Uses of Interface compbio.engine.SyncExecutor\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Uses of Interface compbio.engine.SyncExecutor";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../compbio/engine/SyncExecutor.html" title="interface in compbio.engine"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/engine/\class-useSyncExecutor.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="SyncExecutor.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-<B>Uses of Interface<br>compbio.engine.SyncExecutor</B></H2>\r
-</CENTER>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Packages that use <A HREF="../../../compbio/engine/SyncExecutor.html" title="interface in compbio.engine">SyncExecutor</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.engine"><B>compbio.engine</B></A></TD>\r
-<TD>&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.engine.cluster.drmaa"><B>compbio.engine.cluster.drmaa</B></A></TD>\r
-<TD>An cluster engine classes responsible for execution of Executables on the clusters.&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.engine.local"><B>compbio.engine.local</B></A></TD>\r
-<TD>An local engine classes responsible for execution of Executables on the local computer 
- (the same machine as JVM running these classes).&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.engine"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../compbio/engine/SyncExecutor.html" title="interface in compbio.engine">SyncExecutor</A> in <A HREF="../../../compbio/engine/package-summary.html">compbio.engine</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/engine/package-summary.html">compbio.engine</A> that return <A HREF="../../../compbio/engine/SyncExecutor.html" title="interface in compbio.engine">SyncExecutor</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../compbio/engine/SyncExecutor.html" title="interface in compbio.engine">SyncExecutor</A></CODE></FONT></TD>\r
-<TD><CODE><B>Configurator.</B><B><A HREF="../../../compbio/engine/Configurator.html#getSyncEngine(compbio.engine.client.ConfiguredExecutable)">getSyncEngine</A></B>(<A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;executable)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../compbio/engine/SyncExecutor.html" title="interface in compbio.engine">SyncExecutor</A></CODE></FONT></TD>\r
-<TD><CODE><B>Configurator.</B><B><A HREF="../../../compbio/engine/Configurator.html#getSyncEngine(compbio.engine.client.ConfiguredExecutable, compbio.engine.client.Executable.ExecProvider)">getSyncEngine</A></B>(<A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;executable,\r
-              <A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.engine.cluster.drmaa"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../compbio/engine/SyncExecutor.html" title="interface in compbio.engine">SyncExecutor</A> in <A HREF="../../../compbio/engine/cluster/drmaa/package-summary.html">compbio.engine.cluster.drmaa</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Classes in <A HREF="../../../compbio/engine/cluster/drmaa/package-summary.html">compbio.engine.cluster.drmaa</A> that implement <A HREF="../../../compbio/engine/SyncExecutor.html" title="interface in compbio.engine">SyncExecutor</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;class</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/cluster/drmaa/JobRunner.html" title="class in compbio.engine.cluster.drmaa">JobRunner</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Single cluster job runner class</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.engine.local"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
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-&nbsp;\r
-<P>\r
-\r
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-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Classes in <A HREF="../../../compbio/engine/local/package-summary.html">compbio.engine.local</A> that implement <A HREF="../../../compbio/engine/SyncExecutor.html" title="interface in compbio.engine">SyncExecutor</A></FONT></TH>\r
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-<CODE>&nbsp;class</CODE></FONT></TD>\r
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diff --git a/website/full_javadoc/compbio/engine/client/ClusterNativeSpecExecutable.html b/website/full_javadoc/compbio/engine/client/ClusterNativeSpecExecutable.html

deleted file mode 100644 (file)

index 3eb5b72..0000000
--- a/website/full_javadoc/compbio/engine/client/ClusterNativeSpecExecutable.html
+++ /dev/null
@@ -1,243 +0,0 @@
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-<!-- ========= START OF TOP NAVBAR ======= -->\r
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-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
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-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV CLASS&nbsp;\r
-&nbsp;<A HREF="../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
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-\r
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-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;CONSTR&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
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-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.engine.client</FONT>\r
-<BR>\r
-Interface ClusterNativeSpecExecutable&lt;T&gt;</H2>\r
-<DL>\r
-<DT><B>All Superinterfaces:</B> <DD><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;T&gt;</DD>\r
-</DL>\r
-<DL>\r
-<DT><B>All Known Implementing Classes:</B> <DD><A HREF="../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A></DD>\r
-</DL>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public interface <B>ClusterNativeSpecExecutable&lt;T&gt;</B><DT>extends <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;T&gt;</DL>\r
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-<B>Nested Class Summary</B></FONT></TH>\r
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-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Nested classes/interfaces inherited from interface compbio.engine.client.<A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A></CODE></TD>\r
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-&nbsp;\r
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-\r
-<A NAME="method_summary"><!-- --></A>\r
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-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/ClusterNativeSpecExecutable.html#getNativeSpecs()">getNativeSpecs</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_compbio.engine.client.Executable"><!-- --></A>\r
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-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from interface compbio.engine.client.<A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><A HREF="../../../compbio/engine/client/Executable.html#addParameters(java.util.List)">addParameters</A>, <A HREF="../../../compbio/engine/client/Executable.html#getCreatedFiles()">getCreatedFiles</A>, <A HREF="../../../compbio/engine/client/Executable.html#getError()">getError</A>, <A HREF="../../../compbio/engine/client/Executable.html#getInput()">getInput</A>, <A HREF="../../../compbio/engine/client/Executable.html#getLimit(java.lang.String)">getLimit</A>, <A HREF="../../../compbio/engine/client/Executable.html#getLimits()">getLimits</A>, <A HREF="../../../compbio/engine/client/Executable.html#getOutput()">getOutput</A>, <A HREF="../../../compbio/engine/client/Executable.html#getParameters(compbio.engine.client.Executable.ExecProvider)">getParameters</A>, <A HREF="../../../compbio/engine/client/Executable.html#getResults(java.lang.String)">getResults</A>, <A HREF="../../../compbio/engine/client/Executable.html#loadRunConfiguration(compbio.engine.client.RunConfiguration)">loadRunConfiguration</A></CODE></TD>\r
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-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
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-</TR>\r
-</TABLE>\r
-\r
-<A NAME="getNativeSpecs()"><!-- --></A><H3>\r
-getNativeSpecs</H3>\r
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-java.lang.String <B>getNativeSpecs</B>()</PRE>\r
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-<DD><DL>\r
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-<DD><DL>\r
-</DL>\r
-</DD>\r
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diff --git a/website/full_javadoc/compbio/engine/client/CommandBuilder.html b/website/full_javadoc/compbio/engine/client/CommandBuilder.html

deleted file mode 100644 (file)

index a717442..0000000
--- a/website/full_javadoc/compbio/engine/client/CommandBuilder.html
+++ /dev/null
@@ -1,582 +0,0 @@
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-<SCRIPT type="text/javascript">\r
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-<!-- ========= START OF TOP NAVBAR ======= -->\r
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-&nbsp;<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client"><B>NEXT CLASS</B></A></FONT></TD>\r
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-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
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-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.engine.client</FONT>\r
-<BR>\r
-Class CommandBuilder&lt;T&gt;</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.engine.client.CommandBuilder&lt;T&gt;</B>\r
-</PRE>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public class <B>CommandBuilder&lt;T&gt;</B><DT>extends java.lang.Object</DL>\r
-</PRE>\r
-\r
-<P>\r
-<HR>\r
-\r
-<P>\r
-\r
-<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
-\r
-<A NAME="constructor_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Constructor Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/CommandBuilder.html#CommandBuilder(java.lang.String)">CommandBuilder</A></B>(java.lang.String&nbsp;nameValueSeparator)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/CommandBuilder.html#addParams(java.util.List)">addParams</A></B>(java.util.List&lt;java.lang.String&gt;&nbsp;params)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/CommandBuilder.html#equals(java.lang.Object)">equals</A></B>(java.lang.Object&nbsp;obj)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.util.List&lt;java.lang.String&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/CommandBuilder.html#getCommands()">getCommands</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/CommandBuilder.html#getCommandString()">getCommandString</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/CommandBuilder.html#getParamValue(java.lang.String)">getParamValue</A></B>(java.lang.String&nbsp;paramName)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;int</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/CommandBuilder.html#hashCode()">hashCode</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/CommandBuilder.html#hasParam(java.lang.String)">hasParam</A></B>(java.lang.String&nbsp;paramName)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
-<TR ALIGN="right" VALIGN="">\r
-<TD NOWRAP><FONT SIZE="-1">\r
-<CODE>&lt;T&gt; <A HREF="../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>&lt;T&gt;</CODE></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/CommandBuilder.html#newCommandBuilder(java.util.List, java.lang.String)">newCommandBuilder</A></B>(java.util.List&lt;? extends <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;T&gt;&gt;&nbsp;arguments,\r
-                  java.lang.String&nbsp;nameValueSeparator)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;This produces the same result as getCommands method.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/CommandBuilder.html#removeParam(java.lang.String)">removeParam</A></B>(java.lang.String&nbsp;paramName)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/CommandBuilder.html#setFirst(java.lang.String)">setFirst</A></B>(java.lang.String&nbsp;param)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/CommandBuilder.html#setLast(java.lang.String)">setLast</A></B>(java.lang.String&nbsp;paramName)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/CommandBuilder.html#setLast(java.lang.String, java.lang.String)">setLast</A></B>(java.lang.String&nbsp;paramName,\r
-        java.lang.String&nbsp;paramValue)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/CommandBuilder.html#setParam(java.lang.String)">setParam</A></B>(java.lang.String&nbsp;param)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/CommandBuilder.html#setParam(java.lang.String, java.lang.String)">setParam</A></B>(java.lang.String&nbsp;paramName,\r
-         java.lang.String&nbsp;paramValue)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/CommandBuilder.html#setParams(java.util.List)">setParams</A></B>(java.util.List&lt;java.lang.String&gt;&nbsp;params)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;int</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/CommandBuilder.html#size()">size</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/CommandBuilder.html#toString()">toString</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>getClass, notify, notifyAll, wait, wait, wait</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
-\r
-<A NAME="constructor_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Constructor Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="CommandBuilder(java.lang.String)"><!-- --></A><H3>\r
-CommandBuilder</H3>\r
-<PRE>\r
-public <B>CommandBuilder</B>(java.lang.String&nbsp;nameValueSeparator)</PRE>\r
-<DL>\r
-</DL>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
-<A NAME="method_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="addParams(java.util.List)"><!-- --></A><H3>\r
-addParams</H3>\r
-<PRE>\r
-public void <B>addParams</B>(java.util.List&lt;java.lang.String&gt;&nbsp;params)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="setParams(java.util.List)"><!-- --></A><H3>\r
-setParams</H3>\r
-<PRE>\r
-public void <B>setParams</B>(java.util.List&lt;java.lang.String&gt;&nbsp;params)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="hasParam(java.lang.String)"><!-- --></A><H3>\r
-hasParam</H3>\r
-<PRE>\r
-public boolean <B>hasParam</B>(java.lang.String&nbsp;paramName)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="setFirst(java.lang.String)"><!-- --></A><H3>\r
-setFirst</H3>\r
-<PRE>\r
-public boolean <B>setFirst</B>(java.lang.String&nbsp;param)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="setParam(java.lang.String)"><!-- --></A><H3>\r
-setParam</H3>\r
-<PRE>\r
-public boolean <B>setParam</B>(java.lang.String&nbsp;param)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="setLast(java.lang.String)"><!-- --></A><H3>\r
-setLast</H3>\r
-<PRE>\r
-public boolean <B>setLast</B>(java.lang.String&nbsp;paramName)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="setLast(java.lang.String, java.lang.String)"><!-- --></A><H3>\r
-setLast</H3>\r
-<PRE>\r
-public boolean <B>setLast</B>(java.lang.String&nbsp;paramName,\r
-                       java.lang.String&nbsp;paramValue)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getParamValue(java.lang.String)"><!-- --></A><H3>\r
-getParamValue</H3>\r
-<PRE>\r
-public java.lang.String <B>getParamValue</B>(java.lang.String&nbsp;paramName)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="removeParam(java.lang.String)"><!-- --></A><H3>\r
-removeParam</H3>\r
-<PRE>\r
-public boolean <B>removeParam</B>(java.lang.String&nbsp;paramName)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="setParam(java.lang.String, java.lang.String)"><!-- --></A><H3>\r
-setParam</H3>\r
-<PRE>\r
-public boolean <B>setParam</B>(java.lang.String&nbsp;paramName,\r
-                        java.lang.String&nbsp;paramValue)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getCommands()"><!-- --></A><H3>\r
-getCommands</H3>\r
-<PRE>\r
-public java.util.List&lt;java.lang.String&gt; <B>getCommands</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getCommandString()"><!-- --></A><H3>\r
-getCommandString</H3>\r
-<PRE>\r
-public java.lang.String <B>getCommandString</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="newCommandBuilder(java.util.List, java.lang.String)"><!-- --></A><H3>\r
-newCommandBuilder</H3>\r
-<PRE>\r
-public static &lt;T&gt; <A HREF="../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>&lt;T&gt; <B>newCommandBuilder</B>(java.util.List&lt;? extends <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;T&gt;&gt;&nbsp;arguments,\r
-                                                      java.lang.String&nbsp;nameValueSeparator)</PRE>\r
-<DL>\r
-<DD>This produces the same result as getCommands method. The only difference
- is that it accepts a List of Options as an input\r
-<P>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>arguments</CODE> - \r
-<DT><B>Returns:</B><DD></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="size()"><!-- --></A><H3>\r
-size</H3>\r
-<PRE>\r
-public int <B>size</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="hashCode()"><!-- --></A><H3>\r
-hashCode</H3>\r
-<PRE>\r
-public int <B>hashCode</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Overrides:</B><DD><CODE>hashCode</CODE> in class <CODE>java.lang.Object</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="equals(java.lang.Object)"><!-- --></A><H3>\r
-equals</H3>\r
-<PRE>\r
-public boolean <B>equals</B>(java.lang.Object&nbsp;obj)</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Overrides:</B><DD><CODE>equals</CODE> in class <CODE>java.lang.Object</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="toString()"><!-- --></A><H3>\r
-toString</H3>\r
-<PRE>\r
-public java.lang.String <B>toString</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Overrides:</B><DD><CODE>toString</CODE> in class <CODE>java.lang.Object</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
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-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
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-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
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-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
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diff --git a/website/full_javadoc/compbio/engine/client/ConfExecutable.html b/website/full_javadoc/compbio/engine/client/ConfExecutable.html

deleted file mode 100644 (file)

index a6ea5cc..0000000
--- a/website/full_javadoc/compbio/engine/client/ConfExecutable.html
+++ /dev/null
@@ -1,1000 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:49 GMT 2010 -->\r
-<TITLE>\r
-ConfExecutable\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
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-{\r
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-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
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-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
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-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/ConfExecutable.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
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-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/engine/client/ConfExecutable.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
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-\r
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-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;<A HREF="#field_summary">FIELD</A>&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
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-DETAIL:&nbsp;<A HREF="#field_detail">FIELD</A>&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
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-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.engine.client</FONT>\r
-<BR>\r
-Class ConfExecutable&lt;T&gt;</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.engine.client.ConfExecutable&lt;T&gt;</B>\r
-</PRE>\r
-<DL>\r
-<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;T&gt;, <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;T&gt;, <A HREF="../../../compbio/engine/client/PipedExecutable.html" title="interface in compbio.engine.client">PipedExecutable</A>&lt;T&gt;</DD>\r
-</DL>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public class <B>ConfExecutable&lt;T&gt;</B><DT>extends java.lang.Object<DT>implements <A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;T&gt;</DL>\r
-</PRE>\r
-\r
-<P>\r
-<HR>\r
-\r
-<P>\r
-<!-- ======== NESTED CLASS SUMMARY ======== -->\r
-\r
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-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Nested Class Summary</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="nested_classes_inherited_from_class_compbio.engine.client.Executable"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Nested classes/interfaces inherited from interface compbio.engine.client.<A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A></CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- =========== FIELD SUMMARY =========== -->\r
-\r
-<A NAME="field_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Field Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#CLUSTER_TASK_ID_PREFIX">CLUSTER_TASK_ID_PREFIX</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
-\r
-<A NAME="constructor_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Constructor Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#ConfExecutable(compbio.engine.client.Executable, java.lang.String)">ConfExecutable</A></B>(<A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt;&nbsp;executable,\r
-               java.lang.String&nbsp;taskDirectory)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#addParameters(java.util.List)">addParameters</A></B>(java.util.List&lt;java.lang.String&gt;&nbsp;parameters)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Adds parameter to the list of parameters for a native executable</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getCommand(compbio.engine.client.Executable.ExecProvider)">getCommand</A></B>(<A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.util.List&lt;java.lang.String&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getCreatedFiles()">getCreatedFiles</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.util.Map&lt;java.lang.String,java.lang.String&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getEnvironment()">getEnvironment</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getError()">getError</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getExecProvider()">getExecProvider</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getExecutable()">getExecutable</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getInput()">getInput</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Not all input paths are relative! Input path could be absolute!</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getLimit(java.lang.String)">getLimit</A></B>(java.lang.String&nbsp;presetName)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getLimits()">getLimits</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getOutput()">getOutput</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>&lt;<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getParameters()">getParameters</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>&lt;<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getParameters(compbio.engine.client.Executable.ExecProvider)">getParameters</A></B>(<A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
-<TR ALIGN="right" VALIGN="">\r
-<TD NOWRAP><FONT SIZE="-1">\r
-<CODE>&lt;V&gt; V</CODE></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getResults()">getResults</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
-<TR ALIGN="right" VALIGN="">\r
-<TD NOWRAP><FONT SIZE="-1">\r
-<CODE>&lt;V&gt; V</CODE></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getResults(java.lang.String)">getResults</A></B>(java.lang.String&nbsp;directory)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getRunConfiguration()">getRunConfiguration</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
-<TR ALIGN="right" VALIGN="">\r
-<TD NOWRAP><FONT SIZE="-1">\r
-<CODE>&lt;V&gt; <A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;V&gt;</CODE></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getRunnerLimits(java.lang.Class)">getRunnerLimits</A></B>(java.lang.Class&lt;? extends <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;V&gt;&gt;&nbsp;clazz)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;This method should be executed once and result of its execution reused.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
-<TR ALIGN="right" VALIGN="">\r
-<TD NOWRAP><FONT SIZE="-1">\r
-<CODE>&lt;V&gt; <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&lt;V&gt;</CODE></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getRunnerOptions(java.lang.Class)">getRunnerOptions</A></B>(java.lang.Class&lt;? extends <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;V&gt;&gt;&nbsp;clazz)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
-<TR ALIGN="right" VALIGN="">\r
-<TD NOWRAP><FONT SIZE="-1">\r
-<CODE>&lt;V&gt; <A HREF="../../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>&lt;V&gt;</CODE></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getRunnerPresets(java.lang.Class)">getRunnerPresets</A></B>(java.lang.Class&lt;? extends <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;V&gt;&gt;&nbsp;clazz)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getSupportedRuntimes()">getSupportedRuntimes</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getTaskId()">getTaskId</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getWorkDirectory()">getWorkDirectory</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#loadRunConfiguration(java.io.InputStream)">loadRunConfiguration</A></B>(java.io.InputStream&nbsp;input)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#loadRunConfiguration(compbio.engine.client.RunConfiguration)">loadRunConfiguration</A></B>(<A HREF="../../../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>&nbsp;rconf)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#newConfExecutable(compbio.engine.client.RunConfiguration)">newConfExecutable</A></B>(<A HREF="../../../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>&nbsp;rconf)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#saveRunConfiguration()">saveRunConfiguration</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#setExecProvider(compbio.engine.client.Executable.ExecProvider)">setExecProvider</A></B>(<A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#setWorkDirectory(java.lang.String)">setWorkDirectory</A></B>(java.lang.String&nbsp;workDirectory)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#toString()">toString</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>equals, getClass, hashCode, notify, notifyAll, wait, wait, wait</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ============ FIELD DETAIL =========== -->\r
-\r
-<A NAME="field_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Field Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="CLUSTER_TASK_ID_PREFIX"><!-- --></A><H3>\r
-CLUSTER_TASK_ID_PREFIX</H3>\r
-<PRE>\r
-public static final java.lang.String <B>CLUSTER_TASK_ID_PREFIX</B></PRE>\r
-<DL>\r
-<DL>\r
-<DT><B>See Also:</B><DD><A HREF="../../../constant-values.html#compbio.engine.client.ConfExecutable.CLUSTER_TASK_ID_PREFIX">Constant Field Values</A></DL>\r
-</DL>\r
-\r
-<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
-\r
-<A NAME="constructor_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Constructor Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="ConfExecutable(compbio.engine.client.Executable, java.lang.String)"><!-- --></A><H3>\r
-ConfExecutable</H3>\r
-<PRE>\r
-public <B>ConfExecutable</B>(<A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt;&nbsp;executable,\r
-                      java.lang.String&nbsp;taskDirectory)</PRE>\r
-<DL>\r
-</DL>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
-<A NAME="method_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="getExecProvider()"><!-- --></A><H3>\r
-getExecProvider</H3>\r
-<PRE>\r
-public <A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A> <B>getExecProvider</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html#getExecProvider()">getExecProvider</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="setExecProvider(compbio.engine.client.Executable.ExecProvider)"><!-- --></A><H3>\r
-setExecProvider</H3>\r
-<PRE>\r
-public void <B>setExecProvider</B>(<A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getCommand(compbio.engine.client.Executable.ExecProvider)"><!-- --></A><H3>\r
-getCommand</H3>\r
-<PRE>\r
-public java.lang.String <B>getCommand</B>(<A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider)\r
-                            throws <A HREF="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A></PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html#getCommand(compbio.engine.client.Executable.ExecProvider)">getCommand</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-\r
-<DT><B>Throws:</B>\r
-<DD><CODE><A HREF="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A></CODE></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getSupportedRuntimes()"><!-- --></A><H3>\r
-getSupportedRuntimes</H3>\r
-<PRE>\r
-public <A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A> <B>getSupportedRuntimes</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html#getSupportedRuntimes()">getSupportedRuntimes</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getLimit(java.lang.String)"><!-- --></A><H3>\r
-getLimit</H3>\r
-<PRE>\r
-public <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt; <B>getLimit</B>(java.lang.String&nbsp;presetName)</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#getLimit(java.lang.String)">getLimit</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getLimits()"><!-- --></A><H3>\r
-getLimits</H3>\r
-<PRE>\r
-public <A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt; <B>getLimits</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#getLimits()">getLimits</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getTaskId()"><!-- --></A><H3>\r
-getTaskId</H3>\r
-<PRE>\r
-public java.lang.String <B>getTaskId</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html#getTaskId()">getTaskId</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="setWorkDirectory(java.lang.String)"><!-- --></A><H3>\r
-setWorkDirectory</H3>\r
-<PRE>\r
-public void <B>setWorkDirectory</B>(java.lang.String&nbsp;workDirectory)</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html#setWorkDirectory(java.lang.String)">setWorkDirectory</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getWorkDirectory()"><!-- --></A><H3>\r
-getWorkDirectory</H3>\r
-<PRE>\r
-public java.lang.String <B>getWorkDirectory</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html#getWorkDirectory()">getWorkDirectory</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="addParameters(java.util.List)"><!-- --></A><H3>\r
-addParameters</H3>\r
-<PRE>\r
-public <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt; <B>addParameters</B>(java.util.List&lt;java.lang.String&gt;&nbsp;parameters)</PRE>\r
-<DL>\r
-<DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/engine/client/Executable.html#addParameters(java.util.List)">Executable</A></CODE></B></DD>\r
-<DD>Adds parameter to the list of parameters for a native executable\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#addParameters(java.util.List)">addParameters</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>this Executable</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getOutput()"><!-- --></A><H3>\r
-getOutput</H3>\r
-<PRE>\r
-public java.lang.String <B>getOutput</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#getOutput()">getOutput</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getError()"><!-- --></A><H3>\r
-getError</H3>\r
-<PRE>\r
-public java.lang.String <B>getError</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#getError()">getError</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getCreatedFiles()"><!-- --></A><H3>\r
-getCreatedFiles</H3>\r
-<PRE>\r
-public java.util.List&lt;java.lang.String&gt; <B>getCreatedFiles</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#getCreatedFiles()">getCreatedFiles</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getInput()"><!-- --></A><H3>\r
-getInput</H3>\r
-<PRE>\r
-public java.lang.String <B>getInput</B>()</PRE>\r
-<DL>\r
-<DD>Not all input paths are relative! Input path could be absolute!\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#getInput()">getInput</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-<DT><B>See Also:</B><DD><CODE>compbio.engine.client.Executable#getInputFiles()</CODE></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getParameters()"><!-- --></A><H3>\r
-getParameters</H3>\r
-<PRE>\r
-public <A HREF="../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>&lt;<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt; <B>getParameters</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html#getParameters()">getParameters</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getParameters(compbio.engine.client.Executable.ExecProvider)"><!-- --></A><H3>\r
-getParameters</H3>\r
-<PRE>\r
-public <A HREF="../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>&lt;<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt; <B>getParameters</B>(<A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider)</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#getParameters(compbio.engine.client.Executable.ExecProvider)">getParameters</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getExecutable()"><!-- --></A><H3>\r
-getExecutable</H3>\r
-<PRE>\r
-public <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt; <B>getExecutable</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html#getExecutable()">getExecutable</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getResults()"><!-- --></A><H3>\r
-getResults</H3>\r
-<PRE>\r
-public &lt;V&gt; V <B>getResults</B>()\r
-             throws <A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html#getResults()">getResults</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-\r
-<DT><B>Throws:</B>\r
-<DD><CODE><A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></CODE></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getResults(java.lang.String)"><!-- --></A><H3>\r
-getResults</H3>\r
-<PRE>\r
-public &lt;V&gt; V <B>getResults</B>(java.lang.String&nbsp;directory)\r
-             throws <A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#getResults(java.lang.String)">getResults</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-\r
-<DT><B>Throws:</B>\r
-<DD><CODE><A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></CODE></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getRunnerOptions(java.lang.Class)"><!-- --></A><H3>\r
-getRunnerOptions</H3>\r
-<PRE>\r
-public static &lt;V&gt; <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&lt;V&gt; <B>getRunnerOptions</B>(java.lang.Class&lt;? extends <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;V&gt;&gt;&nbsp;clazz)\r
-                                        throws java.io.IOException</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-<DD><DL>\r
-\r
-<DT><B>Throws:</B>\r
-<DD><CODE>java.io.IOException</CODE></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getRunnerPresets(java.lang.Class)"><!-- --></A><H3>\r
-getRunnerPresets</H3>\r
-<PRE>\r
-public static &lt;V&gt; <A HREF="../../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>&lt;V&gt; <B>getRunnerPresets</B>(java.lang.Class&lt;? extends <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;V&gt;&gt;&nbsp;clazz)\r
-                                         throws java.io.IOException</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-<DD><DL>\r
-\r
-<DT><B>Throws:</B>\r
-<DD><CODE>java.io.IOException</CODE></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getRunnerLimits(java.lang.Class)"><!-- --></A><H3>\r
-getRunnerLimits</H3>\r
-<PRE>\r
-public static &lt;V&gt; <A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;V&gt; <B>getRunnerLimits</B>(java.lang.Class&lt;? extends <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;V&gt;&gt;&nbsp;clazz)\r
-                                        throws java.io.IOException</PRE>\r
-<DL>\r
-<DD>This method should be executed once and result of its execution reused.
- If not used carefully it could slow down the system!\r
-<P>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-<DD><DL>\r
-<DT><B>Type Parameters:</B><DD><CODE>V</CODE> - <DT><B>Parameters:</B><DD><CODE>clazz</CODE> - \r
-<DT><B>Returns:</B><DD>\r
-<DT><B>Throws:</B>\r
-<DD><CODE>java.io.IOException</CODE></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getEnvironment()"><!-- --></A><H3>\r
-getEnvironment</H3>\r
-<PRE>\r
-public java.util.Map&lt;java.lang.String,java.lang.String&gt; <B>getEnvironment</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html#getEnvironment()">getEnvironment</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="loadRunConfiguration(compbio.engine.client.RunConfiguration)"><!-- --></A><H3>\r
-loadRunConfiguration</H3>\r
-<PRE>\r
-public <A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt; <B>loadRunConfiguration</B>(<A HREF="../../../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>&nbsp;rconf)</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#loadRunConfiguration(compbio.engine.client.RunConfiguration)">loadRunConfiguration</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="newConfExecutable(compbio.engine.client.RunConfiguration)"><!-- --></A><H3>\r
-newConfExecutable</H3>\r
-<PRE>\r
-public static <A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt; <B>newConfExecutable</B>(<A HREF="../../../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>&nbsp;rconf)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="saveRunConfiguration()"><!-- --></A><H3>\r
-saveRunConfiguration</H3>\r
-<PRE>\r
-public boolean <B>saveRunConfiguration</B>()\r
-                             throws java.io.IOException</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html#saveRunConfiguration()">saveRunConfiguration</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-\r
-<DT><B>Throws:</B>\r
-<DD><CODE>java.io.IOException</CODE></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getRunConfiguration()"><!-- --></A><H3>\r
-getRunConfiguration</H3>\r
-<PRE>\r
-public <A HREF="../../../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A> <B>getRunConfiguration</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="loadRunConfiguration(java.io.InputStream)"><!-- --></A><H3>\r
-loadRunConfiguration</H3>\r
-<PRE>\r
-public <A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt; <B>loadRunConfiguration</B>(java.io.InputStream&nbsp;input)\r
-                                             throws java.io.IOException</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html#loadRunConfiguration(java.io.InputStream)">loadRunConfiguration</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-\r
-<DT><B>Throws:</B>\r
-<DD><CODE>java.io.IOException</CODE></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="toString()"><!-- --></A><H3>\r
-toString</H3>\r
-<PRE>\r
-public java.lang.String <B>toString</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Overrides:</B><DD><CODE>toString</CODE> in class <CODE>java.lang.Object</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/ConfExecutable.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/engine/client/ConfExecutable.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="ConfExecutable.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;<A HREF="#field_summary">FIELD</A>&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;<A HREF="#field_detail">FIELD</A>&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/engine/client/ConfiguredExecutable.html b/website/full_javadoc/compbio/engine/client/ConfiguredExecutable.html

deleted file mode 100644 (file)

index 1a59a09..0000000
--- a/website/full_javadoc/compbio/engine/client/ConfiguredExecutable.html
+++ /dev/null
@@ -1,504 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:49 GMT 2010 -->\r
-<TITLE>\r
-ConfiguredExecutable\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="ConfiguredExecutable";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
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-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../compbio/engine/client/EnvVariableProcessor.html" title="class in compbio.engine.client"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/engine/client/ConfiguredExecutable.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
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-  }\r
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-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;CONSTR&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;CONSTR&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
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-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.engine.client</FONT>\r
-<BR>\r
-Interface ConfiguredExecutable&lt;T&gt;</H2>\r
-<DL>\r
-<DT><B>All Superinterfaces:</B> <DD><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;T&gt;, <A HREF="../../../compbio/engine/client/PipedExecutable.html" title="interface in compbio.engine.client">PipedExecutable</A>&lt;T&gt;</DD>\r
-</DL>\r
-<DL>\r
-<DT><B>All Known Implementing Classes:</B> <DD><A HREF="../../../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A></DD>\r
-</DL>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public interface <B>ConfiguredExecutable&lt;T&gt;</B><DT>extends <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;T&gt;, <A HREF="../../../compbio/engine/client/PipedExecutable.html" title="interface in compbio.engine.client">PipedExecutable</A>&lt;T&gt;</DL>\r
-</PRE>\r
-\r
-<P>\r
-<HR>\r
-\r
-<P>\r
-<!-- ======== NESTED CLASS SUMMARY ======== -->\r
-\r
-<A NAME="nested_class_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Nested Class Summary</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="nested_classes_inherited_from_class_compbio.engine.client.Executable"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Nested classes/interfaces inherited from interface compbio.engine.client.<A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A></CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html#getCommand(compbio.engine.client.Executable.ExecProvider)">getCommand</A></B>(<A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.util.Map&lt;java.lang.String,java.lang.String&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html#getEnvironment()">getEnvironment</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html#getExecProvider()">getExecProvider</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="type parameter in ConfiguredExecutable">T</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html#getExecutable()">getExecutable</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>&lt;<A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="type parameter in ConfiguredExecutable">T</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html#getParameters()">getParameters</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
-<TR ALIGN="right" VALIGN="">\r
-<TD NOWRAP><FONT SIZE="-1">\r
-<CODE>&lt;V&gt; V</CODE></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html#getResults()">getResults</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html#getSupportedRuntimes()">getSupportedRuntimes</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html#getTaskId()">getTaskId</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html#getWorkDirectory()">getWorkDirectory</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html#loadRunConfiguration(java.io.InputStream)">loadRunConfiguration</A></B>(java.io.InputStream&nbsp;input)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html#saveRunConfiguration()">saveRunConfiguration</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html#setWorkDirectory(java.lang.String)">setWorkDirectory</A></B>(java.lang.String&nbsp;workDirectory)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_compbio.engine.client.Executable"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from interface compbio.engine.client.<A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><A HREF="../../../compbio/engine/client/Executable.html#addParameters(java.util.List)">addParameters</A>, <A HREF="../../../compbio/engine/client/Executable.html#getCreatedFiles()">getCreatedFiles</A>, <A HREF="../../../compbio/engine/client/Executable.html#getError()">getError</A>, <A HREF="../../../compbio/engine/client/Executable.html#getInput()">getInput</A>, <A HREF="../../../compbio/engine/client/Executable.html#getLimit(java.lang.String)">getLimit</A>, <A HREF="../../../compbio/engine/client/Executable.html#getLimits()">getLimits</A>, <A HREF="../../../compbio/engine/client/Executable.html#getOutput()">getOutput</A>, <A HREF="../../../compbio/engine/client/Executable.html#getParameters(compbio.engine.client.Executable.ExecProvider)">getParameters</A>, <A HREF="../../../compbio/engine/client/Executable.html#getResults(java.lang.String)">getResults</A>, <A HREF="../../../compbio/engine/client/Executable.html#loadRunConfiguration(compbio.engine.client.RunConfiguration)">loadRunConfiguration</A></CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
-<A NAME="method_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="getEnvironment()"><!-- --></A><H3>\r
-getEnvironment</H3>\r
-<PRE>\r
-java.util.Map&lt;java.lang.String,java.lang.String&gt; <B>getEnvironment</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getTaskId()"><!-- --></A><H3>\r
-getTaskId</H3>\r
-<PRE>\r
-java.lang.String <B>getTaskId</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getCommand(compbio.engine.client.Executable.ExecProvider)"><!-- --></A><H3>\r
-getCommand</H3>\r
-<PRE>\r
-java.lang.String <B>getCommand</B>(<A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider)\r
-                            throws <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-<DD><DL>\r
-\r
-<DT><B>Throws:</B>\r
-<DD><CODE><A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></CODE></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getSupportedRuntimes()"><!-- --></A><H3>\r
-getSupportedRuntimes</H3>\r
-<PRE>\r
-<A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A> <B>getSupportedRuntimes</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getWorkDirectory()"><!-- --></A><H3>\r
-getWorkDirectory</H3>\r
-<PRE>\r
-java.lang.String <B>getWorkDirectory</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="setWorkDirectory(java.lang.String)"><!-- --></A><H3>\r
-setWorkDirectory</H3>\r
-<PRE>\r
-void <B>setWorkDirectory</B>(java.lang.String&nbsp;workDirectory)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getResults()"><!-- --></A><H3>\r
-getResults</H3>\r
-<PRE>\r
-&lt;V&gt; V <B>getResults</B>()\r
-             throws <A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-<DD><DL>\r
-\r
-<DT><B>Throws:</B>\r
-<DD><CODE><A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></CODE></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getExecutable()"><!-- --></A><H3>\r
-getExecutable</H3>\r
-<PRE>\r
-<A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="type parameter in ConfiguredExecutable">T</A>&gt; <B>getExecutable</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getParameters()"><!-- --></A><H3>\r
-getParameters</H3>\r
-<PRE>\r
-<A HREF="../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>&lt;<A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="type parameter in ConfiguredExecutable">T</A>&gt; <B>getParameters</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="saveRunConfiguration()"><!-- --></A><H3>\r
-saveRunConfiguration</H3>\r
-<PRE>\r
-boolean <B>saveRunConfiguration</B>()\r
-                             throws java.io.IOException</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-<DD><DL>\r
-\r
-<DT><B>Throws:</B>\r
-<DD><CODE>java.io.IOException</CODE></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="loadRunConfiguration(java.io.InputStream)"><!-- --></A><H3>\r
-loadRunConfiguration</H3>\r
-<PRE>\r
-<A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt; <B>loadRunConfiguration</B>(java.io.InputStream&nbsp;input)\r
-                                             throws java.io.IOException</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-<DD><DL>\r
-\r
-<DT><B>Throws:</B>\r
-<DD><CODE>java.io.IOException</CODE></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getExecProvider()"><!-- --></A><H3>\r
-getExecProvider</H3>\r
-<PRE>\r
-<A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A> <B>getExecProvider</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/ConfiguredExecutable.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../compbio/engine/client/EnvVariableProcessor.html" title="class in compbio.engine.client"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/engine/client/ConfiguredExecutable.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="ConfiguredExecutable.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;CONSTR&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;CONSTR&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/engine/client/EnvVariableProcessor.html b/website/full_javadoc/compbio/engine/client/EnvVariableProcessor.html

deleted file mode 100644 (file)

index 096638b..0000000
--- a/website/full_javadoc/compbio/engine/client/EnvVariableProcessor.html
+++ /dev/null
@@ -1,294 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:49 GMT 2010 -->\r
-<TITLE>\r
-EnvVariableProcessor\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="EnvVariableProcessor";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/EnvVariableProcessor.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/engine/client/EnvVariableProcessor.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="EnvVariableProcessor.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
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-  <!--\r
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-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
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-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;<A HREF="#field_summary">FIELD</A>&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;<A HREF="#field_detail">FIELD</A>&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.engine.client</FONT>\r
-<BR>\r
-Class EnvVariableProcessor</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.engine.client.EnvVariableProcessor</B>\r
-</PRE>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public class <B>EnvVariableProcessor</B><DT>extends java.lang.Object</DL>\r
-</PRE>\r
-\r
-<P>\r
-<HR>\r
-\r
-<P>\r
-<!-- =========== FIELD SUMMARY =========== -->\r
-\r
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-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
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-<B>Field Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/EnvVariableProcessor.html#PATH">PATH</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Special variable keys Absolute path(s) will be merged with the content of
- the system PATH variable</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
-\r
-<A NAME="constructor_summary"><!-- --></A>\r
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-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Constructor Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/EnvVariableProcessor.html#EnvVariableProcessor()">EnvVariableProcessor</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;java.util.Map&lt;java.lang.String,java.lang.String&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/EnvVariableProcessor.html#getEnvVariables(java.lang.String, java.lang.Class)">getEnvVariables</A></B>(java.lang.String&nbsp;property,\r
-                java.lang.Class&lt;?&gt;&nbsp;clazz)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ============ FIELD DETAIL =========== -->\r
-\r
-<A NAME="field_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Field Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="PATH"><!-- --></A><H3>\r
-PATH</H3>\r
-<PRE>\r
-public static final java.lang.String <B>PATH</B></PRE>\r
-<DL>\r
-<DD>Special variable keys Absolute path(s) will be merged with the content of
- the system PATH variable\r
-<P>\r
-<DL>\r
-<DT><B>See Also:</B><DD><A HREF="../../../constant-values.html#compbio.engine.client.EnvVariableProcessor.PATH">Constant Field Values</A></DL>\r
-</DL>\r
-\r
-<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
-\r
-<A NAME="constructor_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Constructor Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="EnvVariableProcessor()"><!-- --></A><H3>\r
-EnvVariableProcessor</H3>\r
-<PRE>\r
-public <B>EnvVariableProcessor</B>()</PRE>\r
-<DL>\r
-</DL>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
-<A NAME="method_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="getEnvVariables(java.lang.String, java.lang.Class)"><!-- --></A><H3>\r
-getEnvVariables</H3>\r
-<PRE>\r
-public static java.util.Map&lt;java.lang.String,java.lang.String&gt; <B>getEnvVariables</B>(java.lang.String&nbsp;property,\r
-                                                                               java.lang.Class&lt;?&gt;&nbsp;clazz)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/EnvVariableProcessor.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/engine/client/EnvVariableProcessor.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="EnvVariableProcessor.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;<A HREF="#field_summary">FIELD</A>&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;<A HREF="#field_detail">FIELD</A>&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/engine/client/Executable.ExecProvider.html b/website/full_javadoc/compbio/engine/client/Executable.ExecProvider.html

deleted file mode 100644 (file)

index 085b7fc..0000000
--- a/website/full_javadoc/compbio/engine/client/Executable.ExecProvider.html
+++ /dev/null
@@ -1,341 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:49 GMT 2010 -->\r
-<TITLE>\r
-Executable.ExecProvider\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Executable.ExecProvider";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/Executable.ExecProvider.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../compbio/engine/client/PathValidator.html" title="class in compbio.engine.client"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/engine/client/Executable.ExecProvider.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="Executable.ExecProvider.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;<A HREF="#enum_constant_summary">ENUM CONSTANTS</A>&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;<A HREF="#enum_constant_detail">ENUM CONSTANTS</A>&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.engine.client</FONT>\r
-<BR>\r
-Enum Executable.ExecProvider</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../../resources/inherit.gif" ALT="extended by ">java.lang.Enum&lt;<A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&gt;\r
-      <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.engine.client.Executable.ExecProvider</B>\r
-</PRE>\r
-<DL>\r
-<DT><B>All Implemented Interfaces:</B> <DD>java.io.Serializable, java.lang.Comparable&lt;<A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&gt;</DD>\r
-</DL>\r
-<DL>\r
-<DT><B>Enclosing interface:</B><DD><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/engine/client/Executable.html" title="type parameter in Executable">T</A>&gt;</DD>\r
-</DL>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public static enum <B>Executable.ExecProvider</B><DT>extends java.lang.Enum&lt;<A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&gt;</DL>\r
-</PRE>\r
-\r
-<P>\r
-<HR>\r
-\r
-<P>\r
-<!-- =========== ENUM CONSTANT SUMMARY =========== -->\r
-\r
-<A NAME="enum_constant_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Enum Constant Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/Executable.ExecProvider.html#Any">Any</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/Executable.ExecProvider.html#Cluster">Cluster</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/Executable.ExecProvider.html#Local">Local</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/Executable.ExecProvider.html#valueOf(java.lang.String)">valueOf</A></B>(java.lang.String&nbsp;name)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Returns the enum constant of this type with the specified name.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>[]</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/Executable.ExecProvider.html#values()">values</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Returns an array containing the constants of this enum type, in
-the order they are declared.</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Enum"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Enum</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>compareTo, equals, getDeclaringClass, hashCode, name, ordinal, toString, valueOf</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>getClass, notify, notifyAll, wait, wait, wait</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ============ ENUM CONSTANT DETAIL =========== -->\r
-\r
-<A NAME="enum_constant_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Enum Constant Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="Local"><!-- --></A><H3>\r
-Local</H3>\r
-<PRE>\r
-public static final <A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A> <B>Local</B></PRE>\r
-<DL>\r
-<DL>\r
-</DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="Cluster"><!-- --></A><H3>\r
-Cluster</H3>\r
-<PRE>\r
-public static final <A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A> <B>Cluster</B></PRE>\r
-<DL>\r
-<DL>\r
-</DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="Any"><!-- --></A><H3>\r
-Any</H3>\r
-<PRE>\r
-public static final <A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A> <B>Any</B></PRE>\r
-<DL>\r
-<DL>\r
-</DL>\r
-</DL>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
-<A NAME="method_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="values()"><!-- --></A><H3>\r
-values</H3>\r
-<PRE>\r
-public static <A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>[] <B>values</B>()</PRE>\r
-<DL>\r
-<DD>Returns an array containing the constants of this enum type, in
-the order they are declared.  This method may be used to iterate
-over the constants as follows:
-<pre>
-for (Executable.ExecProvider c : Executable.ExecProvider.values())
-&nbsp;   System.out.println(c);
-</pre>\r
-<P>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>an array containing the constants of this enum type, in
-the order they are declared</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="valueOf(java.lang.String)"><!-- --></A><H3>\r
-valueOf</H3>\r
-<PRE>\r
-public static <A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A> <B>valueOf</B>(java.lang.String&nbsp;name)</PRE>\r
-<DL>\r
-<DD>Returns the enum constant of this type with the specified name.
-The string must match <I>exactly</I> an identifier used to declare an
-enum constant in this type.  (Extraneous whitespace characters are 
-not permitted.)\r
-<P>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>name</CODE> - the name of the enum constant to be returned.\r
-<DT><B>Returns:</B><DD>the enum constant with the specified name\r
-<DT><B>Throws:</B>\r
-<DD><CODE>java.lang.IllegalArgumentException</CODE> - if this enum type has no constant
-with the specified name\r
-<DD><CODE>java.lang.NullPointerException</CODE> - if the argument is null</DL>\r
-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/Executable.ExecProvider.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../compbio/engine/client/PathValidator.html" title="class in compbio.engine.client"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/engine/client/Executable.ExecProvider.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="Executable.ExecProvider.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;<A HREF="#enum_constant_summary">ENUM CONSTANTS</A>&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;<A HREF="#enum_constant_detail">ENUM CONSTANTS</A>&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/engine/client/Executable.html b/website/full_javadoc/compbio/engine/client/Executable.html

deleted file mode 100644 (file)

index 9f7254f..0000000
--- a/website/full_javadoc/compbio/engine/client/Executable.html
+++ /dev/null
@@ -1,423 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:49 GMT 2010 -->\r
-<TITLE>\r
-Executable\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Executable";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/Executable.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/engine/client/EnvVariableProcessor.html" title="class in compbio.engine.client"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/engine/client/Executable.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="Executable.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;<A HREF="#nested_class_summary">NESTED</A>&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;CONSTR&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;CONSTR&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.engine.client</FONT>\r
-<BR>\r
-Interface Executable&lt;T&gt;</H2>\r
-<DL>\r
-<DT><DT><B>Type Parameters:</B><DD><CODE>T</CODE> - </DL>\r
-<DL>\r
-<DT><B>All Known Subinterfaces:</B> <DD><A HREF="../../../compbio/engine/client/ClusterNativeSpecExecutable.html" title="interface in compbio.engine.client">ClusterNativeSpecExecutable</A>&lt;T&gt;, <A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;T&gt;, <A HREF="../../../compbio/engine/client/PipedExecutable.html" title="interface in compbio.engine.client">PipedExecutable</A>&lt;T&gt;</DD>\r
-</DL>\r
-<DL>\r
-<DT><B>All Known Implementing Classes:</B> <DD><A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>, <A HREF="../../../compbio/runner/_impl/BlastAll.html" title="class in compbio.runner._impl">BlastAll</A>, <A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>, <A HREF="../../../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>, <A HREF="../../../compbio/runner/_impl/Disembl.html" title="class in compbio.runner._impl">Disembl</A>, <A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>, <A HREF="../../../compbio/runner/_impl/Mcl.html" title="class in compbio.runner._impl">Mcl</A>, <A HREF="../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>, <A HREF="../../../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>, <A HREF="../../../compbio/runner/_impl/OB.html" title="class in compbio.runner._impl">OB</A>, <A HREF="../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>, <A HREF="../../../compbio/runner/psiblast/PsiBlast.html" title="class in compbio.runner.psiblast">PsiBlast</A>, <A HREF="../../../compbio/runner/_impl/PSIBlast.html" title="class in compbio.runner._impl">PSIBlast</A>, <A HREF="../../../compbio/runner/_impl/Ronn.html" title="class in compbio.runner._impl">Ronn</A>, <A HREF="../../../compbio/runner/_impl/RPSBlast.html" title="class in compbio.runner._impl">RPSBlast</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>, <A HREF="../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A></DD>\r
-</DL>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public interface <B>Executable&lt;T&gt;</B></DL>\r
-</PRE>\r
-\r
-<P>\r
-Interface to a native executable.\r
-<P>\r
-\r
-<P>\r
-<DL>\r
-<DT><B>Author:</B></DT>\r
-  <DD>pvtroshin</DD>\r
-</DL>\r
-<HR>\r
-\r
-<P>\r
-<!-- ======== NESTED CLASS SUMMARY ======== -->\r
-\r
-<A NAME="nested_class_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Nested Class Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;class</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/engine/client/Executable.html" title="type parameter in Executable">T</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/Executable.html#addParameters(java.util.List)">addParameters</A></B>(java.util.List&lt;java.lang.String&gt;&nbsp;parameters)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Adds parameter to the list of parameters for a native executable</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.util.List&lt;java.lang.String&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/Executable.html#getCreatedFiles()">getCreatedFiles</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/Executable.html#getError()">getError</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/Executable.html#getInput()">getInput</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;<A HREF="../../../compbio/engine/client/Executable.html" title="type parameter in Executable">T</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/Executable.html#getLimit(java.lang.String)">getLimit</A></B>(java.lang.String&nbsp;presetName)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;<A HREF="../../../compbio/engine/client/Executable.html" title="type parameter in Executable">T</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/Executable.html#getLimits()">getLimits</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/Executable.html#getOutput()">getOutput</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>&lt;<A HREF="../../../compbio/engine/client/Executable.html" title="type parameter in Executable">T</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/Executable.html#getParameters(compbio.engine.client.Executable.ExecProvider)">getParameters</A></B>(<A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
-<TR ALIGN="right" VALIGN="">\r
-<TD NOWRAP><FONT SIZE="-1">\r
-<CODE>&lt;V&gt; V</CODE></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/Executable.html#getResults(java.lang.String)">getResults</A></B>(java.lang.String&nbsp;directory)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;?&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/Executable.html#loadRunConfiguration(compbio.engine.client.RunConfiguration)">loadRunConfiguration</A></B>(<A HREF="../../../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>&nbsp;rconfig)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
-<A NAME="method_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="addParameters(java.util.List)"><!-- --></A><H3>\r
-addParameters</H3>\r
-<PRE>\r
-<A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/engine/client/Executable.html" title="type parameter in Executable">T</A>&gt; <B>addParameters</B>(java.util.List&lt;java.lang.String&gt;&nbsp;parameters)</PRE>\r
-<DL>\r
-<DD>Adds parameter to the list of parameters for a native executable\r
-<P>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>parameters</CODE> - \r
-<DT><B>Returns:</B><DD>this Executable</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getCreatedFiles()"><!-- --></A><H3>\r
-getCreatedFiles</H3>\r
-<PRE>\r
-java.util.List&lt;java.lang.String&gt; <B>getCreatedFiles</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getInput()"><!-- --></A><H3>\r
-getInput</H3>\r
-<PRE>\r
-java.lang.String <B>getInput</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getOutput()"><!-- --></A><H3>\r
-getOutput</H3>\r
-<PRE>\r
-java.lang.String <B>getOutput</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getError()"><!-- --></A><H3>\r
-getError</H3>\r
-<PRE>\r
-java.lang.String <B>getError</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getParameters(compbio.engine.client.Executable.ExecProvider)"><!-- --></A><H3>\r
-getParameters</H3>\r
-<PRE>\r
-<A HREF="../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>&lt;<A HREF="../../../compbio/engine/client/Executable.html" title="type parameter in Executable">T</A>&gt; <B>getParameters</B>(<A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getResults(java.lang.String)"><!-- --></A><H3>\r
-getResults</H3>\r
-<PRE>\r
-&lt;V&gt; V <B>getResults</B>(java.lang.String&nbsp;directory)\r
-             throws <A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Throws:</B>\r
-<DD><CODE><A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></CODE></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="loadRunConfiguration(compbio.engine.client.RunConfiguration)"><!-- --></A><H3>\r
-loadRunConfiguration</H3>\r
-<PRE>\r
-<A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;?&gt; <B>loadRunConfiguration</B>(<A HREF="../../../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>&nbsp;rconfig)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getLimit(java.lang.String)"><!-- --></A><H3>\r
-getLimit</H3>\r
-<PRE>\r
-<A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;<A HREF="../../../compbio/engine/client/Executable.html" title="type parameter in Executable">T</A>&gt; <B>getLimit</B>(java.lang.String&nbsp;presetName)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getLimits()"><!-- --></A><H3>\r
-getLimits</H3>\r
-<PRE>\r
-<A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;<A HREF="../../../compbio/engine/client/Executable.html" title="type parameter in Executable">T</A>&gt; <B>getLimits</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/Executable.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/engine/client/EnvVariableProcessor.html" title="class in compbio.engine.client"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/engine/client/Executable.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="Executable.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;<A HREF="#nested_class_summary">NESTED</A>&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;CONSTR&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;CONSTR&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/engine/client/PathValidator.html b/website/full_javadoc/compbio/engine/client/PathValidator.html

deleted file mode 100644 (file)

index d83660e..0000000
--- a/website/full_javadoc/compbio/engine/client/PathValidator.html
+++ /dev/null
@@ -1,362 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:49 GMT 2010 -->\r
-<TITLE>\r
-PathValidator\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="PathValidator";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/PathValidator.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
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-</TABLE>\r
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-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../compbio/engine/client/PipedExecutable.html" title="interface in compbio.engine.client"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/engine/client/PathValidator.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
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-&nbsp;<SCRIPT type="text/javascript">\r
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-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
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-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
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-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.engine.client</FONT>\r
-<BR>\r
-Class PathValidator</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.engine.client.PathValidator</B>\r
-</PRE>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public final class <B>PathValidator</B><DT>extends java.lang.Object</DL>\r
-</PRE>\r
-\r
-<P>\r
-<HR>\r
-\r
-<P>\r
-\r
-<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
-\r
-<A NAME="constructor_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Constructor Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/PathValidator.html#PathValidator()">PathValidator</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
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-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/PathValidator.html#isAbsolutePath(java.lang.String)">isAbsolutePath</A></B>(java.lang.String&nbsp;path)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Whether a certain path is absolute or not is operation system dependent!</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/PathValidator.html#isValidDirectory(java.lang.String)">isValidDirectory</A></B>(java.lang.String&nbsp;directory)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/PathValidator.html#isValidExecutable(java.lang.String)">isValidExecutable</A></B>(java.lang.String&nbsp;command)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/PathValidator.html#validateDirectory(java.lang.String)">validateDirectory</A></B>(java.lang.String&nbsp;workDirectory)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/PathValidator.html#validateExecutable(java.lang.String)">validateExecutable</A></B>(java.lang.String&nbsp;command)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/PathValidator.html#validatePathNames(java.util.List, java.lang.String)">validatePathNames</A></B>(java.util.List&lt;java.lang.String&gt;&nbsp;filenames,\r
-                  java.lang.String&nbsp;type)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
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-</TABLE>\r
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-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
-\r
-<A NAME="constructor_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Constructor Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="PathValidator()"><!-- --></A><H3>\r
-PathValidator</H3>\r
-<PRE>\r
-public <B>PathValidator</B>()</PRE>\r
-<DL>\r
-</DL>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
-<A NAME="method_detail"><!-- --></A>\r
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-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
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-<B>Method Detail</B></FONT></TH>\r
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-</TABLE>\r
-\r
-<A NAME="isValidExecutable(java.lang.String)"><!-- --></A><H3>\r
-isValidExecutable</H3>\r
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-<DL>\r
-<DD><DL>\r
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-validateExecutable</H3>\r
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-\r
-<A NAME="isValidDirectory(java.lang.String)"><!-- --></A><H3>\r
-isValidDirectory</H3>\r
-<PRE>\r
-public static boolean <B>isValidDirectory</B>(java.lang.String&nbsp;directory)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="validatePathNames(java.util.List, java.lang.String)"><!-- --></A><H3>\r
-validatePathNames</H3>\r
-<PRE>\r
-public static void <B>validatePathNames</B>(java.util.List&lt;java.lang.String&gt;&nbsp;filenames,\r
-                                     java.lang.String&nbsp;type)\r
-                              throws java.lang.IllegalArgumentException</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>filenames</CODE> - <DD><CODE>type</CODE> - - merely a string to be added to error message to explain what
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-<DT><B>Throws:</B>\r
-<DD><CODE>java.lang.IllegalArgumentException</CODE></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="isAbsolutePath(java.lang.String)"><!-- --></A><H3>\r
-isAbsolutePath</H3>\r
-<PRE>\r
-public static boolean <B>isAbsolutePath</B>(java.lang.String&nbsp;path)</PRE>\r
-<DL>\r
-<DD>Whether a certain path is absolute or not is operation system dependent!\r
-<P>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>path</CODE> - \r
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-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="validateDirectory(java.lang.String)"><!-- --></A><H3>\r
-validateDirectory</H3>\r
-<PRE>\r
-public static void <B>validateDirectory</B>(java.lang.String&nbsp;workDirectory)\r
-                              throws java.lang.IllegalArgumentException</PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Throws:</B>\r
-<DD><CODE>java.lang.IllegalArgumentException</CODE></DL>\r
-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
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-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
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-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
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-  </TR>\r
-</TABLE>\r
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-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../compbio/engine/client/PipedExecutable.html" title="interface in compbio.engine.client"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/engine/client/PathValidator.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="PathValidator.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
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-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
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-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/engine/client/PipedExecutable.html b/website/full_javadoc/compbio/engine/client/PipedExecutable.html

deleted file mode 100644 (file)

index e3e7f54..0000000
--- a/website/full_javadoc/compbio/engine/client/PipedExecutable.html
+++ /dev/null
@@ -1,228 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:49 GMT 2010 -->\r
-<TITLE>\r
-PipedExecutable\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
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-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/PipedExecutable.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/engine/client/PathValidator.html" title="class in compbio.engine.client"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/engine/client/PipedExecutable.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="PipedExecutable.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;CONSTR&nbsp;|&nbsp;METHOD</FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;CONSTR&nbsp;|&nbsp;METHOD</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.engine.client</FONT>\r
-<BR>\r
-Interface PipedExecutable&lt;T&gt;</H2>\r
-<DL>\r
-<DT><DT><B>Type Parameters:</B><DD><CODE>T</CODE> - </DL>\r
-<DL>\r
-<DT><B>All Superinterfaces:</B> <DD><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;T&gt;</DD>\r
-</DL>\r
-<DL>\r
-<DT><B>All Known Subinterfaces:</B> <DD><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;T&gt;</DD>\r
-</DL>\r
-<DL>\r
-<DT><B>All Known Implementing Classes:</B> <DD><A HREF="../../../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>, <A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>, <A HREF="../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>, <A HREF="../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A></DD>\r
-</DL>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public interface <B>PipedExecutable&lt;T&gt;</B><DT>extends <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;T&gt;</DL>\r
-</PRE>\r
-\r
-<P>\r
-This is a marker interface to indicate that the output of the process must be
- captured. It is in generally better for the process to manage its own
- streams, but some executables are not capable of this thus require different
- handling\r
-<P>\r
-\r
-<P>\r
-<DL>\r
-<DT><B>Author:</B></DT>\r
-  <DD>pvtroshin</DD>\r
-</DL>\r
-<HR>\r
-\r
-<P>\r
-<!-- ======== NESTED CLASS SUMMARY ======== -->\r
-\r
-<A NAME="nested_class_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Nested Class Summary</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="nested_classes_inherited_from_class_compbio.engine.client.Executable"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Nested classes/interfaces inherited from interface compbio.engine.client.<A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A></CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_compbio.engine.client.Executable"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from interface compbio.engine.client.<A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><A HREF="../../../compbio/engine/client/Executable.html#addParameters(java.util.List)">addParameters</A>, <A HREF="../../../compbio/engine/client/Executable.html#getCreatedFiles()">getCreatedFiles</A>, <A HREF="../../../compbio/engine/client/Executable.html#getError()">getError</A>, <A HREF="../../../compbio/engine/client/Executable.html#getInput()">getInput</A>, <A HREF="../../../compbio/engine/client/Executable.html#getLimit(java.lang.String)">getLimit</A>, <A HREF="../../../compbio/engine/client/Executable.html#getLimits()">getLimits</A>, <A HREF="../../../compbio/engine/client/Executable.html#getOutput()">getOutput</A>, <A HREF="../../../compbio/engine/client/Executable.html#getParameters(compbio.engine.client.Executable.ExecProvider)">getParameters</A>, <A HREF="../../../compbio/engine/client/Executable.html#getResults(java.lang.String)">getResults</A>, <A HREF="../../../compbio/engine/client/Executable.html#loadRunConfiguration(compbio.engine.client.RunConfiguration)">loadRunConfiguration</A></CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/PipedExecutable.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/engine/client/PathValidator.html" title="class in compbio.engine.client"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/engine/client/PipedExecutable.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="PipedExecutable.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;CONSTR&nbsp;|&nbsp;METHOD</FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;CONSTR&nbsp;|&nbsp;METHOD</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/engine/client/RunConfiguration.html b/website/full_javadoc/compbio/engine/client/RunConfiguration.html

deleted file mode 100644 (file)

index 56783a6..0000000
--- a/website/full_javadoc/compbio/engine/client/RunConfiguration.html
+++ /dev/null
@@ -1,572 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:49 GMT 2010 -->\r
-<TITLE>\r
-RunConfiguration\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="RunConfiguration";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/RunConfiguration.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/engine/client/PipedExecutable.html" title="interface in compbio.engine.client"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/engine/client/RunConfiguration.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="RunConfiguration.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;<A HREF="#field_summary">FIELD</A>&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;<A HREF="#field_detail">FIELD</A>&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.engine.client</FONT>\r
-<BR>\r
-Class RunConfiguration</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.engine.client.RunConfiguration</B>\r
-</PRE>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public class <B>RunConfiguration</B><DT>extends java.lang.Object</DL>\r
-</PRE>\r
-\r
-<P>\r
-Value class for persisting ConfExecutable instances\r
-<P>\r
-\r
-<P>\r
-<DL>\r
-<DT><B>Author:</B></DT>\r
-  <DD>pvtroshin</DD>\r
-</DL>\r
-<HR>\r
-\r
-<P>\r
-<!-- =========== FIELD SUMMARY =========== -->\r
-\r
-<A NAME="field_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Field Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/RunConfiguration.html#rconfigFile">rconfigFile</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
-\r
-<A NAME="constructor_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Constructor Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/RunConfiguration.html#RunConfiguration()">RunConfiguration</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/RunConfiguration.html#RunConfiguration(compbio.engine.client.ConfExecutable)">RunConfiguration</A></B>(<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>&lt;?&gt;&nbsp;cexec)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/RunConfiguration.html#equals(java.lang.Object)">equals</A></B>(java.lang.Object&nbsp;obj)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/RunConfiguration.html#getError()">getError</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/RunConfiguration.html#getInput()">getInput</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/RunConfiguration.html#getOutput()">getOutput</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>&lt;?&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/RunConfiguration.html#getParameters()">getParameters</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/RunConfiguration.html#getRunnerClassName()">getRunnerClassName</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;int</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/RunConfiguration.html#hashCode()">hashCode</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/RunConfiguration.html#load(java.io.InputStream)">load</A></B>(java.io.InputStream&nbsp;input)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/RunConfiguration.html#setError(java.lang.String)">setError</A></B>(java.lang.String&nbsp;error)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/RunConfiguration.html#setInput(java.lang.String)">setInput</A></B>(java.lang.String&nbsp;input)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/RunConfiguration.html#setOutput(java.lang.String)">setOutput</A></B>(java.lang.String&nbsp;output)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/RunConfiguration.html#setParameters(compbio.engine.client.CommandBuilder)">setParameters</A></B>(<A HREF="../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>&lt;?&gt;&nbsp;parameters)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/RunConfiguration.html#toString()">toString</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/RunConfiguration.html#write(compbio.engine.client.RunConfiguration)">write</A></B>(<A HREF="../../../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>&nbsp;rconf)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>getClass, notify, notifyAll, wait, wait, wait</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ============ FIELD DETAIL =========== -->\r
-\r
-<A NAME="field_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Field Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="rconfigFile"><!-- --></A><H3>\r
-rconfigFile</H3>\r
-<PRE>\r
-public static final java.lang.String <B>rconfigFile</B></PRE>\r
-<DL>\r
-<DL>\r
-<DT><B>See Also:</B><DD><A HREF="../../../constant-values.html#compbio.engine.client.RunConfiguration.rconfigFile">Constant Field Values</A></DL>\r
-</DL>\r
-\r
-<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
-\r
-<A NAME="constructor_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Constructor Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="RunConfiguration()"><!-- --></A><H3>\r
-RunConfiguration</H3>\r
-<PRE>\r
-public <B>RunConfiguration</B>()</PRE>\r
-<DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="RunConfiguration(compbio.engine.client.ConfExecutable)"><!-- --></A><H3>\r
-RunConfiguration</H3>\r
-<PRE>\r
-public <B>RunConfiguration</B>(<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>&lt;?&gt;&nbsp;cexec)</PRE>\r
-<DL>\r
-</DL>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
-<A NAME="method_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="write(compbio.engine.client.RunConfiguration)"><!-- --></A><H3>\r
-write</H3>\r
-<PRE>\r
-public static boolean <B>write</B>(<A HREF="../../../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>&nbsp;rconf)\r
-                     throws java.io.IOException</PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Throws:</B>\r
-<DD><CODE>java.io.IOException</CODE></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="load(java.io.InputStream)"><!-- --></A><H3>\r
-load</H3>\r
-<PRE>\r
-public static <A HREF="../../../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A> <B>load</B>(java.io.InputStream&nbsp;input)\r
-                             throws java.io.IOException</PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Throws:</B>\r
-<DD><CODE>java.io.IOException</CODE></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="setOutput(java.lang.String)"><!-- --></A><H3>\r
-setOutput</H3>\r
-<PRE>\r
-public void <B>setOutput</B>(java.lang.String&nbsp;output)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getParameters()"><!-- --></A><H3>\r
-getParameters</H3>\r
-<PRE>\r
-public <A HREF="../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>&lt;?&gt; <B>getParameters</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="setParameters(compbio.engine.client.CommandBuilder)"><!-- --></A><H3>\r
-setParameters</H3>\r
-<PRE>\r
-public void <B>setParameters</B>(<A HREF="../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>&lt;?&gt;&nbsp;parameters)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getOutput()"><!-- --></A><H3>\r
-getOutput</H3>\r
-<PRE>\r
-public java.lang.String <B>getOutput</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="setError(java.lang.String)"><!-- --></A><H3>\r
-setError</H3>\r
-<PRE>\r
-public void <B>setError</B>(java.lang.String&nbsp;error)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getError()"><!-- --></A><H3>\r
-getError</H3>\r
-<PRE>\r
-public java.lang.String <B>getError</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getInput()"><!-- --></A><H3>\r
-getInput</H3>\r
-<PRE>\r
-public java.lang.String <B>getInput</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="setInput(java.lang.String)"><!-- --></A><H3>\r
-setInput</H3>\r
-<PRE>\r
-public void <B>setInput</B>(java.lang.String&nbsp;input)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getRunnerClassName()"><!-- --></A><H3>\r
-getRunnerClassName</H3>\r
-<PRE>\r
-public java.lang.String <B>getRunnerClassName</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="equals(java.lang.Object)"><!-- --></A><H3>\r
-equals</H3>\r
-<PRE>\r
-public boolean <B>equals</B>(java.lang.Object&nbsp;obj)</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Overrides:</B><DD><CODE>equals</CODE> in class <CODE>java.lang.Object</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="hashCode()"><!-- --></A><H3>\r
-hashCode</H3>\r
-<PRE>\r
-public int <B>hashCode</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Overrides:</B><DD><CODE>hashCode</CODE> in class <CODE>java.lang.Object</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="toString()"><!-- --></A><H3>\r
-toString</H3>\r
-<PRE>\r
-public java.lang.String <B>toString</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Overrides:</B><DD><CODE>toString</CODE> in class <CODE>java.lang.Object</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/RunConfiguration.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/engine/client/PipedExecutable.html" title="interface in compbio.engine.client"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/engine/client/RunConfiguration.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="RunConfiguration.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;<A HREF="#field_summary">FIELD</A>&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;<A HREF="#field_detail">FIELD</A>&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/engine/client/SkeletalExecutable.html b/website/full_javadoc/compbio/engine/client/SkeletalExecutable.html

deleted file mode 100644 (file)

index bc14f0c..0000000
--- a/website/full_javadoc/compbio/engine/client/SkeletalExecutable.html
+++ /dev/null
@@ -1,641 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:49 GMT 2010 -->\r
-<TITLE>\r
-SkeletalExecutable\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="SkeletalExecutable";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/SkeletalExecutable.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../compbio/engine/client/Util.html" title="class in compbio.engine.client"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/engine/client/SkeletalExecutable.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="SkeletalExecutable.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.engine.client</FONT>\r
-<BR>\r
-Class SkeletalExecutable&lt;T&gt;</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.engine.client.SkeletalExecutable&lt;T&gt;</B>\r
-</PRE>\r
-<DL>\r
-<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;T&gt;</DD>\r
-</DL>\r
-<DL>\r
-<DT><B>Direct Known Subclasses:</B> <DD><A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>, <A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>, <A HREF="../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>, <A HREF="../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>, <A HREF="../../../compbio/runner/psiblast/PsiBlast.html" title="class in compbio.runner.psiblast">PsiBlast</A>, <A HREF="../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A></DD>\r
-</DL>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public abstract class <B>SkeletalExecutable&lt;T&gt;</B><DT>extends java.lang.Object<DT>implements <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;T&gt;</DL>\r
-</PRE>\r
-\r
-<P>\r
-<HR>\r
-\r
-<P>\r
-<!-- ======== NESTED CLASS SUMMARY ======== -->\r
-\r
-<A NAME="nested_class_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Nested Class Summary</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="nested_classes_inherited_from_class_compbio.engine.client.Executable"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Nested classes/interfaces inherited from interface compbio.engine.client.<A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A></CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-\r
-<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
-\r
-<A NAME="constructor_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Constructor Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#SkeletalExecutable()">SkeletalExecutable</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#SkeletalExecutable(java.lang.String)">SkeletalExecutable</A></B>(java.lang.String&nbsp;parameterKeyValueDelimiter)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#addParameters(java.util.List)">addParameters</A></B>(java.util.List&lt;java.lang.String&gt;&nbsp;parameters)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Adds parameter to the list of parameters for a native executable</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#equals(java.lang.Object)">equals</A></B>(java.lang.Object&nbsp;obj)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getClusterSettings()">getClusterSettings</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.util.List&lt;java.lang.String&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getCreatedFiles()">getCreatedFiles</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;This method cannot really tell whether the files has actually been
- created or not.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getError()">getError</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getInput()">getInput</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getOutput()">getOutput</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>&lt;<A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getParameters(compbio.engine.client.Executable.ExecProvider)">getParameters</A></B>(<A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>abstract &nbsp;java.lang.Class&lt;? extends <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;?&gt;&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getType()">getType</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;int</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#hashCode()">hashCode</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;?&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#loadRunConfiguration(compbio.engine.client.RunConfiguration)">loadRunConfiguration</A></B>(<A HREF="../../../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>&nbsp;rconfig)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>&lt;<A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#setError(java.lang.String)">setError</A></B>(java.lang.String&nbsp;errFile)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>&lt;<A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#setInput(java.lang.String)">setInput</A></B>(java.lang.String&nbsp;inFile)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>&lt;<A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#setOutput(java.lang.String)">setOutput</A></B>(java.lang.String&nbsp;outFile)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#setParameter(java.lang.String)">setParameter</A></B>(java.lang.String&nbsp;parameter)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#toString()">toString</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>getClass, notify, notifyAll, wait, wait, wait</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_compbio.engine.client.Executable"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from interface compbio.engine.client.<A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><A HREF="../../../compbio/engine/client/Executable.html#getLimit(java.lang.String)">getLimit</A>, <A HREF="../../../compbio/engine/client/Executable.html#getLimits()">getLimits</A>, <A HREF="../../../compbio/engine/client/Executable.html#getResults(java.lang.String)">getResults</A></CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
-\r
-<A NAME="constructor_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Constructor Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="SkeletalExecutable()"><!-- --></A><H3>\r
-SkeletalExecutable</H3>\r
-<PRE>\r
-public <B>SkeletalExecutable</B>()</PRE>\r
-<DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="SkeletalExecutable(java.lang.String)"><!-- --></A><H3>\r
-SkeletalExecutable</H3>\r
-<PRE>\r
-public <B>SkeletalExecutable</B>(java.lang.String&nbsp;parameterKeyValueDelimiter)</PRE>\r
-<DL>\r
-</DL>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
-<A NAME="method_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="setInput(java.lang.String)"><!-- --></A><H3>\r
-setInput</H3>\r
-<PRE>\r
-public <A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>&lt;<A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>&gt; <B>setInput</B>(java.lang.String&nbsp;inFile)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="setOutput(java.lang.String)"><!-- --></A><H3>\r
-setOutput</H3>\r
-<PRE>\r
-public <A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>&lt;<A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>&gt; <B>setOutput</B>(java.lang.String&nbsp;outFile)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="setError(java.lang.String)"><!-- --></A><H3>\r
-setError</H3>\r
-<PRE>\r
-public <A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>&lt;<A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>&gt; <B>setError</B>(java.lang.String&nbsp;errFile)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getParameters(compbio.engine.client.Executable.ExecProvider)"><!-- --></A><H3>\r
-getParameters</H3>\r
-<PRE>\r
-public <A HREF="../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>&lt;<A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>&gt; <B>getParameters</B>(<A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider)</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#getParameters(compbio.engine.client.Executable.ExecProvider)">getParameters</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="addParameters(java.util.List)"><!-- --></A><H3>\r
-addParameters</H3>\r
-<PRE>\r
-public <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>&gt; <B>addParameters</B>(java.util.List&lt;java.lang.String&gt;&nbsp;parameters)</PRE>\r
-<DL>\r
-<DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/engine/client/Executable.html#addParameters(java.util.List)">Executable</A></CODE></B></DD>\r
-<DD>Adds parameter to the list of parameters for a native executable\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#addParameters(java.util.List)">addParameters</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>this Executable</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="setParameter(java.lang.String)"><!-- --></A><H3>\r
-setParameter</H3>\r
-<PRE>\r
-public <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>&gt; <B>setParameter</B>(java.lang.String&nbsp;parameter)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getCreatedFiles()"><!-- --></A><H3>\r
-getCreatedFiles</H3>\r
-<PRE>\r
-public java.util.List&lt;java.lang.String&gt; <B>getCreatedFiles</B>()</PRE>\r
-<DL>\r
-<DD>This method cannot really tell whether the files has actually been
- created or not. It must be overridden as required.\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#getCreatedFiles()">getCreatedFiles</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-<DT><B>See Also:</B><DD><A HREF="../../../compbio/engine/client/Executable.html#getCreatedFiles()"><CODE>Executable.getCreatedFiles()</CODE></A></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getInput()"><!-- --></A><H3>\r
-getInput</H3>\r
-<PRE>\r
-public java.lang.String <B>getInput</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#getInput()">getInput</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getOutput()"><!-- --></A><H3>\r
-getOutput</H3>\r
-<PRE>\r
-public java.lang.String <B>getOutput</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#getOutput()">getOutput</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getError()"><!-- --></A><H3>\r
-getError</H3>\r
-<PRE>\r
-public java.lang.String <B>getError</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#getError()">getError</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="toString()"><!-- --></A><H3>\r
-toString</H3>\r
-<PRE>\r
-public java.lang.String <B>toString</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
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-</DD>\r
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-</DD>\r
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-\r
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-<PRE>\r
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-<DL>\r
-<DD><DL>\r
-<DT><B>Overrides:</B><DD><CODE>equals</CODE> in class <CODE>java.lang.Object</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
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-<DT><B>Overrides:</B><DD><CODE>hashCode</CODE> in class <CODE>java.lang.Object</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getClusterSettings()"><!-- --></A><H3>\r
-getClusterSettings</H3>\r
-<PRE>\r
-public java.lang.String <B>getClusterSettings</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
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-\r
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-getType</H3>\r
-<PRE>\r
-public abstract java.lang.Class&lt;? extends <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;?&gt;&gt; <B>getType</B>()</PRE>\r
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-<TR>\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
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-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
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-\r
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-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
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-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
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diff --git a/website/full_javadoc/compbio/engine/client/Util.html b/website/full_javadoc/compbio/engine/client/Util.html

deleted file mode 100644 (file)

index 5574f03..0000000
--- a/website/full_javadoc/compbio/engine/client/Util.html
+++ /dev/null
@@ -1,505 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:49 GMT 2010 -->\r
-<TITLE>\r
-Util\r
-</TITLE>\r
-\r
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-\r
-<SCRIPT type="text/javascript">\r
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-<!-- ========= START OF TOP NAVBAR ======= -->\r
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-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/Util.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
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-</EM>\r
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-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/engine/client/Util.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
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-</PRE>\r
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-<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
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-<B>Constructor Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/Util.html#Util()">Util</A></B>()</CODE>\r
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-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
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-\r
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-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
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-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/Util.html#convertToAbsolute(java.lang.String)">convertToAbsolute</A></B>(java.lang.String&nbsp;relativePath)</CODE>\r
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-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
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-<CODE>static&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/Util.html#getCommand(compbio.engine.client.Executable.ExecProvider, java.lang.Class)">getCommand</A></B>(<A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider,\r
-           java.lang.Class&lt;?&gt;&nbsp;clazz)</CODE>\r
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-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
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-<CODE>static&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/Util.html#getExecProperty(java.lang.String, java.lang.Class)">getExecProperty</A></B>(java.lang.String&nbsp;propertySpec,\r
-                java.lang.Class&lt;?&gt;&nbsp;clazz)</CODE>\r
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-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
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-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/Util.html#getExecProperty(java.lang.String, compbio.engine.client.Executable)">getExecProperty</A></B>(java.lang.String&nbsp;propertySpec,\r
-                <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;?&gt;&nbsp;exec)</CODE>\r
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-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
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-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/Util.html#getFullPath(java.lang.String, java.lang.String)">getFullPath</A></B>(java.lang.String&nbsp;workDirectory,\r
-            java.lang.String&nbsp;fileName)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
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-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/Util.html#getSupportedRuntimes(java.lang.Class)">getSupportedRuntimes</A></B>(java.lang.Class&lt;?&gt;&nbsp;clazz)</CODE>\r
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-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
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-<CODE>static&nbsp;boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/Util.html#isMarked(java.lang.String, compbio.metadata.JobStatus)">isMarked</A></B>(java.lang.String&nbsp;workDirectory,\r
-         <A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A>&nbsp;marker)</CODE>\r
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-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
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-<CODE>static&nbsp;boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/Util.html#isValidJobId(java.lang.String)">isValidJobId</A></B>(java.lang.String&nbsp;key)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
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-<CODE>static&nbsp;<A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/Util.html#loadExecutable(java.lang.String)">loadExecutable</A></B>(java.lang.String&nbsp;taskId)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
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-<TD><CODE><B><A HREF="../../../compbio/engine/client/Util.html#mergeEnvVariables(java.util.Map, java.util.Map)">mergeEnvVariables</A></B>(java.util.Map&lt;java.lang.String,java.lang.String&gt;&nbsp;sysEnvTobeModified,\r
-                  java.util.Map&lt;java.lang.String,java.lang.String&gt;&nbsp;variables)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/Util.html#writeFile(java.lang.String, java.lang.String, java.lang.String, boolean)">writeFile</A></B>(java.lang.String&nbsp;workDirectory,\r
-          java.lang.String&nbsp;fileAndEventName,\r
-          java.lang.String&nbsp;content,\r
-          boolean&nbsp;override)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/Util.html#writeMarker(java.lang.String, compbio.metadata.JobStatus)">writeMarker</A></B>(java.lang.String&nbsp;workDirectory,\r
-            <A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A>&nbsp;fileType)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/Util.html#writeStatFile(java.lang.String, java.lang.String)">writeStatFile</A></B>(java.lang.String&nbsp;workDirectory,\r
-              java.lang.String&nbsp;fileAndEventName)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
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-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
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-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
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-mergeEnvVariables</H3>\r
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-\r
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-<PRE>\r
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-</DD>\r
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-<A NAME="getCommand(compbio.engine.client.Executable.ExecProvider, java.lang.Class)"><!-- --></A><H3>\r
-getCommand</H3>\r
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-\r
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-getSupportedRuntimes</H3>\r
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-loadExecutable</H3>\r
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-<DL>\r
-<DD><DL>\r
-\r
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-<DD><CODE><A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></CODE></DL>\r
-</DD>\r
-</DL>\r
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-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
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-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/Util.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
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-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;NEXT CLASS</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/engine/client/Util.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="Util.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
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-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
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diff --git a/website/full_javadoc/compbio/engine/client/class-use/ClusterNativeSpecExecutable.html b/website/full_javadoc/compbio/engine/client/class-use/ClusterNativeSpecExecutable.html

deleted file mode 100644 (file)

index d57b7bd..0000000
--- a/website/full_javadoc/compbio/engine/client/class-use/ClusterNativeSpecExecutable.html
+++ /dev/null
@@ -1,180 +0,0 @@
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-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Uses of Interface compbio.engine.client.ClusterNativeSpecExecutable\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Uses of Interface compbio.engine.client.ClusterNativeSpecExecutable";\r
-    }\r
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-\r
-</HEAD>\r
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-<BODY BGCOLOR="white" onload="windowTitle();">\r
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-\r
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-<!-- ========= START OF TOP NAVBAR ======= -->\r
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-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
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-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../compbio/engine/client/ClusterNativeSpecExecutable.html" title="interface in compbio.engine.client"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
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-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
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-  <A HREF="../../../../index.html?compbio/engine/client/\class-useClusterNativeSpecExecutable.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="ClusterNativeSpecExecutable.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
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-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
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-\r
-\r
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-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-<B>Uses of Interface<br>compbio.engine.client.ClusterNativeSpecExecutable</B></H2>\r
-</CENTER>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Packages that use <A HREF="../../../../compbio/engine/client/ClusterNativeSpecExecutable.html" title="interface in compbio.engine.client">ClusterNativeSpecExecutable</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.runner.msa"><B>compbio.runner.msa</B></A></TD>\r
-<TD>Wrappers for native executables for multiple sequence alignment (msa)&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.runner.msa"><!-- --></A>\r
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-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../../compbio/engine/client/ClusterNativeSpecExecutable.html" title="interface in compbio.engine.client">ClusterNativeSpecExecutable</A> in <A HREF="../../../../compbio/runner/msa/package-summary.html">compbio.runner.msa</A></FONT></TH>\r
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-<TH ALIGN="left" COLSPAN="2">Classes in <A HREF="../../../../compbio/runner/msa/package-summary.html">compbio.runner.msa</A> that implement <A HREF="../../../../compbio/engine/client/ClusterNativeSpecExecutable.html" title="interface in compbio.engine.client">ClusterNativeSpecExecutable</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;class</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A></B></CODE>\r
-\r
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-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
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-&nbsp;\r
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-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
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-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/engine/client/class-use/CommandBuilder.html b/website/full_javadoc/compbio/engine/client/class-use/CommandBuilder.html

deleted file mode 100644 (file)

index 663f217..0000000
--- a/website/full_javadoc/compbio/engine/client/class-use/CommandBuilder.html
+++ /dev/null
@@ -1,339 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Uses of Class compbio.engine.client.CommandBuilder\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Uses of Class compbio.engine.client.CommandBuilder";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/engine/client/\class-useCommandBuilder.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="CommandBuilder.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-<B>Uses of Class<br>compbio.engine.client.CommandBuilder</B></H2>\r
-</CENTER>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Packages that use <A HREF="../../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.engine.client"><B>compbio.engine.client</B></A></TD>\r
-<TD>Classes and interfaces representing an input for engines.&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.runner"><B>compbio.runner</B></A></TD>\r
-<TD>Utilities commonly used by all runners.&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.runner._impl"><B>compbio.runner._impl</B></A></TD>\r
-<TD>&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.runner.msa"><B>compbio.runner.msa</B></A></TD>\r
-<TD>Wrappers for native executables for multiple sequence alignment (msa)&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.engine.client"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A> in <A HREF="../../../../compbio/engine/client/package-summary.html">compbio.engine.client</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/engine/client/package-summary.html">compbio.engine.client</A> that return <A HREF="../../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>&lt;<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="type parameter in ConfiguredExecutable">T</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>ConfiguredExecutable.</B><B><A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html#getParameters()">getParameters</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>&lt;<A HREF="../../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>ConfExecutable.</B><B><A HREF="../../../../compbio/engine/client/ConfExecutable.html#getParameters()">getParameters</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>&lt;?&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>RunConfiguration.</B><B><A HREF="../../../../compbio/engine/client/RunConfiguration.html#getParameters()">getParameters</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>&lt;<A HREF="../../../../compbio/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>SkeletalExecutable.</B><B><A HREF="../../../../compbio/engine/client/SkeletalExecutable.html#getParameters(compbio.engine.client.Executable.ExecProvider)">getParameters</A></B>(<A HREF="../../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>&lt;<A HREF="../../../../compbio/engine/client/Executable.html" title="type parameter in Executable">T</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>Executable.</B><B><A HREF="../../../../compbio/engine/client/Executable.html#getParameters(compbio.engine.client.Executable.ExecProvider)">getParameters</A></B>(<A HREF="../../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>&lt;<A HREF="../../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>ConfExecutable.</B><B><A HREF="../../../../compbio/engine/client/ConfExecutable.html#getParameters(compbio.engine.client.Executable.ExecProvider)">getParameters</A></B>(<A HREF="../../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
-<TR ALIGN="right" VALIGN="">\r
-<TD NOWRAP><FONT SIZE="-1">\r
-<CODE>&lt;T&gt; <A HREF="../../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>&lt;T&gt;</CODE></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-</CODE></FONT></TD>\r
-<TD><CODE><B>CommandBuilder.</B><B><A HREF="../../../../compbio/engine/client/CommandBuilder.html#newCommandBuilder(java.util.List, java.lang.String)">newCommandBuilder</A></B>(java.util.List&lt;? extends <A HREF="../../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;T&gt;&gt;&nbsp;arguments,\r
-                  java.lang.String&nbsp;nameValueSeparator)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;This produces the same result as getCommands method.</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/engine/client/package-summary.html">compbio.engine.client</A> with parameters of type <A HREF="../../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B>RunConfiguration.</B><B><A HREF="../../../../compbio/engine/client/RunConfiguration.html#setParameters(compbio.engine.client.CommandBuilder)">setParameters</A></B>(<A HREF="../../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>&lt;?&gt;&nbsp;parameters)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.runner"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A> in <A HREF="../../../../compbio/runner/package-summary.html">compbio.runner</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/runner/package-summary.html">compbio.runner</A> that return <A HREF="../../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>&lt;<A HREF="../../../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>_SkeletalCommandBuilder.</B><B><A HREF="../../../../compbio/runner/_SkeletalCommandBuilder.html#getParameters(compbio.engine.client.Executable.ExecProvider)">getParameters</A></B>(<A HREF="../../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.runner._impl"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A> in <A HREF="../../../../compbio/runner/_impl/package-summary.html">compbio.runner._impl</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/runner/_impl/package-summary.html">compbio.runner._impl</A> that return <A HREF="../../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>&lt;<A HREF="../../../../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>NetNglyc.</B><B><A HREF="../../../../compbio/runner/_impl/NetNglyc.html#getParameters(compbio.engine.client.Executable.ExecProvider)">getParameters</A></B>(<A HREF="../../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.runner.msa"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A> in <A HREF="../../../../compbio/runner/msa/package-summary.html">compbio.runner.msa</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/runner/msa/package-summary.html">compbio.runner.msa</A> that return <A HREF="../../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>&lt;<A HREF="../../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>Tcoffee.</B><B><A HREF="../../../../compbio/runner/msa/Tcoffee.html#getParameters(compbio.engine.client.Executable.ExecProvider)">getParameters</A></B>(<A HREF="../../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
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-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/engine/client/\class-useCommandBuilder.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="CommandBuilder.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
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diff --git a/website/full_javadoc/compbio/engine/client/class-use/ConfExecutable.html b/website/full_javadoc/compbio/engine/client/class-use/ConfExecutable.html

deleted file mode 100644 (file)

index e5755d1..0000000
--- a/website/full_javadoc/compbio/engine/client/class-use/ConfExecutable.html
+++ /dev/null
@@ -1,178 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Uses of Class compbio.engine.client.ConfExecutable\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Uses of Class compbio.engine.client.ConfExecutable";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
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-<!-- ========= START OF TOP NAVBAR ======= -->\r
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-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
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-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
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-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/engine/client/\class-useConfExecutable.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="ConfExecutable.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
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-\r
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-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
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-<CENTER>\r
-<H2>\r
-<B>Uses of Class<br>compbio.engine.client.ConfExecutable</B></H2>\r
-</CENTER>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Packages that use <A HREF="../../../../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.engine.client"><B>compbio.engine.client</B></A></TD>\r
-<TD>Classes and interfaces representing an input for engines.&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.engine.client"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A> in <A HREF="../../../../compbio/engine/client/package-summary.html">compbio.engine.client</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Constructors in <A HREF="../../../../compbio/engine/client/package-summary.html">compbio.engine.client</A> with parameters of type <A HREF="../../../../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../../compbio/engine/client/RunConfiguration.html#RunConfiguration(compbio.engine.client.ConfExecutable)">RunConfiguration</A></B>(<A HREF="../../../../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>&lt;?&gt;&nbsp;cexec)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
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-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
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-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/engine/client/\class-useConfExecutable.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="ConfExecutable.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
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-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
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-</HTML>\r
diff --git a/website/full_javadoc/compbio/engine/client/class-use/ConfiguredExecutable.html b/website/full_javadoc/compbio/engine/client/class-use/ConfiguredExecutable.html

deleted file mode 100644 (file)

index 85add53..0000000
--- a/website/full_javadoc/compbio/engine/client/class-use/ConfiguredExecutable.html
+++ /dev/null
@@ -1,744 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Uses of Interface compbio.engine.client.ConfiguredExecutable\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Uses of Interface compbio.engine.client.ConfiguredExecutable";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
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-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/engine/client/\class-useConfiguredExecutable.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="ConfiguredExecutable.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-<B>Uses of Interface<br>compbio.engine.client.ConfiguredExecutable</B></H2>\r
-</CENTER>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Packages that use <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.engine"><B>compbio.engine</B></A></TD>\r
-<TD>&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.engine.client"><B>compbio.engine.client</B></A></TD>\r
-<TD>Classes and interfaces representing an input for engines.&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.engine.cluster.drmaa"><B>compbio.engine.cluster.drmaa</B></A></TD>\r
-<TD>An cluster engine classes responsible for execution of Executables on the clusters.&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.engine.local"><B>compbio.engine.local</B></A></TD>\r
-<TD>An local engine classes responsible for execution of Executables on the local computer 
- (the same machine as JVM running these classes).&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.runner"><B>compbio.runner</B></A></TD>\r
-<TD>Utilities commonly used by all runners.&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.ws.server"><B>compbio.ws.server</B></A></TD>\r
-<TD>&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.engine"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A> in <A HREF="../../../../compbio/engine/package-summary.html">compbio.engine</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/engine/package-summary.html">compbio.engine</A> that return <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
-<TR ALIGN="right" VALIGN="">\r
-<TD NOWRAP><FONT SIZE="-1">\r
-<CODE>&lt;T&gt; <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;T&gt;</CODE></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-</CODE></FONT></TD>\r
-<TD><CODE><B>Configurator.</B><B><A HREF="../../../../compbio/engine/Configurator.html#configureExecutable(compbio.engine.client.Executable)">configureExecutable</A></B>(<A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;T&gt;&nbsp;executable)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
-<TR ALIGN="right" VALIGN="">\r
-<TD NOWRAP><FONT SIZE="-1">\r
-<CODE>&lt;T&gt; <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;T&gt;</CODE></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-</CODE></FONT></TD>\r
-<TD><CODE><B>Configurator.</B><B><A HREF="../../../../compbio/engine/Configurator.html#configureExecutable(compbio.engine.client.Executable, compbio.engine.client.Executable.ExecProvider)">configureExecutable</A></B>(<A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;T&gt;&nbsp;executable,\r
-                    <A HREF="../../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
-<TR ALIGN="right" VALIGN="">\r
-<TD NOWRAP><FONT SIZE="-1">\r
-<CODE>&lt;T&gt; <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;T&gt;</CODE></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-</CODE></FONT></TD>\r
-<TD><CODE><B>Configurator.</B><B><A HREF="../../../../compbio/engine/Configurator.html#configureExecutable(compbio.engine.client.Executable, java.util.List)">configureExecutable</A></B>(<A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;T&gt;&nbsp;executable,\r
-                    java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;dataSet)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>Job.</B><B><A HREF="../../../../compbio/engine/Job.html#getConfExecutable()">getConfExecutable</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>AsyncExecutor.</B><B><A HREF="../../../../compbio/engine/AsyncExecutor.html#getResults(java.lang.String)">getResults</A></B>(java.lang.String&nbsp;jobId)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Retrieve the results of the job.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>SyncExecutor.</B><B><A HREF="../../../../compbio/engine/SyncExecutor.html#waitForResult()">waitForResult</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Call to this method block for as long as it is required for an executable to finish its job.</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/engine/package-summary.html">compbio.engine</A> that return types with arguments of type <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;java.util.concurrent.Future&lt;<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>SubmissionManager.</B><B><A HREF="../../../../compbio/engine/SubmissionManager.html#getTask(java.lang.String)">getTask</A></B>(java.lang.String&nbsp;taskId)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/engine/package-summary.html">compbio.engine</A> with parameters of type <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B>SubmissionManager.</B><B><A HREF="../../../../compbio/engine/SubmissionManager.html#addTask(compbio.engine.client.ConfiguredExecutable, java.util.concurrent.Future)">addTask</A></B>(<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;executable,\r
-        java.util.concurrent.Future&lt;<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&gt;&nbsp;future)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;boolean</CODE></FONT></TD>\r
-<TD><CODE><B>Cleaner.</B><B><A HREF="../../../../compbio/engine/Cleaner.html#deleteFiles(compbio.engine.client.ConfiguredExecutable)">deleteFiles</A></B>(<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;exec)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;This method returns true if all files specified by List files were
- successfully removed or there was no files to remove (files list was
- empty)</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine">AsyncExecutor</A></CODE></FONT></TD>\r
-<TD><CODE><B>Configurator.</B><B><A HREF="../../../../compbio/engine/Configurator.html#getAsyncEngine(compbio.engine.client.ConfiguredExecutable)">getAsyncEngine</A></B>(<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;executable)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine">AsyncExecutor</A></CODE></FONT></TD>\r
-<TD><CODE><B>Configurator.</B><B><A HREF="../../../../compbio/engine/Configurator.html#getAsyncEngine(compbio.engine.client.ConfiguredExecutable, compbio.engine.client.Executable.ExecProvider)">getAsyncEngine</A></B>(<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;executable,\r
-               <A HREF="../../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../../compbio/engine/SyncExecutor.html" title="interface in compbio.engine">SyncExecutor</A></CODE></FONT></TD>\r
-<TD><CODE><B>Configurator.</B><B><A HREF="../../../../compbio/engine/Configurator.html#getSyncEngine(compbio.engine.client.ConfiguredExecutable)">getSyncEngine</A></B>(<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;executable)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../../compbio/engine/SyncExecutor.html" title="interface in compbio.engine">SyncExecutor</A></CODE></FONT></TD>\r
-<TD><CODE><B>Configurator.</B><B><A HREF="../../../../compbio/engine/Configurator.html#getSyncEngine(compbio.engine.client.ConfiguredExecutable, compbio.engine.client.Executable.ExecProvider)">getSyncEngine</A></B>(<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;executable,\r
-              <A HREF="../../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B>SubmissionManager.</B><B><A HREF="../../../../compbio/engine/SubmissionManager.html#removeTask(compbio.engine.client.ConfiguredExecutable)">removeTask</A></B>(<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;executable)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B>AsyncExecutor.</B><B><A HREF="../../../../compbio/engine/AsyncExecutor.html#submitJob(compbio.engine.client.ConfiguredExecutable)">submitJob</A></B>(<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;executable)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Submits job for the execution
- Immediate execution is not guaranteed, this method puts the job in the queue.</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Method parameters in <A HREF="../../../../compbio/engine/package-summary.html">compbio.engine</A> with type arguments of type <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B>SubmissionManager.</B><B><A HREF="../../../../compbio/engine/SubmissionManager.html#addTask(compbio.engine.client.ConfiguredExecutable, java.util.concurrent.Future)">addTask</A></B>(<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;executable,\r
-        java.util.concurrent.Future&lt;<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&gt;&nbsp;future)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Constructors in <A HREF="../../../../compbio/engine/package-summary.html">compbio.engine</A> with parameters of type <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../../compbio/engine/Job.html#Job(java.lang.String, java.lang.String, compbio.engine.client.ConfiguredExecutable)">Job</A></B>(java.lang.String&nbsp;taskId,\r
-    java.lang.String&nbsp;jobId,\r
-    <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;cexecutable)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.engine.client"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A> in <A HREF="../../../../compbio/engine/client/package-summary.html">compbio.engine.client</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Classes in <A HREF="../../../../compbio/engine/client/package-summary.html">compbio.engine.client</A> that implement <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;class</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable&lt;T&gt;</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/engine/client/package-summary.html">compbio.engine.client</A> that return <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>Util.</B><B><A HREF="../../../../compbio/engine/client/Util.html#loadExecutable(java.lang.String)">loadExecutable</A></B>(java.lang.String&nbsp;taskId)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>ConfiguredExecutable.</B><B><A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html#loadRunConfiguration(java.io.InputStream)">loadRunConfiguration</A></B>(java.io.InputStream&nbsp;input)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>ConfExecutable.</B><B><A HREF="../../../../compbio/engine/client/ConfExecutable.html#loadRunConfiguration(java.io.InputStream)">loadRunConfiguration</A></B>(java.io.InputStream&nbsp;input)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>ConfExecutable.</B><B><A HREF="../../../../compbio/engine/client/ConfExecutable.html#loadRunConfiguration(compbio.engine.client.RunConfiguration)">loadRunConfiguration</A></B>(<A HREF="../../../../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>&nbsp;rconf)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>ConfExecutable.</B><B><A HREF="../../../../compbio/engine/client/ConfExecutable.html#newConfExecutable(compbio.engine.client.RunConfiguration)">newConfExecutable</A></B>(<A HREF="../../../../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>&nbsp;rconf)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.engine.cluster.drmaa"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A> in <A HREF="../../../../compbio/engine/cluster/drmaa/package-summary.html">compbio.engine.cluster.drmaa</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/engine/cluster/drmaa/package-summary.html">compbio.engine.cluster.drmaa</A> that return <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>ClusterSession.</B><B><A HREF="../../../../compbio/engine/cluster/drmaa/ClusterSession.html#getResults(java.lang.String)">getResults</A></B>(java.lang.String&nbsp;taskId)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>AsyncJobRunner.</B><B><A HREF="../../../../compbio/engine/cluster/drmaa/AsyncJobRunner.html#getResults(java.lang.String)">getResults</A></B>(java.lang.String&nbsp;jobId)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>JobRunner.</B><B><A HREF="../../../../compbio/engine/cluster/drmaa/JobRunner.html#waitForResult()">waitForResult</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/engine/cluster/drmaa/package-summary.html">compbio.engine.cluster.drmaa</A> with parameters of type <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../../compbio/engine/cluster/drmaa/JobRunner.html" title="class in compbio.engine.cluster.drmaa">JobRunner</A></CODE></FONT></TD>\r
-<TD><CODE><B>JobRunner.</B><B><A HREF="../../../../compbio/engine/cluster/drmaa/JobRunner.html#getInstance(compbio.engine.client.ConfiguredExecutable)">getInstance</A></B>(<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;executable)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B>AsyncJobRunner.</B><B><A HREF="../../../../compbio/engine/cluster/drmaa/AsyncJobRunner.html#submitJob(compbio.engine.client.ConfiguredExecutable)">submitJob</A></B>(<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;executable)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Constructors in <A HREF="../../../../compbio/engine/cluster/drmaa/package-summary.html">compbio.engine.cluster.drmaa</A> with parameters of type <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/JobRunner.html#JobRunner(compbio.engine.client.ConfiguredExecutable)">JobRunner</A></B>(<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;confExec)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.engine.local"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A> in <A HREF="../../../../compbio/engine/local/package-summary.html">compbio.engine.local</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/engine/local/package-summary.html">compbio.engine.local</A> that return <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>ExecutableWrapper.</B><B><A HREF="../../../../compbio/engine/local/ExecutableWrapper.html#call()">call</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;It is vital that output and error streams are captured immediately for
- this call() to succeed.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>LocalEngineUtil.</B><B><A HREF="../../../../compbio/engine/local/LocalEngineUtil.html#getResults(java.util.concurrent.Future, java.lang.String)">getResults</A></B>(java.util.concurrent.Future&lt;<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&gt;&nbsp;future,\r
-           java.lang.String&nbsp;taskId)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>AsyncLocalRunner.</B><B><A HREF="../../../../compbio/engine/local/AsyncLocalRunner.html#getResults(java.lang.String)">getResults</A></B>(java.lang.String&nbsp;taskId)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>LocalRunner.</B><B><A HREF="../../../../compbio/engine/local/LocalRunner.html#waitForResult()">waitForResult</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/engine/local/package-summary.html">compbio.engine.local</A> with parameters of type <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;boolean</CODE></FONT></TD>\r
-<TD><CODE><B>LocalEngineUtil.</B><B><A HREF="../../../../compbio/engine/local/LocalEngineUtil.html#cleanup(compbio.engine.client.ConfiguredExecutable)">cleanup</A></B>(<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;confExecutable)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B>AsyncLocalRunner.</B><B><A HREF="../../../../compbio/engine/local/AsyncLocalRunner.html#submitJob(compbio.engine.client.ConfiguredExecutable)">submitJob</A></B>(<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;executable)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Method parameters in <A HREF="../../../../compbio/engine/local/package-summary.html">compbio.engine.local</A> with type arguments of type <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;boolean</CODE></FONT></TD>\r
-<TD><CODE><B>LocalEngineUtil.</B><B><A HREF="../../../../compbio/engine/local/LocalEngineUtil.html#cancelJob(java.util.concurrent.Future, java.lang.String)">cancelJob</A></B>(java.util.concurrent.Future&lt;<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&gt;&nbsp;future,\r
-          java.lang.String&nbsp;workDirectory)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A></CODE></FONT></TD>\r
-<TD><CODE><B>LocalEngineUtil.</B><B><A HREF="../../../../compbio/engine/local/LocalEngineUtil.html#getJobStatus(java.util.concurrent.Future)">getJobStatus</A></B>(java.util.concurrent.Future&lt;<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&gt;&nbsp;future)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>LocalEngineUtil.</B><B><A HREF="../../../../compbio/engine/local/LocalEngineUtil.html#getResults(java.util.concurrent.Future, java.lang.String)">getResults</A></B>(java.util.concurrent.Future&lt;<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&gt;&nbsp;future,\r
-           java.lang.String&nbsp;taskId)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Constructors in <A HREF="../../../../compbio/engine/local/package-summary.html">compbio.engine.local</A> with parameters of type <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../../compbio/engine/local/ExecutableWrapper.html#ExecutableWrapper(compbio.engine.client.ConfiguredExecutable, java.lang.String)">ExecutableWrapper</A></B>(<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;executable,\r
-                  java.lang.String&nbsp;workDirectory)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../../compbio/engine/local/LocalRunner.html#LocalRunner(compbio.engine.client.ConfiguredExecutable)">LocalRunner</A></B>(<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;executable)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.runner"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A> in <A HREF="../../../../compbio/runner/package-summary.html">compbio.runner</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/runner/package-summary.html">compbio.runner</A> with parameters of type <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B>Util.</B><B><A HREF="../../../../compbio/runner/Util.html#writeInput(java.util.List, compbio.engine.client.ConfiguredExecutable)">writeInput</A></B>(java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-           <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;exec)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.ws.server"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A> in <A HREF="../../../../compbio/ws/server/package-summary.html">compbio.ws.server</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/ws/server/package-summary.html">compbio.ws.server</A> with parameters of type <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
-<TR ALIGN="right" VALIGN="">\r
-<TD NOWRAP><FONT SIZE="-1">\r
-<CODE>&lt;T&gt; java.lang.String</CODE></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-</CODE></FONT></TD>\r
-<TD><CODE><B>WSUtil.</B><B><A HREF="../../../../compbio/ws/server/WSUtil.html#align(java.util.List, compbio.engine.client.ConfiguredExecutable, org.apache.log4j.Logger, javax.xml.ws.WebServiceContext, java.lang.String, compbio.metadata.Limit)">align</A></B>(java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-      <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;T&gt;&nbsp;confExec,\r
-      org.apache.log4j.Logger&nbsp;statLog,\r
-      javax.xml.ws.WebServiceContext&nbsp;wsContext,\r
-      java.lang.String&nbsp;callingMethod,\r
-      <A HREF="../../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;T&gt;&nbsp;limit)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine">AsyncExecutor</A></CODE></FONT></TD>\r
-<TD><CODE><B>WSUtil.</B><B><A HREF="../../../../compbio/ws/server/WSUtil.html#getEngine(compbio.engine.client.ConfiguredExecutable)">getEngine</A></B>(<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;confClustal)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/engine/client/\class-useConfiguredExecutable.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="ConfiguredExecutable.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/engine/client/class-use/EnvVariableProcessor.html b/website/full_javadoc/compbio/engine/client/class-use/EnvVariableProcessor.html

deleted file mode 100644 (file)

index 8647d6e..0000000
--- a/website/full_javadoc/compbio/engine/client/class-use/EnvVariableProcessor.html
+++ /dev/null
@@ -1,144 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Uses of Class compbio.engine.client.EnvVariableProcessor\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Uses of Class compbio.engine.client.EnvVariableProcessor";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../compbio/engine/client/EnvVariableProcessor.html" title="class in compbio.engine.client"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/engine/client/\class-useEnvVariableProcessor.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="EnvVariableProcessor.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-<B>Uses of Class<br>compbio.engine.client.EnvVariableProcessor</B></H2>\r
-</CENTER>\r
-No usage of compbio.engine.client.EnvVariableProcessor\r
-<P>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../compbio/engine/client/EnvVariableProcessor.html" title="class in compbio.engine.client"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/engine/client/\class-useEnvVariableProcessor.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="EnvVariableProcessor.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/engine/client/class-use/Executable.ExecProvider.html b/website/full_javadoc/compbio/engine/client/class-use/Executable.ExecProvider.html

deleted file mode 100644 (file)

index e8cae7f..0000000
--- a/website/full_javadoc/compbio/engine/client/class-use/Executable.ExecProvider.html
+++ /dev/null
@@ -1,516 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Uses of Class compbio.engine.client.Executable.ExecProvider\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Uses of Class compbio.engine.client.Executable.ExecProvider";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/engine/client/\class-useExecutable.ExecProvider.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="Executable.ExecProvider.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-<B>Uses of Class<br>compbio.engine.client.Executable.ExecProvider</B></H2>\r
-</CENTER>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Packages that use <A HREF="../../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.engine"><B>compbio.engine</B></A></TD>\r
-<TD>&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.engine.client"><B>compbio.engine.client</B></A></TD>\r
-<TD>Classes and interfaces representing an input for engines.&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.runner"><B>compbio.runner</B></A></TD>\r
-<TD>Utilities commonly used by all runners.&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.runner._impl"><B>compbio.runner._impl</B></A></TD>\r
-<TD>&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.runner.msa"><B>compbio.runner.msa</B></A></TD>\r
-<TD>Wrappers for native executables for multiple sequence alignment (msa)&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.engine"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A> in <A HREF="../../../../compbio/engine/package-summary.html">compbio.engine</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/engine/package-summary.html">compbio.engine</A> that return <A HREF="../../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A></CODE></FONT></TD>\r
-<TD><CODE><B>LoadBalancer.</B><B><A HREF="../../../../compbio/engine/LoadBalancer.html#getEngine(compbio.engine.client.Executable)">getEngine</A></B>(<A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;?&gt;&nbsp;executable)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
-<TR ALIGN="right" VALIGN="">\r
-<TD NOWRAP><FONT SIZE="-1">\r
-<CODE>&lt;T,V&gt; <A HREF="../../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A></CODE></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-</CODE></FONT></TD>\r
-<TD><CODE><B>LoadBalancer.</B><B><A HREF="../../../../compbio/engine/LoadBalancer.html#getEngine(compbio.engine.client.Executable, java.util.List)">getEngine</A></B>(<A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;V&gt;&nbsp;executable,\r
-          java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;dataSet)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/engine/package-summary.html">compbio.engine</A> with parameters of type <A HREF="../../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
-<TR ALIGN="right" VALIGN="">\r
-<TD NOWRAP><FONT SIZE="-1">\r
-<CODE>&lt;T&gt; <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;T&gt;</CODE></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-</CODE></FONT></TD>\r
-<TD><CODE><B>Configurator.</B><B><A HREF="../../../../compbio/engine/Configurator.html#configureExecutable(compbio.engine.client.Executable, compbio.engine.client.Executable.ExecProvider)">configureExecutable</A></B>(<A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;T&gt;&nbsp;executable,\r
-                    <A HREF="../../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine">AsyncExecutor</A></CODE></FONT></TD>\r
-<TD><CODE><B>Configurator.</B><B><A HREF="../../../../compbio/engine/Configurator.html#getAsyncEngine(compbio.engine.client.ConfiguredExecutable, compbio.engine.client.Executable.ExecProvider)">getAsyncEngine</A></B>(<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;executable,\r
-               <A HREF="../../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../../compbio/engine/SyncExecutor.html" title="interface in compbio.engine">SyncExecutor</A></CODE></FONT></TD>\r
-<TD><CODE><B>Configurator.</B><B><A HREF="../../../../compbio/engine/Configurator.html#getSyncEngine(compbio.engine.client.ConfiguredExecutable, compbio.engine.client.Executable.ExecProvider)">getSyncEngine</A></B>(<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;executable,\r
-              <A HREF="../../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.engine.client"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A> in <A HREF="../../../../compbio/engine/client/package-summary.html">compbio.engine.client</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/engine/client/package-summary.html">compbio.engine.client</A> that return <A HREF="../../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A></CODE></FONT></TD>\r
-<TD><CODE><B>ConfiguredExecutable.</B><B><A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html#getExecProvider()">getExecProvider</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A></CODE></FONT></TD>\r
-<TD><CODE><B>ConfExecutable.</B><B><A HREF="../../../../compbio/engine/client/ConfExecutable.html#getExecProvider()">getExecProvider</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A></CODE></FONT></TD>\r
-<TD><CODE><B>ConfiguredExecutable.</B><B><A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html#getSupportedRuntimes()">getSupportedRuntimes</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A></CODE></FONT></TD>\r
-<TD><CODE><B>ConfExecutable.</B><B><A HREF="../../../../compbio/engine/client/ConfExecutable.html#getSupportedRuntimes()">getSupportedRuntimes</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A></CODE></FONT></TD>\r
-<TD><CODE><B>Util.</B><B><A HREF="../../../../compbio/engine/client/Util.html#getSupportedRuntimes(java.lang.Class)">getSupportedRuntimes</A></B>(java.lang.Class&lt;?&gt;&nbsp;clazz)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A></CODE></FONT></TD>\r
-<TD><CODE><B>Executable.ExecProvider.</B><B><A HREF="../../../../compbio/engine/client/Executable.ExecProvider.html#valueOf(java.lang.String)">valueOf</A></B>(java.lang.String&nbsp;name)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Returns the enum constant of this type with the specified name.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>[]</CODE></FONT></TD>\r
-<TD><CODE><B>Executable.ExecProvider.</B><B><A HREF="../../../../compbio/engine/client/Executable.ExecProvider.html#values()">values</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Returns an array containing the constants of this enum type, in
-the order they are declared.</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/engine/client/package-summary.html">compbio.engine.client</A> with parameters of type <A HREF="../../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B>ConfiguredExecutable.</B><B><A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html#getCommand(compbio.engine.client.Executable.ExecProvider)">getCommand</A></B>(<A HREF="../../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B>ConfExecutable.</B><B><A HREF="../../../../compbio/engine/client/ConfExecutable.html#getCommand(compbio.engine.client.Executable.ExecProvider)">getCommand</A></B>(<A HREF="../../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B>Util.</B><B><A HREF="../../../../compbio/engine/client/Util.html#getCommand(compbio.engine.client.Executable.ExecProvider, java.lang.Class)">getCommand</A></B>(<A HREF="../../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider,\r
-           java.lang.Class&lt;?&gt;&nbsp;clazz)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>&lt;<A HREF="../../../../compbio/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>SkeletalExecutable.</B><B><A HREF="../../../../compbio/engine/client/SkeletalExecutable.html#getParameters(compbio.engine.client.Executable.ExecProvider)">getParameters</A></B>(<A HREF="../../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>&lt;<A HREF="../../../../compbio/engine/client/Executable.html" title="type parameter in Executable">T</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>Executable.</B><B><A HREF="../../../../compbio/engine/client/Executable.html#getParameters(compbio.engine.client.Executable.ExecProvider)">getParameters</A></B>(<A HREF="../../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>&lt;<A HREF="../../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>ConfExecutable.</B><B><A HREF="../../../../compbio/engine/client/ConfExecutable.html#getParameters(compbio.engine.client.Executable.ExecProvider)">getParameters</A></B>(<A HREF="../../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B>ConfExecutable.</B><B><A HREF="../../../../compbio/engine/client/ConfExecutable.html#setExecProvider(compbio.engine.client.Executable.ExecProvider)">setExecProvider</A></B>(<A HREF="../../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.runner"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A> in <A HREF="../../../../compbio/runner/package-summary.html">compbio.runner</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/runner/package-summary.html">compbio.runner</A> with parameters of type <A HREF="../../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>&lt;<A HREF="../../../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>_SkeletalCommandBuilder.</B><B><A HREF="../../../../compbio/runner/_SkeletalCommandBuilder.html#getParameters(compbio.engine.client.Executable.ExecProvider)">getParameters</A></B>(<A HREF="../../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.runner._impl"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A> in <A HREF="../../../../compbio/runner/_impl/package-summary.html">compbio.runner._impl</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/runner/_impl/package-summary.html">compbio.runner._impl</A> with parameters of type <A HREF="../../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B>Mcl.</B><B><A HREF="../../../../compbio/runner/_impl/Mcl.html#getCommand(compbio.engine.client.Executable.ExecProvider)">getCommand</A></B>(<A HREF="../../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B>BlastAll.</B><B><A HREF="../../../../compbio/runner/_impl/BlastAll.html#getCommand(compbio.engine.client.Executable.ExecProvider)">getCommand</A></B>(<A HREF="../../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B>RPSBlast.</B><B><A HREF="../../../../compbio/runner/_impl/RPSBlast.html#getCommand(compbio.engine.client.Executable.ExecProvider)">getCommand</A></B>(<A HREF="../../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B>Ronn.</B><B><A HREF="../../../../compbio/runner/_impl/Ronn.html#getCommand(compbio.engine.client.Executable.ExecProvider)">getCommand</A></B>(<A HREF="../../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B>PSIBlast.</B><B><A HREF="../../../../compbio/runner/_impl/PSIBlast.html#getCommand(compbio.engine.client.Executable.ExecProvider)">getCommand</A></B>(<A HREF="../../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B>Disembl.</B><B><A HREF="../../../../compbio/runner/_impl/Disembl.html#getCommand(compbio.engine.client.Executable.ExecProvider)">getCommand</A></B>(<A HREF="../../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>&lt;<A HREF="../../../../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>NetNglyc.</B><B><A HREF="../../../../compbio/runner/_impl/NetNglyc.html#getParameters(compbio.engine.client.Executable.ExecProvider)">getParameters</A></B>(<A HREF="../../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.runner.msa"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A> in <A HREF="../../../../compbio/runner/msa/package-summary.html">compbio.runner.msa</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/runner/msa/package-summary.html">compbio.runner.msa</A> with parameters of type <A HREF="../../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>&lt;<A HREF="../../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>Tcoffee.</B><B><A HREF="../../../../compbio/runner/msa/Tcoffee.html#getParameters(compbio.engine.client.Executable.ExecProvider)">getParameters</A></B>(<A HREF="../../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/engine/client/\class-useExecutable.ExecProvider.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="Executable.ExecProvider.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
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diff --git a/website/full_javadoc/compbio/engine/client/class-use/Executable.html b/website/full_javadoc/compbio/engine/client/class-use/Executable.html

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--- a/website/full_javadoc/compbio/engine/client/class-use/Executable.html
+++ /dev/null
@@ -1,892 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Uses of Interface compbio.engine.client.Executable\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Uses of Interface compbio.engine.client.Executable";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/engine/client/\class-useExecutable.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="Executable.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-<B>Uses of Interface<br>compbio.engine.client.Executable</B></H2>\r
-</CENTER>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Packages that use <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.engine"><B>compbio.engine</B></A></TD>\r
-<TD>&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.engine.client"><B>compbio.engine.client</B></A></TD>\r
-<TD>Classes and interfaces representing an input for engines.&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.engine.conf"><B>compbio.engine.conf</B></A></TD>\r
-<TD>Classes commonly used by both engines.&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.runner"><B>compbio.runner</B></A></TD>\r
-<TD>Utilities commonly used by all runners.&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.runner._impl"><B>compbio.runner._impl</B></A></TD>\r
-<TD>&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.runner.msa"><B>compbio.runner.msa</B></A></TD>\r
-<TD>Wrappers for native executables for multiple sequence alignment (msa)&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.runner.psiblast"><B>compbio.runner.psiblast</B></A></TD>\r
-<TD>&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.engine"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A> in <A HREF="../../../../compbio/engine/package-summary.html">compbio.engine</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/engine/package-summary.html">compbio.engine</A> with parameters of type <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
-<TR ALIGN="right" VALIGN="">\r
-<TD NOWRAP><FONT SIZE="-1">\r
-<CODE>&lt;T&gt; <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;T&gt;</CODE></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-</CODE></FONT></TD>\r
-<TD><CODE><B>Configurator.</B><B><A HREF="../../../../compbio/engine/Configurator.html#configureExecutable(compbio.engine.client.Executable)">configureExecutable</A></B>(<A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;T&gt;&nbsp;executable)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
-<TR ALIGN="right" VALIGN="">\r
-<TD NOWRAP><FONT SIZE="-1">\r
-<CODE>&lt;T&gt; <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;T&gt;</CODE></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-</CODE></FONT></TD>\r
-<TD><CODE><B>Configurator.</B><B><A HREF="../../../../compbio/engine/Configurator.html#configureExecutable(compbio.engine.client.Executable, compbio.engine.client.Executable.ExecProvider)">configureExecutable</A></B>(<A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;T&gt;&nbsp;executable,\r
-                    <A HREF="../../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
-<TR ALIGN="right" VALIGN="">\r
-<TD NOWRAP><FONT SIZE="-1">\r
-<CODE>&lt;T&gt; <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;T&gt;</CODE></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-</CODE></FONT></TD>\r
-<TD><CODE><B>Configurator.</B><B><A HREF="../../../../compbio/engine/Configurator.html#configureExecutable(compbio.engine.client.Executable, java.util.List)">configureExecutable</A></B>(<A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;T&gt;&nbsp;executable,\r
-                    java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;dataSet)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A></CODE></FONT></TD>\r
-<TD><CODE><B>LoadBalancer.</B><B><A HREF="../../../../compbio/engine/LoadBalancer.html#getEngine(compbio.engine.client.Executable)">getEngine</A></B>(<A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;?&gt;&nbsp;executable)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
-<TR ALIGN="right" VALIGN="">\r
-<TD NOWRAP><FONT SIZE="-1">\r
-<CODE>&lt;T,V&gt; <A HREF="../../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A></CODE></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-</CODE></FONT></TD>\r
-<TD><CODE><B>LoadBalancer.</B><B><A HREF="../../../../compbio/engine/LoadBalancer.html#getEngine(compbio.engine.client.Executable, java.util.List)">getEngine</A></B>(<A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;V&gt;&nbsp;executable,\r
-          java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;dataSet)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.engine.client"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A> in <A HREF="../../../../compbio/engine/client/package-summary.html">compbio.engine.client</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Subinterfaces of <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A> in <A HREF="../../../../compbio/engine/client/package-summary.html">compbio.engine.client</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;interface</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/engine/client/ClusterNativeSpecExecutable.html" title="interface in compbio.engine.client">ClusterNativeSpecExecutable&lt;T&gt;</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;interface</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable&lt;T&gt;</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;interface</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/engine/client/PipedExecutable.html" title="interface in compbio.engine.client">PipedExecutable&lt;T&gt;</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;This is a marker interface to indicate that the output of the process must be
- captured.</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Classes in <A HREF="../../../../compbio/engine/client/package-summary.html">compbio.engine.client</A> that implement <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;class</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable&lt;T&gt;</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;class</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable&lt;T&gt;</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/engine/client/package-summary.html">compbio.engine.client</A> that return <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../../compbio/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>SkeletalExecutable.</B><B><A HREF="../../../../compbio/engine/client/SkeletalExecutable.html#addParameters(java.util.List)">addParameters</A></B>(java.util.List&lt;java.lang.String&gt;&nbsp;parameters)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../../compbio/engine/client/Executable.html" title="type parameter in Executable">T</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>Executable.</B><B><A HREF="../../../../compbio/engine/client/Executable.html#addParameters(java.util.List)">addParameters</A></B>(java.util.List&lt;java.lang.String&gt;&nbsp;parameters)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Adds parameter to the list of parameters for a native executable</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>ConfExecutable.</B><B><A HREF="../../../../compbio/engine/client/ConfExecutable.html#addParameters(java.util.List)">addParameters</A></B>(java.util.List&lt;java.lang.String&gt;&nbsp;parameters)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="type parameter in ConfiguredExecutable">T</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>ConfiguredExecutable.</B><B><A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html#getExecutable()">getExecutable</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>ConfExecutable.</B><B><A HREF="../../../../compbio/engine/client/ConfExecutable.html#getExecutable()">getExecutable</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;?&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>SkeletalExecutable.</B><B><A HREF="../../../../compbio/engine/client/SkeletalExecutable.html#loadRunConfiguration(compbio.engine.client.RunConfiguration)">loadRunConfiguration</A></B>(<A HREF="../../../../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>&nbsp;rconfig)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;?&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>Executable.</B><B><A HREF="../../../../compbio/engine/client/Executable.html#loadRunConfiguration(compbio.engine.client.RunConfiguration)">loadRunConfiguration</A></B>(<A HREF="../../../../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>&nbsp;rconfig)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../../compbio/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>SkeletalExecutable.</B><B><A HREF="../../../../compbio/engine/client/SkeletalExecutable.html#setParameter(java.lang.String)">setParameter</A></B>(java.lang.String&nbsp;parameter)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/engine/client/package-summary.html">compbio.engine.client</A> that return types with arguments of type <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>abstract &nbsp;java.lang.Class&lt;? extends <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;?&gt;&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>SkeletalExecutable.</B><B><A HREF="../../../../compbio/engine/client/SkeletalExecutable.html#getType()">getType</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/engine/client/package-summary.html">compbio.engine.client</A> with parameters of type <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B>Util.</B><B><A HREF="../../../../compbio/engine/client/Util.html#getExecProperty(java.lang.String, compbio.engine.client.Executable)">getExecProperty</A></B>(java.lang.String&nbsp;propertySpec,\r
-                <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;?&gt;&nbsp;exec)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Method parameters in <A HREF="../../../../compbio/engine/client/package-summary.html">compbio.engine.client</A> with type arguments of type <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
-<TR ALIGN="right" VALIGN="">\r
-<TD NOWRAP><FONT SIZE="-1">\r
-<CODE>&lt;V&gt; <A HREF="../../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;V&gt;</CODE></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-</CODE></FONT></TD>\r
-<TD><CODE><B>ConfExecutable.</B><B><A HREF="../../../../compbio/engine/client/ConfExecutable.html#getRunnerLimits(java.lang.Class)">getRunnerLimits</A></B>(java.lang.Class&lt;? extends <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;V&gt;&gt;&nbsp;clazz)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;This method should be executed once and result of its execution reused.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
-<TR ALIGN="right" VALIGN="">\r
-<TD NOWRAP><FONT SIZE="-1">\r
-<CODE>&lt;V&gt; <A HREF="../../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&lt;V&gt;</CODE></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-</CODE></FONT></TD>\r
-<TD><CODE><B>ConfExecutable.</B><B><A HREF="../../../../compbio/engine/client/ConfExecutable.html#getRunnerOptions(java.lang.Class)">getRunnerOptions</A></B>(java.lang.Class&lt;? extends <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;V&gt;&gt;&nbsp;clazz)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
-<TR ALIGN="right" VALIGN="">\r
-<TD NOWRAP><FONT SIZE="-1">\r
-<CODE>&lt;V&gt; <A HREF="../../../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>&lt;V&gt;</CODE></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-</CODE></FONT></TD>\r
-<TD><CODE><B>ConfExecutable.</B><B><A HREF="../../../../compbio/engine/client/ConfExecutable.html#getRunnerPresets(java.lang.Class)">getRunnerPresets</A></B>(java.lang.Class&lt;? extends <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;V&gt;&gt;&nbsp;clazz)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Constructors in <A HREF="../../../../compbio/engine/client/package-summary.html">compbio.engine.client</A> with parameters of type <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../../compbio/engine/client/ConfExecutable.html#ConfExecutable(compbio.engine.client.Executable, java.lang.String)">ConfExecutable</A></B>(<A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt;&nbsp;executable,\r
-               java.lang.String&nbsp;taskDirectory)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.engine.conf"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A> in <A HREF="../../../../compbio/engine/conf/package-summary.html">compbio.engine.conf</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/engine/conf/package-summary.html">compbio.engine.conf</A> that return types with arguments of type <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;java.lang.Class&lt;<A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;?&gt;&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>DirectoryManager.</B><B><A HREF="../../../../compbio/engine/conf/DirectoryManager.html#getClass(java.lang.String)">getClass</A></B>(java.lang.String&nbsp;taskId)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.runner"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A> in <A HREF="../../../../compbio/runner/package-summary.html">compbio.runner</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Classes in <A HREF="../../../../compbio/runner/package-summary.html">compbio.runner</A> that implement <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;class</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/runner/package-summary.html">compbio.runner</A> that return <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;?&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>_SkeletalCommandBuilder.</B><B><A HREF="../../../../compbio/runner/_SkeletalCommandBuilder.html#loadRunConfiguration(compbio.engine.client.RunConfiguration)">loadRunConfiguration</A></B>(<A HREF="../../../../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>&nbsp;rconfig)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Method parameters in <A HREF="../../../../compbio/runner/package-summary.html">compbio.runner</A> with type arguments of type <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;java.util.List&lt;java.lang.String&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>OptionCombinator.</B><B><A HREF="../../../../compbio/runner/OptionCombinator.html#argumentsToCommandString(java.util.List, compbio.metadata.RunnerConfig)">argumentsToCommandString</A></B>(java.util.List&lt;? extends <A HREF="../../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;?&gt;&gt;&nbsp;arguments,\r
-                         <A HREF="../../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&lt;? extends <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;?&gt;&gt;&nbsp;rconfig)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
-<TR ALIGN="right" VALIGN="">\r
-<TD NOWRAP><FONT SIZE="-1">\r
-<CODE>&lt;T&gt; <A HREF="../../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;T&gt;</CODE></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-</CODE></FONT></TD>\r
-<TD><CODE><B>Util.</B><B><A HREF="../../../../compbio/runner/Util.html#getLimits(java.lang.Class)">getLimits</A></B>(java.lang.Class&lt;? extends <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;T&gt;&gt;&nbsp;clazz)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;For now just assume that all parameters which came in needs setting it
- will be a client responsibility to prepare RunnerConfig object then</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
-<TR ALIGN="right" VALIGN="">\r
-<TD NOWRAP><FONT SIZE="-1">\r
-<CODE>&lt;T&gt; <A HREF="../../../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>&lt;T&gt;</CODE></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-</CODE></FONT></TD>\r
-<TD><CODE><B>Util.</B><B><A HREF="../../../../compbio/runner/Util.html#getPresets(java.lang.Class)">getPresets</A></B>(java.lang.Class&lt;? extends <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;T&gt;&gt;&nbsp;clazz)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
-<TR ALIGN="right" VALIGN="">\r
-<TD NOWRAP><FONT SIZE="-1">\r
-<CODE>&lt;T&gt; <A HREF="../../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&lt;T&gt;</CODE></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-</CODE></FONT></TD>\r
-<TD><CODE><B>Util.</B><B><A HREF="../../../../compbio/runner/Util.html#getSupportedOptions(java.lang.Class)">getSupportedOptions</A></B>(java.lang.Class&lt;? extends <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;T&gt;&gt;&nbsp;clazz)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Constructor parameters in <A HREF="../../../../compbio/runner/package-summary.html">compbio.runner</A> with type arguments of type <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../../compbio/runner/OptionCombinator.html#OptionCombinator(compbio.metadata.RunnerConfig)">OptionCombinator</A></B>(<A HREF="../../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&lt;? extends <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;?&gt;&gt;&nbsp;rconfig)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.runner._impl"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A> in <A HREF="../../../../compbio/runner/_impl/package-summary.html">compbio.runner._impl</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Classes in <A HREF="../../../../compbio/runner/_impl/package-summary.html">compbio.runner._impl</A> that implement <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;class</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/runner/_impl/BlastAll.html" title="class in compbio.runner._impl">BlastAll</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;class</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/runner/_impl/Disembl.html" title="class in compbio.runner._impl">Disembl</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;class</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/runner/_impl/Mcl.html" title="class in compbio.runner._impl">Mcl</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;class</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;class</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/runner/_impl/OB.html" title="class in compbio.runner._impl">OB</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;TODO this needs fixing! Executable does not work</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;class</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/runner/_impl/PSIBlast.html" title="class in compbio.runner._impl">PSIBlast</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;class</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/runner/_impl/Ronn.html" title="class in compbio.runner._impl">Ronn</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;class</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/runner/_impl/RPSBlast.html" title="class in compbio.runner._impl">RPSBlast</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/runner/_impl/package-summary.html">compbio.runner._impl</A> that return <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;?&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>NetNglyc.</B><B><A HREF="../../../../compbio/runner/_impl/NetNglyc.html#loadRunConfiguration(compbio.engine.client.RunConfiguration)">loadRunConfiguration</A></B>(<A HREF="../../../../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>&nbsp;rconfig)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.runner.msa"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A> in <A HREF="../../../../compbio/runner/msa/package-summary.html">compbio.runner.msa</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Classes in <A HREF="../../../../compbio/runner/msa/package-summary.html">compbio.runner.msa</A> that implement <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;class</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;class</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;class</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;class</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;class</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/runner/msa/package-summary.html">compbio.runner.msa</A> that return types with arguments of type <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.Class&lt;? extends <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;?&gt;&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>Tcoffee.</B><B><A HREF="../../../../compbio/runner/msa/Tcoffee.html#getType()">getType</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.Class&lt;? extends <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;?&gt;&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>ClustalW.</B><B><A HREF="../../../../compbio/runner/msa/ClustalW.html#getType()">getType</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.Class&lt;? extends <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;?&gt;&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>Probcons.</B><B><A HREF="../../../../compbio/runner/msa/Probcons.html#getType()">getType</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.Class&lt;? extends <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;?&gt;&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>Muscle.</B><B><A HREF="../../../../compbio/runner/msa/Muscle.html#getType()">getType</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.Class&lt;? extends <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;?&gt;&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>Mafft.</B><B><A HREF="../../../../compbio/runner/msa/Mafft.html#getType()">getType</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.runner.psiblast"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A> in <A HREF="../../../../compbio/runner/psiblast/package-summary.html">compbio.runner.psiblast</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Classes in <A HREF="../../../../compbio/runner/psiblast/package-summary.html">compbio.runner.psiblast</A> that implement <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;class</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/runner/psiblast/PsiBlast.html" title="class in compbio.runner.psiblast">PsiBlast</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/runner/psiblast/package-summary.html">compbio.runner.psiblast</A> that return types with arguments of type <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.Class&lt;? extends <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;?&gt;&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>PsiBlast.</B><B><A HREF="../../../../compbio/runner/psiblast/PsiBlast.html#getType()">getType</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/engine/client/\class-useExecutable.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="Executable.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/engine/client/class-use/PathValidator.html b/website/full_javadoc/compbio/engine/client/class-use/PathValidator.html

deleted file mode 100644 (file)

index 9d4b585..0000000
--- a/website/full_javadoc/compbio/engine/client/class-use/PathValidator.html
+++ /dev/null
@@ -1,144 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Uses of Class compbio.engine.client.PathValidator\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Uses of Class compbio.engine.client.PathValidator";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../compbio/engine/client/PathValidator.html" title="class in compbio.engine.client"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/engine/client/\class-usePathValidator.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="PathValidator.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-<B>Uses of Class<br>compbio.engine.client.PathValidator</B></H2>\r
-</CENTER>\r
-No usage of compbio.engine.client.PathValidator\r
-<P>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../compbio/engine/client/PathValidator.html" title="class in compbio.engine.client"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
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-&nbsp;NEXT</FONT></TD>\r
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-  <A HREF="../../../../index.html?compbio/engine/client/\class-usePathValidator.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="PathValidator.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/engine/client/class-use/PipedExecutable.html b/website/full_javadoc/compbio/engine/client/class-use/PipedExecutable.html

deleted file mode 100644 (file)

index 2cb2e67..0000000
--- a/website/full_javadoc/compbio/engine/client/class-use/PipedExecutable.html
+++ /dev/null
@@ -1,241 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Uses of Interface compbio.engine.client.PipedExecutable\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Uses of Interface compbio.engine.client.PipedExecutable";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
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-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
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-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../compbio/engine/client/PipedExecutable.html" title="interface in compbio.engine.client"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/engine/client/\class-usePipedExecutable.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="PipedExecutable.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-<B>Uses of Interface<br>compbio.engine.client.PipedExecutable</B></H2>\r
-</CENTER>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Packages that use <A HREF="../../../../compbio/engine/client/PipedExecutable.html" title="interface in compbio.engine.client">PipedExecutable</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.engine.client"><B>compbio.engine.client</B></A></TD>\r
-<TD>Classes and interfaces representing an input for engines.&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.runner.msa"><B>compbio.runner.msa</B></A></TD>\r
-<TD>Wrappers for native executables for multiple sequence alignment (msa)&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.engine.client"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../../compbio/engine/client/PipedExecutable.html" title="interface in compbio.engine.client">PipedExecutable</A> in <A HREF="../../../../compbio/engine/client/package-summary.html">compbio.engine.client</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Subinterfaces of <A HREF="../../../../compbio/engine/client/PipedExecutable.html" title="interface in compbio.engine.client">PipedExecutable</A> in <A HREF="../../../../compbio/engine/client/package-summary.html">compbio.engine.client</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;interface</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable&lt;T&gt;</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Classes in <A HREF="../../../../compbio/engine/client/package-summary.html">compbio.engine.client</A> that implement <A HREF="../../../../compbio/engine/client/PipedExecutable.html" title="interface in compbio.engine.client">PipedExecutable</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;class</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable&lt;T&gt;</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.runner.msa"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../../compbio/engine/client/PipedExecutable.html" title="interface in compbio.engine.client">PipedExecutable</A> in <A HREF="../../../../compbio/runner/msa/package-summary.html">compbio.runner.msa</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Classes in <A HREF="../../../../compbio/runner/msa/package-summary.html">compbio.runner.msa</A> that implement <A HREF="../../../../compbio/engine/client/PipedExecutable.html" title="interface in compbio.engine.client">PipedExecutable</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;class</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;class</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;class</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
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-&nbsp;\r
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-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
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-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../compbio/engine/client/PipedExecutable.html" title="interface in compbio.engine.client"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/engine/client/\class-usePipedExecutable.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="PipedExecutable.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/engine/client/class-use/RunConfiguration.html b/website/full_javadoc/compbio/engine/client/class-use/RunConfiguration.html

deleted file mode 100644 (file)

index 656c2a0..0000000
--- a/website/full_javadoc/compbio/engine/client/class-use/RunConfiguration.html
+++ /dev/null
@@ -1,294 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Uses of Class compbio.engine.client.RunConfiguration\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Uses of Class compbio.engine.client.RunConfiguration";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/engine/client/\class-useRunConfiguration.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="RunConfiguration.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-<B>Uses of Class<br>compbio.engine.client.RunConfiguration</B></H2>\r
-</CENTER>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Packages that use <A HREF="../../../../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.engine.client"><B>compbio.engine.client</B></A></TD>\r
-<TD>Classes and interfaces representing an input for engines.&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.runner"><B>compbio.runner</B></A></TD>\r
-<TD>Utilities commonly used by all runners.&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.runner._impl"><B>compbio.runner._impl</B></A></TD>\r
-<TD>&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.engine.client"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A> in <A HREF="../../../../compbio/engine/client/package-summary.html">compbio.engine.client</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/engine/client/package-summary.html">compbio.engine.client</A> that return <A HREF="../../../../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A></CODE></FONT></TD>\r
-<TD><CODE><B>ConfExecutable.</B><B><A HREF="../../../../compbio/engine/client/ConfExecutable.html#getRunConfiguration()">getRunConfiguration</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A></CODE></FONT></TD>\r
-<TD><CODE><B>RunConfiguration.</B><B><A HREF="../../../../compbio/engine/client/RunConfiguration.html#load(java.io.InputStream)">load</A></B>(java.io.InputStream&nbsp;input)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/engine/client/package-summary.html">compbio.engine.client</A> with parameters of type <A HREF="../../../../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;?&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>SkeletalExecutable.</B><B><A HREF="../../../../compbio/engine/client/SkeletalExecutable.html#loadRunConfiguration(compbio.engine.client.RunConfiguration)">loadRunConfiguration</A></B>(<A HREF="../../../../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>&nbsp;rconfig)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;?&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>Executable.</B><B><A HREF="../../../../compbio/engine/client/Executable.html#loadRunConfiguration(compbio.engine.client.RunConfiguration)">loadRunConfiguration</A></B>(<A HREF="../../../../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>&nbsp;rconfig)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>ConfExecutable.</B><B><A HREF="../../../../compbio/engine/client/ConfExecutable.html#loadRunConfiguration(compbio.engine.client.RunConfiguration)">loadRunConfiguration</A></B>(<A HREF="../../../../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>&nbsp;rconf)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>ConfExecutable.</B><B><A HREF="../../../../compbio/engine/client/ConfExecutable.html#newConfExecutable(compbio.engine.client.RunConfiguration)">newConfExecutable</A></B>(<A HREF="../../../../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>&nbsp;rconf)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;boolean</CODE></FONT></TD>\r
-<TD><CODE><B>RunConfiguration.</B><B><A HREF="../../../../compbio/engine/client/RunConfiguration.html#write(compbio.engine.client.RunConfiguration)">write</A></B>(<A HREF="../../../../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>&nbsp;rconf)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.runner"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A> in <A HREF="../../../../compbio/runner/package-summary.html">compbio.runner</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/runner/package-summary.html">compbio.runner</A> with parameters of type <A HREF="../../../../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;?&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>_SkeletalCommandBuilder.</B><B><A HREF="../../../../compbio/runner/_SkeletalCommandBuilder.html#loadRunConfiguration(compbio.engine.client.RunConfiguration)">loadRunConfiguration</A></B>(<A HREF="../../../../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>&nbsp;rconfig)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.runner._impl"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A> in <A HREF="../../../../compbio/runner/_impl/package-summary.html">compbio.runner._impl</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/runner/_impl/package-summary.html">compbio.runner._impl</A> with parameters of type <A HREF="../../../../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;?&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>NetNglyc.</B><B><A HREF="../../../../compbio/runner/_impl/NetNglyc.html#loadRunConfiguration(compbio.engine.client.RunConfiguration)">loadRunConfiguration</A></B>(<A HREF="../../../../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>&nbsp;rconfig)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/engine/client/\class-useRunConfiguration.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="RunConfiguration.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/engine/client/class-use/SkeletalExecutable.html b/website/full_javadoc/compbio/engine/client/class-use/SkeletalExecutable.html

deleted file mode 100644 (file)

index 30e7933..0000000
--- a/website/full_javadoc/compbio/engine/client/class-use/SkeletalExecutable.html
+++ /dev/null
@@ -1,286 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Uses of Class compbio.engine.client.SkeletalExecutable\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Uses of Class compbio.engine.client.SkeletalExecutable";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/engine/client/\class-useSkeletalExecutable.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="SkeletalExecutable.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-<B>Uses of Class<br>compbio.engine.client.SkeletalExecutable</B></H2>\r
-</CENTER>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Packages that use <A HREF="../../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.engine.client"><B>compbio.engine.client</B></A></TD>\r
-<TD>Classes and interfaces representing an input for engines.&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.runner.msa"><B>compbio.runner.msa</B></A></TD>\r
-<TD>Wrappers for native executables for multiple sequence alignment (msa)&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.runner.psiblast"><B>compbio.runner.psiblast</B></A></TD>\r
-<TD>&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.engine.client"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A> in <A HREF="../../../../compbio/engine/client/package-summary.html">compbio.engine.client</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/engine/client/package-summary.html">compbio.engine.client</A> that return <A HREF="../../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>&lt;<A HREF="../../../../compbio/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>SkeletalExecutable.</B><B><A HREF="../../../../compbio/engine/client/SkeletalExecutable.html#setError(java.lang.String)">setError</A></B>(java.lang.String&nbsp;errFile)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
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index 32306b8..0000000
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-\r
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-Package compbio.engine.client\r
-</H2>\r
-Classes and interfaces representing an input for engines.\r
-<P>\r
-<B>See:</B>\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<A HREF="#package_description"><B>Description</B></A>\r
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-\r
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-<B>Interface Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../../compbio/engine/client/ClusterNativeSpecExecutable.html" title="interface in compbio.engine.client">ClusterNativeSpecExecutable&lt;T&gt;</A></B></TD>\r
-<TD>&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable&lt;T&gt;</A></B></TD>\r
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-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable&lt;T&gt;</A></B></TD>\r
-<TD>Interface to a native executable.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../../compbio/engine/client/PipedExecutable.html" title="interface in compbio.engine.client">PipedExecutable&lt;T&gt;</A></B></TD>\r
-<TD>This is a marker interface to indicate that the output of the process must be\r
- captured.</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-\r
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-\r
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-<B>Class Summary</B></FONT></TH>\r
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-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder&lt;T&gt;</A></B></TD>\r
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-<TD WIDTH="15%"><B><A HREF="../../../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable&lt;T&gt;</A></B></TD>\r
-<TD>&nbsp;</TD>\r
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-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../../compbio/engine/client/EnvVariableProcessor.html" title="class in compbio.engine.client">EnvVariableProcessor</A></B></TD>\r
-<TD>&nbsp;</TD>\r
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-<B>Enum Summary</B></FONT></TH>\r
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-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A></B></TD>\r
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-&nbsp;\r
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-<P>\r
-<A NAME="package_description"><!-- --></A><H2>\r
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-\r
-<P>\r
-Classes and interfaces representing an input for engines. These classes are known to runners, \r
- which form the next layer of the JABAWS hierarchy.\r
-<P>\r
-\r
-<P>\r
-<DL>\r
-<DT><B>Author:</B></DT>\r
-  <DD>Petr Troshin \r
- \r
-        Date January 2010</DD>\r
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-\r
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diff --git a/website/full_javadoc/compbio/engine/client/package-tree.html b/website/full_javadoc/compbio/engine/client/package-tree.html

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--- a/website/full_javadoc/compbio/engine/client/package-tree.html
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-<!-- ========= END OF TOP NAVBAR ========= -->\r
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-<HR>\r
-<CENTER>\r
-<H2>\r
-Hierarchy For Package compbio.engine.client\r
-</H2>\r
-</CENTER>\r
-<DL>\r
-<DT><B>Package Hierarchies:</B><DD><A HREF="../../../overview-tree.html">All Packages</A></DL>\r
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-<UL>\r
-<LI TYPE="circle">java.lang.Object<UL>\r
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-Interface Hierarchy\r
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-<UL>\r
-<LI TYPE="circle">compbio.engine.client.<A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client"><B>Executable</B></A>&lt;T&gt;<UL>\r
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diff --git a/website/full_javadoc/compbio/engine/client/package-use.html b/website/full_javadoc/compbio/engine/client/package-use.html

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--- a/website/full_javadoc/compbio/engine/client/package-use.html
+++ /dev/null
@@ -1,470 +0,0 @@
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-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
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-</TABLE>\r
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-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
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-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
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-  <A HREF="../../../index.html?compbio/engine/client/package-use.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
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-  <!--\r
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-\r
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-\r
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-<H2>\r
-<B>Uses of Package<br>compbio.engine.client</B></H2>\r
-</CENTER>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Packages that use <A HREF="../../../compbio/engine/client/package-summary.html">compbio.engine.client</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.engine"><B>compbio.engine</B></A></TD>\r
-<TD>&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.engine.client"><B>compbio.engine.client</B></A></TD>\r
-<TD>Classes and interfaces representing an input for engines.&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.engine.cluster.drmaa"><B>compbio.engine.cluster.drmaa</B></A></TD>\r
-<TD>An cluster engine classes responsible for execution of Executables on the clusters.&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.engine.conf"><B>compbio.engine.conf</B></A></TD>\r
-<TD>Classes commonly used by both engines.&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.engine.local"><B>compbio.engine.local</B></A></TD>\r
-<TD>An local engine classes responsible for execution of Executables on the local computer 
- (the same machine as JVM running these classes).&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.runner"><B>compbio.runner</B></A></TD>\r
-<TD>Utilities commonly used by all runners.&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.runner._impl"><B>compbio.runner._impl</B></A></TD>\r
-<TD>&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.runner.msa"><B>compbio.runner.msa</B></A></TD>\r
-<TD>Wrappers for native executables for multiple sequence alignment (msa)&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.runner.psiblast"><B>compbio.runner.psiblast</B></A></TD>\r
-<TD>&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.ws.server"><B>compbio.ws.server</B></A></TD>\r
-<TD>&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.engine"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Classes in <A HREF="../../../compbio/engine/client/package-summary.html">compbio.engine.client</A> used by <A HREF="../../../compbio/engine/package-summary.html">compbio.engine</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../../compbio/engine/client/class-use/ConfiguredExecutable.html#compbio.engine"><B>ConfiguredExecutable</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../../compbio/engine/client/class-use/Executable.html#compbio.engine"><B>Executable</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Interface to a native executable.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../../compbio/engine/client/class-use/Executable.ExecProvider.html#compbio.engine"><B>Executable.ExecProvider</B></A></B>\r
-\r
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-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../../compbio/engine/client/class-use/CommandBuilder.html#compbio.engine.client"><B>CommandBuilder</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../../compbio/engine/client/class-use/ConfExecutable.html#compbio.engine.client"><B>ConfExecutable</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
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-\r
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-<TR BGCOLOR="white" CLASS="TableRowColor">\r
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-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Interface to a native executable.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../../compbio/engine/client/class-use/Executable.ExecProvider.html#compbio.engine.client"><B>Executable.ExecProvider</B></A></B>\r
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-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
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-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../../compbio/engine/client/class-use/PipedExecutable.html#compbio.engine.client"><B>PipedExecutable</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;This is a marker interface to indicate that the output of the process must be
- captured.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../../compbio/engine/client/class-use/RunConfiguration.html#compbio.engine.client"><B>RunConfiguration</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Value class for persisting ConfExecutable instances</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../../compbio/engine/client/class-use/SkeletalExecutable.html#compbio.engine.client"><B>SkeletalExecutable</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.engine.cluster.drmaa"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Classes in <A HREF="../../../compbio/engine/client/package-summary.html">compbio.engine.client</A> used by <A HREF="../../../compbio/engine/cluster/drmaa/package-summary.html">compbio.engine.cluster.drmaa</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../../compbio/engine/client/class-use/ConfiguredExecutable.html#compbio.engine.cluster.drmaa"><B>ConfiguredExecutable</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.engine.conf"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Classes in <A HREF="../../../compbio/engine/client/package-summary.html">compbio.engine.client</A> used by <A HREF="../../../compbio/engine/conf/package-summary.html">compbio.engine.conf</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../../compbio/engine/client/class-use/Executable.html#compbio.engine.conf"><B>Executable</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Interface to a native executable.</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.engine.local"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Classes in <A HREF="../../../compbio/engine/client/package-summary.html">compbio.engine.client</A> used by <A HREF="../../../compbio/engine/local/package-summary.html">compbio.engine.local</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../../compbio/engine/client/class-use/ConfiguredExecutable.html#compbio.engine.local"><B>ConfiguredExecutable</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.runner"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
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-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../../compbio/engine/client/class-use/CommandBuilder.html#compbio.runner"><B>CommandBuilder</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../../compbio/engine/client/class-use/Executable.html#compbio.runner"><B>Executable</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Interface to a native executable.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../../compbio/engine/client/class-use/Executable.ExecProvider.html#compbio.runner"><B>Executable.ExecProvider</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../../compbio/engine/client/class-use/RunConfiguration.html#compbio.runner"><B>RunConfiguration</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Value class for persisting ConfExecutable instances</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.runner._impl"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Classes in <A HREF="../../../compbio/engine/client/package-summary.html">compbio.engine.client</A> used by <A HREF="../../../compbio/runner/_impl/package-summary.html">compbio.runner._impl</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../../compbio/engine/client/class-use/CommandBuilder.html#compbio.runner._impl"><B>CommandBuilder</B></A></B>\r
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-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../../compbio/engine/client/class-use/Executable.html#compbio.runner._impl"><B>Executable</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Interface to a native executable.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../../compbio/engine/client/class-use/Executable.ExecProvider.html#compbio.runner._impl"><B>Executable.ExecProvider</B></A></B>\r
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-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../../compbio/engine/client/class-use/RunConfiguration.html#compbio.runner._impl"><B>RunConfiguration</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Value class for persisting ConfExecutable instances</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.runner.msa"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Classes in <A HREF="../../../compbio/engine/client/package-summary.html">compbio.engine.client</A> used by <A HREF="../../../compbio/runner/msa/package-summary.html">compbio.runner.msa</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
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-\r
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-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
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-<TR BGCOLOR="white" CLASS="TableRowColor">\r
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-\r
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-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
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-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
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-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;This is a marker interface to indicate that the output of the process must be
- captured.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../../compbio/engine/client/class-use/SkeletalExecutable.html#compbio.runner.msa"><B>SkeletalExecutable</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.runner.psiblast"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Classes in <A HREF="../../../compbio/engine/client/package-summary.html">compbio.engine.client</A> used by <A HREF="../../../compbio/runner/psiblast/package-summary.html">compbio.runner.psiblast</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../../compbio/engine/client/class-use/Executable.html#compbio.runner.psiblast"><B>Executable</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Interface to a native executable.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../../compbio/engine/client/class-use/SkeletalExecutable.html#compbio.runner.psiblast"><B>SkeletalExecutable</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.ws.server"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Classes in <A HREF="../../../compbio/engine/client/package-summary.html">compbio.engine.client</A> used by <A HREF="../../../compbio/ws/server/package-summary.html">compbio.ws.server</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../../compbio/engine/client/class-use/ConfiguredExecutable.html#compbio.ws.server"><B>ConfiguredExecutable</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
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-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
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-<TR>\r
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-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Class</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
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-  </TR>\r
-</TABLE>\r
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-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
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-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/engine/client/package-use.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="package-use.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
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-<A NAME="skip-navbar_bottom"></A>\r
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diff --git a/website/full_javadoc/compbio/engine/cluster/drmaa/AsyncJobRunner.html b/website/full_javadoc/compbio/engine/cluster/drmaa/AsyncJobRunner.html

deleted file mode 100644 (file)

index 779a787..0000000
--- a/website/full_javadoc/compbio/engine/cluster/drmaa/AsyncJobRunner.html
+++ /dev/null
@@ -1,412 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:49 GMT 2010 -->\r
-<TITLE>\r
-AsyncJobRunner\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="AsyncJobRunner";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/AsyncJobRunner.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../../compbio/engine/cluster/drmaa/_JobStatus.html" title="class in compbio.engine.cluster.drmaa"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../../compbio/engine/cluster/drmaa/ClusterSession.html" title="class in compbio.engine.cluster.drmaa"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/engine/cluster/drmaa/AsyncJobRunner.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="AsyncJobRunner.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
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-\r
-\r
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-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
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-\r
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-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.engine.cluster.drmaa</FONT>\r
-<BR>\r
-Class AsyncJobRunner</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../../../resources/inherit.gif" ALT="extended by "><B>compbio.engine.cluster.drmaa.AsyncJobRunner</B>\r
-</PRE>\r
-<DL>\r
-<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine">AsyncExecutor</A></DD>\r
-</DL>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public class <B>AsyncJobRunner</B><DT>extends java.lang.Object<DT>implements <A HREF="../../../../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine">AsyncExecutor</A></DL>\r
-</PRE>\r
-\r
-<P>\r
-Single cluster job runner class\r
-<P>\r
-\r
-<P>\r
-<DL>\r
-<DT><B>Author:</B></DT>\r
-  <DD>pvtroshin</DD>\r
-</DL>\r
-<HR>\r
-\r
-<P>\r
-\r
-<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
-\r
-<A NAME="constructor_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Constructor Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/AsyncJobRunner.html#AsyncJobRunner()">AsyncJobRunner</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/AsyncJobRunner.html#cancelJob(java.lang.String)">cancelJob</A></B>(java.lang.String&nbsp;jobId)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Stop running job.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/AsyncJobRunner.html#cleanup(java.lang.String)">cleanup</A></B>(java.lang.String&nbsp;jobId)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Remove all files and a job directory for a jobid.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/AsyncJobRunner.html#getJobStatus(java.lang.String)">getJobStatus</A></B>(java.lang.String&nbsp;jobId)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;This will never return clust.engine.JobStatus.CANCELLED as for sun grid
- engine cancelled job is the same as failed.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/AsyncJobRunner.html#getResults(java.lang.String)">getResults</A></B>(java.lang.String&nbsp;jobId)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Retrieve the results of the job.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/AsyncJobRunner.html#getWorkDirectory(java.lang.String)">getWorkDirectory</A></B>(java.lang.String&nbsp;jobId)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/AsyncJobRunner.html#submitJob(compbio.engine.client.ConfiguredExecutable)">submitJob</A></B>(<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;executable)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Submits job for the execution
- Immediate execution is not guaranteed, this method puts the job in the queue.</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
-\r
-<A NAME="constructor_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Constructor Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="AsyncJobRunner()"><!-- --></A><H3>\r
-AsyncJobRunner</H3>\r
-<PRE>\r
-public <B>AsyncJobRunner</B>()</PRE>\r
-<DL>\r
-</DL>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
-<A NAME="method_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="submitJob(compbio.engine.client.ConfiguredExecutable)"><!-- --></A><H3>\r
-submitJob</H3>\r
-<PRE>\r
-public java.lang.String <B>submitJob</B>(<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;executable)\r
-                           throws <A HREF="../../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></PRE>\r
-<DL>\r
-<DD><B>Description copied from interface: <CODE><A HREF="../../../../compbio/engine/AsyncExecutor.html#submitJob(compbio.engine.client.ConfiguredExecutable)">AsyncExecutor</A></CODE></B></DD>\r
-<DD>Submits job for the execution
- Immediate execution is not guaranteed, this method puts the job in the queue. 
- All it guarantees that the job will be eventually executed. 
- The start of execution will depend on the number of jobs in the queue.\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../compbio/engine/AsyncExecutor.html#submitJob(compbio.engine.client.ConfiguredExecutable)">submitJob</A></CODE> in interface <CODE><A HREF="../../../../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine">AsyncExecutor</A></CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>unique job identifier\r
-<DT><B>Throws:</B>\r
-<DD><CODE><A HREF="../../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></CODE> - if submission fails. This usually happens due to the problem on a server side.</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="cancelJob(java.lang.String)"><!-- --></A><H3>\r
-cancelJob</H3>\r
-<PRE>\r
-public boolean <B>cancelJob</B>(java.lang.String&nbsp;jobId)</PRE>\r
-<DL>\r
-<DD><B>Description copied from interface: <CODE><A HREF="../../../../compbio/engine/AsyncExecutor.html#cancelJob(java.lang.String)">AsyncExecutor</A></CODE></B></DD>\r
-<DD>Stop running job. Please not that this method does not guarantee to remove the job directory and files in it.\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../compbio/engine/AsyncExecutor.html#cancelJob(java.lang.String)">cancelJob</A></CODE> in interface <CODE><A HREF="../../../../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine">AsyncExecutor</A></CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>true if job was cancelled successfully, false otherwise</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getJobStatus(java.lang.String)"><!-- --></A><H3>\r
-getJobStatus</H3>\r
-<PRE>\r
-public <A HREF="../../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A> <B>getJobStatus</B>(java.lang.String&nbsp;jobId)</PRE>\r
-<DL>\r
-<DD>This will never return clust.engine.JobStatus.CANCELLED as for sun grid
- engine cancelled job is the same as failed. Cancelled jobs needs to be
- tracked manually!\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../compbio/engine/AsyncExecutor.html#getJobStatus(java.lang.String)">getJobStatus</A></CODE> in interface <CODE><A HREF="../../../../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine">AsyncExecutor</A></CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>The JobStatus object representing the status of the job<DT><B>See Also:</B><DD><A HREF="../../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata"><CODE>JobStatus</CODE></A></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="cleanup(java.lang.String)"><!-- --></A><H3>\r
-cleanup</H3>\r
-<PRE>\r
-public boolean <B>cleanup</B>(java.lang.String&nbsp;jobId)</PRE>\r
-<DL>\r
-<DD><B>Description copied from interface: <CODE><A HREF="../../../../compbio/engine/AsyncExecutor.html#cleanup(java.lang.String)">AsyncExecutor</A></CODE></B></DD>\r
-<DD>Remove all files and a job directory for a jobid.\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../compbio/engine/AsyncExecutor.html#cleanup(java.lang.String)">cleanup</A></CODE> in interface <CODE><A HREF="../../../../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine">AsyncExecutor</A></CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>true if job directory was successfully removed, false otherwise.</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getResults(java.lang.String)"><!-- --></A><H3>\r
-getResults</H3>\r
-<PRE>\r
-public <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt; <B>getResults</B>(java.lang.String&nbsp;jobId)\r
-                                   throws <A HREF="../../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></PRE>\r
-<DL>\r
-<DD><B>Description copied from interface: <CODE><A HREF="../../../../compbio/engine/AsyncExecutor.html#getResults(java.lang.String)">AsyncExecutor</A></CODE></B></DD>\r
-<DD>Retrieve the results of the job. Please not that current implementations of this method 
- blocks if the task is running until the end of the calculation.\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../compbio/engine/AsyncExecutor.html#getResults(java.lang.String)">getResults</A></CODE> in interface <CODE><A HREF="../../../../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine">AsyncExecutor</A></CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>jobId</CODE> - job identifier obtained at the job submission\r
-<DT><B>Returns:</B><DD>ConfiguredExecutable object from which result can be obtained\r
-<DT><B>Throws:</B>\r
-<DD><CODE><A HREF="../../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></CODE> - if the result is not available for whatever reason. 
- Could be due to execution failure, or due to the results being removed from the server at 
- the time of request.</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getWorkDirectory(java.lang.String)"><!-- --></A><H3>\r
-getWorkDirectory</H3>\r
-<PRE>\r
-public java.lang.String <B>getWorkDirectory</B>(java.lang.String&nbsp;jobId)</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../compbio/engine/AsyncExecutor.html#getWorkDirectory(java.lang.String)">getWorkDirectory</A></CODE> in interface <CODE><A HREF="../../../../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine">AsyncExecutor</A></CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>jobId</CODE> - unique job identifier\r
-<DT><B>Returns:</B><DD>task working directory</DL>\r
-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/AsyncJobRunner.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../../compbio/engine/cluster/drmaa/_JobStatus.html" title="class in compbio.engine.cluster.drmaa"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../../compbio/engine/cluster/drmaa/ClusterSession.html" title="class in compbio.engine.cluster.drmaa"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/engine/cluster/drmaa/AsyncJobRunner.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="AsyncJobRunner.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/engine/cluster/drmaa/ClusterSession.html b/website/full_javadoc/compbio/engine/cluster/drmaa/ClusterSession.html

deleted file mode 100644 (file)

index 51b0e22..0000000
--- a/website/full_javadoc/compbio/engine/cluster/drmaa/ClusterSession.html
+++ /dev/null
@@ -1,471 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:49 GMT 2010 -->\r
-<TITLE>\r
-ClusterSession\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="ClusterSession";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/ClusterSession.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../../compbio/engine/cluster/drmaa/AsyncJobRunner.html" title="class in compbio.engine.cluster.drmaa"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../../compbio/engine/cluster/drmaa/ClusterUtil.html" title="class in compbio.engine.cluster.drmaa"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/engine/cluster/drmaa/ClusterSession.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="ClusterSession.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;<A HREF="#field_summary">FIELD</A>&nbsp;|&nbsp;CONSTR&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;<A HREF="#field_detail">FIELD</A>&nbsp;|&nbsp;CONSTR&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.engine.cluster.drmaa</FONT>\r
-<BR>\r
-Class ClusterSession</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../../../resources/inherit.gif" ALT="extended by "><B>compbio.engine.cluster.drmaa.ClusterSession</B>\r
-</PRE>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public final class <B>ClusterSession</B><DT>extends java.lang.Object</DL>\r
-</PRE>\r
-\r
-<P>\r
-<HR>\r
-\r
-<P>\r
-<!-- =========== FIELD SUMMARY =========== -->\r
-\r
-<A NAME="field_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Field Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/ClusterSession.html#JOBID">JOBID</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/ClusterSession.html#close()">close</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../../compbio/engine/ClusterJobId.html" title="class in compbio.engine">ClusterJobId</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/ClusterSession.html#getClusterJobId(java.lang.String)">getClusterJobId</A></B>(java.lang.String&nbsp;taskId)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;int</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/ClusterSession.html#getJobStatus(compbio.engine.ClusterJobId)">getJobStatus</A></B>(<A HREF="../../../../compbio/engine/ClusterJobId.html" title="class in compbio.engine">ClusterJobId</A>&nbsp;jobId)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Apparently completed jobs cannot be found! If this happened most likely
- that the job is not running any more and Most likely it has been
- cancelled, finished or failed.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/ClusterSession.html#getJobStatus(int)">getJobStatus</A></B>(int&nbsp;status)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<B>Deprecated.</B>&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/ClusterSession.html#getResults(java.lang.String)">getResults</A></B>(java.lang.String&nbsp;taskId)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;org.ggf.drmaa.Session</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/ClusterSession.html#getSession()">getSession</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/ClusterSession.html#getStatistics(org.ggf.drmaa.JobInfo)">getStatistics</A></B>(org.ggf.drmaa.JobInfo&nbsp;status)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/ClusterSession.html#removeJob(java.lang.String)">removeJob</A></B>(java.lang.String&nbsp;taskId)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;org.ggf.drmaa.JobInfo</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/ClusterSession.html#waitForJob(java.lang.String)">waitForJob</A></B>(java.lang.String&nbsp;taskId)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;org.ggf.drmaa.JobInfo</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/ClusterSession.html#waitForJob(java.lang.String, long)">waitForJob</A></B>(java.lang.String&nbsp;jobId,\r
-           long&nbsp;waitingTime)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>\r
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-\r
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-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Field Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="JOBID"><!-- --></A><H3>\r
-JOBID</H3>\r
-<PRE>\r
-public static final java.lang.String <B>JOBID</B></PRE>\r
-<DL>\r
-<DL>\r
-<DT><B>See Also:</B><DD><A HREF="../../../../constant-values.html#compbio.engine.cluster.drmaa.ClusterSession.JOBID">Constant Field Values</A></DL>\r
-</DL>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
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-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="getSession()"><!-- --></A><H3>\r
-getSession</H3>\r
-<PRE>\r
-public org.ggf.drmaa.Session <B>getSession</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="close()"><!-- --></A><H3>\r
-close</H3>\r
-<PRE>\r
-public void <B>close</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="removeJob(java.lang.String)"><!-- --></A><H3>\r
-removeJob</H3>\r
-<PRE>\r
-public void <B>removeJob</B>(java.lang.String&nbsp;taskId)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="waitForJob(java.lang.String)"><!-- --></A><H3>\r
-waitForJob</H3>\r
-<PRE>\r
-public org.ggf.drmaa.JobInfo <B>waitForJob</B>(java.lang.String&nbsp;taskId)\r
-                                 throws org.ggf.drmaa.DrmaaException,\r
-                                        java.io.IOException</PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Throws:</B>\r
-<DD><CODE>org.ggf.drmaa.DrmaaException</CODE>\r
-<DD><CODE>java.io.IOException</CODE></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getClusterJobId(java.lang.String)"><!-- --></A><H3>\r
-getClusterJobId</H3>\r
-<PRE>\r
-public static <A HREF="../../../../compbio/engine/ClusterJobId.html" title="class in compbio.engine">ClusterJobId</A> <B>getClusterJobId</B>(java.lang.String&nbsp;taskId)\r
-                                    throws java.io.IOException</PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Throws:</B>\r
-<DD><CODE>java.io.IOException</CODE></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="waitForJob(java.lang.String, long)"><!-- --></A><H3>\r
-waitForJob</H3>\r
-<PRE>\r
-public org.ggf.drmaa.JobInfo <B>waitForJob</B>(java.lang.String&nbsp;jobId,\r
-                                        long&nbsp;waitingTime)\r
-                                 throws org.ggf.drmaa.DrmaaException,\r
-                                        java.io.IOException</PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Throws:</B>\r
-<DD><CODE>org.ggf.drmaa.DrmaaException</CODE>\r
-<DD><CODE>java.io.IOException</CODE></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getResults(java.lang.String)"><!-- --></A><H3>\r
-getResults</H3>\r
-<PRE>\r
-public <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt; <B>getResults</B>(java.lang.String&nbsp;taskId)\r
-                                   throws org.ggf.drmaa.DrmaaException,\r
-                                          <A HREF="../../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Throws:</B>\r
-<DD><CODE>org.ggf.drmaa.DrmaaException</CODE>\r
-<DD><CODE><A HREF="../../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></CODE></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getStatistics(org.ggf.drmaa.JobInfo)"><!-- --></A><H3>\r
-getStatistics</H3>\r
-<PRE>\r
-public static <A HREF="../../../../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</A> <B>getStatistics</B>(org.ggf.drmaa.JobInfo&nbsp;status)\r
-                                      throws org.ggf.drmaa.DrmaaException</PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Throws:</B>\r
-<DD><CODE>org.ggf.drmaa.DrmaaException</CODE></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getJobStatus(compbio.engine.ClusterJobId)"><!-- --></A><H3>\r
-getJobStatus</H3>\r
-<PRE>\r
-public int <B>getJobStatus</B>(<A HREF="../../../../compbio/engine/ClusterJobId.html" title="class in compbio.engine">ClusterJobId</A>&nbsp;jobId)\r
-                 throws org.ggf.drmaa.DrmaaException,\r
-                        org.ggf.drmaa.InvalidJobException</PRE>\r
-<DL>\r
-<DD>Apparently completed jobs cannot be found! If this happened most likely
- that the job is not running any more and Most likely it has been
- cancelled, finished or failed.\r
-<P>\r
-<DD><DL>\r
-\r
-<DT><B>Throws:</B>\r
-<DD><CODE>org.ggf.drmaa.InvalidJobException</CODE> - if the job is no longer in the queue or running. basically it
-             will throw this exception for all finished or cancelled jobs\r
-<DD><CODE>org.ggf.drmaa.DrmaaException</CODE></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getJobStatus(int)"><!-- --></A><H3>\r
-getJobStatus</H3>\r
-<PRE>\r
-<FONT SIZE="-1">@Deprecated\r
-</FONT>public static java.lang.String <B>getJobStatus</B>(int&nbsp;status)\r
-                                     throws org.ggf.drmaa.DrmaaException</PRE>\r
-<DL>\r
-<DD><B>Deprecated.</B>&nbsp;\r
-<P>\r
-<DD>Method for getting jobs status by quering the cluster, It returns status
- in therms of a Sessions, not a JobStatus Should only be used for testing!\r
-<P>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>status</CODE> - \r
-<DT><B>Returns:</B><DD>\r
-<DT><B>Throws:</B>\r
-<DD><CODE>org.ggf.drmaa.DrmaaException</CODE></DL>\r
-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
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-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
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-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/ClusterSession.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
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-  </TR>\r
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-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../../compbio/engine/cluster/drmaa/AsyncJobRunner.html" title="class in compbio.engine.cluster.drmaa"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../../compbio/engine/cluster/drmaa/ClusterUtil.html" title="class in compbio.engine.cluster.drmaa"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/engine/cluster/drmaa/ClusterSession.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
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-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
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-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;<A HREF="#field_summary">FIELD</A>&nbsp;|&nbsp;CONSTR&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;<A HREF="#field_detail">FIELD</A>&nbsp;|&nbsp;CONSTR&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
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diff --git a/website/full_javadoc/compbio/engine/cluster/drmaa/ClusterUtil.html b/website/full_javadoc/compbio/engine/cluster/drmaa/ClusterUtil.html

deleted file mode 100644 (file)

index ad68763..0000000
--- a/website/full_javadoc/compbio/engine/cluster/drmaa/ClusterUtil.html
+++ /dev/null
@@ -1,314 +0,0 @@
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-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
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-\r
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-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
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-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
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-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/ClusterUtil.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
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-&nbsp;<A HREF="../../../../compbio/engine/cluster/drmaa/ClusterSession.html" title="class in compbio.engine.cluster.drmaa"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../../compbio/engine/cluster/drmaa/JobRunner.html" title="class in compbio.engine.cluster.drmaa"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/engine/cluster/drmaa/ClusterUtil.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="ClusterUtil.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
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-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
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-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;<A HREF="#field_summary">FIELD</A>&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
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-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
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-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.engine.cluster.drmaa</FONT>\r
-<BR>\r
-Class ClusterUtil</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../../../resources/inherit.gif" ALT="extended by "><B>compbio.engine.cluster.drmaa.ClusterUtil</B>\r
-</PRE>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public class <B>ClusterUtil</B><DT>extends java.lang.Object</DL>\r
-</PRE>\r
-\r
-<P>\r
-<HR>\r
-\r
-<P>\r
-<!-- =========== FIELD SUMMARY =========== -->\r
-\r
-<A NAME="field_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Field Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;java.text.NumberFormat</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/ClusterUtil.html#CLUSTER_STAT_IN_SEC">CLUSTER_STAT_IN_SEC</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
-\r
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-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Constructor Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/ClusterUtil.html#ClusterUtil()">ClusterUtil</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
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-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/ClusterUtil.html#cancelJob(java.lang.String, compbio.engine.cluster.drmaa.ClusterSession)">cancelJob</A></B>(java.lang.String&nbsp;jobId,\r
-          <A HREF="../../../../compbio/engine/cluster/drmaa/ClusterSession.html" title="class in compbio.engine.cluster.drmaa">ClusterSession</A>&nbsp;csession)</CODE>\r
-\r
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-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;org.ggf.drmaa.JobInfo</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/ClusterUtil.html#waitForResult(compbio.engine.cluster.drmaa.ClusterSession, java.lang.String)">waitForResult</A></B>(<A HREF="../../../../compbio/engine/cluster/drmaa/ClusterSession.html" title="class in compbio.engine.cluster.drmaa">ClusterSession</A>&nbsp;csession,\r
-              java.lang.String&nbsp;jobId)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
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-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
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-<TR BGCOLOR="white" CLASS="TableRowColor">\r
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-<B>Field Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="CLUSTER_STAT_IN_SEC"><!-- --></A><H3>\r
-CLUSTER_STAT_IN_SEC</H3>\r
-<PRE>\r
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-<DL>\r
-<DL>\r
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-\r
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-<B>Constructor Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="ClusterUtil()"><!-- --></A><H3>\r
-ClusterUtil</H3>\r
-<PRE>\r
-public <B>ClusterUtil</B>()</PRE>\r
-<DL>\r
-</DL>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
-<A NAME="method_detail"><!-- --></A>\r
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-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="cancelJob(java.lang.String, compbio.engine.cluster.drmaa.ClusterSession)"><!-- --></A><H3>\r
-cancelJob</H3>\r
-<PRE>\r
-public static final boolean <B>cancelJob</B>(java.lang.String&nbsp;jobId,\r
-                                      <A HREF="../../../../compbio/engine/cluster/drmaa/ClusterSession.html" title="class in compbio.engine.cluster.drmaa">ClusterSession</A>&nbsp;csession)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="waitForResult(compbio.engine.cluster.drmaa.ClusterSession, java.lang.String)"><!-- --></A><H3>\r
-waitForResult</H3>\r
-<PRE>\r
-public static final org.ggf.drmaa.JobInfo <B>waitForResult</B>(<A HREF="../../../../compbio/engine/cluster/drmaa/ClusterSession.html" title="class in compbio.engine.cluster.drmaa">ClusterSession</A>&nbsp;csession,\r
-                                                        java.lang.String&nbsp;jobId)\r
-                                                 throws <A HREF="../../../../compbio/metadata/JobExecutionException.html" title="class in compbio.metadata">JobExecutionException</A></PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Throws:</B>\r
-<DD><CODE><A HREF="../../../../compbio/metadata/JobExecutionException.html" title="class in compbio.metadata">JobExecutionException</A></CODE></DL>\r
-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
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-<TR>\r
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-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
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-\r
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-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../../compbio/engine/cluster/drmaa/ClusterSession.html" title="class in compbio.engine.cluster.drmaa"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../../compbio/engine/cluster/drmaa/JobRunner.html" title="class in compbio.engine.cluster.drmaa"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/engine/cluster/drmaa/ClusterUtil.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
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-  if(window==top) {\r
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-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;<A HREF="#field_detail">FIELD</A>&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
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diff --git a/website/full_javadoc/compbio/engine/cluster/drmaa/JobRunner.html b/website/full_javadoc/compbio/engine/cluster/drmaa/JobRunner.html

deleted file mode 100644 (file)

index da7c2e3..0000000
--- a/website/full_javadoc/compbio/engine/cluster/drmaa/JobRunner.html
+++ /dev/null
@@ -1,487 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:49 GMT 2010 -->\r
-<TITLE>\r
-JobRunner\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="JobRunner";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
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-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
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-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/JobRunner.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
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-&nbsp;<A HREF="../../../../compbio/engine/cluster/drmaa/ClusterUtil.html" title="class in compbio.engine.cluster.drmaa"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/engine/cluster/drmaa/JobRunner.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="JobRunner.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
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-\r
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-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
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-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.engine.cluster.drmaa</FONT>\r
-<BR>\r
-Class JobRunner</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../../../resources/inherit.gif" ALT="extended by "><B>compbio.engine.cluster.drmaa.JobRunner</B>\r
-</PRE>\r
-<DL>\r
-<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../compbio/engine/SyncExecutor.html" title="interface in compbio.engine">SyncExecutor</A></DD>\r
-</DL>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public class <B>JobRunner</B><DT>extends java.lang.Object<DT>implements <A HREF="../../../../compbio/engine/SyncExecutor.html" title="interface in compbio.engine">SyncExecutor</A></DL>\r
-</PRE>\r
-\r
-<P>\r
-Single cluster job runner class\r
-<P>\r
-\r
-<P>\r
-<DL>\r
-<DT><B>Author:</B></DT>\r
-  <DD>pvtroshin</DD>\r
-</DL>\r
-<HR>\r
-\r
-<P>\r
-\r
-<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
-\r
-<A NAME="constructor_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Constructor Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/JobRunner.html#JobRunner(compbio.engine.client.ConfiguredExecutable)">JobRunner</A></B>(<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;confExec)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
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-\r
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-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/JobRunner.html#cancelJob()">cancelJob</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Stops running job.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/JobRunner.html#cleanup()">cleanup</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Clean up after the job</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/JobRunner.html#deepClean()">deepClean</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/JobRunner.html#executeJob()">executeJob</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Execute the job</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../../compbio/engine/cluster/drmaa/JobRunner.html" title="class in compbio.engine.cluster.drmaa">JobRunner</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/JobRunner.html#getInstance(compbio.engine.client.ConfiguredExecutable)">getInstance</A></B>(<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;executable)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;org.ggf.drmaa.JobInfo</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/JobRunner.html#getJobInfo()">getJobInfo</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;This method will block before the calculation has completed and then
- return the object containing a job execution statistics</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/JobRunner.html#getJobStatus()">getJobStatus</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Query the status of the job by its id.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/JobRunner.html#getWorkDirectory()">getWorkDirectory</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/JobRunner.html#waitForResult()">waitForResult</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Call to this method block for as long as it is required for an executable to finish its job.</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
-\r
-<A NAME="constructor_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Constructor Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="JobRunner(compbio.engine.client.ConfiguredExecutable)"><!-- --></A><H3>\r
-JobRunner</H3>\r
-<PRE>\r
-public <B>JobRunner</B>(<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;confExec)\r
-          throws <A HREF="../../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></PRE>\r
-<DL>\r
-<DL>\r
-\r
-<DT><B>Throws:</B>\r
-<DD><CODE><A HREF="../../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></CODE></DL>\r
-</DL>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
-<A NAME="method_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="deepClean()"><!-- --></A><H3>\r
-deepClean</H3>\r
-<PRE>\r
-public boolean <B>deepClean</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="cleanup()"><!-- --></A><H3>\r
-cleanup</H3>\r
-<PRE>\r
-public boolean <B>cleanup</B>()</PRE>\r
-<DL>\r
-<DD><B>Description copied from interface: <CODE><A HREF="../../../../compbio/engine/SyncExecutor.html#cleanup()">SyncExecutor</A></CODE></B></DD>\r
-<DD>Clean up after the job\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../compbio/engine/SyncExecutor.html#cleanup()">cleanup</A></CODE> in interface <CODE><A HREF="../../../../compbio/engine/SyncExecutor.html" title="interface in compbio.engine">SyncExecutor</A></CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>true if all the files created by this job have been removed successfully, false otherwise</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="cancelJob()"><!-- --></A><H3>\r
-cancelJob</H3>\r
-<PRE>\r
-public boolean <B>cancelJob</B>()</PRE>\r
-<DL>\r
-<DD><B>Description copied from interface: <CODE><A HREF="../../../../compbio/engine/SyncExecutor.html#cancelJob()">SyncExecutor</A></CODE></B></DD>\r
-<DD>Stops running job. 
- Clean up is not performed.\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../compbio/engine/SyncExecutor.html#cancelJob()">cancelJob</A></CODE> in interface <CODE><A HREF="../../../../compbio/engine/SyncExecutor.html" title="interface in compbio.engine">SyncExecutor</A></CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>true if job was cancelled successfully, false otherwise</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getWorkDirectory()"><!-- --></A><H3>\r
-getWorkDirectory</H3>\r
-<PRE>\r
-public java.lang.String <B>getWorkDirectory</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../compbio/engine/SyncExecutor.html#getWorkDirectory()">getWorkDirectory</A></CODE> in interface <CODE><A HREF="../../../../compbio/engine/SyncExecutor.html" title="interface in compbio.engine">SyncExecutor</A></CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>working directory if the task</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="executeJob()"><!-- --></A><H3>\r
-executeJob</H3>\r
-<PRE>\r
-public void <B>executeJob</B>()\r
-                throws <A HREF="../../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></PRE>\r
-<DL>\r
-<DD><B>Description copied from interface: <CODE><A HREF="../../../../compbio/engine/SyncExecutor.html#executeJob()">SyncExecutor</A></CODE></B></DD>\r
-<DD>Execute the job\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../compbio/engine/SyncExecutor.html#executeJob()">executeJob</A></CODE> in interface <CODE><A HREF="../../../../compbio/engine/SyncExecutor.html" title="interface in compbio.engine">SyncExecutor</A></CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-\r
-<DT><B>Throws:</B>\r
-<DD><CODE><A HREF="../../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></CODE> - if submission fails</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getJobInfo()"><!-- --></A><H3>\r
-getJobInfo</H3>\r
-<PRE>\r
-public org.ggf.drmaa.JobInfo <B>getJobInfo</B>()\r
-                                 throws <A HREF="../../../../compbio/metadata/JobExecutionException.html" title="class in compbio.metadata">JobExecutionException</A></PRE>\r
-<DL>\r
-<DD>This method will block before the calculation has completed and then
- return the object containing a job execution statistics\r
-<P>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>\r
-<DT><B>Throws:</B>\r
-<DD><CODE><A HREF="../../../../compbio/metadata/JobExecutionException.html" title="class in compbio.metadata">JobExecutionException</A></CODE></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="waitForResult()"><!-- --></A><H3>\r
-waitForResult</H3>\r
-<PRE>\r
-public <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt; <B>waitForResult</B>()\r
-                                      throws <A HREF="../../../../compbio/metadata/JobExecutionException.html" title="class in compbio.metadata">JobExecutionException</A></PRE>\r
-<DL>\r
-<DD><B>Description copied from interface: <CODE><A HREF="../../../../compbio/engine/SyncExecutor.html#waitForResult()">SyncExecutor</A></CODE></B></DD>\r
-<DD>Call to this method block for as long as it is required for an executable to finish its job. 
- If the calculation has been completed already, the this method returns results immediately. 
- This could return the result directly, but that would be type unsafe\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../compbio/engine/SyncExecutor.html#waitForResult()">waitForResult</A></CODE> in interface <CODE><A HREF="../../../../compbio/engine/SyncExecutor.html" title="interface in compbio.engine">SyncExecutor</A></CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>object from wich the result can be obtained\r
-<DT><B>Throws:</B>\r
-<DD><CODE><A HREF="../../../../compbio/metadata/JobExecutionException.html" title="class in compbio.metadata">JobExecutionException</A></CODE></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getJobStatus()"><!-- --></A><H3>\r
-getJobStatus</H3>\r
-<PRE>\r
-public <A HREF="../../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A> <B>getJobStatus</B>()</PRE>\r
-<DL>\r
-<DD><B>Description copied from interface: <CODE><A HREF="../../../../compbio/engine/SyncExecutor.html#getJobStatus()">SyncExecutor</A></CODE></B></DD>\r
-<DD>Query the status of the job by its id.\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../compbio/engine/SyncExecutor.html#getJobStatus()">getJobStatus</A></CODE> in interface <CODE><A HREF="../../../../compbio/engine/SyncExecutor.html" title="interface in compbio.engine">SyncExecutor</A></CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>- JobStatus</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getInstance(compbio.engine.client.ConfiguredExecutable)"><!-- --></A><H3>\r
-getInstance</H3>\r
-<PRE>\r
-public static <A HREF="../../../../compbio/engine/cluster/drmaa/JobRunner.html" title="class in compbio.engine.cluster.drmaa">JobRunner</A> <B>getInstance</B>(<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;executable)\r
-                             throws <A HREF="../../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-<DD><DL>\r
-\r
-<DT><B>Throws:</B>\r
-<DD><CODE><A HREF="../../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></CODE></DL>\r
-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
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-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/JobRunner.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
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-  </TR>\r
-</TABLE>\r
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-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
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-\r
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-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../../compbio/engine/cluster/drmaa/ClusterUtil.html" title="class in compbio.engine.cluster.drmaa"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/engine/cluster/drmaa/JobRunner.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="JobRunner.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
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-\r
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-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
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-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/engine/cluster/drmaa/StatisticManager.html b/website/full_javadoc/compbio/engine/cluster/drmaa/StatisticManager.html

deleted file mode 100644 (file)

index da1ad93..0000000
--- a/website/full_javadoc/compbio/engine/cluster/drmaa/StatisticManager.html
+++ /dev/null
@@ -1,759 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:49 GMT 2010 -->\r
-<TITLE>\r
-StatisticManager\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="StatisticManager";\r
-    }\r
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-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
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-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/StatisticManager.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../../compbio/engine/cluster/drmaa/JobRunner.html" title="class in compbio.engine.cluster.drmaa"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;NEXT CLASS</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/engine/cluster/drmaa/StatisticManager.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="StatisticManager.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
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-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.engine.cluster.drmaa</FONT>\r
-<BR>\r
-Class StatisticManager</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../../../resources/inherit.gif" ALT="extended by "><B>compbio.engine.cluster.drmaa.StatisticManager</B>\r
-</PRE>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public class <B>StatisticManager</B><DT>extends java.lang.Object</DL>\r
-</PRE>\r
-\r
-<P>\r
-<HR>\r
-\r
-<P>\r
-\r
-<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
-\r
-<A NAME="constructor_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Constructor Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/StatisticManager.html#StatisticManager(org.ggf.drmaa.JobInfo)">StatisticManager</A></B>(org.ggf.drmaa.JobInfo&nbsp;status)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/StatisticManager.html#getAllStats()">getAllStats</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/StatisticManager.html#getCalculationTime()">getCalculationTime</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/StatisticManager.html#getCPUTimeStat()">getCPUTimeStat</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/StatisticManager.html#getCPUUsageTime()">getCPUUsageTime</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/StatisticManager.html#getDataTransfered()">getDataTransfered</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
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-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/StatisticManager.html#getExecutionStat()">getExecutionStat</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
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-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/StatisticManager.html#getExitStatus()">getExitStatus</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
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-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/StatisticManager.html#getIOWait()">getIOWait</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/StatisticManager.html#getJobId()">getJobId</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/StatisticManager.html#getJobPriority()">getJobPriority</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/StatisticManager.html#getMaxVMem()">getMaxVMem</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/StatisticManager.html#getMemoryStat()">getMemoryStat</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.util.Map&lt;java.lang.String,java.lang.String&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/StatisticManager.html#getRawUsage()">getRawUsage</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/StatisticManager.html#getStartTime()">getStartTime</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/StatisticManager.html#getSubmissionTime()">getSubmissionTime</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/StatisticManager.html#getTimeStat()">getTimeStat</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/StatisticManager.html#getUsedSysTime()">getUsedSysTime</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/StatisticManager.html#getUsedUserTime()">getUsedUserTime</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/StatisticManager.html#getVMem()">getVMem</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/StatisticManager.html#hasDump()">hasDump</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/StatisticManager.html#hasExited()">hasExited</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/StatisticManager.html#hasSignaled()">hasSignaled</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/StatisticManager.html#termSignal()">termSignal</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/StatisticManager.html#toString()">toString</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/StatisticManager.html#wasAborted()">wasAborted</A></B>()</CODE>\r
-\r
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-</TABLE>\r
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-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>equals, getClass, hashCode, notify, notifyAll, wait, wait, wait</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
-\r
-<A NAME="constructor_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Constructor Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="StatisticManager(org.ggf.drmaa.JobInfo)"><!-- --></A><H3>\r
-StatisticManager</H3>\r
-<PRE>\r
-public <B>StatisticManager</B>(org.ggf.drmaa.JobInfo&nbsp;status)\r
-                 throws org.ggf.drmaa.DrmaaException</PRE>\r
-<DL>\r
-<DL>\r
-\r
-<DT><B>Throws:</B>\r
-<DD><CODE>org.ggf.drmaa.DrmaaException</CODE></DL>\r
-</DL>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
-<A NAME="method_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="getJobId()"><!-- --></A><H3>\r
-getJobId</H3>\r
-<PRE>\r
-public java.lang.String <B>getJobId</B>()\r
-                          throws org.ggf.drmaa.DrmaaException</PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Throws:</B>\r
-<DD><CODE>org.ggf.drmaa.DrmaaException</CODE></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="hasExited()"><!-- --></A><H3>\r
-hasExited</H3>\r
-<PRE>\r
-public boolean <B>hasExited</B>()\r
-                  throws org.ggf.drmaa.DrmaaException</PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Throws:</B>\r
-<DD><CODE>org.ggf.drmaa.DrmaaException</CODE></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="hasSignaled()"><!-- --></A><H3>\r
-hasSignaled</H3>\r
-<PRE>\r
-public boolean <B>hasSignaled</B>()\r
-                    throws org.ggf.drmaa.DrmaaException</PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Throws:</B>\r
-<DD><CODE>org.ggf.drmaa.DrmaaException</CODE></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="hasDump()"><!-- --></A><H3>\r
-hasDump</H3>\r
-<PRE>\r
-public boolean <B>hasDump</B>()\r
-                throws org.ggf.drmaa.DrmaaException</PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Throws:</B>\r
-<DD><CODE>org.ggf.drmaa.DrmaaException</CODE></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="termSignal()"><!-- --></A><H3>\r
-termSignal</H3>\r
-<PRE>\r
-public java.lang.String <B>termSignal</B>()\r
-                            throws org.ggf.drmaa.DrmaaException</PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Throws:</B>\r
-<DD><CODE>org.ggf.drmaa.DrmaaException</CODE></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="wasAborted()"><!-- --></A><H3>\r
-wasAborted</H3>\r
-<PRE>\r
-public boolean <B>wasAborted</B>()\r
-                   throws org.ggf.drmaa.DrmaaException</PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Throws:</B>\r
-<DD><CODE>org.ggf.drmaa.DrmaaException</CODE></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getSubmissionTime()"><!-- --></A><H3>\r
-getSubmissionTime</H3>\r
-<PRE>\r
-public java.lang.String <B>getSubmissionTime</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getVMem()"><!-- --></A><H3>\r
-getVMem</H3>\r
-<PRE>\r
-public java.lang.String <B>getVMem</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getMaxVMem()"><!-- --></A><H3>\r
-getMaxVMem</H3>\r
-<PRE>\r
-public java.lang.String <B>getMaxVMem</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getUsedSysTime()"><!-- --></A><H3>\r
-getUsedSysTime</H3>\r
-<PRE>\r
-public java.lang.String <B>getUsedSysTime</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getUsedUserTime()"><!-- --></A><H3>\r
-getUsedUserTime</H3>\r
-<PRE>\r
-public java.lang.String <B>getUsedUserTime</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getCalculationTime()"><!-- --></A><H3>\r
-getCalculationTime</H3>\r
-<PRE>\r
-public java.lang.String <B>getCalculationTime</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getEndTime()"><!-- --></A><H3>\r
-getEndTime</H3>\r
-<PRE>\r
-public java.lang.String <B>getEndTime</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getStartTime()"><!-- --></A><H3>\r
-getStartTime</H3>\r
-<PRE>\r
-public java.lang.String <B>getStartTime</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getIOWait()"><!-- --></A><H3>\r
-getIOWait</H3>\r
-<PRE>\r
-public java.lang.String <B>getIOWait</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getCPUUsageTime()"><!-- --></A><H3>\r
-getCPUUsageTime</H3>\r
-<PRE>\r
-public java.lang.String <B>getCPUUsageTime</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getDataTransfered()"><!-- --></A><H3>\r
-getDataTransfered</H3>\r
-<PRE>\r
-public java.lang.String <B>getDataTransfered</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getJobPriority()"><!-- --></A><H3>\r
-getJobPriority</H3>\r
-<PRE>\r
-public java.lang.String <B>getJobPriority</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getExitStatus()"><!-- --></A><H3>\r
-getExitStatus</H3>\r
-<PRE>\r
-public java.lang.String <B>getExitStatus</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getAllStats()"><!-- --></A><H3>\r
-getAllStats</H3>\r
-<PRE>\r
-public java.lang.String <B>getAllStats</B>()\r
-                             throws org.ggf.drmaa.DrmaaException</PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Throws:</B>\r
-<DD><CODE>org.ggf.drmaa.DrmaaException</CODE></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getExecutionStat()"><!-- --></A><H3>\r
-getExecutionStat</H3>\r
-<PRE>\r
-public java.lang.String <B>getExecutionStat</B>()\r
-                                  throws org.ggf.drmaa.DrmaaException</PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Throws:</B>\r
-<DD><CODE>org.ggf.drmaa.DrmaaException</CODE></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getMemoryStat()"><!-- --></A><H3>\r
-getMemoryStat</H3>\r
-<PRE>\r
-public java.lang.String <B>getMemoryStat</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getCPUTimeStat()"><!-- --></A><H3>\r
-getCPUTimeStat</H3>\r
-<PRE>\r
-public java.lang.String <B>getCPUTimeStat</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getTimeStat()"><!-- --></A><H3>\r
-getTimeStat</H3>\r
-<PRE>\r
-public java.lang.String <B>getTimeStat</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getRawUsage()"><!-- --></A><H3>\r
-getRawUsage</H3>\r
-<PRE>\r
-public java.util.Map&lt;java.lang.String,java.lang.String&gt; <B>getRawUsage</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="toString()"><!-- --></A><H3>\r
-toString</H3>\r
-<PRE>\r
-public java.lang.String <B>toString</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Overrides:</B><DD><CODE>toString</CODE> in class <CODE>java.lang.Object</CODE></DL>\r
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-<DD><DL>\r
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-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
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-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
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diff --git a/website/full_javadoc/compbio/engine/cluster/drmaa/_DrmaaExample.html b/website/full_javadoc/compbio/engine/cluster/drmaa/_DrmaaExample.html

deleted file mode 100644 (file)

index 158c30c..0000000
--- a/website/full_javadoc/compbio/engine/cluster/drmaa/_DrmaaExample.html
+++ /dev/null
@@ -1,255 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:49 GMT 2010 -->\r
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-_DrmaaExample\r
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-<META NAME="date" CONTENT="2010-02-17">\r
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-\r
-<SCRIPT type="text/javascript">\r
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-    if (location.href.indexOf('is-external=true') == -1) {\r
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-<FONT SIZE="-1">\r
-compbio.engine.cluster.drmaa</FONT>\r
-<BR>\r
-Class _DrmaaExample</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../../../resources/inherit.gif" ALT="extended by "><B>compbio.engine.cluster.drmaa._DrmaaExample</B>\r
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-<DT><PRE>public class <B>_DrmaaExample</B><DT>extends java.lang.Object</DL>\r
-</PRE>\r
-\r
-<P>\r
-<HR>\r
-\r
-<P>\r
-\r
-<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
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-<B>Constructor Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/_DrmaaExample.html#_DrmaaExample()">_DrmaaExample</A></B>()</CODE>\r
-\r
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-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
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-<TR BGCOLOR="white" CLASS="TableRowColor">\r
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-<CODE>static&nbsp;void</CODE></FONT></TD>\r
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-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
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-&nbsp;\r
-<P>\r
-\r
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-_DrmaaExample</H3>\r
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-&nbsp;<SCRIPT type="text/javascript">\r
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-  if(window==top) {\r
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-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
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diff --git a/website/full_javadoc/compbio/engine/cluster/drmaa/_JobStatus.html b/website/full_javadoc/compbio/engine/cluster/drmaa/_JobStatus.html

deleted file mode 100644 (file)

index 6aaaf54..0000000
--- a/website/full_javadoc/compbio/engine/cluster/drmaa/_JobStatus.html
+++ /dev/null
@@ -1,252 +0,0 @@
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-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:49 GMT 2010 -->\r
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-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
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diff --git a/website/full_javadoc/compbio/engine/cluster/drmaa/class-use/AsyncJobRunner.html b/website/full_javadoc/compbio/engine/cluster/drmaa/class-use/AsyncJobRunner.html

deleted file mode 100644 (file)

index 1c73aaf..0000000
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deleted file mode 100644 (file)

index 17e4869..0000000
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-<B>Uses of Class<br>compbio.engine.cluster.drmaa.StatisticManager</B></H2>\r
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-<TR BGCOLOR="white" CLASS="TableRowColor">\r
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-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../../compbio/engine/cluster/drmaa/package-summary.html">compbio.engine.cluster.drmaa</A> that return <A HREF="../../../../../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</A></FONT></TH>\r
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deleted file mode 100644 (file)

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diff --git a/website/full_javadoc/compbio/engine/cluster/drmaa/package-summary.html b/website/full_javadoc/compbio/engine/cluster/drmaa/package-summary.html

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-Package compbio.engine.cluster.drmaa\r
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-An cluster engine classes responsible for execution of Executables on the clusters.\r
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-<TR BGCOLOR="white" CLASS="TableRowColor">\r
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-<A NAME="package_description"><!-- --></A><H2>\r
-Package compbio.engine.cluster.drmaa Description\r
-</H2>\r
-\r
-<P>\r
-An cluster engine classes responsible for execution of Executables on the clusters.
- Implementation uses DRMAA library.  
- Classes in this package depend on the data model classes. 
- They form a second layer of Jalview Web Services v2.\r
-<P>\r
-\r
-<P>\r
-<DL>\r
-<DT><B>Author:</B></DT>\r
-  <DD>Petr Troshin 
- 
-        Date January 2010</DD>\r
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diff --git a/website/full_javadoc/compbio/engine/cluster/drmaa/package-use.html b/website/full_javadoc/compbio/engine/cluster/drmaa/package-use.html

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-<B>Uses of Package<br>compbio.engine.cluster.drmaa</B></H2>\r
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-<TD><A HREF="#compbio.engine.cluster.drmaa"><B>compbio.engine.cluster.drmaa</B></A></TD>\r
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diff --git a/website/full_javadoc/compbio/engine/cluster/dundee/_Queue.html b/website/full_javadoc/compbio/engine/cluster/dundee/_Queue.html

deleted file mode 100644 (file)

index 613a3c0..0000000
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+++ /dev/null
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-<!--NewPage-->\r
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-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-_Queue\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
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-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="_Queue";\r
-    }\r
-}\r
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-&nbsp;PREV CLASS&nbsp;\r
-&nbsp;<A HREF="../../../../compbio/engine/cluster/dundee/_QueueConstraints.html" title="class in compbio.engine.cluster.dundee"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/engine/cluster/dundee/_Queue.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
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-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;<A HREF="#enum_constant_summary">ENUM CONSTANTS</A>&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;<A HREF="#enum_constant_detail">ENUM CONSTANTS</A>&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
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-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
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-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.engine.cluster.dundee</FONT>\r
-<BR>\r
-Enum _Queue</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../../../resources/inherit.gif" ALT="extended by ">java.lang.Enum&lt;<A HREF="../../../../compbio/engine/cluster/dundee/_Queue.html" title="enum in compbio.engine.cluster.dundee">_Queue</A>&gt;\r
-      <IMG SRC="../../../../resources/inherit.gif" ALT="extended by "><B>compbio.engine.cluster.dundee._Queue</B>\r
-</PRE>\r
-<DL>\r
-<DT><B>All Implemented Interfaces:</B> <DD>java.io.Serializable, java.lang.Comparable&lt;<A HREF="../../../../compbio/engine/cluster/dundee/_Queue.html" title="enum in compbio.engine.cluster.dundee">_Queue</A>&gt;</DD>\r
-</DL>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public enum <B>_Queue</B><DT>extends java.lang.Enum&lt;<A HREF="../../../../compbio/engine/cluster/dundee/_Queue.html" title="enum in compbio.engine.cluster.dundee">_Queue</A>&gt;</DL>\r
-</PRE>\r
-\r
-<P>\r
-<HR>\r
-\r
-<P>\r
-<!-- =========== ENUM CONSTANT SUMMARY =========== -->\r
-\r
-<A NAME="enum_constant_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Enum Constant Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../../compbio/engine/cluster/dundee/_Queue.html#BIGINT">BIGINT</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../../compbio/engine/cluster/dundee/_Queue.html#BIGMEM">BIGMEM</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../../compbio/engine/cluster/dundee/_Queue.html#BIT64">BIT64</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../../compbio/engine/cluster/dundee/_Queue.html#DEVEL">DEVEL</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Order of the constraint reflect the priority of the queue</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../../compbio/engine/cluster/dundee/_Queue.html#PRIBIT64">PRIBIT64</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;int</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/engine/cluster/dundee/_Queue.html#getMemoryLimit()">getMemoryLimit</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;return max memory limit in Mb</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../../compbio/engine/cluster/dundee/_Queue.html" title="enum in compbio.engine.cluster.dundee">_Queue</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/engine/cluster/dundee/_Queue.html#getQueue(int, int)">getQueue</A></B>(int&nbsp;maxMemory,\r
-         int&nbsp;timeLimitInHours)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/engine/cluster/dundee/_Queue.html" title="enum in compbio.engine.cluster.dundee">_Queue</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/engine/cluster/dundee/_Queue.html#getQueue(java.lang.String)">getQueue</A></B>(java.lang.String&nbsp;queueName)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../../compbio/engine/cluster/dundee/_Queue.html" title="enum in compbio.engine.cluster.dundee">_Queue</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/engine/cluster/dundee/_Queue.html#getQueueByMemoryRequirements(int)">getQueueByMemoryRequirements</A></B>(int&nbsp;maxMemory)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;int</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/engine/cluster/dundee/_Queue.html#getTimeLimit()">getTimeLimit</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0 - unlimited</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/engine/cluster/dundee/_Queue.html#hasTimeLimit()">hasTimeLimit</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/engine/cluster/dundee/_Queue.html#toString()">toString</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../../compbio/engine/cluster/dundee/_Queue.html" title="enum in compbio.engine.cluster.dundee">_Queue</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/engine/cluster/dundee/_Queue.html#valueOf(java.lang.String)">valueOf</A></B>(java.lang.String&nbsp;name)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Returns the enum constant of this type with the specified name.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../../compbio/engine/cluster/dundee/_Queue.html" title="enum in compbio.engine.cluster.dundee">_Queue</A>[]</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/engine/cluster/dundee/_Queue.html#values()">values</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Returns an array containing the constants of this enum type, in
-the order they are declared.</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Enum"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Enum</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>compareTo, equals, getDeclaringClass, hashCode, name, ordinal, valueOf</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>getClass, notify, notifyAll, wait, wait, wait</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ============ ENUM CONSTANT DETAIL =========== -->\r
-\r
-<A NAME="enum_constant_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Enum Constant Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="DEVEL"><!-- --></A><H3>\r
-DEVEL</H3>\r
-<PRE>\r
-public static final <A HREF="../../../../compbio/engine/cluster/dundee/_Queue.html" title="enum in compbio.engine.cluster.dundee">_Queue</A> <B>DEVEL</B></PRE>\r
-<DL>\r
-<DD>Order of the constraint reflect the priority of the queue\r
-<P>\r
-<DL>\r
-</DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="PRIBIT64"><!-- --></A><H3>\r
-PRIBIT64</H3>\r
-<PRE>\r
-public static final <A HREF="../../../../compbio/engine/cluster/dundee/_Queue.html" title="enum in compbio.engine.cluster.dundee">_Queue</A> <B>PRIBIT64</B></PRE>\r
-<DL>\r
-<DL>\r
-</DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="BIT64"><!-- --></A><H3>\r
-BIT64</H3>\r
-<PRE>\r
-public static final <A HREF="../../../../compbio/engine/cluster/dundee/_Queue.html" title="enum in compbio.engine.cluster.dundee">_Queue</A> <B>BIT64</B></PRE>\r
-<DL>\r
-<DL>\r
-</DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="BIGINT"><!-- --></A><H3>\r
-BIGINT</H3>\r
-<PRE>\r
-public static final <A HREF="../../../../compbio/engine/cluster/dundee/_Queue.html" title="enum in compbio.engine.cluster.dundee">_Queue</A> <B>BIGINT</B></PRE>\r
-<DL>\r
-<DL>\r
-</DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="BIGMEM"><!-- --></A><H3>\r
-BIGMEM</H3>\r
-<PRE>\r
-public static final <A HREF="../../../../compbio/engine/cluster/dundee/_Queue.html" title="enum in compbio.engine.cluster.dundee">_Queue</A> <B>BIGMEM</B></PRE>\r
-<DL>\r
-<DL>\r
-</DL>\r
-</DL>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
-<A NAME="method_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="values()"><!-- --></A><H3>\r
-values</H3>\r
-<PRE>\r
-public static <A HREF="../../../../compbio/engine/cluster/dundee/_Queue.html" title="enum in compbio.engine.cluster.dundee">_Queue</A>[] <B>values</B>()</PRE>\r
-<DL>\r
-<DD>Returns an array containing the constants of this enum type, in
-the order they are declared.  This method may be used to iterate
-over the constants as follows:
-<pre>
-for (_Queue c : _Queue.values())
-&nbsp;   System.out.println(c);
-</pre>\r
-<P>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>an array containing the constants of this enum type, in
-the order they are declared</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="valueOf(java.lang.String)"><!-- --></A><H3>\r
-valueOf</H3>\r
-<PRE>\r
-public static <A HREF="../../../../compbio/engine/cluster/dundee/_Queue.html" title="enum in compbio.engine.cluster.dundee">_Queue</A> <B>valueOf</B>(java.lang.String&nbsp;name)</PRE>\r
-<DL>\r
-<DD>Returns the enum constant of this type with the specified name.
-The string must match <I>exactly</I> an identifier used to declare an
-enum constant in this type.  (Extraneous whitespace characters are 
-not permitted.)\r
-<P>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>name</CODE> - the name of the enum constant to be returned.\r
-<DT><B>Returns:</B><DD>the enum constant with the specified name\r
-<DT><B>Throws:</B>\r
-<DD><CODE>java.lang.IllegalArgumentException</CODE> - if this enum type has no constant
-with the specified name\r
-<DD><CODE>java.lang.NullPointerException</CODE> - if the argument is null</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="toString()"><!-- --></A><H3>\r
-toString</H3>\r
-<PRE>\r
-public java.lang.String <B>toString</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Overrides:</B><DD><CODE>toString</CODE> in class <CODE>java.lang.Enum&lt;<A HREF="../../../../compbio/engine/cluster/dundee/_Queue.html" title="enum in compbio.engine.cluster.dundee">_Queue</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getTimeLimit()"><!-- --></A><H3>\r
-getTimeLimit</H3>\r
-<PRE>\r
-public int <B>getTimeLimit</B>()</PRE>\r
-<DL>\r
-<DD>0 - unlimited\r
-<P>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>max runtime in hours</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="hasTimeLimit()"><!-- --></A><H3>\r
-hasTimeLimit</H3>\r
-<PRE>\r
-public boolean <B>hasTimeLimit</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>true if the queue has time limit, false overwise</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getMemoryLimit()"><!-- --></A><H3>\r
-getMemoryLimit</H3>\r
-<PRE>\r
-public int <B>getMemoryLimit</B>()</PRE>\r
-<DL>\r
-<DD>return max memory limit in Mb\r
-<P>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getQueueByMemoryRequirements(int)"><!-- --></A><H3>\r
-getQueueByMemoryRequirements</H3>\r
-<PRE>\r
-public static <A HREF="../../../../compbio/engine/cluster/dundee/_Queue.html" title="enum in compbio.engine.cluster.dundee">_Queue</A> <B>getQueueByMemoryRequirements</B>(int&nbsp;maxMemory)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getQueue(int, int)"><!-- --></A><H3>\r
-getQueue</H3>\r
-<PRE>\r
-public static <A HREF="../../../../compbio/engine/cluster/dundee/_Queue.html" title="enum in compbio.engine.cluster.dundee">_Queue</A> <B>getQueue</B>(int&nbsp;maxMemory,\r
-                              int&nbsp;timeLimitInHours)</PRE>\r
-<DL>\r
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-</DD>\r
-</DL>\r
-<HR>\r
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-<A NAME="getQueue(java.lang.String)"><!-- --></A><H3>\r
-getQueue</H3>\r
-<PRE>\r
-public <A HREF="../../../../compbio/engine/cluster/dundee/_Queue.html" title="enum in compbio.engine.cluster.dundee">_Queue</A> <B>getQueue</B>(java.lang.String&nbsp;queueName)</PRE>\r
-<DL>\r
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-</DD>\r
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-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/engine/cluster/dundee/_Queue.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
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diff --git a/website/full_javadoc/compbio/engine/cluster/dundee/_QueueConstraints.html b/website/full_javadoc/compbio/engine/cluster/dundee/_QueueConstraints.html

deleted file mode 100644 (file)

index f951552..0000000
--- a/website/full_javadoc/compbio/engine/cluster/dundee/_QueueConstraints.html
+++ /dev/null
@@ -1,281 +0,0 @@
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-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/_QueueConstraints.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
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-  </TR>\r
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-</SCRIPT>\r
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-\r
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-<FONT SIZE="-1">\r
-compbio.engine.cluster.dundee</FONT>\r
-<BR>\r
-Class _QueueConstraints</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../../../resources/inherit.gif" ALT="extended by "><B>compbio.engine.cluster.dundee._QueueConstraints</B>\r
-</PRE>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public final class <B>_QueueConstraints</B><DT>extends java.lang.Object</DL>\r
-</PRE>\r
-\r
-<P>\r
-<HR>\r
-\r
-<P>\r
-<!-- =========== FIELD SUMMARY =========== -->\r
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-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;int</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/engine/cluster/dundee/_QueueConstraints.html#FIRST_MEMORY_LIMIT">FIRST_MEMORY_LIMIT</A></B></CODE>\r
-\r
-<BR>\r
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-<CODE>static&nbsp;int</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/engine/cluster/dundee/_QueueConstraints.html#LONG_TIME_LIMIT">LONG_TIME_LIMIT</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
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-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;int</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/engine/cluster/dundee/_QueueConstraints.html#MAX_MEMORY_LIMIT">MAX_MEMORY_LIMIT</A></B></CODE>\r
-\r
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-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;int</CODE></FONT></TD>\r
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-\r
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-\r
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-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
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-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
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-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>\r
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-<B>Field Detail</B></FONT></TH>\r
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-</TABLE>\r
-\r
-<A NAME="SHORT_TIME_LIMIT"><!-- --></A><H3>\r
-SHORT_TIME_LIMIT</H3>\r
-<PRE>\r
-public static final int <B>SHORT_TIME_LIMIT</B></PRE>\r
-<DL>\r
-<DL>\r
-<DT><B>See Also:</B><DD><A HREF="../../../../constant-values.html#compbio.engine.cluster.dundee._QueueConstraints.SHORT_TIME_LIMIT">Constant Field Values</A></DL>\r
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-<HR>\r
-\r
-<A NAME="LONG_TIME_LIMIT"><!-- --></A><H3>\r
-LONG_TIME_LIMIT</H3>\r
-<PRE>\r
-public static final int <B>LONG_TIME_LIMIT</B></PRE>\r
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-<DL>\r
-<DT><B>See Also:</B><DD><A HREF="../../../../constant-values.html#compbio.engine.cluster.dundee._QueueConstraints.LONG_TIME_LIMIT">Constant Field Values</A></DL>\r
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-\r
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-<PRE>\r
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-<DL>\r
-<DL>\r
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-<HR>\r
-\r
-<A NAME="MAX_MEMORY_LIMIT"><!-- --></A><H3>\r
-MAX_MEMORY_LIMIT</H3>\r
-<PRE>\r
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-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
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-\r
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-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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-  </TR>\r
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-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
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diff --git a/website/full_javadoc/compbio/engine/cluster/dundee/class-use/_Queue.html b/website/full_javadoc/compbio/engine/cluster/dundee/class-use/_Queue.html

deleted file mode 100644 (file)

index d5b990c..0000000
--- a/website/full_javadoc/compbio/engine/cluster/dundee/class-use/_Queue.html
+++ /dev/null
@@ -1,243 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Uses of Class compbio.engine.cluster.dundee._Queue\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Uses of Class compbio.engine.cluster.dundee._Queue";\r
-    }\r
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-\r
-</HEAD>\r
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-<BODY BGCOLOR="white" onload="windowTitle();">\r
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-\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../../compbio/engine/cluster/dundee/_Queue.html" title="enum in compbio.engine.cluster.dundee"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
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-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../../index.html?compbio/engine/cluster/dundee/\class-use_Queue.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
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-\r
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-<CENTER>\r
-<H2>\r
-<B>Uses of Class<br>compbio.engine.cluster.dundee._Queue</B></H2>\r
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-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Packages that use <A HREF="../../../../../compbio/engine/cluster/dundee/_Queue.html" title="enum in compbio.engine.cluster.dundee">_Queue</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.engine.cluster.dundee"><B>compbio.engine.cluster.dundee</B></A></TD>\r
-<TD>&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.runner"><B>compbio.runner</B></A></TD>\r
-<TD>Utilities commonly used by all runners.&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.engine.cluster.dundee"><!-- --></A>\r
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-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../../../compbio/engine/cluster/dundee/_Queue.html" title="enum in compbio.engine.cluster.dundee">_Queue</A> in <A HREF="../../../../../compbio/engine/cluster/dundee/package-summary.html">compbio.engine.cluster.dundee</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
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-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../../compbio/engine/cluster/dundee/package-summary.html">compbio.engine.cluster.dundee</A> that return <A HREF="../../../../../compbio/engine/cluster/dundee/_Queue.html" title="enum in compbio.engine.cluster.dundee">_Queue</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../../../compbio/engine/cluster/dundee/_Queue.html" title="enum in compbio.engine.cluster.dundee">_Queue</A></CODE></FONT></TD>\r
-<TD><CODE><B>_Queue.</B><B><A HREF="../../../../../compbio/engine/cluster/dundee/_Queue.html#getQueue(int, int)">getQueue</A></B>(int&nbsp;maxMemory,\r
-         int&nbsp;timeLimitInHours)</CODE>\r
-\r
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-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
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-<CODE>&nbsp;<A HREF="../../../../../compbio/engine/cluster/dundee/_Queue.html" title="enum in compbio.engine.cluster.dundee">_Queue</A></CODE></FONT></TD>\r
-<TD><CODE><B>_Queue.</B><B><A HREF="../../../../../compbio/engine/cluster/dundee/_Queue.html#getQueue(java.lang.String)">getQueue</A></B>(java.lang.String&nbsp;queueName)</CODE>\r
-\r
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-<CODE>static&nbsp;<A HREF="../../../../../compbio/engine/cluster/dundee/_Queue.html" title="enum in compbio.engine.cluster.dundee">_Queue</A></CODE></FONT></TD>\r
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-\r
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-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Returns the enum constant of this type with the specified name.</TD>\r
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-<CODE>static&nbsp;<A HREF="../../../../../compbio/engine/cluster/dundee/_Queue.html" title="enum in compbio.engine.cluster.dundee">_Queue</A>[]</CODE></FONT></TD>\r
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-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Returns an array containing the constants of this enum type, in
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-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../../../compbio/engine/cluster/dundee/_Queue.html" title="enum in compbio.engine.cluster.dundee">_Queue</A> in <A HREF="../../../../../compbio/runner/package-summary.html">compbio.runner</A></FONT></TH>\r
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-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../../compbio/runner/package-summary.html">compbio.runner</A> that return <A HREF="../../../../../compbio/engine/cluster/dundee/_Queue.html" title="enum in compbio.engine.cluster.dundee">_Queue</A></FONT></TH>\r
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-<CODE>&nbsp;<A HREF="../../../../../compbio/engine/cluster/dundee/_Queue.html" title="enum in compbio.engine.cluster.dundee">_Queue</A></CODE></FONT></TD>\r
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-&nbsp;<SCRIPT type="text/javascript">\r
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-<A NAME="skip-navbar_bottom"></A>\r
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diff --git a/website/full_javadoc/compbio/engine/cluster/dundee/class-use/_QueueConstraints.html b/website/full_javadoc/compbio/engine/cluster/dundee/class-use/_QueueConstraints.html

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-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
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-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
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-<A NAME="navbar_top_firstrow"><!-- --></A>\r
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-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
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-  <A HREF="../../../../../index.html?compbio/engine/cluster/dundee/\class-use_QueueConstraints.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="_QueueConstraints.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
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-</SCRIPT>\r
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-\r
-\r
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-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
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-<CENTER>\r
-<H2>\r
-<B>Uses of Class<br>compbio.engine.cluster.dundee._QueueConstraints</B></H2>\r
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-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
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-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
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diff --git a/website/full_javadoc/compbio/engine/cluster/dundee/package-use.html b/website/full_javadoc/compbio/engine/cluster/dundee/package-use.html

deleted file mode 100644 (file)

index 998ba3c..0000000
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-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.engine.cluster.dundee"><B>compbio.engine.cluster.dundee</B></A></TD>\r
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-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.runner"><B>compbio.runner</B></A></TD>\r
-<TD>Utilities commonly used by all runners.&nbsp;</TD>\r
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-&nbsp;\r
-<P>\r
-<A NAME="compbio.engine.cluster.dundee"><!-- --></A>\r
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-Classes in <A HREF="../../../../compbio/engine/cluster/dundee/package-summary.html">compbio.engine.cluster.dundee</A> used by <A HREF="../../../../compbio/engine/cluster/dundee/package-summary.html">compbio.engine.cluster.dundee</A></FONT></TH>\r
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-Classes in <A HREF="../../../../compbio/engine/cluster/dundee/package-summary.html">compbio.engine.cluster.dundee</A> used by <A HREF="../../../../compbio/runner/package-summary.html">compbio.runner</A></FONT></TH>\r
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diff --git a/website/full_javadoc/compbio/engine/conf/DirectoryManager.html b/website/full_javadoc/compbio/engine/conf/DirectoryManager.html

deleted file mode 100644 (file)

index f4e425b..0000000
--- a/website/full_javadoc/compbio/engine/conf/DirectoryManager.html
+++ /dev/null
@@ -1,307 +0,0 @@
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-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/DirectoryManager.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/engine/conf/_Key.html" title="class in compbio.engine.conf"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../compbio/engine/conf/PropertyHelperManager.html" title="class in compbio.engine.conf"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/engine/conf/DirectoryManager.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="DirectoryManager.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;<A HREF="#field_summary">FIELD</A>&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;<A HREF="#field_detail">FIELD</A>&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/engine/conf/PropertyHelperManager.html b/website/full_javadoc/compbio/engine/conf/PropertyHelperManager.html

deleted file mode 100644 (file)

index d4816f8..0000000
--- a/website/full_javadoc/compbio/engine/conf/PropertyHelperManager.html
+++ /dev/null
@@ -1,332 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:49 GMT 2010 -->\r
-<TITLE>\r
-PropertyHelperManager\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="PropertyHelperManager";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/PropertyHelperManager.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/engine/conf/DirectoryManager.html" title="class in compbio.engine.conf"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../compbio/engine/conf/RunnerConfigMarshaller.html" title="class in compbio.engine.conf"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/engine/conf/PropertyHelperManager.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="PropertyHelperManager.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;<A HREF="#field_summary">FIELD</A>&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;<A HREF="#field_detail">FIELD</A>&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.engine.conf</FONT>\r
-<BR>\r
-Class PropertyHelperManager</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.engine.conf.PropertyHelperManager</B>\r
-</PRE>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public final class <B>PropertyHelperManager</B><DT>extends java.lang.Object</DL>\r
-</PRE>\r
-\r
-<P>\r
-<HR>\r
-\r
-<P>\r
-<!-- =========== FIELD SUMMARY =========== -->\r
-\r
-<A NAME="field_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Field Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/conf/PropertyHelperManager.html#confDir">confDir</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
-\r
-<A NAME="constructor_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Constructor Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/engine/conf/PropertyHelperManager.html#PropertyHelperManager()">PropertyHelperManager</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/conf/PropertyHelperManager.html#getLocalPath()">getLocalPath</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Method return the absolute path to the project root directory.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;compbio.util.PropertyHelper</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/conf/PropertyHelperManager.html#getPropertyHelper()">getPropertyHelper</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Ways to fix path problem: 1) find a path to WEB-INF directory based on
- the path to a known class.</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ============ FIELD DETAIL =========== -->\r
-\r
-<A NAME="field_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Field Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="confDir"><!-- --></A><H3>\r
-confDir</H3>\r
-<PRE>\r
-public static final java.lang.String <B>confDir</B></PRE>\r
-<DL>\r
-<DL>\r
-</DL>\r
-</DL>\r
-\r
-<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
-\r
-<A NAME="constructor_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Constructor Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="PropertyHelperManager()"><!-- --></A><H3>\r
-PropertyHelperManager</H3>\r
-<PRE>\r
-public <B>PropertyHelperManager</B>()</PRE>\r
-<DL>\r
-</DL>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
-<A NAME="method_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="getPropertyHelper()"><!-- --></A><H3>\r
-getPropertyHelper</H3>\r
-<PRE>\r
-public static compbio.util.PropertyHelper <B>getPropertyHelper</B>()</PRE>\r
-<DL>\r
-<DD>Ways to fix path problem: 1) find a path to WEB-INF directory based on
- the path to a known class. Then prepend this absolute path to the rest of
- paths pros: no input from user cons: relocation of the source may cause
- problems 2) Require users to add configuration directories to the class
- path and then load entries from it. pros: cons: Many paths needs to be
- added. Put significant burden on the user. Hard to tell web appl server
- to add these entries to its class path. 3) Ask for project source
- directory explicitly in the configuration. pros cons: similar to 1, but
- this initial configuration file must reside in well known location! Why
- ask users what can be found automatically? 4) Have everything in the
- location already in class path for tomcat. cons: only classes and
- lib/*.jar are added, eclipse will remove non classses from classes dir.
- 
- Try 1 - succeed.\r
-<P>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getLocalPath()"><!-- --></A><H3>\r
-getLocalPath</H3>\r
-<PRE>\r
-public static java.lang.String <B>getLocalPath</B>()</PRE>\r
-<DL>\r
-<DD>Method return the absolute path to the project root directory. It assumes
- the following structure of the project project root conf settings
- binaries WEB-INF classes compbio engine conf If the structure changes it
- must be reflected in this method\r
-<P>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>\r
-<DT><B>Throws:</B>\r
-<DD><CODE>javax.naming.ConfigurationException</CODE></DL>\r
-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/PropertyHelperManager.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/engine/conf/DirectoryManager.html" title="class in compbio.engine.conf"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../compbio/engine/conf/RunnerConfigMarshaller.html" title="class in compbio.engine.conf"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/engine/conf/PropertyHelperManager.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="PropertyHelperManager.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;<A HREF="#field_summary">FIELD</A>&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;<A HREF="#field_detail">FIELD</A>&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/engine/conf/RunnerConfigMarshaller.html b/website/full_javadoc/compbio/engine/conf/RunnerConfigMarshaller.html

deleted file mode 100644 (file)

index 6457ed8..0000000
--- a/website/full_javadoc/compbio/engine/conf/RunnerConfigMarshaller.html
+++ /dev/null
@@ -1,507 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:49 GMT 2010 -->\r
-<TITLE>\r
-RunnerConfigMarshaller\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
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-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="RunnerConfigMarshaller";\r
-    }\r
-}\r
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-\r
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-<FONT SIZE="-1">\r
-compbio.engine.conf</FONT>\r
-<BR>\r
-Class RunnerConfigMarshaller&lt;T&gt;</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.engine.conf.RunnerConfigMarshaller&lt;T&gt;</B>\r
-</PRE>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public class <B>RunnerConfigMarshaller&lt;T&gt;</B><DT>extends java.lang.Object</DL>\r
-</PRE>\r
-\r
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-<HR>\r
-\r
-<P>\r
-\r
-<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
-\r
-<A NAME="constructor_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Constructor Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/engine/conf/RunnerConfigMarshaller.html#RunnerConfigMarshaller(java.lang.Class)">RunnerConfigMarshaller</A></B>(java.lang.Class&lt;?&gt;&nbsp;rootClass)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/engine/conf/RunnerConfigMarshaller.html#RunnerConfigMarshaller(java.lang.Class, java.lang.Class...)">RunnerConfigMarshaller</A></B>(java.lang.Class&lt;?&gt;&nbsp;rootClass,\r
-                       java.lang.Class&lt;?&gt;...&nbsp;classes)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;javax.xml.validation.Schema</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/conf/RunnerConfigMarshaller.html#getSchema(java.lang.String)">getSchema</A></B>(java.lang.String&nbsp;schemafile)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;javax.xml.validation.Validator</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/conf/RunnerConfigMarshaller.html#getValidator(javax.xml.validation.Schema)">getValidator</A></B>(javax.xml.validation.Schema&nbsp;schema)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;javax.xml.validation.Validator</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/conf/RunnerConfigMarshaller.html#getValidator(java.lang.String)">getValidator</A></B>(java.lang.String&nbsp;schemafile)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
-<TR ALIGN="right" VALIGN="">\r
-<TD NOWRAP><FONT SIZE="-1">\r
-<CODE>&lt;V&gt; V</CODE></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/conf/RunnerConfigMarshaller.html#read(java.io.InputStream, java.lang.Class)">read</A></B>(java.io.InputStream&nbsp;instream,\r
-     java.lang.Class&lt;V&gt;&nbsp;resultElemType)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
-<TR ALIGN="right" VALIGN="">\r
-<TD NOWRAP><FONT SIZE="-1">\r
-<CODE>&lt;V&gt; V</CODE></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/conf/RunnerConfigMarshaller.html#read(java.io.InputStream, java.lang.Class, java.lang.Class...)">read</A></B>(java.io.InputStream&nbsp;instream,\r
-     java.lang.Class&lt;V&gt;&nbsp;resultElemType,\r
-     java.lang.Class&lt;?&gt;...&nbsp;classes)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
-<TR ALIGN="right" VALIGN="">\r
-<TD NOWRAP><FONT SIZE="-1">\r
-<CODE>&lt;V&gt; V</CODE></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/conf/RunnerConfigMarshaller.html#readAndValidate(java.io.InputStream, java.lang.Class)">readAndValidate</A></B>(java.io.InputStream&nbsp;document,\r
-                java.lang.Class&lt;V&gt;&nbsp;resultElemType)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/conf/RunnerConfigMarshaller.html#validate(javax.xml.validation.Validator, java.lang.String)">validate</A></B>(javax.xml.validation.Validator&nbsp;validator,\r
-         java.lang.String&nbsp;document)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/conf/RunnerConfigMarshaller.html#write(java.lang.Object, java.io.OutputStream)">write</A></B>(java.lang.Object&nbsp;xmlRootElement,\r
-      java.io.OutputStream&nbsp;out)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/conf/RunnerConfigMarshaller.html#writeAndValidate(java.lang.Object, java.lang.String, java.io.OutputStream)">writeAndValidate</A></B>(java.lang.Object&nbsp;xmlRootElement,\r
-                 java.lang.String&nbsp;schemafile,\r
-                 java.io.OutputStream&nbsp;out)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
-\r
-<A NAME="constructor_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Constructor Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="RunnerConfigMarshaller(java.lang.Class)"><!-- --></A><H3>\r
-RunnerConfigMarshaller</H3>\r
-<PRE>\r
-public <B>RunnerConfigMarshaller</B>(java.lang.Class&lt;?&gt;&nbsp;rootClass)\r
-                       throws javax.xml.bind.JAXBException</PRE>\r
-<DL>\r
-<DL>\r
-\r
-<DT><B>Throws:</B>\r
-<DD><CODE>javax.xml.bind.JAXBException</CODE></DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="RunnerConfigMarshaller(java.lang.Class, java.lang.Class...)"><!-- --></A><H3>\r
-RunnerConfigMarshaller</H3>\r
-<PRE>\r
-public <B>RunnerConfigMarshaller</B>(java.lang.Class&lt;?&gt;&nbsp;rootClass,\r
-                              java.lang.Class&lt;?&gt;...&nbsp;classes)\r
-                       throws javax.xml.bind.JAXBException</PRE>\r
-<DL>\r
-<DL>\r
-\r
-<DT><B>Throws:</B>\r
-<DD><CODE>javax.xml.bind.JAXBException</CODE></DL>\r
-</DL>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
-<A NAME="method_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="write(java.lang.Object, java.io.OutputStream)"><!-- --></A><H3>\r
-write</H3>\r
-<PRE>\r
-public void <B>write</B>(java.lang.Object&nbsp;xmlRootElement,\r
-                  java.io.OutputStream&nbsp;out)\r
-           throws javax.xml.bind.JAXBException,\r
-                  java.io.IOException</PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Throws:</B>\r
-<DD><CODE>javax.xml.bind.JAXBException</CODE>\r
-<DD><CODE>java.io.IOException</CODE></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="writeAndValidate(java.lang.Object, java.lang.String, java.io.OutputStream)"><!-- --></A><H3>\r
-writeAndValidate</H3>\r
-<PRE>\r
-public void <B>writeAndValidate</B>(java.lang.Object&nbsp;xmlRootElement,\r
-                             java.lang.String&nbsp;schemafile,\r
-                             java.io.OutputStream&nbsp;out)\r
-                      throws javax.xml.bind.JAXBException,\r
-                             java.io.IOException,\r
-                             org.xml.sax.SAXException</PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Throws:</B>\r
-<DD><CODE>javax.xml.bind.JAXBException</CODE>\r
-<DD><CODE>java.io.IOException</CODE>\r
-<DD><CODE>org.xml.sax.SAXException</CODE></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getSchema(java.lang.String)"><!-- --></A><H3>\r
-getSchema</H3>\r
-<PRE>\r
-public static javax.xml.validation.Schema <B>getSchema</B>(java.lang.String&nbsp;schemafile)\r
-                                             throws org.xml.sax.SAXException</PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Throws:</B>\r
-<DD><CODE>org.xml.sax.SAXException</CODE></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getValidator(java.lang.String)"><!-- --></A><H3>\r
-getValidator</H3>\r
-<PRE>\r
-public static javax.xml.validation.Validator <B>getValidator</B>(java.lang.String&nbsp;schemafile)\r
-                                                   throws org.xml.sax.SAXException</PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>\r
-<DT><B>Throws:</B>\r
-<DD><CODE>org.xml.sax.SAXException</CODE></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getValidator(javax.xml.validation.Schema)"><!-- --></A><H3>\r
-getValidator</H3>\r
-<PRE>\r
-public static javax.xml.validation.Validator <B>getValidator</B>(javax.xml.validation.Schema&nbsp;schema)\r
-                                                   throws org.xml.sax.SAXException</PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Throws:</B>\r
-<DD><CODE>org.xml.sax.SAXException</CODE></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="validate(javax.xml.validation.Validator, java.lang.String)"><!-- --></A><H3>\r
-validate</H3>\r
-<PRE>\r
-public static boolean <B>validate</B>(javax.xml.validation.Validator&nbsp;validator,\r
-                               java.lang.String&nbsp;document)\r
-                        throws java.io.IOException,\r
-                               org.xml.sax.SAXException</PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Throws:</B>\r
-<DD><CODE>java.io.IOException</CODE>\r
-<DD><CODE>org.xml.sax.SAXException</CODE></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="readAndValidate(java.io.InputStream, java.lang.Class)"><!-- --></A><H3>\r
-readAndValidate</H3>\r
-<PRE>\r
-public &lt;V&gt; V <B>readAndValidate</B>(java.io.InputStream&nbsp;document,\r
-                             java.lang.Class&lt;V&gt;&nbsp;resultElemType)\r
-                  throws javax.xml.bind.JAXBException,\r
-                         java.io.IOException,\r
-                         org.xml.sax.SAXException</PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Throws:</B>\r
-<DD><CODE>javax.xml.bind.JAXBException</CODE>\r
-<DD><CODE>java.io.IOException</CODE>\r
-<DD><CODE>org.xml.sax.SAXException</CODE></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="read(java.io.InputStream, java.lang.Class)"><!-- --></A><H3>\r
-read</H3>\r
-<PRE>\r
-public &lt;V&gt; V <B>read</B>(java.io.InputStream&nbsp;instream,\r
-                  java.lang.Class&lt;V&gt;&nbsp;resultElemType)\r
-       throws javax.xml.bind.JAXBException</PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Throws:</B>\r
-<DD><CODE>javax.xml.bind.JAXBException</CODE></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="read(java.io.InputStream, java.lang.Class, java.lang.Class...)"><!-- --></A><H3>\r
-read</H3>\r
-<PRE>\r
-public &lt;V&gt; V <B>read</B>(java.io.InputStream&nbsp;instream,\r
-                  java.lang.Class&lt;V&gt;&nbsp;resultElemType,\r
-                  java.lang.Class&lt;?&gt;...&nbsp;classes)\r
-       throws javax.xml.bind.JAXBException</PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Throws:</B>\r
-<DD><CODE>javax.xml.bind.JAXBException</CODE></DL>\r
-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/RunnerConfigMarshaller.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/engine/conf/PropertyHelperManager.html" title="class in compbio.engine.conf"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;NEXT CLASS</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/engine/conf/RunnerConfigMarshaller.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="RunnerConfigMarshaller.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
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diff --git a/website/full_javadoc/compbio/engine/conf/_Key.html b/website/full_javadoc/compbio/engine/conf/_Key.html

deleted file mode 100644 (file)

index 68d1965..0000000
--- a/website/full_javadoc/compbio/engine/conf/_Key.html
+++ /dev/null
@@ -1,354 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:49 GMT 2010 -->\r
-<TITLE>\r
-_Key\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="_Key";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/_Key.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV CLASS&nbsp;\r
-&nbsp;<A HREF="../../../compbio/engine/conf/DirectoryManager.html" title="class in compbio.engine.conf"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/engine/conf/_Key.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="_Key.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
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-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
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-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
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-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;<A HREF="#field_summary">FIELD</A>&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
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-</TR>\r
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-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
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-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.engine.conf</FONT>\r
-<BR>\r
-Class _Key</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.engine.conf._Key</B>\r
-</PRE>\r
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-\r
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-<!-- =========== FIELD SUMMARY =========== -->\r
-\r
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-<B>Field Summary</B></FONT></TH>\r
-</TR>\r
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-<CODE>static&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/conf/_Key.html#DELIM">DELIM</A></B></CODE>\r
-\r
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-<B>Constructor Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/engine/conf/_Key.html#_Key(java.lang.Class)">_Key</A></B>(java.lang.Class&lt;?&gt;&nbsp;clazz)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
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-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
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-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/conf/_Key.html#equals(java.lang.Object)">equals</A></B>(java.lang.Object&nbsp;obj)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;int</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/conf/_Key.html#hashCode()">hashCode</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../compbio/engine/conf/_Key.html" title="class in compbio.engine.conf">_Key</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/conf/_Key.html#parse(java.lang.String)">parse</A></B>(java.lang.String&nbsp;key)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/conf/_Key.html#toString()">toString</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>getClass, notify, notifyAll, wait, wait, wait</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ============ FIELD DETAIL =========== -->\r
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-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
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-<B>Field Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="DELIM"><!-- --></A><H3>\r
-DELIM</H3>\r
-<PRE>\r
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-<DL>\r
-<DL>\r
-<DT><B>See Also:</B><DD><A HREF="../../../constant-values.html#compbio.engine.conf._Key.DELIM">Constant Field Values</A></DL>\r
-</DL>\r
-\r
-<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
-\r
-<A NAME="constructor_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Constructor Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="_Key(java.lang.Class)"><!-- --></A><H3>\r
-_Key</H3>\r
-<PRE>\r
-public <B>_Key</B>(java.lang.Class&lt;?&gt;&nbsp;clazz)</PRE>\r
-<DL>\r
-</DL>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
-<A NAME="method_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="equals(java.lang.Object)"><!-- --></A><H3>\r
-equals</H3>\r
-<PRE>\r
-public boolean <B>equals</B>(java.lang.Object&nbsp;obj)</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Overrides:</B><DD><CODE>equals</CODE> in class <CODE>java.lang.Object</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="toString()"><!-- --></A><H3>\r
-toString</H3>\r
-<PRE>\r
-public java.lang.String <B>toString</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Overrides:</B><DD><CODE>toString</CODE> in class <CODE>java.lang.Object</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="hashCode()"><!-- --></A><H3>\r
-hashCode</H3>\r
-<PRE>\r
-public int <B>hashCode</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Overrides:</B><DD><CODE>hashCode</CODE> in class <CODE>java.lang.Object</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="parse(java.lang.String)"><!-- --></A><H3>\r
-parse</H3>\r
-<PRE>\r
-public static <A HREF="../../../compbio/engine/conf/_Key.html" title="class in compbio.engine.conf">_Key</A> <B>parse</B>(java.lang.String&nbsp;key)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/_Key.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV CLASS&nbsp;\r
-&nbsp;<A HREF="../../../compbio/engine/conf/DirectoryManager.html" title="class in compbio.engine.conf"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/engine/conf/_Key.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="_Key.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;<A HREF="#field_summary">FIELD</A>&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;<A HREF="#field_detail">FIELD</A>&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/engine/conf/class-use/DirectoryManager.html b/website/full_javadoc/compbio/engine/conf/class-use/DirectoryManager.html

deleted file mode 100644 (file)

index 8152d4c..0000000
--- a/website/full_javadoc/compbio/engine/conf/class-use/DirectoryManager.html
+++ /dev/null
@@ -1,144 +0,0 @@
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-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Uses of Class compbio.engine.conf.DirectoryManager\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
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diff --git a/website/full_javadoc/compbio/engine/conf/class-use/PropertyHelperManager.html b/website/full_javadoc/compbio/engine/conf/class-use/PropertyHelperManager.html

deleted file mode 100644 (file)

index e8d0067..0000000
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-\r
-<SCRIPT type="text/javascript">\r
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-    if (location.href.indexOf('is-external=true') == -1) {\r
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-No usage of compbio.engine.conf.PropertyHelperManager\r
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diff --git a/website/full_javadoc/compbio/engine/conf/class-use/RunnerConfigMarshaller.html b/website/full_javadoc/compbio/engine/conf/class-use/RunnerConfigMarshaller.html

deleted file mode 100644 (file)

index deeac1c..0000000
--- a/website/full_javadoc/compbio/engine/conf/class-use/RunnerConfigMarshaller.html
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-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
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-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
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-<CENTER>\r
-<H2>\r
-<B>Uses of Class<br>compbio.engine.conf.RunnerConfigMarshaller</B></H2>\r
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-No usage of compbio.engine.conf.RunnerConfigMarshaller\r
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-<HR>\r
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diff --git a/website/full_javadoc/compbio/engine/conf/class-use/_Key.html b/website/full_javadoc/compbio/engine/conf/class-use/_Key.html

deleted file mode 100644 (file)

index 223d824..0000000
--- a/website/full_javadoc/compbio/engine/conf/class-use/_Key.html
+++ /dev/null
@@ -1,180 +0,0 @@
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-  </TR>\r
-</TABLE>\r
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-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
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-  <A HREF="../../../../index.html?compbio/engine/conf/\class-use_Key.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
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-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
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-</SCRIPT>\r
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-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
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-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-<B>Uses of Class<br>compbio.engine.conf._Key</B></H2>\r
-</CENTER>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Packages that use <A HREF="../../../../compbio/engine/conf/_Key.html" title="class in compbio.engine.conf">_Key</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.engine.conf"><B>compbio.engine.conf</B></A></TD>\r
-<TD>Classes commonly used by both engines.&nbsp;</TD>\r
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-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.engine.conf"><!-- --></A>\r
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-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../../compbio/engine/conf/_Key.html" title="class in compbio.engine.conf">_Key</A> in <A HREF="../../../../compbio/engine/conf/package-summary.html">compbio.engine.conf</A></FONT></TH>\r
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-\r
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-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/engine/conf/package-summary.html">compbio.engine.conf</A> that return <A HREF="../../../../compbio/engine/conf/_Key.html" title="class in compbio.engine.conf">_Key</A></FONT></TH>\r
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-<CODE>static&nbsp;<A HREF="../../../../compbio/engine/conf/_Key.html" title="class in compbio.engine.conf">_Key</A></CODE></FONT></TD>\r
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diff --git a/website/full_javadoc/compbio/engine/conf/package-frame.html b/website/full_javadoc/compbio/engine/conf/package-frame.html

deleted file mode 100644 (file)

index 29f4ef3..0000000
--- a/website/full_javadoc/compbio/engine/conf/package-frame.html
+++ /dev/null
@@ -1,38 +0,0 @@
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diff --git a/website/full_javadoc/compbio/engine/conf/package-summary.html b/website/full_javadoc/compbio/engine/conf/package-summary.html

deleted file mode 100644 (file)

index 7dc8a3b..0000000
--- a/website/full_javadoc/compbio/engine/conf/package-summary.html
+++ /dev/null
@@ -1,188 +0,0 @@
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-<META NAME="date" CONTENT="2010-02-17">\r
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-<!-- ========= START OF TOP NAVBAR ======= -->\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Class</FONT>&nbsp;</TD>\r
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-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
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-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/engine/conf/package-summary.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
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-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
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-<H2>\r
-Package compbio.engine.conf\r
-</H2>\r
-Classes commonly used by both engines.\r
-<P>\r
-<B>See:</B>\r
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-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Class Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../../compbio/engine/conf/_Key.html" title="class in compbio.engine.conf">_Key</A></B></TD>\r
-<TD>&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../../compbio/engine/conf/DirectoryManager.html" title="class in compbio.engine.conf">DirectoryManager</A></B></TD>\r
-<TD>&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../../compbio/engine/conf/PropertyHelperManager.html" title="class in compbio.engine.conf">PropertyHelperManager</A></B></TD>\r
-<TD>&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../../compbio/engine/conf/RunnerConfigMarshaller.html" title="class in compbio.engine.conf">RunnerConfigMarshaller&lt;T&gt;</A></B></TD>\r
-<TD>&nbsp;</TD>\r
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-</TABLE>\r
-&nbsp;\r
-\r
-<P>\r
-<A NAME="package_description"><!-- --></A><H2>\r
-Package compbio.engine.conf Description\r
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-\r
-<P>\r
-Classes commonly used by both engines.\r
-<P>\r
-\r
-<P>\r
-<DL>\r
-<DT><B>Author:</B></DT>\r
-  <DD>Petr Troshin 
- 
-        Date January 2010</DD>\r
-</DL>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
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diff --git a/website/full_javadoc/compbio/engine/conf/package-use.html b/website/full_javadoc/compbio/engine/conf/package-use.html

deleted file mode 100644 (file)

index 46402ba..0000000
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diff --git a/website/full_javadoc/compbio/engine/local/AsyncLocalRunner.html b/website/full_javadoc/compbio/engine/local/AsyncLocalRunner.html

deleted file mode 100644 (file)

index 4e4459d..0000000
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+++ /dev/null
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
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-&nbsp;<A HREF="../../../compbio/engine/local/ExecutableWrapper.html" title="class in compbio.engine.local"><B>NEXT CLASS</B></A></FONT></TD>\r
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-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
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-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.engine.local</FONT>\r
-<BR>\r
-Class AsyncLocalRunner</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.engine.local.AsyncLocalRunner</B>\r
-</PRE>\r
-<DL>\r
-<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine">AsyncExecutor</A></DD>\r
-</DL>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public final class <B>AsyncLocalRunner</B><DT>extends java.lang.Object<DT>implements <A HREF="../../../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine">AsyncExecutor</A></DL>\r
-</PRE>\r
-\r
-<P>\r
-<HR>\r
-\r
-<P>\r
-\r
-<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
-\r
-<A NAME="constructor_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Constructor Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/engine/local/AsyncLocalRunner.html#AsyncLocalRunner()">AsyncLocalRunner</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/local/AsyncLocalRunner.html#cancelJob(java.lang.String)">cancelJob</A></B>(java.lang.String&nbsp;jobId)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Stop running job.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/local/AsyncLocalRunner.html#cleanup(java.lang.String)">cleanup</A></B>(java.lang.String&nbsp;jobId)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Remove all files and a job directory for a jobid.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/local/AsyncLocalRunner.html#getJobStatus(java.lang.String)">getJobStatus</A></B>(java.lang.String&nbsp;jobId)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Query the status of the job</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/local/AsyncLocalRunner.html#getResults(java.lang.String)">getResults</A></B>(java.lang.String&nbsp;taskId)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Retrieve the results of the job.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/local/AsyncLocalRunner.html#getWorkDirectory(java.lang.String)">getWorkDirectory</A></B>(java.lang.String&nbsp;jobId)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/local/AsyncLocalRunner.html#submitJob(compbio.engine.client.ConfiguredExecutable)">submitJob</A></B>(<A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;executable)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Submits job for the execution
- Immediate execution is not guaranteed, this method puts the job in the queue.</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
-\r
-<A NAME="constructor_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Constructor Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="AsyncLocalRunner()"><!-- --></A><H3>\r
-AsyncLocalRunner</H3>\r
-<PRE>\r
-public <B>AsyncLocalRunner</B>()</PRE>\r
-<DL>\r
-</DL>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
-<A NAME="method_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="getWorkDirectory(java.lang.String)"><!-- --></A><H3>\r
-getWorkDirectory</H3>\r
-<PRE>\r
-public java.lang.String <B>getWorkDirectory</B>(java.lang.String&nbsp;jobId)</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/AsyncExecutor.html#getWorkDirectory(java.lang.String)">getWorkDirectory</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine">AsyncExecutor</A></CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>jobId</CODE> - unique job identifier\r
-<DT><B>Returns:</B><DD>task working directory</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="cancelJob(java.lang.String)"><!-- --></A><H3>\r
-cancelJob</H3>\r
-<PRE>\r
-public boolean <B>cancelJob</B>(java.lang.String&nbsp;jobId)</PRE>\r
-<DL>\r
-<DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/engine/AsyncExecutor.html#cancelJob(java.lang.String)">AsyncExecutor</A></CODE></B></DD>\r
-<DD>Stop running job. Please not that this method does not guarantee to remove the job directory and files in it.\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/AsyncExecutor.html#cancelJob(java.lang.String)">cancelJob</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine">AsyncExecutor</A></CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>true if job was cancelled successfully, false otherwise</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getJobStatus(java.lang.String)"><!-- --></A><H3>\r
-getJobStatus</H3>\r
-<PRE>\r
-public <A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A> <B>getJobStatus</B>(java.lang.String&nbsp;jobId)</PRE>\r
-<DL>\r
-<DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/engine/AsyncExecutor.html#getJobStatus(java.lang.String)">AsyncExecutor</A></CODE></B></DD>\r
-<DD>Query the status of the job\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/AsyncExecutor.html#getJobStatus(java.lang.String)">getJobStatus</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine">AsyncExecutor</A></CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>The JobStatus object representing the status of the job<DT><B>See Also:</B><DD><A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata"><CODE>JobStatus</CODE></A></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="submitJob(compbio.engine.client.ConfiguredExecutable)"><!-- --></A><H3>\r
-submitJob</H3>\r
-<PRE>\r
-public java.lang.String <B>submitJob</B>(<A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;executable)\r
-                           throws <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></PRE>\r
-<DL>\r
-<DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/engine/AsyncExecutor.html#submitJob(compbio.engine.client.ConfiguredExecutable)">AsyncExecutor</A></CODE></B></DD>\r
-<DD>Submits job for the execution
- Immediate execution is not guaranteed, this method puts the job in the queue. 
- All it guarantees that the job will be eventually executed. 
- The start of execution will depend on the number of jobs in the queue.\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/AsyncExecutor.html#submitJob(compbio.engine.client.ConfiguredExecutable)">submitJob</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine">AsyncExecutor</A></CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>unique job identifier\r
-<DT><B>Throws:</B>\r
-<DD><CODE><A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></CODE> - if submission fails. This usually happens due to the problem on a server side.</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="cleanup(java.lang.String)"><!-- --></A><H3>\r
-cleanup</H3>\r
-<PRE>\r
-public boolean <B>cleanup</B>(java.lang.String&nbsp;jobId)</PRE>\r
-<DL>\r
-<DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/engine/AsyncExecutor.html#cleanup(java.lang.String)">AsyncExecutor</A></CODE></B></DD>\r
-<DD>Remove all files and a job directory for a jobid.\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/AsyncExecutor.html#cleanup(java.lang.String)">cleanup</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine">AsyncExecutor</A></CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>jobId</CODE> - \r
-<DT><B>Returns:</B><DD></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getResults(java.lang.String)"><!-- --></A><H3>\r
-getResults</H3>\r
-<PRE>\r
-public <A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt; <B>getResults</B>(java.lang.String&nbsp;taskId)\r
-                                   throws <A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></PRE>\r
-<DL>\r
-<DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/engine/AsyncExecutor.html#getResults(java.lang.String)">AsyncExecutor</A></CODE></B></DD>\r
-<DD>Retrieve the results of the job. Please not that current implementations of this method 
- blocks if the task is running until the end of the calculation.\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/AsyncExecutor.html#getResults(java.lang.String)">getResults</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine">AsyncExecutor</A></CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>taskId</CODE> - job identifier obtained at the job submission\r
-<DT><B>Returns:</B><DD>ConfiguredExecutable object from which result can be obtained\r
-<DT><B>Throws:</B>\r
-<DD><CODE><A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></CODE> - if the result is not available for whatever reason. 
- Could be due to execution failure, or due to the results being removed from the server at 
- the time of request.</DL>\r
-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/AsyncLocalRunner.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
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-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/engine/local/_TrackingExecutor.html" title="class in compbio.engine.local"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../compbio/engine/local/ExecutableWrapper.html" title="class in compbio.engine.local"><B>NEXT CLASS</B></A></FONT></TD>\r
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-&nbsp;<A HREF="AsyncLocalRunner.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
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-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/engine/local/ExecutableWrapper.html b/website/full_javadoc/compbio/engine/local/ExecutableWrapper.html

deleted file mode 100644 (file)

index 421469f..0000000
--- a/website/full_javadoc/compbio/engine/local/ExecutableWrapper.html
+++ /dev/null
@@ -1,331 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-ExecutableWrapper\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="ExecutableWrapper";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/ExecutableWrapper.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/engine/local/AsyncLocalRunner.html" title="class in compbio.engine.local"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../compbio/engine/local/LocalEngineUtil.html" title="class in compbio.engine.local"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/engine/local/ExecutableWrapper.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="ExecutableWrapper.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;<A HREF="#field_summary">FIELD</A>&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;<A HREF="#field_detail">FIELD</A>&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.engine.local</FONT>\r
-<BR>\r
-Class ExecutableWrapper</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.engine.local.ExecutableWrapper</B>\r
-</PRE>\r
-<DL>\r
-<DT><B>All Implemented Interfaces:</B> <DD>java.util.concurrent.Callable&lt;<A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&gt;</DD>\r
-</DL>\r
-<HR>\r
-<DL>\r
-<DT><PRE><FONT SIZE="-1">@Immutable\r
-</FONT>public final class <B>ExecutableWrapper</B><DT>extends java.lang.Object<DT>implements java.util.concurrent.Callable&lt;<A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&gt;</DL>\r
-</PRE>\r
-\r
-<P>\r
-<HR>\r
-\r
-<P>\r
-<!-- =========== FIELD SUMMARY =========== -->\r
-\r
-<A NAME="field_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Field Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/local/ExecutableWrapper.html#PROC_ERR_FILE">PROC_ERR_FILE</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/local/ExecutableWrapper.html#PROC_OUT_FILE">PROC_OUT_FILE</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
-\r
-<A NAME="constructor_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Constructor Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/engine/local/ExecutableWrapper.html#ExecutableWrapper(compbio.engine.client.ConfiguredExecutable, java.lang.String)">ExecutableWrapper</A></B>(<A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;executable,\r
-                  java.lang.String&nbsp;workDirectory)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/local/ExecutableWrapper.html#call()">call</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;It is vital that output and error streams are captured immediately for
- this call() to succeed.</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ============ FIELD DETAIL =========== -->\r
-\r
-<A NAME="field_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Field Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="PROC_OUT_FILE"><!-- --></A><H3>\r
-PROC_OUT_FILE</H3>\r
-<PRE>\r
-public static final java.lang.String <B>PROC_OUT_FILE</B></PRE>\r
-<DL>\r
-<DL>\r
-<DT><B>See Also:</B><DD><A HREF="../../../constant-values.html#compbio.engine.local.ExecutableWrapper.PROC_OUT_FILE">Constant Field Values</A></DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="PROC_ERR_FILE"><!-- --></A><H3>\r
-PROC_ERR_FILE</H3>\r
-<PRE>\r
-public static final java.lang.String <B>PROC_ERR_FILE</B></PRE>\r
-<DL>\r
-<DL>\r
-<DT><B>See Also:</B><DD><A HREF="../../../constant-values.html#compbio.engine.local.ExecutableWrapper.PROC_ERR_FILE">Constant Field Values</A></DL>\r
-</DL>\r
-\r
-<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
-\r
-<A NAME="constructor_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Constructor Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="ExecutableWrapper(compbio.engine.client.ConfiguredExecutable, java.lang.String)"><!-- --></A><H3>\r
-ExecutableWrapper</H3>\r
-<PRE>\r
-public <B>ExecutableWrapper</B>(<A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;executable,\r
-                         java.lang.String&nbsp;workDirectory)\r
-                  throws <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></PRE>\r
-<DL>\r
-<DL>\r
-\r
-<DT><B>Throws:</B>\r
-<DD><CODE><A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></CODE></DL>\r
-</DL>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
-<A NAME="method_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="call()"><!-- --></A><H3>\r
-call</H3>\r
-<PRE>\r
-public <A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt; <B>call</B>()\r
-                             throws java.io.IOException</PRE>\r
-<DL>\r
-<DD>It is vital that output and error streams are captured immediately for
- this call() to succeed. Thus each instance if ExecutableWrapper has 2 its
- own thread ready to capture the output. If executor could not execute
- capture immediately this could lead to the call method to stale, as
- execution could not proceed without output being captured. Every call to
- call() method will use 2 threads\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE>call</CODE> in interface <CODE>java.util.concurrent.Callable&lt;<A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-\r
-<DT><B>Throws:</B>\r
-<DD><CODE>java.io.IOException</CODE></DL>\r
-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/ExecutableWrapper.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/engine/local/AsyncLocalRunner.html" title="class in compbio.engine.local"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../compbio/engine/local/LocalEngineUtil.html" title="class in compbio.engine.local"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/engine/local/ExecutableWrapper.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="ExecutableWrapper.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;<A HREF="#field_summary">FIELD</A>&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;<A HREF="#field_detail">FIELD</A>&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/engine/local/LocalEngineUtil.html b/website/full_javadoc/compbio/engine/local/LocalEngineUtil.html

deleted file mode 100644 (file)

index a4edf4a..0000000
--- a/website/full_javadoc/compbio/engine/local/LocalEngineUtil.html
+++ /dev/null
@@ -1,335 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-LocalEngineUtil\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="LocalEngineUtil";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/LocalEngineUtil.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
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-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/engine/local/ExecutableWrapper.html" title="class in compbio.engine.local"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../compbio/engine/local/LocalExecutorService.html" title="class in compbio.engine.local"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/engine/local/LocalEngineUtil.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
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-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
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-</SCRIPT>\r
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-\r
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-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
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-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.engine.local</FONT>\r
-<BR>\r
-Class LocalEngineUtil</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.engine.local.LocalEngineUtil</B>\r
-</PRE>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public final class <B>LocalEngineUtil</B><DT>extends java.lang.Object</DL>\r
-</PRE>\r
-\r
-<P>\r
-<HR>\r
-\r
-<P>\r
-\r
-<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
-\r
-<A NAME="constructor_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Constructor Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/engine/local/LocalEngineUtil.html#LocalEngineUtil()">LocalEngineUtil</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/local/LocalEngineUtil.html#cancelJob(java.util.concurrent.Future, java.lang.String)">cancelJob</A></B>(java.util.concurrent.Future&lt;<A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&gt;&nbsp;future,\r
-          java.lang.String&nbsp;workDirectory)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/local/LocalEngineUtil.html#cleanup(compbio.engine.client.ConfiguredExecutable)">cleanup</A></B>(<A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;confExecutable)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/local/LocalEngineUtil.html#getJobStatus(java.util.concurrent.Future)">getJobStatus</A></B>(java.util.concurrent.Future&lt;<A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&gt;&nbsp;future)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/local/LocalEngineUtil.html#getRecordedJobStatus(java.lang.String)">getRecordedJobStatus</A></B>(java.lang.String&nbsp;jobId)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/local/LocalEngineUtil.html#getResults(java.util.concurrent.Future, java.lang.String)">getResults</A></B>(java.util.concurrent.Future&lt;<A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&gt;&nbsp;future,\r
-           java.lang.String&nbsp;taskId)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
-\r
-<A NAME="constructor_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Constructor Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="LocalEngineUtil()"><!-- --></A><H3>\r
-LocalEngineUtil</H3>\r
-<PRE>\r
-public <B>LocalEngineUtil</B>()</PRE>\r
-<DL>\r
-</DL>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
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-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
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-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="cancelJob(java.util.concurrent.Future, java.lang.String)"><!-- --></A><H3>\r
-cancelJob</H3>\r
-<PRE>\r
-public static boolean <B>cancelJob</B>(java.util.concurrent.Future&lt;<A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&gt;&nbsp;future,\r
-                                java.lang.String&nbsp;workDirectory)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getJobStatus(java.util.concurrent.Future)"><!-- --></A><H3>\r
-getJobStatus</H3>\r
-<PRE>\r
-public static <A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A> <B>getJobStatus</B>(java.util.concurrent.Future&lt;<A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&gt;&nbsp;future)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getRecordedJobStatus(java.lang.String)"><!-- --></A><H3>\r
-getRecordedJobStatus</H3>\r
-<PRE>\r
-public static <A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A> <B>getRecordedJobStatus</B>(java.lang.String&nbsp;jobId)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="cleanup(compbio.engine.client.ConfiguredExecutable)"><!-- --></A><H3>\r
-cleanup</H3>\r
-<PRE>\r
-public static boolean <B>cleanup</B>(<A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;confExecutable)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getResults(java.util.concurrent.Future, java.lang.String)"><!-- --></A><H3>\r
-getResults</H3>\r
-<PRE>\r
-public static <A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt; <B>getResults</B>(java.util.concurrent.Future&lt;<A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&gt;&nbsp;future,\r
-                                                 java.lang.String&nbsp;taskId)\r
-                                          throws <A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Throws:</B>\r
-<DD><CODE><A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></CODE></DL>\r
-</DD>\r
-</DL>\r
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-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
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-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
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-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
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-</TR>\r
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-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/engine/local/ExecutableWrapper.html" title="class in compbio.engine.local"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../compbio/engine/local/LocalExecutorService.html" title="class in compbio.engine.local"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/engine/local/LocalEngineUtil.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="LocalEngineUtil.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
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-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/engine/local/LocalExecutorService.html b/website/full_javadoc/compbio/engine/local/LocalExecutorService.html

deleted file mode 100644 (file)

index 9cf5fd7..0000000
--- a/website/full_javadoc/compbio/engine/local/LocalExecutorService.html
+++ /dev/null
@@ -1,310 +0,0 @@
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-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-LocalExecutorService\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
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-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="LocalExecutorService";\r
-    }\r
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-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
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-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
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-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/engine/local/LocalEngineUtil.html" title="class in compbio.engine.local"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../compbio/engine/local/LocalRunner.html" title="class in compbio.engine.local"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/engine/local/LocalExecutorService.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="LocalExecutorService.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
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-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
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-<NOSCRIPT>\r
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-\r
-\r
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-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;<A HREF="#nested_classes_inherited_from_class_java.util.concurrent.ThreadPoolExecutor">NESTED</A>&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;CONSTR&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
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-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.engine.local</FONT>\r
-<BR>\r
-Class LocalExecutorService</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../../resources/inherit.gif" ALT="extended by ">java.util.concurrent.AbstractExecutorService\r
-      <IMG SRC="../../../resources/inherit.gif" ALT="extended by ">java.util.concurrent.ThreadPoolExecutor\r
-          <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.engine.local.LocalExecutorService</B>\r
-</PRE>\r
-<DL>\r
-<DT><B>All Implemented Interfaces:</B> <DD>java.util.concurrent.Executor, java.util.concurrent.ExecutorService</DD>\r
-</DL>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public final class <B>LocalExecutorService</B><DT>extends java.util.concurrent.ThreadPoolExecutor</DL>\r
-</PRE>\r
-\r
-<P>\r
-<HR>\r
-\r
-<P>\r
-<!-- ======== NESTED CLASS SUMMARY ======== -->\r
-\r
-<A NAME="nested_class_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Nested Class Summary</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="nested_classes_inherited_from_class_java.util.concurrent.ThreadPoolExecutor"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Nested classes/interfaces inherited from class java.util.concurrent.ThreadPoolExecutor</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>java.util.concurrent.ThreadPoolExecutor.AbortPolicy, java.util.concurrent.ThreadPoolExecutor.CallerRunsPolicy, java.util.concurrent.ThreadPoolExecutor.DiscardOldestPolicy, java.util.concurrent.ThreadPoolExecutor.DiscardPolicy</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/local/LocalExecutorService.html#canAcceptMoreWork()">canAcceptMoreWork</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;If the Executor queue is empty</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../compbio/engine/local/LocalExecutorService.html" title="class in compbio.engine.local">LocalExecutorService</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/local/LocalExecutorService.html#getExecutor()">getExecutor</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;This method returns the single instance of CachedThreadPoolExecutor which
- it cashes internally</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/local/LocalExecutorService.html#shutDown()">shutDown</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;This stops all executing processes via interruption.</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.util.concurrent.ThreadPoolExecutor"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.util.concurrent.ThreadPoolExecutor</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>allowCoreThreadTimeOut, allowsCoreThreadTimeOut, awaitTermination, execute, getActiveCount, getCompletedTaskCount, getCorePoolSize, getKeepAliveTime, getLargestPoolSize, getMaximumPoolSize, getPoolSize, getQueue, getRejectedExecutionHandler, getTaskCount, getThreadFactory, isShutdown, isTerminated, isTerminating, prestartAllCoreThreads, prestartCoreThread, purge, remove, setCorePoolSize, setKeepAliveTime, setMaximumPoolSize, setRejectedExecutionHandler, setThreadFactory, shutdown, shutdownNow</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.util.concurrent.AbstractExecutorService"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.util.concurrent.AbstractExecutorService</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>invokeAll, invokeAll, invokeAny, invokeAny, submit, submit, submit</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
-<A NAME="method_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="getExecutor()"><!-- --></A><H3>\r
-getExecutor</H3>\r
-<PRE>\r
-public static <A HREF="../../../compbio/engine/local/LocalExecutorService.html" title="class in compbio.engine.local">LocalExecutorService</A> <B>getExecutor</B>()</PRE>\r
-<DL>\r
-<DD>This method returns the single instance of CachedThreadPoolExecutor which
- it cashes internally\r
-<P>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="shutDown()"><!-- --></A><H3>\r
-shutDown</H3>\r
-<PRE>\r
-public static void <B>shutDown</B>()</PRE>\r
-<DL>\r
-<DD>This stops all executing processes via interruption. Thus it is vital
- that all processes that use this service respond to interruption\r
-<P>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="canAcceptMoreWork()"><!-- --></A><H3>\r
-canAcceptMoreWork</H3>\r
-<PRE>\r
-public boolean <B>canAcceptMoreWork</B>()</PRE>\r
-<DL>\r
-<DD>If the Executor queue is empty\r
-<P>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>true is not all threads are busy, false overwise</DL>\r
-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/LocalExecutorService.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/engine/local/LocalEngineUtil.html" title="class in compbio.engine.local"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../compbio/engine/local/LocalRunner.html" title="class in compbio.engine.local"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/engine/local/LocalExecutorService.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="LocalExecutorService.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;<A HREF="#nested_classes_inherited_from_class_java.util.concurrent.ThreadPoolExecutor">NESTED</A>&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;CONSTR&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;CONSTR&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/engine/local/LocalRunner.html b/website/full_javadoc/compbio/engine/local/LocalRunner.html

deleted file mode 100644 (file)

index b64d9db..0000000
--- a/website/full_javadoc/compbio/engine/local/LocalRunner.html
+++ /dev/null
@@ -1,398 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-LocalRunner\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="LocalRunner";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/LocalRunner.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/engine/local/LocalExecutorService.html" title="class in compbio.engine.local"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../compbio/engine/local/StreamGobbler.html" title="class in compbio.engine.local"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/engine/local/LocalRunner.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="LocalRunner.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.engine.local</FONT>\r
-<BR>\r
-Class LocalRunner</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.engine.local.LocalRunner</B>\r
-</PRE>\r
-<DL>\r
-<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../compbio/engine/SyncExecutor.html" title="interface in compbio.engine">SyncExecutor</A></DD>\r
-</DL>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public final class <B>LocalRunner</B><DT>extends java.lang.Object<DT>implements <A HREF="../../../compbio/engine/SyncExecutor.html" title="interface in compbio.engine">SyncExecutor</A></DL>\r
-</PRE>\r
-\r
-<P>\r
-<HR>\r
-\r
-<P>\r
-\r
-<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
-\r
-<A NAME="constructor_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Constructor Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/engine/local/LocalRunner.html#LocalRunner(compbio.engine.client.ConfiguredExecutable)">LocalRunner</A></B>(<A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;executable)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/local/LocalRunner.html#cancelJob()">cancelJob</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Stops running job.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/local/LocalRunner.html#cleanup()">cleanup</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Clean up after the job</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/local/LocalRunner.html#executeJob()">executeJob</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Execute the job</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/local/LocalRunner.html#getJobStatus()">getJobStatus</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Query the status of the job by its id.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/local/LocalRunner.html#getWorkDirectory()">getWorkDirectory</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/local/LocalRunner.html#waitForResult()">waitForResult</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Call to this method block for as long as it is required for an executable to finish its job.</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
-\r
-<A NAME="constructor_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Constructor Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="LocalRunner(compbio.engine.client.ConfiguredExecutable)"><!-- --></A><H3>\r
-LocalRunner</H3>\r
-<PRE>\r
-public <B>LocalRunner</B>(<A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;executable)</PRE>\r
-<DL>\r
-</DL>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
-<A NAME="method_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="getWorkDirectory()"><!-- --></A><H3>\r
-getWorkDirectory</H3>\r
-<PRE>\r
-public java.lang.String <B>getWorkDirectory</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/SyncExecutor.html#getWorkDirectory()">getWorkDirectory</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/SyncExecutor.html" title="interface in compbio.engine">SyncExecutor</A></CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>working directory if the task</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="cancelJob()"><!-- --></A><H3>\r
-cancelJob</H3>\r
-<PRE>\r
-public boolean <B>cancelJob</B>()</PRE>\r
-<DL>\r
-<DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/engine/SyncExecutor.html#cancelJob()">SyncExecutor</A></CODE></B></DD>\r
-<DD>Stops running job. 
- Clean up is not performed.\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/SyncExecutor.html#cancelJob()">cancelJob</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/SyncExecutor.html" title="interface in compbio.engine">SyncExecutor</A></CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>true if job was cancelled successfully, false otherwise</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getJobStatus()"><!-- --></A><H3>\r
-getJobStatus</H3>\r
-<PRE>\r
-public <A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A> <B>getJobStatus</B>()</PRE>\r
-<DL>\r
-<DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/engine/SyncExecutor.html#getJobStatus()">SyncExecutor</A></CODE></B></DD>\r
-<DD>Query the status of the job by its id.\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/SyncExecutor.html#getJobStatus()">getJobStatus</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/SyncExecutor.html" title="interface in compbio.engine">SyncExecutor</A></CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>- JobStatus</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="executeJob()"><!-- --></A><H3>\r
-executeJob</H3>\r
-<PRE>\r
-public void <B>executeJob</B>()\r
-                throws <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></PRE>\r
-<DL>\r
-<DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/engine/SyncExecutor.html#executeJob()">SyncExecutor</A></CODE></B></DD>\r
-<DD>Execute the job\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/SyncExecutor.html#executeJob()">executeJob</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/SyncExecutor.html" title="interface in compbio.engine">SyncExecutor</A></CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-\r
-<DT><B>Throws:</B>\r
-<DD><CODE><A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></CODE> - if submission fails</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="waitForResult()"><!-- --></A><H3>\r
-waitForResult</H3>\r
-<PRE>\r
-public <A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt; <B>waitForResult</B>()\r
-                                      throws <A HREF="../../../compbio/metadata/JobExecutionException.html" title="class in compbio.metadata">JobExecutionException</A></PRE>\r
-<DL>\r
-<DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/engine/SyncExecutor.html#waitForResult()">SyncExecutor</A></CODE></B></DD>\r
-<DD>Call to this method block for as long as it is required for an executable to finish its job. 
- If the calculation has been completed already, the this method returns results immediately. 
- This could return the result directly, but that would be type unsafe\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/SyncExecutor.html#waitForResult()">waitForResult</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/SyncExecutor.html" title="interface in compbio.engine">SyncExecutor</A></CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>object from wich the result can be obtained\r
-<DT><B>Throws:</B>\r
-<DD><CODE>java.util.concurrent.CancellationException</CODE>\r
-<DD><CODE><A HREF="../../../compbio/metadata/JobExecutionException.html" title="class in compbio.metadata">JobExecutionException</A></CODE></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="cleanup()"><!-- --></A><H3>\r
-cleanup</H3>\r
-<PRE>\r
-public boolean <B>cleanup</B>()</PRE>\r
-<DL>\r
-<DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/engine/SyncExecutor.html#cleanup()">SyncExecutor</A></CODE></B></DD>\r
-<DD>Clean up after the job\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/SyncExecutor.html#cleanup()">cleanup</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/SyncExecutor.html" title="interface in compbio.engine">SyncExecutor</A></CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>true if all the files created by this job have been removed successfully, false otherwise</DL>\r
-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/LocalRunner.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/engine/local/LocalExecutorService.html" title="class in compbio.engine.local"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../compbio/engine/local/StreamGobbler.html" title="class in compbio.engine.local"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/engine/local/LocalRunner.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="LocalRunner.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/engine/local/StreamGobbler.html b/website/full_javadoc/compbio/engine/local/StreamGobbler.html

deleted file mode 100644 (file)

index 4ddf4c6..0000000
--- a/website/full_javadoc/compbio/engine/local/StreamGobbler.html
+++ /dev/null
@@ -1,226 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-StreamGobbler\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="StreamGobbler";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/StreamGobbler.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/engine/local/LocalRunner.html" title="class in compbio.engine.local"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;NEXT CLASS</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/engine/local/StreamGobbler.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="StreamGobbler.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;CONSTR&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;CONSTR&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.engine.local</FONT>\r
-<BR>\r
-Class StreamGobbler</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.engine.local.StreamGobbler</B>\r
-</PRE>\r
-<DL>\r
-<DT><B>All Implemented Interfaces:</B> <DD>java.lang.Runnable</DD>\r
-</DL>\r
-<HR>\r
-<DL>\r
-<DT><PRE><FONT SIZE="-1">@ThreadSafe\r
-</FONT>public class <B>StreamGobbler</B><DT>extends java.lang.Object<DT>implements java.lang.Runnable</DL>\r
-</PRE>\r
-\r
-<P>\r
-<HR>\r
-\r
-<P>\r
-\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/local/StreamGobbler.html#run()">run</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
-<A NAME="method_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="run()"><!-- --></A><H3>\r
-run</H3>\r
-<PRE>\r
-public void <B>run</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE>run</CODE> in interface <CODE>java.lang.Runnable</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/StreamGobbler.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
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-\r
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-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/engine/local/LocalRunner.html" title="class in compbio.engine.local"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;NEXT CLASS</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/engine/local/StreamGobbler.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
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-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
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-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;CONSTR&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
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-<A NAME="skip-navbar_bottom"></A>\r
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diff --git a/website/full_javadoc/compbio/engine/local/_TrackingExecutor.html b/website/full_javadoc/compbio/engine/local/_TrackingExecutor.html

deleted file mode 100644 (file)

index e10952d..0000000
--- a/website/full_javadoc/compbio/engine/local/_TrackingExecutor.html
+++ /dev/null
@@ -1,427 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-_TrackingExecutor\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="_TrackingExecutor";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
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-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/_TrackingExecutor.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
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-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV CLASS&nbsp;\r
-&nbsp;<A HREF="../../../compbio/engine/local/AsyncLocalRunner.html" title="class in compbio.engine.local"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/engine/local/_TrackingExecutor.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
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-  <!--\r
-  if(window==top) {\r
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-\r
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-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.engine.local</FONT>\r
-<BR>\r
-Class _TrackingExecutor</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../../resources/inherit.gif" ALT="extended by ">java.util.concurrent.AbstractExecutorService\r
-      <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.engine.local._TrackingExecutor</B>\r
-</PRE>\r
-<DL>\r
-<DT><B>All Implemented Interfaces:</B> <DD>java.util.concurrent.Executor, java.util.concurrent.ExecutorService</DD>\r
-</DL>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public class <B>_TrackingExecutor</B><DT>extends java.util.concurrent.AbstractExecutorService</DL>\r
-</PRE>\r
-\r
-<P>\r
-This executor extends standard Java ExecutorService by adding the method to
- obtain all Runnables which were running and did not complete upon executor
- termination. For this to work properly Runnables must propagate an
- Interruption exceptions, not swallow them, which a good Runnable should do
- anyway.
- 
- TODO it may be better to persists task from different place\r
-<P>\r
-\r
-<P>\r
-<DL>\r
-<DT><B>Author:</B></DT>\r
-  <DD>pvtroshin</DD>\r
-</DL>\r
-<HR>\r
-\r
-<P>\r
-\r
-<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
-\r
-<A NAME="constructor_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Constructor Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/engine/local/_TrackingExecutor.html#_TrackingExecutor(java.util.concurrent.ExecutorService)">_TrackingExecutor</A></B>(java.util.concurrent.ExecutorService&nbsp;executor)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/local/_TrackingExecutor.html#awaitTermination(long, java.util.concurrent.TimeUnit)">awaitTermination</A></B>(long&nbsp;timeout,\r
-                 java.util.concurrent.TimeUnit&nbsp;unit)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/local/_TrackingExecutor.html#execute(java.lang.Runnable)">execute</A></B>(java.lang.Runnable&nbsp;runnable)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.util.List</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/local/_TrackingExecutor.html#getCancelledTasks()">getCancelledTasks</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/local/_TrackingExecutor.html#isShutdown()">isShutdown</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/local/_TrackingExecutor.html#isTerminated()">isTerminated</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/local/_TrackingExecutor.html#shutdown()">shutdown</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.util.List&lt;java.lang.Runnable&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/local/_TrackingExecutor.html#shutdownNow()">shutdownNow</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
-<TR ALIGN="right" VALIGN="">\r
-<TD NOWRAP><FONT SIZE="-1">\r
-<CODE>&lt;T&gt; java.util.concurrent.Future&lt;T&gt;</CODE></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/local/_TrackingExecutor.html#submit(java.util.concurrent.Callable)">submit</A></B>(java.util.concurrent.Callable&lt;T&gt;&nbsp;task)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.util.concurrent.AbstractExecutorService"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.util.concurrent.AbstractExecutorService</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>invokeAll, invokeAll, invokeAny, invokeAny, submit, submit</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
-\r
-<A NAME="constructor_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Constructor Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="_TrackingExecutor(java.util.concurrent.ExecutorService)"><!-- --></A><H3>\r
-_TrackingExecutor</H3>\r
-<PRE>\r
-public <B>_TrackingExecutor</B>(java.util.concurrent.ExecutorService&nbsp;executor)</PRE>\r
-<DL>\r
-</DL>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
-<A NAME="method_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="getCancelledTasks()"><!-- --></A><H3>\r
-getCancelledTasks</H3>\r
-<PRE>\r
-public java.util.List <B>getCancelledTasks</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="execute(java.lang.Runnable)"><!-- --></A><H3>\r
-execute</H3>\r
-<PRE>\r
-public void <B>execute</B>(java.lang.Runnable&nbsp;runnable)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="submit(java.util.concurrent.Callable)"><!-- --></A><H3>\r
-submit</H3>\r
-<PRE>\r
-public &lt;T&gt; java.util.concurrent.Future&lt;T&gt; <B>submit</B>(java.util.concurrent.Callable&lt;T&gt;&nbsp;task)</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE>submit</CODE> in interface <CODE>java.util.concurrent.ExecutorService</CODE><DT><B>Overrides:</B><DD><CODE>submit</CODE> in class <CODE>java.util.concurrent.AbstractExecutorService</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="awaitTermination(long, java.util.concurrent.TimeUnit)"><!-- --></A><H3>\r
-awaitTermination</H3>\r
-<PRE>\r
-public boolean <B>awaitTermination</B>(long&nbsp;timeout,\r
-                                java.util.concurrent.TimeUnit&nbsp;unit)\r
-                         throws java.lang.InterruptedException</PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Throws:</B>\r
-<DD><CODE>java.lang.InterruptedException</CODE></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="isShutdown()"><!-- --></A><H3>\r
-isShutdown</H3>\r
-<PRE>\r
-public boolean <B>isShutdown</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="isTerminated()"><!-- --></A><H3>\r
-isTerminated</H3>\r
-<PRE>\r
-public boolean <B>isTerminated</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="shutdown()"><!-- --></A><H3>\r
-shutdown</H3>\r
-<PRE>\r
-public void <B>shutdown</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="shutdownNow()"><!-- --></A><H3>\r
-shutdownNow</H3>\r
-<PRE>\r
-public java.util.List&lt;java.lang.Runnable&gt; <B>shutdownNow</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/_TrackingExecutor.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
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-  </TR>\r
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diff --git a/website/full_javadoc/compbio/engine/local/class-use/AsyncLocalRunner.html b/website/full_javadoc/compbio/engine/local/class-use/AsyncLocalRunner.html

deleted file mode 100644 (file)

index a5689d9..0000000
--- a/website/full_javadoc/compbio/engine/local/class-use/AsyncLocalRunner.html
+++ /dev/null
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-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
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-    if (location.href.indexOf('is-external=true') == -1) {\r
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-<B>Uses of Class<br>compbio.engine.local.AsyncLocalRunner</B></H2>\r
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-\r
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diff --git a/website/full_javadoc/compbio/engine/local/class-use/ExecutableWrapper.html b/website/full_javadoc/compbio/engine/local/class-use/ExecutableWrapper.html

deleted file mode 100644 (file)

index ecbab56..0000000
--- a/website/full_javadoc/compbio/engine/local/class-use/ExecutableWrapper.html
+++ /dev/null
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-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
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-Uses of Class compbio.engine.local.ExecutableWrapper\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
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-\r
-<SCRIPT type="text/javascript">\r
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-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
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-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
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-  <A HREF="../../../../index.html?compbio/engine/local/\class-useExecutableWrapper.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
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-\r
-\r
-</FONT></TD>\r
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-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-<B>Uses of Class<br>compbio.engine.local.ExecutableWrapper</B></H2>\r
-</CENTER>\r
-No usage of compbio.engine.local.ExecutableWrapper\r
-<P>\r
-<HR>\r
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-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
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-\r
-\r
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-\r
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diff --git a/website/full_javadoc/compbio/engine/local/class-use/LocalEngineUtil.html b/website/full_javadoc/compbio/engine/local/class-use/LocalEngineUtil.html

deleted file mode 100644 (file)

index 2e55194..0000000
--- a/website/full_javadoc/compbio/engine/local/class-use/LocalEngineUtil.html
+++ /dev/null
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-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
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-\r
-<META NAME="date" CONTENT="2010-02-17">\r
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-    if (location.href.indexOf('is-external=true') == -1) {\r
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-\r
-\r
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-  </TR>\r
-</TABLE>\r
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-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
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-</TR>\r
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-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
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-  <A HREF="../../../../index.html?compbio/engine/local/\class-useLocalEngineUtil.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="LocalEngineUtil.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
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-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
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-\r
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-<B>Uses of Class<br>compbio.engine.local.LocalEngineUtil</B></H2>\r
-</CENTER>\r
-No usage of compbio.engine.local.LocalEngineUtil\r
-<P>\r
-<HR>\r
-\r
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-  </TR>\r
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-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
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-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
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-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
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-</FONT></TD>\r
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-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
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diff --git a/website/full_javadoc/compbio/engine/local/class-use/LocalExecutorService.html b/website/full_javadoc/compbio/engine/local/class-use/LocalExecutorService.html

deleted file mode 100644 (file)

index 1b52d1f..0000000
--- a/website/full_javadoc/compbio/engine/local/class-use/LocalExecutorService.html
+++ /dev/null
@@ -1,182 +0,0 @@
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-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Uses of Class compbio.engine.local.LocalExecutorService\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Uses of Class compbio.engine.local.LocalExecutorService";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
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-\r
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-<!-- ========= START OF TOP NAVBAR ======= -->\r
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-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
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-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
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-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-<B>Uses of Class<br>compbio.engine.local.LocalExecutorService</B></H2>\r
-</CENTER>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Packages that use <A HREF="../../../../compbio/engine/local/LocalExecutorService.html" title="class in compbio.engine.local">LocalExecutorService</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.engine.local"><B>compbio.engine.local</B></A></TD>\r
-<TD>An local engine classes responsible for execution of Executables on the local computer 
- (the same machine as JVM running these classes).&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.engine.local"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../../compbio/engine/local/LocalExecutorService.html" title="class in compbio.engine.local">LocalExecutorService</A> in <A HREF="../../../../compbio/engine/local/package-summary.html">compbio.engine.local</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/engine/local/package-summary.html">compbio.engine.local</A> that return <A HREF="../../../../compbio/engine/local/LocalExecutorService.html" title="class in compbio.engine.local">LocalExecutorService</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../../compbio/engine/local/LocalExecutorService.html" title="class in compbio.engine.local">LocalExecutorService</A></CODE></FONT></TD>\r
-<TD><CODE><B>LocalExecutorService.</B><B><A HREF="../../../../compbio/engine/local/LocalExecutorService.html#getExecutor()">getExecutor</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;This method returns the single instance of CachedThreadPoolExecutor which
- it cashes internally</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
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-<TR>\r
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-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
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-  <A HREF="../../../../index.html?compbio/engine/local/\class-useLocalExecutorService.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="LocalExecutorService.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
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-</SCRIPT>\r
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-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
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-\r
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-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
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-\r
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-</HTML>\r
diff --git a/website/full_javadoc/compbio/engine/local/class-use/LocalRunner.html b/website/full_javadoc/compbio/engine/local/class-use/LocalRunner.html

deleted file mode 100644 (file)

index c8d8e6b..0000000
--- a/website/full_javadoc/compbio/engine/local/class-use/LocalRunner.html
+++ /dev/null
@@ -1,144 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Uses of Class compbio.engine.local.LocalRunner\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Uses of Class compbio.engine.local.LocalRunner";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
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-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
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-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../compbio/engine/local/LocalRunner.html" title="class in compbio.engine.local"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
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-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/engine/local/\class-useLocalRunner.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="LocalRunner.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
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-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-<B>Uses of Class<br>compbio.engine.local.LocalRunner</B></H2>\r
-</CENTER>\r
-No usage of compbio.engine.local.LocalRunner\r
-<P>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
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-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
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-  </TR>\r
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diff --git a/website/full_javadoc/compbio/engine/local/class-use/StreamGobbler.html b/website/full_javadoc/compbio/engine/local/class-use/StreamGobbler.html

deleted file mode 100644 (file)

index 017c86e..0000000
--- a/website/full_javadoc/compbio/engine/local/class-use/StreamGobbler.html
+++ /dev/null
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-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
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-Uses of Class compbio.engine.local.StreamGobbler\r
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-\r
-<META NAME="date" CONTENT="2010-02-17">\r
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-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Uses of Class compbio.engine.local.StreamGobbler";\r
-    }\r
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-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
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-</HEAD>\r
-\r
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-  </TR>\r
-</TABLE>\r
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-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
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-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
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-\r
-\r
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-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-<B>Uses of Class<br>compbio.engine.local.StreamGobbler</B></H2>\r
-</CENTER>\r
-No usage of compbio.engine.local.StreamGobbler\r
-<P>\r
-<HR>\r
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-\r
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-\r
-<HR>\r
-\r
-</BODY>\r
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diff --git a/website/full_javadoc/compbio/engine/local/class-use/_TrackingExecutor.html b/website/full_javadoc/compbio/engine/local/class-use/_TrackingExecutor.html

deleted file mode 100644 (file)

index db6bec9..0000000
--- a/website/full_javadoc/compbio/engine/local/class-use/_TrackingExecutor.html
+++ /dev/null
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-<!--NewPage-->\r
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-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
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-Uses of Class compbio.engine.local._TrackingExecutor\r
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-\r
-<META NAME="date" CONTENT="2010-02-17">\r
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-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Uses of Class compbio.engine.local._TrackingExecutor";\r
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-  <A HREF="../../../../index.html?compbio/engine/local/\class-use_TrackingExecutor.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
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-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
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-</SCRIPT>\r
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-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-<B>Uses of Class<br>compbio.engine.local._TrackingExecutor</B></H2>\r
-</CENTER>\r
-No usage of compbio.engine.local._TrackingExecutor\r
-<P>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
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diff --git a/website/full_javadoc/compbio/engine/local/package-frame.html b/website/full_javadoc/compbio/engine/local/package-frame.html

deleted file mode 100644 (file)

index 02fb20e..0000000
--- a/website/full_javadoc/compbio/engine/local/package-frame.html
+++ /dev/null
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-</TR>\r
-</TABLE>\r
-\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/engine/local/package-summary.html b/website/full_javadoc/compbio/engine/local/package-summary.html

deleted file mode 100644 (file)

index b9dc15d..0000000
--- a/website/full_javadoc/compbio/engine/local/package-summary.html
+++ /dev/null
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-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Class</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-use.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
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-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/engine/conf/package-summary.html"><B>PREV PACKAGE</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../compbio/metadata/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/engine/local/package-summary.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="package-summary.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
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-\r
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-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<H2>\r
-Package compbio.engine.local\r
-</H2>\r
-An local engine classes responsible for execution of Executables on the local computer 
- (the same machine as JVM running these classes).\r
-<P>\r
-<B>See:</B>\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<A HREF="#package_description"><B>Description</B></A>\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Class Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../../compbio/engine/local/_TrackingExecutor.html" title="class in compbio.engine.local">_TrackingExecutor</A></B></TD>\r
-<TD>This executor extends standard Java ExecutorService by adding the method to
- obtain all Runnables which were running and did not complete upon executor
- termination.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../../compbio/engine/local/AsyncLocalRunner.html" title="class in compbio.engine.local">AsyncLocalRunner</A></B></TD>\r
-<TD>&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../../compbio/engine/local/ExecutableWrapper.html" title="class in compbio.engine.local">ExecutableWrapper</A></B></TD>\r
-<TD>&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../../compbio/engine/local/LocalEngineUtil.html" title="class in compbio.engine.local">LocalEngineUtil</A></B></TD>\r
-<TD>&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../../compbio/engine/local/LocalExecutorService.html" title="class in compbio.engine.local">LocalExecutorService</A></B></TD>\r
-<TD>&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../../compbio/engine/local/LocalRunner.html" title="class in compbio.engine.local">LocalRunner</A></B></TD>\r
-<TD>&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../../compbio/engine/local/StreamGobbler.html" title="class in compbio.engine.local">StreamGobbler</A></B></TD>\r
-<TD>&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-\r
-<P>\r
-<A NAME="package_description"><!-- --></A><H2>\r
-Package compbio.engine.local Description\r
-</H2>\r
-\r
-<P>\r
-An local engine classes responsible for execution of Executables on the local computer 
- (the same machine as JVM running these classes).
- Implementation uses Java 6 Executor framework to execute native programmes in parallel in different threads.  
- Classes in this package depend on the data model classes. 
- They form a second layer of Jalview Web Services v2.\r
-<P>\r
-\r
-<P>\r
-<DL>\r
-<DT><B>Author:</B></DT>\r
-  <DD>Petr Troshin 
- 
-        Date January 2010</DD>\r
-</DL>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Class</FONT>&nbsp;</TD>\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/engine/conf/package-summary.html"><B>PREV PACKAGE</B></A>&nbsp;\r
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-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
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-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
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-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
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-</FONT></TD>\r
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-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/engine/local/package-tree.html b/website/full_javadoc/compbio/engine/local/package-tree.html

deleted file mode 100644 (file)

index f34b8b2..0000000
--- a/website/full_javadoc/compbio/engine/local/package-tree.html
+++ /dev/null
@@ -1,162 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
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-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-compbio.engine.local Class Hierarchy\r
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-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
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-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Class</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Use</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
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-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/engine/conf/package-tree.html"><B>PREV</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../compbio/metadata/package-tree.html"><B>NEXT</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/engine/local/package-tree.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
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-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-Hierarchy For Package compbio.engine.local\r
-</H2>\r
-</CENTER>\r
-<DL>\r
-<DT><B>Package Hierarchies:</B><DD><A HREF="../../../overview-tree.html">All Packages</A></DL>\r
-<HR>\r
-<H2>\r
-Class Hierarchy\r
-</H2>\r
-<UL>\r
-<LI TYPE="circle">java.lang.Object<UL>\r
-<LI TYPE="circle">java.util.concurrent.AbstractExecutorService (implements java.util.concurrent.ExecutorService)\r
-<UL>\r
-<LI TYPE="circle">compbio.engine.local.<A HREF="../../../compbio/engine/local/_TrackingExecutor.html" title="class in compbio.engine.local"><B>_TrackingExecutor</B></A><LI TYPE="circle">java.util.concurrent.ThreadPoolExecutor<UL>\r
-<LI TYPE="circle">compbio.engine.local.<A HREF="../../../compbio/engine/local/LocalExecutorService.html" title="class in compbio.engine.local"><B>LocalExecutorService</B></A></UL>\r
-</UL>\r
-<LI TYPE="circle">compbio.engine.local.<A HREF="../../../compbio/engine/local/AsyncLocalRunner.html" title="class in compbio.engine.local"><B>AsyncLocalRunner</B></A> (implements compbio.engine.<A HREF="../../../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine">AsyncExecutor</A>)\r
-<LI TYPE="circle">compbio.engine.local.<A HREF="../../../compbio/engine/local/ExecutableWrapper.html" title="class in compbio.engine.local"><B>ExecutableWrapper</B></A> (implements java.util.concurrent.Callable&lt;V&gt;)\r
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-<LI TYPE="circle">compbio.engine.local.<A HREF="../../../compbio/engine/local/StreamGobbler.html" title="class in compbio.engine.local"><B>StreamGobbler</B></A> (implements java.lang.Runnable)\r
-</UL>\r
-</UL>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Class</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Use</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
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-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/engine/conf/package-tree.html"><B>PREV</B></A>&nbsp;\r
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-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
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-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
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-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
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-\r
-<HR>\r
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-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/engine/local/package-use.html b/website/full_javadoc/compbio/engine/local/package-use.html

deleted file mode 100644 (file)

index 75e20de..0000000
--- a/website/full_javadoc/compbio/engine/local/package-use.html
+++ /dev/null
@@ -1,171 +0,0 @@
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-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Uses of Package compbio.engine.local\r
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-\r
-<META NAME="date" CONTENT="2010-02-17">\r
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-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
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-<!-- ========= START OF TOP NAVBAR ======= -->\r
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-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
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-</TD>\r
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-\r
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-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
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-  <A HREF="../../../index.html?compbio/engine/local/package-use.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
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-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
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-<H2>\r
-<B>Uses of Package<br>compbio.engine.local</B></H2>\r
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-\r
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-<TD><A HREF="#compbio.engine.local"><B>compbio.engine.local</B></A></TD>\r
-<TD>An local engine classes responsible for execution of Executables on the local computer 
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deleted file mode 100644 (file)

index 5855a35..0000000
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diff --git a/website/full_javadoc/compbio/engine/package-summary.html b/website/full_javadoc/compbio/engine/package-summary.html

deleted file mode 100644 (file)

index da7acf2..0000000
--- a/website/full_javadoc/compbio/engine/package-summary.html
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-<TR BGCOLOR="white" CLASS="TableRowColor">\r
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diff --git a/website/full_javadoc/compbio/engine/package-tree.html b/website/full_javadoc/compbio/engine/package-tree.html

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diff --git a/website/full_javadoc/compbio/engine/package-use.html b/website/full_javadoc/compbio/engine/package-use.html

deleted file mode 100644 (file)

index 0c8ff4d..0000000
--- a/website/full_javadoc/compbio/engine/package-use.html
+++ /dev/null
@@ -1,274 +0,0 @@
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-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
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-<B>Uses of Package<br>compbio.engine</B></H2>\r
-</CENTER>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Packages that use <A HREF="../../compbio/engine/package-summary.html">compbio.engine</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.engine"><B>compbio.engine</B></A></TD>\r
-<TD>&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.engine.cluster.drmaa"><B>compbio.engine.cluster.drmaa</B></A></TD>\r
-<TD>An cluster engine classes responsible for execution of Executables on the clusters.&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.engine.local"><B>compbio.engine.local</B></A></TD>\r
-<TD>An local engine classes responsible for execution of Executables on the local computer 
- (the same machine as JVM running these classes).&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.ws.server"><B>compbio.ws.server</B></A></TD>\r
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-<P>\r
-<A NAME="compbio.engine"><!-- --></A>\r
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-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Classes in <A HREF="../../compbio/engine/package-summary.html">compbio.engine</A> used by <A HREF="../../compbio/engine/package-summary.html">compbio.engine</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/engine/class-use/AsyncExecutor.html#compbio.engine"><B>AsyncExecutor</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;An asynchronous executor engine, capable of running, cancelling, 
- obtaining results calculated by a native executable wrapper in Executable interface.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/engine/class-use/ClusterJobId.html#compbio.engine"><B>ClusterJobId</B></A></B>\r
-\r
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-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
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-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/engine/class-use/FilePuller.html#compbio.engine"><B>FilePuller</B></A></B>\r
-\r
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-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/engine/class-use/Job.html#compbio.engine"><B>Job</B></A></B>\r
-\r
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-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
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-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/engine/class-use/SyncExecutor.html#compbio.engine"><B>SyncExecutor</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Synchronous executor, is an engine to run the Executable synchronously.</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.engine.cluster.drmaa"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Classes in <A HREF="../../compbio/engine/package-summary.html">compbio.engine</A> used by <A HREF="../../compbio/engine/cluster/drmaa/package-summary.html">compbio.engine.cluster.drmaa</A></FONT></TH>\r
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-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/engine/class-use/AsyncExecutor.html#compbio.engine.cluster.drmaa"><B>AsyncExecutor</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;An asynchronous executor engine, capable of running, cancelling, 
- obtaining results calculated by a native executable wrapper in Executable interface.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/engine/class-use/ClusterJobId.html#compbio.engine.cluster.drmaa"><B>ClusterJobId</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/engine/class-use/SyncExecutor.html#compbio.engine.cluster.drmaa"><B>SyncExecutor</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Synchronous executor, is an engine to run the Executable synchronously.</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.engine.local"><!-- --></A>\r
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-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Classes in <A HREF="../../compbio/engine/package-summary.html">compbio.engine</A> used by <A HREF="../../compbio/engine/local/package-summary.html">compbio.engine.local</A></FONT></TH>\r
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-<TD><B><A HREF="../../compbio/engine/class-use/AsyncExecutor.html#compbio.engine.local"><B>AsyncExecutor</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;An asynchronous executor engine, capable of running, cancelling, 
- obtaining results calculated by a native executable wrapper in Executable interface.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
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-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Synchronous executor, is an engine to run the Executable synchronously.</TD>\r
-</TR>\r
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-&nbsp;\r
-<P>\r
-<A NAME="compbio.ws.server"><!-- --></A>\r
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-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;An asynchronous executor engine, capable of running, cancelling, 
- obtaining results calculated by a native executable wrapper in Executable interface.</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
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-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../index.html?compbio/engine/package-use.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="package-use.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
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-  <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>\r
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-\r
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-</TABLE>\r
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-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
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-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/metadata/Argument.html b/website/full_javadoc/compbio/metadata/Argument.html

deleted file mode 100644 (file)

index 656cb78..0000000
--- a/website/full_javadoc/compbio/metadata/Argument.html
+++ /dev/null
@@ -1,327 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Argument\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Argument";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/Argument.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
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-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV CLASS&nbsp;\r
-&nbsp;<A HREF="../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../index.html?compbio/metadata/Argument.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="Argument.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;CONSTR&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;CONSTR&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.metadata</FONT>\r
-<BR>\r
-Interface Argument&lt;T&gt;</H2>\r
-<DL>\r
-<DT><DT><B>Type Parameters:</B><DD><CODE>T</CODE> - executable type</DL>\r
-<DL>\r
-<DT><B>All Known Implementing Classes:</B> <DD><A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>, <A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A></DD>\r
-</DL>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public interface <B>Argument&lt;T&gt;</B></DL>\r
-</PRE>\r
-\r
-<P>\r
-An unmodifiable view for the options and parameters, with one exception - it
- allows to set a value\r
-<P>\r
-\r
-<P>\r
-<DL>\r
-<DT><B>Author:</B></DT>\r
-  <DD>pvtroshin
- 
-         Date December 2009</DD>\r
-<DT><B>See Also:</B><DD><A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata"><CODE>Parameter</CODE></A>, \r
-<A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata"><CODE>Option</CODE></A></DL>\r
-<HR>\r
-\r
-<P>\r
-\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/Argument.html#getDefaultValue()">getDefaultValue</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/Argument.html#getDescription()">getDescription</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.net.URL</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/Argument.html#getFurtherDetails()">getFurtherDetails</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/Argument.html#getName()">getName</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.util.List&lt;java.lang.String&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/Argument.html#getPossibleValues()">getPossibleValues</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/Argument.html#setValue(java.lang.String)">setValue</A></B>(java.lang.String&nbsp;defaultValue)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Set default values for the parameter or an option</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
-<A NAME="method_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="getFurtherDetails()"><!-- --></A><H3>\r
-getFurtherDetails</H3>\r
-<PRE>\r
-java.net.URL <B>getFurtherDetails</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getDefaultValue()"><!-- --></A><H3>\r
-getDefaultValue</H3>\r
-<PRE>\r
-java.lang.String <B>getDefaultValue</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getDescription()"><!-- --></A><H3>\r
-getDescription</H3>\r
-<PRE>\r
-java.lang.String <B>getDescription</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getName()"><!-- --></A><H3>\r
-getName</H3>\r
-<PRE>\r
-java.lang.String <B>getName</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getPossibleValues()"><!-- --></A><H3>\r
-getPossibleValues</H3>\r
-<PRE>\r
-java.util.List&lt;java.lang.String&gt; <B>getPossibleValues</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>List of values allowed for an Argument</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="setValue(java.lang.String)"><!-- --></A><H3>\r
-setValue</H3>\r
-<PRE>\r
-void <B>setValue</B>(java.lang.String&nbsp;defaultValue)\r
-              throws <A HREF="../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></PRE>\r
-<DL>\r
-<DD>Set default values for the parameter or an option\r
-<P>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>defaultValue</CODE> - the value to be set\r
-<DT><B>Throws:</B>\r
-<DD><CODE><A HREF="../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></CODE> - - when the value to be set is illegal. Wrong value for
-             numeric parameter is the value defined outside it , for
-             string type parameter, wrong value is the one which is not
-             listed in possible values list<DT><B>See Also:</B><DD><A HREF="../../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata"><CODE>ValueConstrain</CODE></A></DL>\r
-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/Argument.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
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-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV CLASS&nbsp;\r
-&nbsp;<A HREF="../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../index.html?compbio/metadata/Argument.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
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-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
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-  }\r
-  //-->\r
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-  <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>\r
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-\r
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-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
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-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;CONSTR&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
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diff --git a/website/full_javadoc/compbio/metadata/ChunkHolder.html b/website/full_javadoc/compbio/metadata/ChunkHolder.html

deleted file mode 100644 (file)

index 9b66ead..0000000
--- a/website/full_javadoc/compbio/metadata/ChunkHolder.html
+++ /dev/null
@@ -1,350 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-ChunkHolder\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="ChunkHolder";\r
-    }\r
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-<BODY BGCOLOR="white" onload="windowTitle();">\r
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-\r
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-<!-- ========= START OF TOP NAVBAR ======= -->\r
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-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/ChunkHolder.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../compbio/metadata/Argument.html" title="interface in compbio.metadata"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../compbio/metadata/JobExecutionException.html" title="class in compbio.metadata"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../index.html?compbio/metadata/ChunkHolder.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="ChunkHolder.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>\r
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-\r
-\r
-</FONT></TD>\r
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-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.metadata</FONT>\r
-<BR>\r
-Class ChunkHolder</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../resources/inherit.gif" ALT="extended by "><B>compbio.metadata.ChunkHolder</B>\r
-</PRE>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public class <B>ChunkHolder</B><DT>extends java.lang.Object</DL>\r
-</PRE>\r
-\r
-<P>\r
-Represents a chunk of string data together with the position in a file from
- where corresponding to of the data.\r
-<P>\r
-\r
-<P>\r
-<DL>\r
-<DT><B>Author:</B></DT>\r
-  <DD>pvtroshin
- 
-         Date December 2009</DD>\r
-</DL>\r
-<HR>\r
-\r
-<P>\r
-\r
-<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
-\r
-<A NAME="constructor_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Constructor Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../compbio/metadata/ChunkHolder.html#ChunkHolder(java.lang.String, long)">ChunkHolder</A></B>(java.lang.String&nbsp;chunk,\r
-            long&nbsp;position)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/ChunkHolder.html#equals(java.lang.Object)">equals</A></B>(java.lang.Object&nbsp;obj)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/ChunkHolder.html#getChunk()">getChunk</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;long</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/ChunkHolder.html#getNextPosition()">getNextPosition</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;int</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/ChunkHolder.html#hashCode()">hashCode</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/ChunkHolder.html#toString()">toString</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>getClass, notify, notifyAll, wait, wait, wait</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
-\r
-<A NAME="constructor_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Constructor Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="ChunkHolder(java.lang.String, long)"><!-- --></A><H3>\r
-ChunkHolder</H3>\r
-<PRE>\r
-public <B>ChunkHolder</B>(java.lang.String&nbsp;chunk,\r
-                   long&nbsp;position)</PRE>\r
-<DL>\r
-</DL>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
-<A NAME="method_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="getChunk()"><!-- --></A><H3>\r
-getChunk</H3>\r
-<PRE>\r
-public java.lang.String <B>getChunk</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getNextPosition()"><!-- --></A><H3>\r
-getNextPosition</H3>\r
-<PRE>\r
-public long <B>getNextPosition</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="equals(java.lang.Object)"><!-- --></A><H3>\r
-equals</H3>\r
-<PRE>\r
-public boolean <B>equals</B>(java.lang.Object&nbsp;obj)</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Overrides:</B><DD><CODE>equals</CODE> in class <CODE>java.lang.Object</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="toString()"><!-- --></A><H3>\r
-toString</H3>\r
-<PRE>\r
-public java.lang.String <B>toString</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Overrides:</B><DD><CODE>toString</CODE> in class <CODE>java.lang.Object</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="hashCode()"><!-- --></A><H3>\r
-hashCode</H3>\r
-<PRE>\r
-public int <B>hashCode</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Overrides:</B><DD><CODE>hashCode</CODE> in class <CODE>java.lang.Object</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/ChunkHolder.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../compbio/metadata/Argument.html" title="interface in compbio.metadata"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../compbio/metadata/JobExecutionException.html" title="class in compbio.metadata"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../index.html?compbio/metadata/ChunkHolder.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="ChunkHolder.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/metadata/JobExecutionException.html b/website/full_javadoc/compbio/metadata/JobExecutionException.html

deleted file mode 100644 (file)

index 6e1b992..0000000
--- a/website/full_javadoc/compbio/metadata/JobExecutionException.html
+++ /dev/null
@@ -1,279 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-JobExecutionException\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="JobExecutionException";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/JobExecutionException.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../index.html?compbio/metadata/JobExecutionException.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
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-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>\r
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-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#methods_inherited_from_class_java.lang.Throwable">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;METHOD</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.metadata</FONT>\r
-<BR>\r
-Class JobExecutionException</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../resources/inherit.gif" ALT="extended by ">java.lang.Throwable\r
-      <IMG SRC="../../resources/inherit.gif" ALT="extended by ">java.lang.Exception\r
-          <IMG SRC="../../resources/inherit.gif" ALT="extended by "><B>compbio.metadata.JobExecutionException</B>\r
-</PRE>\r
-<DL>\r
-<DT><B>All Implemented Interfaces:</B> <DD>java.io.Serializable</DD>\r
-</DL>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public class <B>JobExecutionException</B><DT>extends java.lang.Exception</DL>\r
-</PRE>\r
-\r
-<P>\r
-JobExecutionException is thrown wherever the results of the calculation
- cannot be obtained. For cluster execution it hides DrmaaException\r
-<P>\r
-\r
-<P>\r
-<DL>\r
-<DT><B>Author:</B></DT>\r
-  <DD>pvtroshin
- 
-         Date October 2009</DD>\r
-<DT><B>See Also:</B><DD><A HREF="../../serialized-form.html#compbio.metadata.JobExecutionException">Serialized Form</A></DL>\r
-<HR>\r
-\r
-<P>\r
-\r
-<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
-\r
-<A NAME="constructor_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Constructor Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../compbio/metadata/JobExecutionException.html#JobExecutionException(java.lang.String)">JobExecutionException</A></B>(java.lang.String&nbsp;message)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../compbio/metadata/JobExecutionException.html#JobExecutionException(java.lang.String, java.lang.Throwable)">JobExecutionException</A></B>(java.lang.String&nbsp;message,\r
-                      java.lang.Throwable&nbsp;cause)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../compbio/metadata/JobExecutionException.html#JobExecutionException(java.lang.Throwable)">JobExecutionException</A></B>(java.lang.Throwable&nbsp;cause)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Throwable"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Throwable</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>fillInStackTrace, getCause, getLocalizedMessage, getMessage, getStackTrace, initCause, printStackTrace, printStackTrace, printStackTrace, setStackTrace, toString</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>equals, getClass, hashCode, notify, notifyAll, wait, wait, wait</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
-\r
-<A NAME="constructor_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Constructor Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="JobExecutionException(java.lang.String)"><!-- --></A><H3>\r
-JobExecutionException</H3>\r
-<PRE>\r
-public <B>JobExecutionException</B>(java.lang.String&nbsp;message)</PRE>\r
-<DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="JobExecutionException(java.lang.Throwable)"><!-- --></A><H3>\r
-JobExecutionException</H3>\r
-<PRE>\r
-public <B>JobExecutionException</B>(java.lang.Throwable&nbsp;cause)</PRE>\r
-<DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="JobExecutionException(java.lang.String, java.lang.Throwable)"><!-- --></A><H3>\r
-JobExecutionException</H3>\r
-<PRE>\r
-public <B>JobExecutionException</B>(java.lang.String&nbsp;message,\r
-                             java.lang.Throwable&nbsp;cause)</PRE>\r
-<DL>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/JobExecutionException.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../index.html?compbio/metadata/JobExecutionException.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="JobExecutionException.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#methods_inherited_from_class_java.lang.Throwable">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;METHOD</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/metadata/JobStatus.html b/website/full_javadoc/compbio/metadata/JobStatus.html

deleted file mode 100644 (file)

index 7d716e8..0000000
--- a/website/full_javadoc/compbio/metadata/JobStatus.html
+++ /dev/null
@@ -1,465 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-JobStatus\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="JobStatus";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/JobStatus.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../compbio/metadata/JobExecutionException.html" title="class in compbio.metadata"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../index.html?compbio/metadata/JobStatus.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="JobStatus.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;<A HREF="#enum_constant_summary">ENUM CONSTANTS</A>&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;<A HREF="#enum_constant_detail">ENUM CONSTANTS</A>&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.metadata</FONT>\r
-<BR>\r
-Enum JobStatus</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../resources/inherit.gif" ALT="extended by ">java.lang.Enum&lt;<A HREF="../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A>&gt;\r
-      <IMG SRC="../../resources/inherit.gif" ALT="extended by "><B>compbio.metadata.JobStatus</B>\r
-</PRE>\r
-<DL>\r
-<DT><B>All Implemented Interfaces:</B> <DD>java.io.Serializable, java.lang.Comparable&lt;<A HREF="../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A>&gt;</DD>\r
-</DL>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public enum <B>JobStatus</B><DT>extends java.lang.Enum&lt;<A HREF="../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A>&gt;</DL>\r
-</PRE>\r
-\r
-<P>\r
-The status of the job.\r
-<P>\r
-\r
-<P>\r
-<DL>\r
-<DT><B>Author:</B></DT>\r
-  <DD>pvtroshin
- 
-         Date October 2009</DD>\r
-</DL>\r
-<HR>\r
-\r
-<P>\r
-<!-- =========== ENUM CONSTANT SUMMARY =========== -->\r
-\r
-<A NAME="enum_constant_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Enum Constant Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../compbio/metadata/JobStatus.html#CANCELLED">CANCELLED</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Jobs that has been cancelled</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../compbio/metadata/JobStatus.html#COLLECTED">COLLECTED</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Results has been collected</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../compbio/metadata/JobStatus.html#FAILED">FAILED</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Failed jobs</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../compbio/metadata/JobStatus.html#FINISHED">FINISHED</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Finished jobs</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../compbio/metadata/JobStatus.html#PENDING">PENDING</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Jobs which are in the queue and awaiting execution reported for cluster
- jobs only</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../compbio/metadata/JobStatus.html#RUNNING">RUNNING</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Jobs that are running</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../compbio/metadata/JobStatus.html#STARTED">STARTED</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Job calculation has been started.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../compbio/metadata/JobStatus.html#SUBMITTED">SUBMITTED</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Job has been submitted.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../compbio/metadata/JobStatus.html#UNDEFINED">UNDEFINED</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Represents jobs with unknown status</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/JobStatus.html#valueOf(java.lang.String)">valueOf</A></B>(java.lang.String&nbsp;name)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Returns the enum constant of this type with the specified name.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A>[]</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/JobStatus.html#values()">values</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Returns an array containing the constants of this enum type, in
-the order they are declared.</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Enum"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Enum</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>compareTo, equals, getDeclaringClass, hashCode, name, ordinal, toString, valueOf</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>getClass, notify, notifyAll, wait, wait, wait</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ============ ENUM CONSTANT DETAIL =========== -->\r
-\r
-<A NAME="enum_constant_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Enum Constant Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="PENDING"><!-- --></A><H3>\r
-PENDING</H3>\r
-<PRE>\r
-public static final <A HREF="../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A> <B>PENDING</B></PRE>\r
-<DL>\r
-<DD>Jobs which are in the queue and awaiting execution reported for cluster
- jobs only\r
-<P>\r
-<DL>\r
-</DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="RUNNING"><!-- --></A><H3>\r
-RUNNING</H3>\r
-<PRE>\r
-public static final <A HREF="../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A> <B>RUNNING</B></PRE>\r
-<DL>\r
-<DD>Jobs that are running\r
-<P>\r
-<DL>\r
-</DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="CANCELLED"><!-- --></A><H3>\r
-CANCELLED</H3>\r
-<PRE>\r
-public static final <A HREF="../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A> <B>CANCELLED</B></PRE>\r
-<DL>\r
-<DD>Jobs that has been cancelled\r
-<P>\r
-<DL>\r
-</DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="FINISHED"><!-- --></A><H3>\r
-FINISHED</H3>\r
-<PRE>\r
-public static final <A HREF="../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A> <B>FINISHED</B></PRE>\r
-<DL>\r
-<DD>Finished jobs\r
-<P>\r
-<DL>\r
-</DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="FAILED"><!-- --></A><H3>\r
-FAILED</H3>\r
-<PRE>\r
-public static final <A HREF="../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A> <B>FAILED</B></PRE>\r
-<DL>\r
-<DD>Failed jobs\r
-<P>\r
-<DL>\r
-</DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="UNDEFINED"><!-- --></A><H3>\r
-UNDEFINED</H3>\r
-<PRE>\r
-public static final <A HREF="../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A> <B>UNDEFINED</B></PRE>\r
-<DL>\r
-<DD>Represents jobs with unknown status\r
-<P>\r
-<DL>\r
-</DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="STARTED"><!-- --></A><H3>\r
-STARTED</H3>\r
-<PRE>\r
-public static final <A HREF="../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A> <B>STARTED</B></PRE>\r
-<DL>\r
-<DD>Job calculation has been started. First status reported by the local
- engine\r
-<P>\r
-<DL>\r
-</DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="SUBMITTED"><!-- --></A><H3>\r
-SUBMITTED</H3>\r
-<PRE>\r
-public static final <A HREF="../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A> <B>SUBMITTED</B></PRE>\r
-<DL>\r
-<DD>Job has been submitted. This status is only set for cluster jobs\r
-<P>\r
-<DL>\r
-</DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="COLLECTED"><!-- --></A><H3>\r
-COLLECTED</H3>\r
-<PRE>\r
-public static final <A HREF="../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A> <B>COLLECTED</B></PRE>\r
-<DL>\r
-<DD>Results has been collected\r
-<P>\r
-<DL>\r
-</DL>\r
-</DL>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
-<A NAME="method_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="values()"><!-- --></A><H3>\r
-values</H3>\r
-<PRE>\r
-public static <A HREF="../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A>[] <B>values</B>()</PRE>\r
-<DL>\r
-<DD>Returns an array containing the constants of this enum type, in
-the order they are declared.  This method may be used to iterate
-over the constants as follows:
-<pre>
-for (JobStatus c : JobStatus.values())
-&nbsp;   System.out.println(c);
-</pre>\r
-<P>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>an array containing the constants of this enum type, in
-the order they are declared</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="valueOf(java.lang.String)"><!-- --></A><H3>\r
-valueOf</H3>\r
-<PRE>\r
-public static <A HREF="../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A> <B>valueOf</B>(java.lang.String&nbsp;name)</PRE>\r
-<DL>\r
-<DD>Returns the enum constant of this type with the specified name.
-The string must match <I>exactly</I> an identifier used to declare an
-enum constant in this type.  (Extraneous whitespace characters are 
-not permitted.)\r
-<P>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>name</CODE> - the name of the enum constant to be returned.\r
-<DT><B>Returns:</B><DD>the enum constant with the specified name\r
-<DT><B>Throws:</B>\r
-<DD><CODE>java.lang.IllegalArgumentException</CODE> - if this enum type has no constant
-with the specified name\r
-<DD><CODE>java.lang.NullPointerException</CODE> - if the argument is null</DL>\r
-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/JobStatus.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../compbio/metadata/JobExecutionException.html" title="class in compbio.metadata"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../index.html?compbio/metadata/JobStatus.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="JobStatus.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;<A HREF="#enum_constant_summary">ENUM CONSTANTS</A>&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;<A HREF="#enum_constant_detail">ENUM CONSTANTS</A>&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/metadata/JobSubmissionException.html b/website/full_javadoc/compbio/metadata/JobSubmissionException.html

deleted file mode 100644 (file)

index c290dba..0000000
--- a/website/full_javadoc/compbio/metadata/JobSubmissionException.html
+++ /dev/null
@@ -1,283 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-JobSubmissionException\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="JobSubmissionException";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/JobSubmissionException.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../compbio/metadata/Limit.html" title="class in compbio.metadata"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../index.html?compbio/metadata/JobSubmissionException.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="JobSubmissionException.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#methods_inherited_from_class_java.lang.Throwable">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;METHOD</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.metadata</FONT>\r
-<BR>\r
-Class JobSubmissionException</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../resources/inherit.gif" ALT="extended by ">java.lang.Throwable\r
-      <IMG SRC="../../resources/inherit.gif" ALT="extended by ">java.lang.Exception\r
-          <IMG SRC="../../resources/inherit.gif" ALT="extended by "><B>compbio.metadata.JobSubmissionException</B>\r
-</PRE>\r
-<DL>\r
-<DT><B>All Implemented Interfaces:</B> <DD>java.io.Serializable</DD>\r
-</DL>\r
-<DL>\r
-<DT><B>Direct Known Subclasses:</B> <DD><A HREF="../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A>, <A HREF="../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A></DD>\r
-</DL>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public class <B>JobSubmissionException</B><DT>extends java.lang.Exception</DL>\r
-</PRE>\r
-\r
-<P>\r
-Exception for generic problems with JobSubmission it is often thrown as a
- wrapper for the lower level exceptions like IOException or DrmaaException. If
- this exception is thrown the task has not been calculated\r
-<P>\r
-\r
-<P>\r
-<DL>\r
-<DT><B>Author:</B></DT>\r
-  <DD>pvtroshin
- 
-         Date December 2009</DD>\r
-<DT><B>See Also:</B><DD><A HREF="../../serialized-form.html#compbio.metadata.JobSubmissionException">Serialized Form</A></DL>\r
-<HR>\r
-\r
-<P>\r
-\r
-<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
-\r
-<A NAME="constructor_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Constructor Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../compbio/metadata/JobSubmissionException.html#JobSubmissionException(java.lang.String)">JobSubmissionException</A></B>(java.lang.String&nbsp;message)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../compbio/metadata/JobSubmissionException.html#JobSubmissionException(java.lang.String, java.lang.Throwable)">JobSubmissionException</A></B>(java.lang.String&nbsp;message,\r
-                       java.lang.Throwable&nbsp;cause)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../compbio/metadata/JobSubmissionException.html#JobSubmissionException(java.lang.Throwable)">JobSubmissionException</A></B>(java.lang.Throwable&nbsp;cause)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Throwable"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Throwable</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>fillInStackTrace, getCause, getLocalizedMessage, getMessage, getStackTrace, initCause, printStackTrace, printStackTrace, printStackTrace, setStackTrace, toString</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>equals, getClass, hashCode, notify, notifyAll, wait, wait, wait</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
-\r
-<A NAME="constructor_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Constructor Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="JobSubmissionException(java.lang.String)"><!-- --></A><H3>\r
-JobSubmissionException</H3>\r
-<PRE>\r
-public <B>JobSubmissionException</B>(java.lang.String&nbsp;message)</PRE>\r
-<DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="JobSubmissionException(java.lang.Throwable)"><!-- --></A><H3>\r
-JobSubmissionException</H3>\r
-<PRE>\r
-public <B>JobSubmissionException</B>(java.lang.Throwable&nbsp;cause)</PRE>\r
-<DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="JobSubmissionException(java.lang.String, java.lang.Throwable)"><!-- --></A><H3>\r
-JobSubmissionException</H3>\r
-<PRE>\r
-public <B>JobSubmissionException</B>(java.lang.String&nbsp;message,\r
-                              java.lang.Throwable&nbsp;cause)</PRE>\r
-<DL>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
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-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/JobSubmissionException.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
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-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../compbio/metadata/Limit.html" title="class in compbio.metadata"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../index.html?compbio/metadata/JobSubmissionException.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="JobSubmissionException.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
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-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#methods_inherited_from_class_java.lang.Throwable">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;METHOD</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
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-<HR>\r
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-</HTML>\r
diff --git a/website/full_javadoc/compbio/metadata/Limit.html b/website/full_javadoc/compbio/metadata/Limit.html

deleted file mode 100644 (file)

index f2f4095..0000000
--- a/website/full_javadoc/compbio/metadata/Limit.html
+++ /dev/null
@@ -1,459 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Limit\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Limit";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/Limit.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../index.html?compbio/metadata/Limit.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="Limit.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.metadata</FONT>\r
-<BR>\r
-Class Limit&lt;T&gt;</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../resources/inherit.gif" ALT="extended by "><B>compbio.metadata.Limit&lt;T&gt;</B>\r
-</PRE>\r
-<DL>\r
-<DT><DT><B>Type Parameters:</B><DD><CODE>T</CODE> - the type of an executable for which this limit is defined.</DL>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public class <B>Limit&lt;T&gt;</B><DT>extends java.lang.Object</DL>\r
-</PRE>\r
-\r
-<P>\r
-A value object containing a maximum number of sequences and a maximum average
- sequence length for a preset.\r
-<P>\r
-\r
-<P>\r
-<DL>\r
-<DT><B>Author:</B></DT>\r
-  <DD>pvtroshin
- 
-         Date January 2010</DD>\r
-<DT><B>See Also:</B><DD><A HREF="../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata"><CODE>LimitsManager</CODE></A></DL>\r
-<HR>\r
-\r
-<P>\r
-\r
-<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
-\r
-<A NAME="constructor_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Constructor Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../compbio/metadata/Limit.html#Limit(int, int, java.lang.String)">Limit</A></B>(int&nbsp;seqNumber,\r
-      int&nbsp;seqLength,\r
-      java.lang.String&nbsp;preset)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../compbio/metadata/Limit.html#Limit(int, int, java.lang.String, boolean)">Limit</A></B>(int&nbsp;seqNumber,\r
-      int&nbsp;seqLength,\r
-      java.lang.String&nbsp;preset,\r
-      boolean&nbsp;isDefault)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/Limit.html#equals(java.lang.Object)">equals</A></B>(java.lang.Object&nbsp;obj)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;int</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/Limit.html#getAvgSeqLength()">getAvgSeqLength</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;int</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/Limit.html#getAvgSequenceLength(java.util.List)">getAvgSequenceLength</A></B>(java.util.List&lt;<A HREF="../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;data)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Calculates an average sequence length of the dataset</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/Limit.html#getPreset()">getPreset</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;int</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/Limit.html#getSeqNumber()">getSeqNumber</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;int</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/Limit.html#hashCode()">hashCode</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/Limit.html#isDefault()">isDefault</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/Limit.html#isExceeded(java.util.List)">isExceeded</A></B>(java.util.List&lt;<A HREF="../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;data)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Checks if the number of sequences or their average length in the dataset
- exceeds limits the values defined by this Limit</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/Limit.html#toString()">toString</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>getClass, notify, notifyAll, wait, wait, wait</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
-\r
-<A NAME="constructor_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Constructor Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="Limit(int, int, java.lang.String)"><!-- --></A><H3>\r
-Limit</H3>\r
-<PRE>\r
-public <B>Limit</B>(int&nbsp;seqNumber,\r
-             int&nbsp;seqLength,\r
-             java.lang.String&nbsp;preset)</PRE>\r
-<DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="Limit(int, int, java.lang.String, boolean)"><!-- --></A><H3>\r
-Limit</H3>\r
-<PRE>\r
-public <B>Limit</B>(int&nbsp;seqNumber,\r
-             int&nbsp;seqLength,\r
-             java.lang.String&nbsp;preset,\r
-             boolean&nbsp;isDefault)</PRE>\r
-<DL>\r
-</DL>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
-<A NAME="method_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="getPreset()"><!-- --></A><H3>\r
-getPreset</H3>\r
-<PRE>\r
-public java.lang.String <B>getPreset</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getAvgSeqLength()"><!-- --></A><H3>\r
-getAvgSeqLength</H3>\r
-<PRE>\r
-public int <B>getAvgSeqLength</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getSeqNumber()"><!-- --></A><H3>\r
-getSeqNumber</H3>\r
-<PRE>\r
-public int <B>getSeqNumber</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="isDefault()"><!-- --></A><H3>\r
-isDefault</H3>\r
-<PRE>\r
-public boolean <B>isDefault</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="hashCode()"><!-- --></A><H3>\r
-hashCode</H3>\r
-<PRE>\r
-public int <B>hashCode</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Overrides:</B><DD><CODE>hashCode</CODE> in class <CODE>java.lang.Object</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="equals(java.lang.Object)"><!-- --></A><H3>\r
-equals</H3>\r
-<PRE>\r
-public boolean <B>equals</B>(java.lang.Object&nbsp;obj)</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Overrides:</B><DD><CODE>equals</CODE> in class <CODE>java.lang.Object</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="toString()"><!-- --></A><H3>\r
-toString</H3>\r
-<PRE>\r
-public java.lang.String <B>toString</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Overrides:</B><DD><CODE>toString</CODE> in class <CODE>java.lang.Object</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="isExceeded(java.util.List)"><!-- --></A><H3>\r
-isExceeded</H3>\r
-<PRE>\r
-public boolean <B>isExceeded</B>(java.util.List&lt;<A HREF="../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;data)</PRE>\r
-<DL>\r
-<DD>Checks if the number of sequences or their average length in the dataset
- exceeds limits the values defined by this Limit\r
-<P>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>data</CODE> - \r
-<DT><B>Returns:</B><DD>true if a limit is exceeded (what is the dataset is larger then
-         the limit), false otherwise.</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getAvgSequenceLength(java.util.List)"><!-- --></A><H3>\r
-getAvgSequenceLength</H3>\r
-<PRE>\r
-public static int <B>getAvgSequenceLength</B>(java.util.List&lt;<A HREF="../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;data)</PRE>\r
-<DL>\r
-<DD>Calculates an average sequence length of the dataset\r
-<P>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>data</CODE> - \r
-<DT><B>Returns:</B><DD>an average sequence length in the input dataset</DL>\r
-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
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-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/Limit.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
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-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../index.html?compbio/metadata/Limit.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
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-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
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-  <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>\r
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-\r
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-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
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-<HR>\r
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-</HTML>\r
diff --git a/website/full_javadoc/compbio/metadata/LimitExceededException.html b/website/full_javadoc/compbio/metadata/LimitExceededException.html

deleted file mode 100644 (file)

index 910baa8..0000000
--- a/website/full_javadoc/compbio/metadata/LimitExceededException.html
+++ /dev/null
@@ -1,357 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-LimitExceededException\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
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-    }\r
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-</SCRIPT>\r
-<NOSCRIPT>\r
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-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
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-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
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-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
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-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
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-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../compbio/metadata/Limit.html" title="class in compbio.metadata"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../index.html?compbio/metadata/LimitExceededException.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
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-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
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-  <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>\r
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-\r
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-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.metadata</FONT>\r
-<BR>\r
-Class LimitExceededException</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../resources/inherit.gif" ALT="extended by ">java.lang.Throwable\r
-      <IMG SRC="../../resources/inherit.gif" ALT="extended by ">java.lang.Exception\r
-          <IMG SRC="../../resources/inherit.gif" ALT="extended by "><A HREF="../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">compbio.metadata.JobSubmissionException</A>\r
-              <IMG SRC="../../resources/inherit.gif" ALT="extended by "><B>compbio.metadata.LimitExceededException</B>\r
-</PRE>\r
-<DL>\r
-<DT><B>All Implemented Interfaces:</B> <DD>java.io.Serializable</DD>\r
-</DL>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public class <B>LimitExceededException</B><DT>extends <A HREF="../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></DL>\r
-</PRE>\r
-\r
-<P>\r
-Thrown if the task larger in size that the limit that applies to the
- calculation.\r
-<P>\r
-\r
-<P>\r
-<DL>\r
-<DT><B>Author:</B></DT>\r
-  <DD>pvtroshin
- 
-         Date February 2010</DD>\r
-<DT><B>See Also:</B><DD><A HREF="../../compbio/metadata/Limit.html" title="class in compbio.metadata"><CODE>Limit</CODE></A>, \r
-<A HREF="../../serialized-form.html#compbio.metadata.LimitExceededException">Serialized Form</A></DL>\r
-<HR>\r
-\r
-<P>\r
-\r
-<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
-\r
-<A NAME="constructor_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Constructor Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../compbio/metadata/LimitExceededException.html#LimitExceededException(java.lang.String)">LimitExceededException</A></B>(java.lang.String&nbsp;message)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;int</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/LimitExceededException.html#getActualNumberofSequences()">getActualNumberofSequences</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;int</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/LimitExceededException.html#getNumberOfSequencesAllowed()">getNumberOfSequencesAllowed</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;int</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/LimitExceededException.html#getSequenceLenghtActual()">getSequenceLenghtActual</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;int</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/LimitExceededException.html#getSequenceLenghtAllowed()">getSequenceLenghtAllowed</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/LimitExceededException.html#newLimitExceeded(compbio.metadata.Limit, java.util.List)">newLimitExceeded</A></B>(<A HREF="../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;?&gt;&nbsp;limit,\r
-                 java.util.List&lt;<A HREF="../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;seqs)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Throwable"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Throwable</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>fillInStackTrace, getCause, getLocalizedMessage, getMessage, getStackTrace, initCause, printStackTrace, printStackTrace, printStackTrace, setStackTrace, toString</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>equals, getClass, hashCode, notify, notifyAll, wait, wait, wait</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
-\r
-<A NAME="constructor_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Constructor Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="LimitExceededException(java.lang.String)"><!-- --></A><H3>\r
-LimitExceededException</H3>\r
-<PRE>\r
-public <B>LimitExceededException</B>(java.lang.String&nbsp;message)</PRE>\r
-<DL>\r
-</DL>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
-<A NAME="method_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="newLimitExceeded(compbio.metadata.Limit, java.util.List)"><!-- --></A><H3>\r
-newLimitExceeded</H3>\r
-<PRE>\r
-public static <A HREF="../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A> <B>newLimitExceeded</B>(<A HREF="../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;?&gt;&nbsp;limit,\r
-                                                      java.util.List&lt;<A HREF="../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;seqs)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getNumberOfSequencesAllowed()"><!-- --></A><H3>\r
-getNumberOfSequencesAllowed</H3>\r
-<PRE>\r
-public int <B>getNumberOfSequencesAllowed</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getActualNumberofSequences()"><!-- --></A><H3>\r
-getActualNumberofSequences</H3>\r
-<PRE>\r
-public int <B>getActualNumberofSequences</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getSequenceLenghtAllowed()"><!-- --></A><H3>\r
-getSequenceLenghtAllowed</H3>\r
-<PRE>\r
-public int <B>getSequenceLenghtAllowed</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getSequenceLenghtActual()"><!-- --></A><H3>\r
-getSequenceLenghtActual</H3>\r
-<PRE>\r
-public int <B>getSequenceLenghtActual</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
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-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/LimitExceededException.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
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-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../compbio/metadata/Limit.html" title="class in compbio.metadata"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../index.html?compbio/metadata/LimitExceededException.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="LimitExceededException.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/metadata/LimitsManager.html b/website/full_javadoc/compbio/metadata/LimitsManager.html

deleted file mode 100644 (file)

index 88195c6..0000000
--- a/website/full_javadoc/compbio/metadata/LimitsManager.html
+++ /dev/null
@@ -1,363 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-LimitsManager\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="LimitsManager";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/LimitsManager.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../index.html?compbio/metadata/LimitsManager.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="LimitsManager.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.metadata</FONT>\r
-<BR>\r
-Class LimitsManager&lt;T&gt;</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../resources/inherit.gif" ALT="extended by "><B>compbio.metadata.LimitsManager&lt;T&gt;</B>\r
-</PRE>\r
-<DL>\r
-<DT><DT><B>Type Parameters:</B><DD><CODE>T</CODE> - executable type</DL>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public class <B>LimitsManager&lt;T&gt;</B><DT>extends java.lang.Object</DL>\r
-</PRE>\r
-\r
-<P>\r
-A collection of Limits\r
-<P>\r
-\r
-<P>\r
-<DL>\r
-<DT><B>Author:</B></DT>\r
-  <DD>pvtroshin
- 
-         Date January 2010</DD>\r
-<DT><B>See Also:</B><DD><A HREF="../../compbio/metadata/Limit.html" title="class in compbio.metadata"><CODE>Limit</CODE></A></DL>\r
-<HR>\r
-\r
-<P>\r
-\r
-<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
-\r
-<A NAME="constructor_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Constructor Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../compbio/metadata/LimitsManager.html#LimitsManager()">LimitsManager</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;<A HREF="../../compbio/metadata/LimitsManager.html" title="type parameter in LimitsManager">T</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/LimitsManager.html#getDefaultLimit()">getDefaultLimit</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;<A HREF="../../compbio/metadata/LimitsManager.html" title="type parameter in LimitsManager">T</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/LimitsManager.html#getLimitByName(java.lang.String)">getLimitByName</A></B>(java.lang.String&nbsp;presetName)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.util.List&lt;<A HREF="../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;<A HREF="../../compbio/metadata/LimitsManager.html" title="type parameter in LimitsManager">T</A>&gt;&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/LimitsManager.html#getLimits()">getLimits</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/LimitsManager.html#toString()">toString</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/LimitsManager.html#validate(compbio.metadata.PresetManager)">validate</A></B>(<A HREF="../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>&lt;<A HREF="../../compbio/metadata/LimitsManager.html" title="type parameter in LimitsManager">T</A>&gt;&nbsp;presets)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Validate Limits</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>equals, getClass, hashCode, notify, notifyAll, wait, wait, wait</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
-\r
-<A NAME="constructor_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Constructor Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="LimitsManager()"><!-- --></A><H3>\r
-LimitsManager</H3>\r
-<PRE>\r
-public <B>LimitsManager</B>()</PRE>\r
-<DL>\r
-</DL>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
-<A NAME="method_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="getLimits()"><!-- --></A><H3>\r
-getLimits</H3>\r
-<PRE>\r
-public java.util.List&lt;<A HREF="../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;<A HREF="../../compbio/metadata/LimitsManager.html" title="type parameter in LimitsManager">T</A>&gt;&gt; <B>getLimits</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>all limits defined for an executable T</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="toString()"><!-- --></A><H3>\r
-toString</H3>\r
-<PRE>\r
-public java.lang.String <B>toString</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Overrides:</B><DD><CODE>toString</CODE> in class <CODE>java.lang.Object</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getLimitByName(java.lang.String)"><!-- --></A><H3>\r
-getLimitByName</H3>\r
-<PRE>\r
-public <A HREF="../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;<A HREF="../../compbio/metadata/LimitsManager.html" title="type parameter in LimitsManager">T</A>&gt; <B>getLimitByName</B>(java.lang.String&nbsp;presetName)</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>presetName</CODE> - \r
-<DT><B>Returns:</B><DD>Limit defined for the executable T and presetName. If no limit is
-         defined for the presetName then default Limit is returned. If
-         presetName is empty or null than the default Limit will be
-         returned. If not limit defined for the type T than NULL will be
-         returned</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getDefaultLimit()"><!-- --></A><H3>\r
-getDefaultLimit</H3>\r
-<PRE>\r
-public <A HREF="../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;<A HREF="../../compbio/metadata/LimitsManager.html" title="type parameter in LimitsManager">T</A>&gt; <B>getDefaultLimit</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>the default Limit for an executable type T</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="validate(compbio.metadata.PresetManager)"><!-- --></A><H3>\r
-validate</H3>\r
-<PRE>\r
-public void <B>validate</B>(<A HREF="../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>&lt;<A HREF="../../compbio/metadata/LimitsManager.html" title="type parameter in LimitsManager">T</A>&gt;&nbsp;presets)\r
-              throws javax.xml.bind.ValidationException</PRE>\r
-<DL>\r
-<DD>Validate Limits\r
-<P>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>presets</CODE> - \r
-<DT><B>Throws:</B>\r
-<DD><CODE>javax.xml.bind.ValidationException</CODE> - if any of the Limit defined is found to be invalid. That is
-             when
- 
-             1) No default limit is defined
- 
-             2) More than 1 default limit is defined
- 
-             3) Limit's preset name does not match any presets for type T<DT><B>See Also:</B><DD><A HREF="../../compbio/metadata/Limit.html" title="class in compbio.metadata"><CODE>Limit</CODE></A>, \r
-<A HREF="../../compbio/metadata/Preset.html" title="class in compbio.metadata"><CODE>Preset</CODE></A></DL>\r
-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/LimitsManager.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../index.html?compbio/metadata/LimitsManager.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="LimitsManager.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/metadata/Option.html b/website/full_javadoc/compbio/metadata/Option.html

deleted file mode 100644 (file)

index 1bb99d9..0000000
--- a/website/full_javadoc/compbio/metadata/Option.html
+++ /dev/null
@@ -1,714 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Option\r
-</TITLE>\r
-\r
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-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Option";\r
-    }\r
-}\r
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-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
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-\r
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-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.metadata</FONT>\r
-<BR>\r
-Class Option&lt;T&gt;</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../resources/inherit.gif" ALT="extended by "><B>compbio.metadata.Option&lt;T&gt;</B>\r
-</PRE>\r
-<DL>\r
-<DT><DT><B>Type Parameters:</B><DD><CODE>T</CODE> - type of executable</DL>\r
-<DL>\r
-<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</A>&lt;T&gt;</DD>\r
-</DL>\r
-<DL>\r
-<DT><B>Direct Known Subclasses:</B> <DD><A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A></DD>\r
-</DL>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public class <B>Option&lt;T&gt;</B><DT>extends java.lang.Object<DT>implements <A HREF="../../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</A>&lt;T&gt;</DL>\r
-</PRE>\r
-\r
-<P>\r
-Command line option/flag or multiple exclusive options with no value. Example
- -protein, -dna, -auto\r
-<P>\r
-\r
-<P>\r
-<DL>\r
-<DT><B>Author:</B></DT>\r
-  <DD>pvtroshin
- 
-         Date October 2009</DD>\r
-</DL>\r
-<HR>\r
-\r
-<P>\r
-\r
-<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
-\r
-<A NAME="constructor_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Constructor Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../compbio/metadata/Option.html#Option(java.lang.String, java.lang.String)">Option</A></B>(java.lang.String&nbsp;name,\r
-       java.lang.String&nbsp;description)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.util.Set&lt;java.lang.String&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/Option.html#addOptionNames(java.lang.String...)">addOptionNames</A></B>(java.lang.String...&nbsp;value)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Adds an option to the optionName list</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/Option.html#equals(java.lang.Object)">equals</A></B>(java.lang.Object&nbsp;obj)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/Option.html#getDefaultValue()">getDefaultValue</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;A default value of the option.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/Option.html#getDescription()">getDescription</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;A long description of the Option</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.net.URL</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/Option.html#getFurtherDetails()">getFurtherDetails</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The URL where further details about the option can be found</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/Option.html#getName()">getName</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Human readable name of the option</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.util.List&lt;java.lang.String&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/Option.html#getOptionNames()">getOptionNames</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.util.List&lt;java.lang.String&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/Option.html#getPossibleValues()">getPossibleValues</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;List of possible optionNames</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;int</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/Option.html#hashCode()">hashCode</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/Option.html#isRequired()">isRequired</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Flag that indicated that this option must be specified in the command
- line for an executable to run</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/Option.html#setDefaultValue(java.lang.String)">setDefaultValue</A></B>(java.lang.String&nbsp;defaultVal)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Sets one of the values defined in optionList as default.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/Option.html#setDescription(java.lang.String)">setDescription</A></B>(java.lang.String&nbsp;description)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/Option.html#setFurtherDetails(java.net.URL)">setFurtherDetails</A></B>(java.net.URL&nbsp;furtherDetails)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/Option.html#setName(java.lang.String)">setName</A></B>(java.lang.String&nbsp;name)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/Option.html#setOptionNames(java.util.Set)">setOptionNames</A></B>(java.util.Set&lt;java.lang.String&gt;&nbsp;optionNames)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/Option.html#setRequired(boolean)">setRequired</A></B>(boolean&nbsp;isRequired)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/Option.html#setValue(java.lang.String)">setValue</A></B>(java.lang.String&nbsp;dValue)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Set default values for the parameter or an option</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/Option.html#toCommand(java.lang.String)">toCommand</A></B>(java.lang.String&nbsp;nameValueSeparator)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Convert the option to the command string.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/Option.html#toString()">toString</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>getClass, notify, notifyAll, wait, wait, wait</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
-\r
-<A NAME="constructor_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Constructor Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="Option(java.lang.String, java.lang.String)"><!-- --></A><H3>\r
-Option</H3>\r
-<PRE>\r
-public <B>Option</B>(java.lang.String&nbsp;name,\r
-              java.lang.String&nbsp;description)</PRE>\r
-<DL>\r
-</DL>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
-<A NAME="method_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="getName()"><!-- --></A><H3>\r
-getName</H3>\r
-<PRE>\r
-public java.lang.String <B>getName</B>()</PRE>\r
-<DL>\r
-<DD>Human readable name of the option\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../compbio/metadata/Argument.html#getName()">getName</A></CODE> in interface <CODE><A HREF="../../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</A>&lt;<A HREF="../../compbio/metadata/Option.html" title="type parameter in Option">T</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="setName(java.lang.String)"><!-- --></A><H3>\r
-setName</H3>\r
-<PRE>\r
-public void <B>setName</B>(java.lang.String&nbsp;name)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getDescription()"><!-- --></A><H3>\r
-getDescription</H3>\r
-<PRE>\r
-public java.lang.String <B>getDescription</B>()</PRE>\r
-<DL>\r
-<DD>A long description of the Option\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../compbio/metadata/Argument.html#getDescription()">getDescription</A></CODE> in interface <CODE><A HREF="../../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</A>&lt;<A HREF="../../compbio/metadata/Option.html" title="type parameter in Option">T</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="setDescription(java.lang.String)"><!-- --></A><H3>\r
-setDescription</H3>\r
-<PRE>\r
-public void <B>setDescription</B>(java.lang.String&nbsp;description)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getFurtherDetails()"><!-- --></A><H3>\r
-getFurtherDetails</H3>\r
-<PRE>\r
-public java.net.URL <B>getFurtherDetails</B>()</PRE>\r
-<DL>\r
-<DD>The URL where further details about the option can be found\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../compbio/metadata/Argument.html#getFurtherDetails()">getFurtherDetails</A></CODE> in interface <CODE><A HREF="../../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</A>&lt;<A HREF="../../compbio/metadata/Option.html" title="type parameter in Option">T</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="setFurtherDetails(java.net.URL)"><!-- --></A><H3>\r
-setFurtherDetails</H3>\r
-<PRE>\r
-public void <B>setFurtherDetails</B>(java.net.URL&nbsp;furtherDetails)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getDefaultValue()"><!-- --></A><H3>\r
-getDefaultValue</H3>\r
-<PRE>\r
-public java.lang.String <B>getDefaultValue</B>()</PRE>\r
-<DL>\r
-<DD>A default value of the option. Defaults to command line argument name
- e.g. -auto\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../compbio/metadata/Argument.html#getDefaultValue()">getDefaultValue</A></CODE> in interface <CODE><A HREF="../../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</A>&lt;<A HREF="../../compbio/metadata/Option.html" title="type parameter in Option">T</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="setDefaultValue(java.lang.String)"><!-- --></A><H3>\r
-setDefaultValue</H3>\r
-<PRE>\r
-public void <B>setDefaultValue</B>(java.lang.String&nbsp;defaultVal)\r
-                     throws <A HREF="../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></PRE>\r
-<DL>\r
-<DD>Sets one of the values defined in optionList as default. Attempting set
- the value not listed there will result in WrongParameter exception\r
-<P>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>defaultVal</CODE> - \r
-<DT><B>Throws:</B>\r
-<DD><CODE><A HREF="../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></CODE> - is thrown if the defaultValue is not found in optionList</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="isRequired()"><!-- --></A><H3>\r
-isRequired</H3>\r
-<PRE>\r
-public boolean <B>isRequired</B>()</PRE>\r
-<DL>\r
-<DD>Flag that indicated that this option must be specified in the command
- line for an executable to run\r
-<P>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>true is the option is required, false otherwise</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="setRequired(boolean)"><!-- --></A><H3>\r
-setRequired</H3>\r
-<PRE>\r
-public void <B>setRequired</B>(boolean&nbsp;isRequired)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getOptionNames()"><!-- --></A><H3>\r
-getOptionNames</H3>\r
-<PRE>\r
-public java.util.List&lt;java.lang.String&gt; <B>getOptionNames</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>List of option names</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="setOptionNames(java.util.Set)"><!-- --></A><H3>\r
-setOptionNames</H3>\r
-<PRE>\r
-public void <B>setOptionNames</B>(java.util.Set&lt;java.lang.String&gt;&nbsp;optionNames)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="addOptionNames(java.lang.String...)"><!-- --></A><H3>\r
-addOptionNames</H3>\r
-<PRE>\r
-public java.util.Set&lt;java.lang.String&gt; <B>addOptionNames</B>(java.lang.String...&nbsp;value)</PRE>\r
-<DL>\r
-<DD>Adds an option to the optionName list\r
-<P>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>value</CODE> - \r
-<DT><B>Returns:</B><DD>modified optionName list</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="toString()"><!-- --></A><H3>\r
-toString</H3>\r
-<PRE>\r
-public java.lang.String <B>toString</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Overrides:</B><DD><CODE>toString</CODE> in class <CODE>java.lang.Object</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="toCommand(java.lang.String)"><!-- --></A><H3>\r
-toCommand</H3>\r
-<PRE>\r
-public java.lang.String <B>toCommand</B>(java.lang.String&nbsp;nameValueSeparator)</PRE>\r
-<DL>\r
-<DD>Convert the option to the command string.\r
-<P>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>If only one optionName is defined, than it is returned, if many
-         option names are defined, then the defaultValue is returned.
-         Option must have a default value if there are many optionNames to
-         be valid.</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="equals(java.lang.Object)"><!-- --></A><H3>\r
-equals</H3>\r
-<PRE>\r
-public boolean <B>equals</B>(java.lang.Object&nbsp;obj)</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Overrides:</B><DD><CODE>equals</CODE> in class <CODE>java.lang.Object</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="hashCode()"><!-- --></A><H3>\r
-hashCode</H3>\r
-<PRE>\r
-public int <B>hashCode</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Overrides:</B><DD><CODE>hashCode</CODE> in class <CODE>java.lang.Object</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getPossibleValues()"><!-- --></A><H3>\r
-getPossibleValues</H3>\r
-<PRE>\r
-public java.util.List&lt;java.lang.String&gt; <B>getPossibleValues</B>()</PRE>\r
-<DL>\r
-<DD>List of possible optionNames\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../compbio/metadata/Argument.html#getPossibleValues()">getPossibleValues</A></CODE> in interface <CODE><A HREF="../../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</A>&lt;<A HREF="../../compbio/metadata/Option.html" title="type parameter in Option">T</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>List of values allowed for an Argument</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="setValue(java.lang.String)"><!-- --></A><H3>\r
-setValue</H3>\r
-<PRE>\r
-public void <B>setValue</B>(java.lang.String&nbsp;dValue)\r
-              throws <A HREF="../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></PRE>\r
-<DL>\r
-<DD><B>Description copied from interface: <CODE><A HREF="../../compbio/metadata/Argument.html#setValue(java.lang.String)">Argument</A></CODE></B></DD>\r
-<DD>Set default values for the parameter or an option\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../compbio/metadata/Argument.html#setValue(java.lang.String)">setValue</A></CODE> in interface <CODE><A HREF="../../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</A>&lt;<A HREF="../../compbio/metadata/Option.html" title="type parameter in Option">T</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>dValue</CODE> - the value to be set\r
-<DT><B>Throws:</B>\r
-<DD><CODE><A HREF="../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></CODE> - - when the value to be set is illegal. Wrong value for
-             numeric parameter is the value defined outside it , for
-             string type parameter, wrong value is the one which is not
-             listed in possible values list<DT><B>See Also:</B><DD><A HREF="../../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata"><CODE>ValueConstrain</CODE></A></DL>\r
-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
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-<TR>\r
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-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/Option.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
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-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../index.html?compbio/metadata/Option.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="Option.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
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-<HR>\r
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-</HTML>\r
diff --git a/website/full_javadoc/compbio/metadata/Parameter.html b/website/full_javadoc/compbio/metadata/Parameter.html

deleted file mode 100644 (file)

index 45505e0..0000000
--- a/website/full_javadoc/compbio/metadata/Parameter.html
+++ /dev/null
@@ -1,572 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Parameter\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Parameter";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/Parameter.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../compbio/metadata/Preset.html" title="class in compbio.metadata"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../index.html?compbio/metadata/Parameter.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="Parameter.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.metadata</FONT>\r
-<BR>\r
-Class Parameter&lt;T&gt;</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../resources/inherit.gif" ALT="extended by "><A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">compbio.metadata.Option</A>&lt;T&gt;\r
-      <IMG SRC="../../resources/inherit.gif" ALT="extended by "><B>compbio.metadata.Parameter&lt;T&gt;</B>\r
-</PRE>\r
-<DL>\r
-<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</A>&lt;T&gt;</DD>\r
-</DL>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public class <B>Parameter&lt;T&gt;</B><DT>extends <A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;T&gt;</DL>\r
-</PRE>\r
-\r
-<P>\r
-A single value containing option supported by the web service e.g.
- seqType=protein. Where seqType is a optionName and protein is one of
- possibleValues\r
-<P>\r
-\r
-<P>\r
-<DL>\r
-<DT><B>Author:</B></DT>\r
-  <DD>pvtroshin
- 
-         Date November 2009</DD>\r
-<DT><B>See Also:</B><DD><A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata"><CODE>Option</CODE></A>, \r
-<A HREF="../../compbio/metadata/Argument.html" title="interface in compbio.metadata"><CODE>Argument</CODE></A></DL>\r
-<HR>\r
-\r
-<P>\r
-\r
-<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
-\r
-<A NAME="constructor_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Constructor Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../compbio/metadata/Parameter.html#Parameter(java.lang.String, java.lang.String)">Parameter</A></B>(java.lang.String&nbsp;name,\r
-          java.lang.String&nbsp;description)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.util.Set&lt;java.lang.String&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/Parameter.html#addOptionNames(java.lang.String...)">addOptionNames</A></B>(java.lang.String...&nbsp;value)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Adds an option to the optionName list</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.util.Set&lt;java.lang.String&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/Parameter.html#addPossibleValues(java.lang.String...)">addPossibleValues</A></B>(java.lang.String...&nbsp;value)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/Parameter.html#equals(java.lang.Object)">equals</A></B>(java.lang.Object&nbsp;obj)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/Parameter.html#getOptionName()">getOptionName</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.util.List&lt;java.lang.String&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/Parameter.html#getPossibleValues()">getPossibleValues</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;List is more convenient to work with</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/Parameter.html#getValidValue()">getValidValue</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;int</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/Parameter.html#hashCode()">hashCode</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/Parameter.html#setDefaultValue(java.lang.String)">setDefaultValue</A></B>(java.lang.String&nbsp;defaultVal)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Sets one of the values defined in optionList as default.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/Parameter.html#setOptionName(java.lang.String)">setOptionName</A></B>(java.lang.String&nbsp;optionName)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/Parameter.html#setOptionNames(java.util.Set)">setOptionNames</A></B>(java.util.Set&lt;java.lang.String&gt;&nbsp;optionName)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/Parameter.html#setPossibleValues(java.util.Set)">setPossibleValues</A></B>(java.util.Set&lt;java.lang.String&gt;&nbsp;possibleValues)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/Parameter.html#setValidValue(compbio.metadata.ValueConstrain)">setValidValue</A></B>(<A HREF="../../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A>&nbsp;validValue)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/Parameter.html#toCommand(java.lang.String)">toCommand</A></B>(java.lang.String&nbsp;nameValueSeparator)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Convert the option to the command string.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/Parameter.html#toString()">toString</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_compbio.metadata.Option"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class compbio.metadata.<A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A></B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><A HREF="../../compbio/metadata/Option.html#getDefaultValue()">getDefaultValue</A>, <A HREF="../../compbio/metadata/Option.html#getDescription()">getDescription</A>, <A HREF="../../compbio/metadata/Option.html#getFurtherDetails()">getFurtherDetails</A>, <A HREF="../../compbio/metadata/Option.html#getName()">getName</A>, <A HREF="../../compbio/metadata/Option.html#getOptionNames()">getOptionNames</A>, <A HREF="../../compbio/metadata/Option.html#isRequired()">isRequired</A>, <A HREF="../../compbio/metadata/Option.html#setDescription(java.lang.String)">setDescription</A>, <A HREF="../../compbio/metadata/Option.html#setFurtherDetails(java.net.URL)">setFurtherDetails</A>, <A HREF="../../compbio/metadata/Option.html#setName(java.lang.String)">setName</A>, <A HREF="../../compbio/metadata/Option.html#setRequired(boolean)">setRequired</A>, <A HREF="../../compbio/metadata/Option.html#setValue(java.lang.String)">setValue</A></CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>getClass, notify, notifyAll, wait, wait, wait</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
-\r
-<A NAME="constructor_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Constructor Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="Parameter(java.lang.String, java.lang.String)"><!-- --></A><H3>\r
-Parameter</H3>\r
-<PRE>\r
-public <B>Parameter</B>(java.lang.String&nbsp;name,\r
-                 java.lang.String&nbsp;description)</PRE>\r
-<DL>\r
-</DL>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
-<A NAME="method_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="getValidValue()"><!-- --></A><H3>\r
-getValidValue</H3>\r
-<PRE>\r
-public <A HREF="../../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A> <B>getValidValue</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="setValidValue(compbio.metadata.ValueConstrain)"><!-- --></A><H3>\r
-setValidValue</H3>\r
-<PRE>\r
-public void <B>setValidValue</B>(<A HREF="../../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A>&nbsp;validValue)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="toString()"><!-- --></A><H3>\r
-toString</H3>\r
-<PRE>\r
-public java.lang.String <B>toString</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Overrides:</B><DD><CODE><A HREF="../../compbio/metadata/Option.html#toString()">toString</A></CODE> in class <CODE><A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../compbio/metadata/Parameter.html" title="type parameter in Parameter">T</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="toCommand(java.lang.String)"><!-- --></A><H3>\r
-toCommand</H3>\r
-<PRE>\r
-public java.lang.String <B>toCommand</B>(java.lang.String&nbsp;nameValueSeparator)</PRE>\r
-<DL>\r
-<DD><B>Description copied from class: <CODE><A HREF="../../compbio/metadata/Option.html#toCommand(java.lang.String)">Option</A></CODE></B></DD>\r
-<DD>Convert the option to the command string.\r
-<P>\r
-<DD><DL>\r
-<DT><B>Overrides:</B><DD><CODE><A HREF="../../compbio/metadata/Option.html#toCommand(java.lang.String)">toCommand</A></CODE> in class <CODE><A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../compbio/metadata/Parameter.html" title="type parameter in Parameter">T</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>If only one optionName is defined, than it is returned, if many
-         option names are defined, then the defaultValue is returned.
-         Option must have a default value if there are many optionNames to
-         be valid.</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="equals(java.lang.Object)"><!-- --></A><H3>\r
-equals</H3>\r
-<PRE>\r
-public boolean <B>equals</B>(java.lang.Object&nbsp;obj)</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Overrides:</B><DD><CODE><A HREF="../../compbio/metadata/Option.html#equals(java.lang.Object)">equals</A></CODE> in class <CODE><A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../compbio/metadata/Parameter.html" title="type parameter in Parameter">T</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getPossibleValues()"><!-- --></A><H3>\r
-getPossibleValues</H3>\r
-<PRE>\r
-public java.util.List&lt;java.lang.String&gt; <B>getPossibleValues</B>()</PRE>\r
-<DL>\r
-<DD>List is more convenient to work with\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../compbio/metadata/Argument.html#getPossibleValues()">getPossibleValues</A></CODE> in interface <CODE><A HREF="../../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</A>&lt;<A HREF="../../compbio/metadata/Parameter.html" title="type parameter in Parameter">T</A>&gt;</CODE><DT><B>Overrides:</B><DD><CODE><A HREF="../../compbio/metadata/Option.html#getPossibleValues()">getPossibleValues</A></CODE> in class <CODE><A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../compbio/metadata/Parameter.html" title="type parameter in Parameter">T</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>List of String</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="setPossibleValues(java.util.Set)"><!-- --></A><H3>\r
-setPossibleValues</H3>\r
-<PRE>\r
-public void <B>setPossibleValues</B>(java.util.Set&lt;java.lang.String&gt;&nbsp;possibleValues)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="addPossibleValues(java.lang.String...)"><!-- --></A><H3>\r
-addPossibleValues</H3>\r
-<PRE>\r
-public java.util.Set&lt;java.lang.String&gt; <B>addPossibleValues</B>(java.lang.String...&nbsp;value)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="hashCode()"><!-- --></A><H3>\r
-hashCode</H3>\r
-<PRE>\r
-public int <B>hashCode</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Overrides:</B><DD><CODE><A HREF="../../compbio/metadata/Option.html#hashCode()">hashCode</A></CODE> in class <CODE><A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../compbio/metadata/Parameter.html" title="type parameter in Parameter">T</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="setOptionNames(java.util.Set)"><!-- --></A><H3>\r
-setOptionNames</H3>\r
-<PRE>\r
-public void <B>setOptionNames</B>(java.util.Set&lt;java.lang.String&gt;&nbsp;optionName)</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Overrides:</B><DD><CODE><A HREF="../../compbio/metadata/Option.html#setOptionNames(java.util.Set)">setOptionNames</A></CODE> in class <CODE><A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../compbio/metadata/Parameter.html" title="type parameter in Parameter">T</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="addOptionNames(java.lang.String...)"><!-- --></A><H3>\r
-addOptionNames</H3>\r
-<PRE>\r
-public java.util.Set&lt;java.lang.String&gt; <B>addOptionNames</B>(java.lang.String...&nbsp;value)</PRE>\r
-<DL>\r
-<DD><B>Description copied from class: <CODE><A HREF="../../compbio/metadata/Option.html#addOptionNames(java.lang.String...)">Option</A></CODE></B></DD>\r
-<DD>Adds an option to the optionName list\r
-<P>\r
-<DD><DL>\r
-<DT><B>Overrides:</B><DD><CODE><A HREF="../../compbio/metadata/Option.html#addOptionNames(java.lang.String...)">addOptionNames</A></CODE> in class <CODE><A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../compbio/metadata/Parameter.html" title="type parameter in Parameter">T</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>modified optionName list</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getOptionName()"><!-- --></A><H3>\r
-getOptionName</H3>\r
-<PRE>\r
-public java.lang.String <B>getOptionName</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="setOptionName(java.lang.String)"><!-- --></A><H3>\r
-setOptionName</H3>\r
-<PRE>\r
-public void <B>setOptionName</B>(java.lang.String&nbsp;optionName)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="setDefaultValue(java.lang.String)"><!-- --></A><H3>\r
-setDefaultValue</H3>\r
-<PRE>\r
-public void <B>setDefaultValue</B>(java.lang.String&nbsp;defaultVal)\r
-                     throws <A HREF="../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></PRE>\r
-<DL>\r
-<DD><B>Description copied from class: <CODE><A HREF="../../compbio/metadata/Option.html#setDefaultValue(java.lang.String)">Option</A></CODE></B></DD>\r
-<DD>Sets one of the values defined in optionList as default. Attempting set
- the value not listed there will result in WrongParameter exception\r
-<P>\r
-<DD><DL>\r
-<DT><B>Overrides:</B><DD><CODE><A HREF="../../compbio/metadata/Option.html#setDefaultValue(java.lang.String)">setDefaultValue</A></CODE> in class <CODE><A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../compbio/metadata/Parameter.html" title="type parameter in Parameter">T</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-\r
-<DT><B>Throws:</B>\r
-<DD><CODE><A HREF="../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></CODE> - is thrown if the defaultValue is not found in optionList</DL>\r
-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
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-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/Parameter.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
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-  </TR>\r
-</TABLE>\r
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-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../compbio/metadata/Preset.html" title="class in compbio.metadata"><B>NEXT CLASS</B></A></FONT></TD>\r
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-  <A HREF="../../index.html?compbio/metadata/Parameter.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
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-  if(window==top) {\r
-    document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
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-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/metadata/Preset.html b/website/full_javadoc/compbio/metadata/Preset.html

deleted file mode 100644 (file)

index 2995b06..0000000
--- a/website/full_javadoc/compbio/metadata/Preset.html
+++ /dev/null
@@ -1,455 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Preset\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Preset";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/Preset.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../compbio/metadata/PresetManager.html" title="class in compbio.metadata"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../index.html?compbio/metadata/Preset.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="Preset.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.metadata</FONT>\r
-<BR>\r
-Class Preset&lt;T&gt;</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../resources/inherit.gif" ALT="extended by "><B>compbio.metadata.Preset&lt;T&gt;</B>\r
-</PRE>\r
-<DL>\r
-<DT><DT><B>Type Parameters:</B><DD><CODE>T</CODE> - executable type</DL>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public class <B>Preset&lt;T&gt;</B><DT>extends java.lang.Object</DL>\r
-</PRE>\r
-\r
-<P>\r
-Collection of Options and Parameters with their values\r
-<P>\r
-\r
-<P>\r
-<DL>\r
-<DT><B>Author:</B></DT>\r
-  <DD>pvtroshin
- 
-         Date December 2009</DD>\r
-<DT><B>See Also:</B><DD><A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata"><CODE>Option</CODE></A>, \r
-<A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata"><CODE>Parameter</CODE></A></DL>\r
-<HR>\r
-\r
-<P>\r
-\r
-<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
-\r
-<A NAME="constructor_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Constructor Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../compbio/metadata/Preset.html#Preset()">Preset</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/Preset.html#equals(java.lang.Object)">equals</A></B>(java.lang.Object&nbsp;obj)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.util.List&lt;<A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../compbio/metadata/Preset.html" title="type parameter in Preset">T</A>&gt;&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/Preset.html#getArguments(compbio.metadata.RunnerConfig)">getArguments</A></B>(<A HREF="../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&lt;<A HREF="../../compbio/metadata/Preset.html" title="type parameter in Preset">T</A>&gt;&nbsp;rconfig)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Converts list of options as String to type Option</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/Preset.html#getDescription()">getDescription</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/Preset.html#getName()">getName</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.util.List&lt;java.lang.String&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/Preset.html#getOptions()">getOptions</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;int</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/Preset.html#hashCode()">hashCode</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/Preset.html#setDescription(java.lang.String)">setDescription</A></B>(java.lang.String&nbsp;description)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/Preset.html#setName(java.lang.String)">setName</A></B>(java.lang.String&nbsp;name)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/Preset.html#setOptions(java.util.List)">setOptions</A></B>(java.util.List&lt;java.lang.String&gt;&nbsp;option)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/Preset.html#toString()">toString</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>getClass, notify, notifyAll, wait, wait, wait</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
-\r
-<A NAME="constructor_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Constructor Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="Preset()"><!-- --></A><H3>\r
-Preset</H3>\r
-<PRE>\r
-public <B>Preset</B>()</PRE>\r
-<DL>\r
-</DL>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
-<A NAME="method_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="setOptions(java.util.List)"><!-- --></A><H3>\r
-setOptions</H3>\r
-<PRE>\r
-public void <B>setOptions</B>(java.util.List&lt;java.lang.String&gt;&nbsp;option)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="setName(java.lang.String)"><!-- --></A><H3>\r
-setName</H3>\r
-<PRE>\r
-public void <B>setName</B>(java.lang.String&nbsp;name)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="setDescription(java.lang.String)"><!-- --></A><H3>\r
-setDescription</H3>\r
-<PRE>\r
-public void <B>setDescription</B>(java.lang.String&nbsp;description)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getOptions()"><!-- --></A><H3>\r
-getOptions</H3>\r
-<PRE>\r
-public java.util.List&lt;java.lang.String&gt; <B>getOptions</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>a List of Options as a String</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getName()"><!-- --></A><H3>\r
-getName</H3>\r
-<PRE>\r
-public java.lang.String <B>getName</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>- name of the Preset</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getDescription()"><!-- --></A><H3>\r
-getDescription</H3>\r
-<PRE>\r
-public java.lang.String <B>getDescription</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>- a long description of the Preset</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getArguments(compbio.metadata.RunnerConfig)"><!-- --></A><H3>\r
-getArguments</H3>\r
-<PRE>\r
-public java.util.List&lt;<A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../compbio/metadata/Preset.html" title="type parameter in Preset">T</A>&gt;&gt; <B>getArguments</B>(<A HREF="../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&lt;<A HREF="../../compbio/metadata/Preset.html" title="type parameter in Preset">T</A>&gt;&nbsp;rconfig)\r
-                                       throws <A HREF="../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></PRE>\r
-<DL>\r
-<DD>Converts list of options as String to type Option\r
-<P>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>rconfig</CODE> - \r
-<DT><B>Returns:</B><DD>List of Options\r
-<DT><B>Throws:</B>\r
-<DD><CODE><A HREF="../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></CODE> - if the value of the parameter is invalid @see
-             <A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata"><CODE>Parameter</CODE></A></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="toString()"><!-- --></A><H3>\r
-toString</H3>\r
-<PRE>\r
-public java.lang.String <B>toString</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Overrides:</B><DD><CODE>toString</CODE> in class <CODE>java.lang.Object</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="hashCode()"><!-- --></A><H3>\r
-hashCode</H3>\r
-<PRE>\r
-public int <B>hashCode</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Overrides:</B><DD><CODE>hashCode</CODE> in class <CODE>java.lang.Object</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="equals(java.lang.Object)"><!-- --></A><H3>\r
-equals</H3>\r
-<PRE>\r
-public boolean <B>equals</B>(java.lang.Object&nbsp;obj)</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Overrides:</B><DD><CODE>equals</CODE> in class <CODE>java.lang.Object</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/Preset.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../compbio/metadata/PresetManager.html" title="class in compbio.metadata"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../index.html?compbio/metadata/Preset.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="Preset.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/metadata/PresetManager.html b/website/full_javadoc/compbio/metadata/PresetManager.html

deleted file mode 100644 (file)

index 17b792a..0000000
--- a/website/full_javadoc/compbio/metadata/PresetManager.html
+++ /dev/null
@@ -1,428 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-PresetManager\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="PresetManager";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/PresetManager.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../compbio/metadata/Preset.html" title="class in compbio.metadata"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../index.html?compbio/metadata/PresetManager.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="PresetManager.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;<A HREF="#field_summary">FIELD</A>&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;<A HREF="#field_detail">FIELD</A>&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.metadata</FONT>\r
-<BR>\r
-Class PresetManager&lt;T&gt;</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../resources/inherit.gif" ALT="extended by "><B>compbio.metadata.PresetManager&lt;T&gt;</B>\r
-</PRE>\r
-<DL>\r
-<DT><DT><B>Type Parameters:</B><DD><CODE>T</CODE> - type of executable.</DL>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public class <B>PresetManager&lt;T&gt;</B><DT>extends java.lang.Object</DL>\r
-</PRE>\r
-\r
-<P>\r
-Collection of presets and methods to manipulate them @see <A HREF="../../compbio/metadata/Preset.html" title="class in compbio.metadata"><CODE>Preset</CODE></A>\r
-<P>\r
-\r
-<P>\r
-<DL>\r
-<DT><B>Author:</B></DT>\r
-  <DD>pvtroshin
- 
-         Date December 2009</DD>\r
-</DL>\r
-<HR>\r
-\r
-<P>\r
-<!-- =========== FIELD SUMMARY =========== -->\r
-\r
-<A NAME="field_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Field Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/PresetManager.html#LOCAL_ENGINE_LIMIT_PRESET">LOCAL_ENGINE_LIMIT_PRESET</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
-\r
-<A NAME="constructor_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Constructor Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../compbio/metadata/PresetManager.html#PresetManager()">PresetManager</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>&lt;<A HREF="../../compbio/metadata/PresetManager.html" title="type parameter in PresetManager">T</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/PresetManager.html#getPresetByName(java.lang.String)">getPresetByName</A></B>(java.lang.String&nbsp;presetName)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.util.List&lt;<A HREF="../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>&lt;<A HREF="../../compbio/metadata/PresetManager.html" title="type parameter in PresetManager">T</A>&gt;&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/PresetManager.html#getPresets()">getPresets</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/PresetManager.html#getRunnerClassName()">getRunnerClassName</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/PresetManager.html#setPresets(java.util.List)">setPresets</A></B>(java.util.List&lt;<A HREF="../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>&lt;<A HREF="../../compbio/metadata/PresetManager.html" title="type parameter in PresetManager">T</A>&gt;&gt;&nbsp;presets)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/PresetManager.html#setRunnerClassName(java.lang.String)">setRunnerClassName</A></B>(java.lang.String&nbsp;runnerClassName)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/PresetManager.html#toString()">toString</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/PresetManager.html#validate(compbio.metadata.RunnerConfig)">validate</A></B>(<A HREF="../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&lt;<A HREF="../../compbio/metadata/PresetManager.html" title="type parameter in PresetManager">T</A>&gt;&nbsp;options)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Checks whether preset option and parameter are defined in RunnerConfig
- object.</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>equals, getClass, hashCode, notify, notifyAll, wait, wait, wait</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ============ FIELD DETAIL =========== -->\r
-\r
-<A NAME="field_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Field Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="LOCAL_ENGINE_LIMIT_PRESET"><!-- --></A><H3>\r
-LOCAL_ENGINE_LIMIT_PRESET</H3>\r
-<PRE>\r
-public static final java.lang.String <B>LOCAL_ENGINE_LIMIT_PRESET</B></PRE>\r
-<DL>\r
-<DL>\r
-<DT><B>See Also:</B><DD><A HREF="../../constant-values.html#compbio.metadata.PresetManager.LOCAL_ENGINE_LIMIT_PRESET">Constant Field Values</A></DL>\r
-</DL>\r
-\r
-<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
-\r
-<A NAME="constructor_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Constructor Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="PresetManager()"><!-- --></A><H3>\r
-PresetManager</H3>\r
-<PRE>\r
-public <B>PresetManager</B>()</PRE>\r
-<DL>\r
-</DL>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
-<A NAME="method_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="getPresets()"><!-- --></A><H3>\r
-getPresets</H3>\r
-<PRE>\r
-public java.util.List&lt;<A HREF="../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>&lt;<A HREF="../../compbio/metadata/PresetManager.html" title="type parameter in PresetManager">T</A>&gt;&gt; <B>getPresets</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="setPresets(java.util.List)"><!-- --></A><H3>\r
-setPresets</H3>\r
-<PRE>\r
-public void <B>setPresets</B>(java.util.List&lt;<A HREF="../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>&lt;<A HREF="../../compbio/metadata/PresetManager.html" title="type parameter in PresetManager">T</A>&gt;&gt;&nbsp;presets)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getRunnerClassName()"><!-- --></A><H3>\r
-getRunnerClassName</H3>\r
-<PRE>\r
-public java.lang.String <B>getRunnerClassName</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>fully qualified class name of type T</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="setRunnerClassName(java.lang.String)"><!-- --></A><H3>\r
-setRunnerClassName</H3>\r
-<PRE>\r
-public void <B>setRunnerClassName</B>(java.lang.String&nbsp;runnerClassName)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getPresetByName(java.lang.String)"><!-- --></A><H3>\r
-getPresetByName</H3>\r
-<PRE>\r
-public <A HREF="../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>&lt;<A HREF="../../compbio/metadata/PresetManager.html" title="type parameter in PresetManager">T</A>&gt; <B>getPresetByName</B>(java.lang.String&nbsp;presetName)</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>presetName</CODE> - \r
-<DT><B>Returns:</B><DD>preset by its name, null if no preset found</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="validate(compbio.metadata.RunnerConfig)"><!-- --></A><H3>\r
-validate</H3>\r
-<PRE>\r
-public void <B>validate</B>(<A HREF="../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&lt;<A HREF="../../compbio/metadata/PresetManager.html" title="type parameter in PresetManager">T</A>&gt;&nbsp;options)\r
-              throws javax.xml.bind.ValidationException</PRE>\r
-<DL>\r
-<DD>Checks whether preset option and parameter are defined in RunnerConfig
- object.
- 
- TODO handle parameters with values properly!\r
-<P>\r
-<DD><DL>\r
-\r
-<DT><B>Throws:</B>\r
-<DD><CODE>javax.xml.bind.ValidationException</CODE> - if preset is found to be invalid.</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="toString()"><!-- --></A><H3>\r
-toString</H3>\r
-<PRE>\r
-public java.lang.String <B>toString</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Overrides:</B><DD><CODE>toString</CODE> in class <CODE>java.lang.Object</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/PresetManager.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../compbio/metadata/Preset.html" title="class in compbio.metadata"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../index.html?compbio/metadata/PresetManager.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="PresetManager.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;<A HREF="#field_summary">FIELD</A>&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;<A HREF="#field_detail">FIELD</A>&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
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diff --git a/website/full_javadoc/compbio/metadata/ResultNotAvailableException.html b/website/full_javadoc/compbio/metadata/ResultNotAvailableException.html

deleted file mode 100644 (file)

index c0d8b57..0000000
--- a/website/full_javadoc/compbio/metadata/ResultNotAvailableException.html
+++ /dev/null
@@ -1,280 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-ResultNotAvailableException\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="ResultNotAvailableException";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/ResultNotAvailableException.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
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-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../compbio/metadata/PresetManager.html" title="class in compbio.metadata"><B>PREV CLASS</B></A>&nbsp;\r
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-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../index.html?compbio/metadata/ResultNotAvailableException.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="ResultNotAvailableException.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#methods_inherited_from_class_java.lang.Throwable">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;METHOD</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.metadata</FONT>\r
-<BR>\r
-Class ResultNotAvailableException</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../resources/inherit.gif" ALT="extended by ">java.lang.Throwable\r
-      <IMG SRC="../../resources/inherit.gif" ALT="extended by ">java.lang.Exception\r
-          <IMG SRC="../../resources/inherit.gif" ALT="extended by "><B>compbio.metadata.ResultNotAvailableException</B>\r
-</PRE>\r
-<DL>\r
-<DT><B>All Implemented Interfaces:</B> <DD>java.io.Serializable</DD>\r
-</DL>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public class <B>ResultNotAvailableException</B><DT>extends java.lang.Exception</DL>\r
-</PRE>\r
-\r
-<P>\r
-ResultNotAvailableException is thrown wherever the results of the calculation
- cannot be obtained. For cluster execution it hides lower level exceptions
- like DrmaaException\r
-<P>\r
-\r
-<P>\r
-<DL>\r
-<DT><B>Author:</B></DT>\r
-  <DD>pvtroshin
- 
-         Date October 2009</DD>\r
-<DT><B>See Also:</B><DD><A HREF="../../serialized-form.html#compbio.metadata.ResultNotAvailableException">Serialized Form</A></DL>\r
-<HR>\r
-\r
-<P>\r
-\r
-<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
-\r
-<A NAME="constructor_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Constructor Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../compbio/metadata/ResultNotAvailableException.html#ResultNotAvailableException(java.lang.String)">ResultNotAvailableException</A></B>(java.lang.String&nbsp;message)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../compbio/metadata/ResultNotAvailableException.html#ResultNotAvailableException(java.lang.String, java.lang.Throwable)">ResultNotAvailableException</A></B>(java.lang.String&nbsp;message,\r
-                            java.lang.Throwable&nbsp;cause)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../compbio/metadata/ResultNotAvailableException.html#ResultNotAvailableException(java.lang.Throwable)">ResultNotAvailableException</A></B>(java.lang.Throwable&nbsp;cause)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Throwable"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Throwable</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>fillInStackTrace, getCause, getLocalizedMessage, getMessage, getStackTrace, initCause, printStackTrace, printStackTrace, printStackTrace, setStackTrace, toString</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>equals, getClass, hashCode, notify, notifyAll, wait, wait, wait</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
-\r
-<A NAME="constructor_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Constructor Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="ResultNotAvailableException(java.lang.String)"><!-- --></A><H3>\r
-ResultNotAvailableException</H3>\r
-<PRE>\r
-public <B>ResultNotAvailableException</B>(java.lang.String&nbsp;message)</PRE>\r
-<DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="ResultNotAvailableException(java.lang.Throwable)"><!-- --></A><H3>\r
-ResultNotAvailableException</H3>\r
-<PRE>\r
-public <B>ResultNotAvailableException</B>(java.lang.Throwable&nbsp;cause)</PRE>\r
-<DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="ResultNotAvailableException(java.lang.String, java.lang.Throwable)"><!-- --></A><H3>\r
-ResultNotAvailableException</H3>\r
-<PRE>\r
-public <B>ResultNotAvailableException</B>(java.lang.String&nbsp;message,\r
-                                   java.lang.Throwable&nbsp;cause)</PRE>\r
-<DL>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/ResultNotAvailableException.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
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-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../compbio/metadata/PresetManager.html" title="class in compbio.metadata"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../index.html?compbio/metadata/ResultNotAvailableException.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="ResultNotAvailableException.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#methods_inherited_from_class_java.lang.Throwable">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;METHOD</FONT></TD>\r
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-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
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-</HTML>\r
diff --git a/website/full_javadoc/compbio/metadata/RunnerConfig.html b/website/full_javadoc/compbio/metadata/RunnerConfig.html

deleted file mode 100644 (file)

index 7f59fd8..0000000
--- a/website/full_javadoc/compbio/metadata/RunnerConfig.html
+++ /dev/null
@@ -1,640 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-RunnerConfig\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="RunnerConfig";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
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-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/RunnerConfig.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
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-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../index.html?compbio/metadata/RunnerConfig.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="RunnerConfig.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
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-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
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-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.metadata</FONT>\r
-<BR>\r
-Class RunnerConfig&lt;T&gt;</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../resources/inherit.gif" ALT="extended by "><B>compbio.metadata.RunnerConfig&lt;T&gt;</B>\r
-</PRE>\r
-<DL>\r
-<DT><DT><B>Type Parameters:</B><DD><CODE>T</CODE> - type of an Executable</DL>\r
-<HR>\r
-<DL>\r
-<DT><PRE><FONT SIZE="-1">@NotThreadSafe\r
-</FONT>public class <B>RunnerConfig&lt;T&gt;</B><DT>extends java.lang.Object</DL>\r
-</PRE>\r
-\r
-<P>\r
-The list of <A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata"><CODE>Parameter</CODE></A>s and <A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata"><CODE>Option</CODE></A>s supported by executable.\r
-<P>\r
-\r
-<P>\r
-<DL>\r
-<DT><B>Author:</B></DT>\r
-  <DD>pvtroshin
- 
-         Date October 2009</DD>\r
-</DL>\r
-<HR>\r
-\r
-<P>\r
-\r
-<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
-\r
-<A NAME="constructor_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Constructor Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../compbio/metadata/RunnerConfig.html#RunnerConfig()">RunnerConfig</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/RunnerConfig.html#addOption(compbio.metadata.Option)">addOption</A></B>(<A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>&gt;&nbsp;option)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/RunnerConfig.html#addParameter(compbio.metadata.Parameter)">addParameter</A></B>(<A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>&lt;<A HREF="../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>&gt;&nbsp;param)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&lt;<A HREF="../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/RunnerConfig.html#copyAndValidateRConfig(compbio.metadata.RunnerConfig)">copyAndValidateRConfig</A></B>(<A HREF="../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&lt;?&gt;&nbsp;runnerConf)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/RunnerConfig.html#equals(java.lang.Object)">equals</A></B>(java.lang.Object&nbsp;obj)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/RunnerConfig.html#getArgument(java.lang.String)">getArgument</A></B>(java.lang.String&nbsp;name)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Returns the argument by its name if found, NULL otherwise</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/RunnerConfig.html#getArgumentByOptionName(java.lang.String)">getArgumentByOptionName</A></B>(java.lang.String&nbsp;optionName)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Returns the argument by option name, NULL if the argument is not found</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.util.List&lt;<A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>&gt;&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/RunnerConfig.html#getArguments()">getArguments</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.util.List&lt;<A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>&gt;&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/RunnerConfig.html#getOptions()">getOptions</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.util.List&lt;<A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>&lt;<A HREF="../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>&gt;&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/RunnerConfig.html#getParameters()">getParameters</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/RunnerConfig.html#getPrmSeparator()">getPrmSeparator</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/RunnerConfig.html#getRunnerClassName()">getRunnerClassName</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/RunnerConfig.html#removeArgument(java.lang.String)">removeArgument</A></B>(java.lang.String&nbsp;name)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Removes the argument <A HREF="../../compbio/metadata/Argument.html" title="interface in compbio.metadata"><CODE>Argument</CODE></A> if found.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/RunnerConfig.html#removeArgumentByOptionName(java.lang.String)">removeArgumentByOptionName</A></B>(java.lang.String&nbsp;optionName)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Removes the argument</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/RunnerConfig.html#setOptions(java.util.List)">setOptions</A></B>(java.util.List&lt;<A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>&gt;&gt;&nbsp;parameters)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/RunnerConfig.html#setParameters(java.util.List)">setParameters</A></B>(java.util.List&lt;<A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>&lt;<A HREF="../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>&gt;&gt;&nbsp;parameters)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/RunnerConfig.html#setPrmSeparator(java.lang.String)">setPrmSeparator</A></B>(java.lang.String&nbsp;prmSeparator)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/RunnerConfig.html#setRunnerClassName(java.lang.String)">setRunnerClassName</A></B>(java.lang.String&nbsp;runnerClassName)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/RunnerConfig.html#toString()">toString</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/RunnerConfig.html#validate()">validate</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Validate the arguments</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>getClass, hashCode, notify, notifyAll, wait, wait, wait</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
-\r
-<A NAME="constructor_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Constructor Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="RunnerConfig()"><!-- --></A><H3>\r
-RunnerConfig</H3>\r
-<PRE>\r
-public <B>RunnerConfig</B>()</PRE>\r
-<DL>\r
-</DL>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
-<A NAME="method_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="copyAndValidateRConfig(compbio.metadata.RunnerConfig)"><!-- --></A><H3>\r
-copyAndValidateRConfig</H3>\r
-<PRE>\r
-public <A HREF="../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&lt;<A HREF="../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>&gt; <B>copyAndValidateRConfig</B>(<A HREF="../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&lt;?&gt;&nbsp;runnerConf)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getOptions()"><!-- --></A><H3>\r
-getOptions</H3>\r
-<PRE>\r
-public java.util.List&lt;<A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>&gt;&gt; <B>getOptions</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>list of <A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata"><CODE>Option</CODE></A> supported by type T</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="addParameter(compbio.metadata.Parameter)"><!-- --></A><H3>\r
-addParameter</H3>\r
-<PRE>\r
-public void <B>addParameter</B>(<A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>&lt;<A HREF="../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>&gt;&nbsp;param)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="addOption(compbio.metadata.Option)"><!-- --></A><H3>\r
-addOption</H3>\r
-<PRE>\r
-public void <B>addOption</B>(<A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>&gt;&nbsp;option)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getArguments()"><!-- --></A><H3>\r
-getArguments</H3>\r
-<PRE>\r
-public java.util.List&lt;<A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>&gt;&gt; <B>getArguments</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>list of <A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata"><CODE>Option</CODE></A> and <A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata"><CODE>Parameter</CODE></A> supported by type T</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getPrmSeparator()"><!-- --></A><H3>\r
-getPrmSeparator</H3>\r
-<PRE>\r
-public java.lang.String <B>getPrmSeparator</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>name value separator character</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="setPrmSeparator(java.lang.String)"><!-- --></A><H3>\r
-setPrmSeparator</H3>\r
-<PRE>\r
-public void <B>setPrmSeparator</B>(java.lang.String&nbsp;prmSeparator)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="setOptions(java.util.List)"><!-- --></A><H3>\r
-setOptions</H3>\r
-<PRE>\r
-public void <B>setOptions</B>(java.util.List&lt;<A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>&gt;&gt;&nbsp;parameters)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getRunnerClassName()"><!-- --></A><H3>\r
-getRunnerClassName</H3>\r
-<PRE>\r
-public java.lang.String <B>getRunnerClassName</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>fully qualified class name for type T</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="setRunnerClassName(java.lang.String)"><!-- --></A><H3>\r
-setRunnerClassName</H3>\r
-<PRE>\r
-public void <B>setRunnerClassName</B>(java.lang.String&nbsp;runnerClassName)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="setParameters(java.util.List)"><!-- --></A><H3>\r
-setParameters</H3>\r
-<PRE>\r
-public void <B>setParameters</B>(java.util.List&lt;<A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>&lt;<A HREF="../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>&gt;&gt;&nbsp;parameters)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getParameters()"><!-- --></A><H3>\r
-getParameters</H3>\r
-<PRE>\r
-public java.util.List&lt;<A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>&lt;<A HREF="../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>&gt;&gt; <B>getParameters</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>List of <A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata"><CODE>Parameter</CODE></A> supported by type T.</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="toString()"><!-- --></A><H3>\r
-toString</H3>\r
-<PRE>\r
-public java.lang.String <B>toString</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
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-<P>\r
-<DD><DL>\r
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-<P>\r
-<DD><DL>\r
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-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getArgumentByOptionName(java.lang.String)"><!-- --></A><H3>\r
-getArgumentByOptionName</H3>\r
-<PRE>\r
-public <A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>&gt; <B>getArgumentByOptionName</B>(java.lang.String&nbsp;optionName)</PRE>\r
-<DL>\r
-<DD>Returns the argument by option name, NULL if the argument is not found\r
-<P>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>optionName</CODE> - - the name of the option\r
-<DT><B>Returns:</B><DD>Option</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="removeArgumentByOptionName(java.lang.String)"><!-- --></A><H3>\r
-removeArgumentByOptionName</H3>\r
-<PRE>\r
-public boolean <B>removeArgumentByOptionName</B>(java.lang.String&nbsp;optionName)</PRE>\r
-<DL>\r
-<DD>Removes the argument\r
-<P>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>optionName</CODE> - \r
-<DT><B>Returns:</B><DD>true if argument with optionName exists and was removed, false
-         otherwise</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="validate()"><!-- --></A><H3>\r
-validate</H3>\r
-<PRE>\r
-public void <B>validate</B>()\r
-              throws javax.xml.bind.ValidationException</PRE>\r
-<DL>\r
-<DD>Validate the arguments\r
-<P>\r
-<DD><DL>\r
-\r
-<DT><B>Throws:</B>\r
-<DD><CODE>javax.xml.bind.ValidationException</CODE> - if any of the arguments found invalid which is when
-             <dl>
-             <li>Parameter value outside <A HREF="../../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata"><CODE>ValueConstrain</CODE></A> boundary</li>
-             <li>Parameter name is not listed in possible values</li>
-             </dl></DL>\r
-</DD>\r
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-<!-- ========= END OF CLASS DATA ========= -->\r
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-&nbsp;<A HREF="../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata"><B>PREV CLASS</B></A>&nbsp;\r
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-    document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');\r
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-\r
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-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
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diff --git a/website/full_javadoc/compbio/metadata/UnsupportedRuntimeException.html b/website/full_javadoc/compbio/metadata/UnsupportedRuntimeException.html

deleted file mode 100644 (file)

index b7d4950..0000000
--- a/website/full_javadoc/compbio/metadata/UnsupportedRuntimeException.html
+++ /dev/null
@@ -1,265 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-UnsupportedRuntimeException\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
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-<BODY BGCOLOR="white" onload="windowTitle();">\r
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-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
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-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/UnsupportedRuntimeException.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
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-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
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-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
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-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../index.html?compbio/metadata/UnsupportedRuntimeException.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
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-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>\r
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-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#methods_inherited_from_class_java.lang.Throwable">METHOD</A></FONT></TD>\r
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-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.metadata</FONT>\r
-<BR>\r
-Class UnsupportedRuntimeException</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../resources/inherit.gif" ALT="extended by ">java.lang.Throwable\r
-      <IMG SRC="../../resources/inherit.gif" ALT="extended by ">java.lang.Exception\r
-          <IMG SRC="../../resources/inherit.gif" ALT="extended by "><A HREF="../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">compbio.metadata.JobSubmissionException</A>\r
-              <IMG SRC="../../resources/inherit.gif" ALT="extended by "><B>compbio.metadata.UnsupportedRuntimeException</B>\r
-</PRE>\r
-<DL>\r
-<DT><B>All Implemented Interfaces:</B> <DD>java.io.Serializable</DD>\r
-</DL>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public class <B>UnsupportedRuntimeException</B><DT>extends <A HREF="../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></DL>\r
-</PRE>\r
-\r
-<P>\r
-Indicates that the server could not execute native executables. e.g. If Mafft\r
- (unix executable) is asked to be run on Windows. In context of JABAWS this\r
- exception indicates that the service is deployed but is not able to run.\r
-<P>\r
-\r
-<P>\r
-<DL>\r
-<DT><B>Author:</B></DT>\r
-  <DD>pvtroshin\r
- \r
-         Date February 2010</DD>\r
-<DT><B>See Also:</B><DD><A HREF="../../serialized-form.html#compbio.metadata.UnsupportedRuntimeException">Serialized Form</A></DL>\r
-<HR>\r
-\r
-<P>\r
-\r
-<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
-\r
-<A NAME="constructor_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
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-<B>Constructor Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../compbio/metadata/UnsupportedRuntimeException.html#UnsupportedRuntimeException(java.lang.String)">UnsupportedRuntimeException</A></B>(java.lang.String&nbsp;message)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../compbio/metadata/UnsupportedRuntimeException.html#UnsupportedRuntimeException(java.lang.Throwable)">UnsupportedRuntimeException</A></B>(java.lang.Throwable&nbsp;cause)</CODE>\r
-\r
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-</TR>\r
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-\r
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-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Throwable"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
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-<TH ALIGN="left"><B>Methods inherited from class java.lang.Throwable</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>fillInStackTrace, getCause, getLocalizedMessage, getMessage, getStackTrace, initCause, printStackTrace, printStackTrace, printStackTrace, setStackTrace, toString</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>equals, getClass, hashCode, notify, notifyAll, wait, wait, wait</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
-\r
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-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Constructor Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="UnsupportedRuntimeException(java.lang.String)"><!-- --></A><H3>\r
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-<PRE>\r
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-<A NAME="UnsupportedRuntimeException(java.lang.Throwable)"><!-- --></A><H3>\r
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-public <B>UnsupportedRuntimeException</B>(java.lang.Throwable&nbsp;cause)</PRE>\r
-<DL>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
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-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
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-&nbsp;<A HREF="../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata"><B>PREV CLASS</B></A>&nbsp;\r
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-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#methods_inherited_from_class_java.lang.Throwable">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;METHOD</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
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diff --git a/website/full_javadoc/compbio/metadata/ValueConstrain.Type.html b/website/full_javadoc/compbio/metadata/ValueConstrain.Type.html

deleted file mode 100644 (file)

index 62a7160..0000000
--- a/website/full_javadoc/compbio/metadata/ValueConstrain.Type.html
+++ /dev/null
@@ -1,325 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-ValueConstrain.Type\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="ValueConstrain.Type";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/ValueConstrain.Type.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
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-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../index.html?compbio/metadata/ValueConstrain.Type.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="ValueConstrain.Type.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;<A HREF="#enum_constant_summary">ENUM CONSTANTS</A>&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;<A HREF="#enum_constant_detail">ENUM CONSTANTS</A>&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.metadata</FONT>\r
-<BR>\r
-Enum ValueConstrain.Type</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../resources/inherit.gif" ALT="extended by ">java.lang.Enum&lt;<A HREF="../../compbio/metadata/ValueConstrain.Type.html" title="enum in compbio.metadata">ValueConstrain.Type</A>&gt;\r
-      <IMG SRC="../../resources/inherit.gif" ALT="extended by "><B>compbio.metadata.ValueConstrain.Type</B>\r
-</PRE>\r
-<DL>\r
-<DT><B>All Implemented Interfaces:</B> <DD>java.io.Serializable, java.lang.Comparable&lt;<A HREF="../../compbio/metadata/ValueConstrain.Type.html" title="enum in compbio.metadata">ValueConstrain.Type</A>&gt;</DD>\r
-</DL>\r
-<DL>\r
-<DT><B>Enclosing class:</B><DD><A HREF="../../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A></DD>\r
-</DL>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public static enum <B>ValueConstrain.Type</B><DT>extends java.lang.Enum&lt;<A HREF="../../compbio/metadata/ValueConstrain.Type.html" title="enum in compbio.metadata">ValueConstrain.Type</A>&gt;</DL>\r
-</PRE>\r
-\r
-<P>\r
-<HR>\r
-\r
-<P>\r
-<!-- =========== ENUM CONSTANT SUMMARY =========== -->\r
-\r
-<A NAME="enum_constant_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Enum Constant Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../compbio/metadata/ValueConstrain.Type.html#Float">Float</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../compbio/metadata/ValueConstrain.Type.html#Integer">Integer</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../compbio/metadata/ValueConstrain.Type.html" title="enum in compbio.metadata">ValueConstrain.Type</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/ValueConstrain.Type.html#valueOf(java.lang.String)">valueOf</A></B>(java.lang.String&nbsp;name)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Returns the enum constant of this type with the specified name.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../compbio/metadata/ValueConstrain.Type.html" title="enum in compbio.metadata">ValueConstrain.Type</A>[]</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/ValueConstrain.Type.html#values()">values</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Returns an array containing the constants of this enum type, in
-the order they are declared.</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Enum"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Enum</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>compareTo, equals, getDeclaringClass, hashCode, name, ordinal, toString, valueOf</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>getClass, notify, notifyAll, wait, wait, wait</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ============ ENUM CONSTANT DETAIL =========== -->\r
-\r
-<A NAME="enum_constant_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Enum Constant Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="Integer"><!-- --></A><H3>\r
-Integer</H3>\r
-<PRE>\r
-public static final <A HREF="../../compbio/metadata/ValueConstrain.Type.html" title="enum in compbio.metadata">ValueConstrain.Type</A> <B>Integer</B></PRE>\r
-<DL>\r
-<DL>\r
-</DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="Float"><!-- --></A><H3>\r
-Float</H3>\r
-<PRE>\r
-public static final <A HREF="../../compbio/metadata/ValueConstrain.Type.html" title="enum in compbio.metadata">ValueConstrain.Type</A> <B>Float</B></PRE>\r
-<DL>\r
-<DL>\r
-</DL>\r
-</DL>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
-<A NAME="method_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="values()"><!-- --></A><H3>\r
-values</H3>\r
-<PRE>\r
-public static <A HREF="../../compbio/metadata/ValueConstrain.Type.html" title="enum in compbio.metadata">ValueConstrain.Type</A>[] <B>values</B>()</PRE>\r
-<DL>\r
-<DD>Returns an array containing the constants of this enum type, in
-the order they are declared.  This method may be used to iterate
-over the constants as follows:
-<pre>
-for (ValueConstrain.Type c : ValueConstrain.Type.values())
-&nbsp;   System.out.println(c);
-</pre>\r
-<P>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>an array containing the constants of this enum type, in
-the order they are declared</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="valueOf(java.lang.String)"><!-- --></A><H3>\r
-valueOf</H3>\r
-<PRE>\r
-public static <A HREF="../../compbio/metadata/ValueConstrain.Type.html" title="enum in compbio.metadata">ValueConstrain.Type</A> <B>valueOf</B>(java.lang.String&nbsp;name)</PRE>\r
-<DL>\r
-<DD>Returns the enum constant of this type with the specified name.
-The string must match <I>exactly</I> an identifier used to declare an
-enum constant in this type.  (Extraneous whitespace characters are 
-not permitted.)\r
-<P>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>name</CODE> - the name of the enum constant to be returned.\r
-<DT><B>Returns:</B><DD>the enum constant with the specified name\r
-<DT><B>Throws:</B>\r
-<DD><CODE>java.lang.IllegalArgumentException</CODE> - if this enum type has no constant
-with the specified name\r
-<DD><CODE>java.lang.NullPointerException</CODE> - if the argument is null</DL>\r
-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/ValueConstrain.Type.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
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-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../index.html?compbio/metadata/ValueConstrain.Type.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="ValueConstrain.Type.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;<A HREF="#enum_constant_summary">ENUM CONSTANTS</A>&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;<A HREF="#enum_constant_detail">ENUM CONSTANTS</A>&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
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diff --git a/website/full_javadoc/compbio/metadata/ValueConstrain.html b/website/full_javadoc/compbio/metadata/ValueConstrain.html

deleted file mode 100644 (file)

index 0d924f6..0000000
--- a/website/full_javadoc/compbio/metadata/ValueConstrain.html
+++ /dev/null
@@ -1,440 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-ValueConstrain\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="ValueConstrain";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/ValueConstrain.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
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-</TABLE>\r
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-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../compbio/metadata/ValueConstrain.Type.html" title="enum in compbio.metadata"><B>NEXT CLASS</B></A></FONT></TD>\r
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-  <A HREF="../../index.html?compbio/metadata/ValueConstrain.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
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-\r
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-  SUMMARY:&nbsp;<A HREF="#nested_class_summary">NESTED</A>&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
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-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
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-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.metadata</FONT>\r
-<BR>\r
-Class ValueConstrain</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../resources/inherit.gif" ALT="extended by "><B>compbio.metadata.ValueConstrain</B>\r
-</PRE>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public class <B>ValueConstrain</B><DT>extends java.lang.Object</DL>\r
-</PRE>\r
-\r
-<P>\r
-The type and the lower and upper boundaries for numerical value.\r
-<P>\r
-\r
-<P>\r
-<DL>\r
-<DT><B>Author:</B></DT>\r
-  <DD>pvtroshin
- 
-         Date November 2009</DD>\r
-</DL>\r
-<HR>\r
-\r
-<P>\r
-<!-- ======== NESTED CLASS SUMMARY ======== -->\r
-\r
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-<B>Nested Class Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;class</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/ValueConstrain.Type.html" title="enum in compbio.metadata">ValueConstrain.Type</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
-\r
-<A NAME="constructor_summary"><!-- --></A>\r
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-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Constructor Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../compbio/metadata/ValueConstrain.html#ValueConstrain()">ValueConstrain</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
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-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/ValueConstrain.html#equals(java.lang.Object)">equals</A></B>(java.lang.Object&nbsp;obj)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.Number</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/ValueConstrain.html#getMax()">getMax</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.Number</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/ValueConstrain.html#getMin()">getMin</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../compbio/metadata/ValueConstrain.Type.html" title="enum in compbio.metadata">ValueConstrain.Type</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/ValueConstrain.html#getType()">getType</A></B>()</CODE>\r
-\r
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-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
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-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;int</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/ValueConstrain.html#hashCode()">hashCode</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/ValueConstrain.html#setMax(java.lang.String)">setMax</A></B>(java.lang.String&nbsp;max)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/ValueConstrain.html#setMin(java.lang.String)">setMin</A></B>(java.lang.String&nbsp;min)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/ValueConstrain.html#setType(compbio.metadata.ValueConstrain.Type)">setType</A></B>(<A HREF="../../compbio/metadata/ValueConstrain.Type.html" title="enum in compbio.metadata">ValueConstrain.Type</A>&nbsp;type)</CODE>\r
-\r
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-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
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-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/ValueConstrain.html#toString()">toString</A></B>()</CODE>\r
-\r
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-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
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-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
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-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>getClass, notify, notifyAll, wait, wait, wait</CODE></TD>\r
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-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
-\r
-<A NAME="constructor_detail"><!-- --></A>\r
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-<B>Constructor Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="ValueConstrain()"><!-- --></A><H3>\r
-ValueConstrain</H3>\r
-<PRE>\r
-public <B>ValueConstrain</B>()</PRE>\r
-<DL>\r
-</DL>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
-<A NAME="method_detail"><!-- --></A>\r
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-getType</H3>\r
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-public <A HREF="../../compbio/metadata/ValueConstrain.Type.html" title="enum in compbio.metadata">ValueConstrain.Type</A> <B>getType</B>()</PRE>\r
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-<DD><DL>\r
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-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="setType(compbio.metadata.ValueConstrain.Type)"><!-- --></A><H3>\r
-setType</H3>\r
-<PRE>\r
-public void <B>setType</B>(<A HREF="../../compbio/metadata/ValueConstrain.Type.html" title="enum in compbio.metadata">ValueConstrain.Type</A>&nbsp;type)</PRE>\r
-<DL>\r
-<DD><DL>\r
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-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getMax()"><!-- --></A><H3>\r
-getMax</H3>\r
-<PRE>\r
-public java.lang.Number <B>getMax</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
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-</DD>\r
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-<HR>\r
-\r
-<A NAME="setMax(java.lang.String)"><!-- --></A><H3>\r
-setMax</H3>\r
-<PRE>\r
-public void <B>setMax</B>(java.lang.String&nbsp;max)</PRE>\r
-<DL>\r
-<DD><DL>\r
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-</DL>\r
-<HR>\r
-\r
-<A NAME="getMin()"><!-- --></A><H3>\r
-getMin</H3>\r
-<PRE>\r
-public java.lang.Number <B>getMin</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="setMin(java.lang.String)"><!-- --></A><H3>\r
-setMin</H3>\r
-<PRE>\r
-public void <B>setMin</B>(java.lang.String&nbsp;min)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="equals(java.lang.Object)"><!-- --></A><H3>\r
-equals</H3>\r
-<PRE>\r
-public boolean <B>equals</B>(java.lang.Object&nbsp;obj)</PRE>\r
-<DL>\r
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-</DL>\r
-<HR>\r
-\r
-<A NAME="toString()"><!-- --></A><H3>\r
-toString</H3>\r
-<PRE>\r
-public java.lang.String <B>toString</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Overrides:</B><DD><CODE>toString</CODE> in class <CODE>java.lang.Object</CODE></DL>\r
-</DD>\r
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-\r
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-hashCode</H3>\r
-<PRE>\r
-public int <B>hashCode</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Overrides:</B><DD><CODE>hashCode</CODE> in class <CODE>java.lang.Object</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
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-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
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-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata"><B>PREV CLASS</B></A>&nbsp;\r
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-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../index.html?compbio/metadata/ValueConstrain.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
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diff --git a/website/full_javadoc/compbio/metadata/WrongParameterException.html b/website/full_javadoc/compbio/metadata/WrongParameterException.html

deleted file mode 100644 (file)

index 9d95892..0000000
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+++ /dev/null
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-</TABLE>\r
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-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../compbio/metadata/ValueConstrain.Type.html" title="enum in compbio.metadata"><B>PREV CLASS</B></A>&nbsp;\r
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-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
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-    document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
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-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#methods_inherited_from_class_java.lang.Throwable">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;METHOD</FONT></TD>\r
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-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.metadata</FONT>\r
-<BR>\r
-Class WrongParameterException</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../resources/inherit.gif" ALT="extended by ">java.lang.Throwable\r
-      <IMG SRC="../../resources/inherit.gif" ALT="extended by ">java.lang.Exception\r
-          <IMG SRC="../../resources/inherit.gif" ALT="extended by "><B>compbio.metadata.WrongParameterException</B>\r
-</PRE>\r
-<DL>\r
-<DT><B>All Implemented Interfaces:</B> <DD>java.io.Serializable</DD>\r
-</DL>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public class <B>WrongParameterException</B><DT>extends java.lang.Exception</DL>\r
-</PRE>\r
-\r
-<P>\r
-WrongParameterException is thrown wherever the <A HREF="../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata"><CODE>RunnerConfig</CODE></A> object
- does not match the actual runnable or then attempting to set the value of
- <A HREF="../../compbio/metadata/Argument.html" title="interface in compbio.metadata"><CODE>Argument</CODE></A> to invalid value.\r
-<P>\r
-\r
-<P>\r
-<DL>\r
-<DT><B>Author:</B></DT>\r
-  <DD>pvtroshin
- 
-         Date October 2009</DD>\r
-<DT><B>See Also:</B><DD><A HREF="../../serialized-form.html#compbio.metadata.WrongParameterException">Serialized Form</A></DL>\r
-<HR>\r
-\r
-<P>\r
-\r
-<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
-\r
-<A NAME="constructor_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Constructor Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../compbio/metadata/WrongParameterException.html#WrongParameterException(compbio.metadata.Option)">WrongParameterException</A></B>(<A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;?&gt;&nbsp;option)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../compbio/metadata/WrongParameterException.html#WrongParameterException(java.lang.String)">WrongParameterException</A></B>(java.lang.String&nbsp;message)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../compbio/metadata/WrongParameterException.html#WrongParameterException(java.lang.String, java.lang.Throwable)">WrongParameterException</A></B>(java.lang.String&nbsp;message,\r
-                        java.lang.Throwable&nbsp;cause)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../compbio/metadata/WrongParameterException.html#WrongParameterException(java.lang.Throwable)">WrongParameterException</A></B>(java.lang.Throwable&nbsp;cause)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Throwable"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Throwable</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>fillInStackTrace, getCause, getLocalizedMessage, getMessage, getStackTrace, initCause, printStackTrace, printStackTrace, printStackTrace, setStackTrace, toString</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>equals, getClass, hashCode, notify, notifyAll, wait, wait, wait</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
-\r
-<A NAME="constructor_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Constructor Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="WrongParameterException(compbio.metadata.Option)"><!-- --></A><H3>\r
-WrongParameterException</H3>\r
-<PRE>\r
-public <B>WrongParameterException</B>(<A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;?&gt;&nbsp;option)</PRE>\r
-<DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="WrongParameterException(java.lang.String)"><!-- --></A><H3>\r
-WrongParameterException</H3>\r
-<PRE>\r
-public <B>WrongParameterException</B>(java.lang.String&nbsp;message)</PRE>\r
-<DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="WrongParameterException(java.lang.Throwable)"><!-- --></A><H3>\r
-WrongParameterException</H3>\r
-<PRE>\r
-public <B>WrongParameterException</B>(java.lang.Throwable&nbsp;cause)</PRE>\r
-<DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="WrongParameterException(java.lang.String, java.lang.Throwable)"><!-- --></A><H3>\r
-WrongParameterException</H3>\r
-<PRE>\r
-public <B>WrongParameterException</B>(java.lang.String&nbsp;message,\r
-                               java.lang.Throwable&nbsp;cause)</PRE>\r
-<DL>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
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-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
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-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../compbio/metadata/ValueConstrain.Type.html" title="enum in compbio.metadata"><B>PREV CLASS</B></A>&nbsp;\r
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-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;METHOD</FONT></TD>\r
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diff --git a/website/full_javadoc/compbio/metadata/class-use/Argument.html b/website/full_javadoc/compbio/metadata/class-use/Argument.html

deleted file mode 100644 (file)

index 11f5c1a..0000000
--- a/website/full_javadoc/compbio/metadata/class-use/Argument.html
+++ /dev/null
@@ -1,189 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Uses of Interface compbio.metadata.Argument\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Uses of Interface compbio.metadata.Argument";\r
-    }\r
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-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
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-\r
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-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../compbio/metadata/Argument.html" title="interface in compbio.metadata"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
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-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
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-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
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-&nbsp;<A HREF="Argument.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
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-</SCRIPT>\r
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-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
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-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-<B>Uses of Interface<br>compbio.metadata.Argument</B></H2>\r
-</CENTER>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Packages that use <A HREF="../../../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.metadata"><B>compbio.metadata</B></A></TD>\r
-<TD>A meta-data model for multiple sequence alignment web services 
- Classes in this package have no dependencies to other sources in the project.&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.metadata"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</A> in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Classes in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A> that implement <A HREF="../../../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;class</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option&lt;T&gt;</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Command line option/flag or multiple exclusive options with no value.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;class</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter&lt;T&gt;</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;A single value containing option supported by the web service e.g.</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../compbio/metadata/Argument.html" title="interface in compbio.metadata"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/metadata/\class-useArgument.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="Argument.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/metadata/class-use/ChunkHolder.html b/website/full_javadoc/compbio/metadata/class-use/ChunkHolder.html

deleted file mode 100644 (file)

index 30abc70..0000000
--- a/website/full_javadoc/compbio/metadata/class-use/ChunkHolder.html
+++ /dev/null
@@ -1,356 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Uses of Class compbio.metadata.ChunkHolder\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Uses of Class compbio.metadata.ChunkHolder";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/metadata/\class-useChunkHolder.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="ChunkHolder.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-<B>Uses of Class<br>compbio.metadata.ChunkHolder</B></H2>\r
-</CENTER>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Packages that use <A HREF="../../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.data.msa"><B>compbio.data.msa</B></A></TD>\r
-<TD>&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.data.msa.jaxws"><B>compbio.data.msa.jaxws</B></A></TD>\r
-<TD>&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.engine"><B>compbio.engine</B></A></TD>\r
-<TD>&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.ws.server"><B>compbio.ws.server</B></A></TD>\r
-<TD>&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.data.msa"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A> in <A HREF="../../../compbio/data/msa/package-summary.html">compbio.data.msa</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/data/msa/package-summary.html">compbio.data.msa</A> that return <A HREF="../../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A></CODE></FONT></TD>\r
-<TD><CODE><B>MsaWS.</B><B><A HREF="../../../compbio/data/msa/MsaWS.html#pullExecStatistics(java.lang.String, long)">pullExecStatistics</A></B>(java.lang.String&nbsp;jobId,\r
-                   long&nbsp;position)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Reads 1kb chunk from the statistics file which is specific to a given web
- service from the position.</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.data.msa.jaxws"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A> in <A HREF="../../../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A> that return <A HREF="../../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A></CODE></FONT></TD>\r
-<TD><CODE><B>PullFileResponse.</B><B><A HREF="../../../compbio/data/msa/jaxws/PullFileResponse.html#getReturn()">getReturn</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A></CODE></FONT></TD>\r
-<TD><CODE><B>PullExecStatisticsResponse.</B><B><A HREF="../../../compbio/data/msa/jaxws/PullExecStatisticsResponse.html#getReturn()">getReturn</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A> with parameters of type <A HREF="../../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B>PullFileResponse.</B><B><A HREF="../../../compbio/data/msa/jaxws/PullFileResponse.html#setReturn(compbio.metadata.ChunkHolder)">setReturn</A></B>(<A HREF="../../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A>&nbsp;_return)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B>PullExecStatisticsResponse.</B><B><A HREF="../../../compbio/data/msa/jaxws/PullExecStatisticsResponse.html#setReturn(compbio.metadata.ChunkHolder)">setReturn</A></B>(<A HREF="../../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A>&nbsp;_return)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.engine"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A> in <A HREF="../../../compbio/engine/package-summary.html">compbio.engine</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/engine/package-summary.html">compbio.engine</A> that return <A HREF="../../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A></CODE></FONT></TD>\r
-<TD><CODE><B>FilePuller.</B><B><A HREF="../../../compbio/engine/FilePuller.html#pull(long)">pull</A></B>(long&nbsp;position)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A></CODE></FONT></TD>\r
-<TD><CODE><B>ProgressGetter.</B><B><A HREF="../../../compbio/engine/ProgressGetter.html#pull(java.lang.String, long)">pull</A></B>(java.lang.String&nbsp;file,\r
-     long&nbsp;position)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.ws.server"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A> in <A HREF="../../../compbio/ws/server/package-summary.html">compbio.ws.server</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/ws/server/package-summary.html">compbio.ws.server</A> that return <A HREF="../../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A></CODE></FONT></TD>\r
-<TD><CODE><B>TcoffeeWS.</B><B><A HREF="../../../compbio/ws/server/TcoffeeWS.html#pullExecStatistics(java.lang.String, long)">pullExecStatistics</A></B>(java.lang.String&nbsp;jobId,\r
-                   long&nbsp;position)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A></CODE></FONT></TD>\r
-<TD><CODE><B>ProbconsWS.</B><B><A HREF="../../../compbio/ws/server/ProbconsWS.html#pullExecStatistics(java.lang.String, long)">pullExecStatistics</A></B>(java.lang.String&nbsp;jobId,\r
-                   long&nbsp;position)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A></CODE></FONT></TD>\r
-<TD><CODE><B>MuscleWS.</B><B><A HREF="../../../compbio/ws/server/MuscleWS.html#pullExecStatistics(java.lang.String, long)">pullExecStatistics</A></B>(java.lang.String&nbsp;jobId,\r
-                   long&nbsp;position)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A></CODE></FONT></TD>\r
-<TD><CODE><B>MafftWS.</B><B><A HREF="../../../compbio/ws/server/MafftWS.html#pullExecStatistics(java.lang.String, long)">pullExecStatistics</A></B>(java.lang.String&nbsp;jobId,\r
-                   long&nbsp;position)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A></CODE></FONT></TD>\r
-<TD><CODE><B>ClustalWS.</B><B><A HREF="../../../compbio/ws/server/ClustalWS.html#pullExecStatistics(java.lang.String, long)">pullExecStatistics</A></B>(java.lang.String&nbsp;jobId,\r
-                   long&nbsp;position)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A></CODE></FONT></TD>\r
-<TD><CODE><B>WSUtil.</B><B><A HREF="../../../compbio/ws/server/WSUtil.html#pullFile(java.lang.String, long)">pullFile</A></B>(java.lang.String&nbsp;jobId,\r
-         long&nbsp;position)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/metadata/\class-useChunkHolder.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="ChunkHolder.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/metadata/class-use/JobExecutionException.html b/website/full_javadoc/compbio/metadata/class-use/JobExecutionException.html

deleted file mode 100644 (file)

index 2efb5f4..0000000
--- a/website/full_javadoc/compbio/metadata/class-use/JobExecutionException.html
+++ /dev/null
@@ -1,257 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Uses of Class compbio.metadata.JobExecutionException\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Uses of Class compbio.metadata.JobExecutionException";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../compbio/metadata/JobExecutionException.html" title="class in compbio.metadata"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/metadata/\class-useJobExecutionException.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="JobExecutionException.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-<B>Uses of Class<br>compbio.metadata.JobExecutionException</B></H2>\r
-</CENTER>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Packages that use <A HREF="../../../compbio/metadata/JobExecutionException.html" title="class in compbio.metadata">JobExecutionException</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.engine"><B>compbio.engine</B></A></TD>\r
-<TD>&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.engine.cluster.drmaa"><B>compbio.engine.cluster.drmaa</B></A></TD>\r
-<TD>An cluster engine classes responsible for execution of Executables on the clusters.&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.engine.local"><B>compbio.engine.local</B></A></TD>\r
-<TD>An local engine classes responsible for execution of Executables on the local computer 
- (the same machine as JVM running these classes).&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.engine"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../compbio/metadata/JobExecutionException.html" title="class in compbio.metadata">JobExecutionException</A> in <A HREF="../../../compbio/engine/package-summary.html">compbio.engine</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/engine/package-summary.html">compbio.engine</A> that throw <A HREF="../../../compbio/metadata/JobExecutionException.html" title="class in compbio.metadata">JobExecutionException</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>SyncExecutor.</B><B><A HREF="../../../compbio/engine/SyncExecutor.html#waitForResult()">waitForResult</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Call to this method block for as long as it is required for an executable to finish its job.</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.engine.cluster.drmaa"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../compbio/metadata/JobExecutionException.html" title="class in compbio.metadata">JobExecutionException</A> in <A HREF="../../../compbio/engine/cluster/drmaa/package-summary.html">compbio.engine.cluster.drmaa</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/engine/cluster/drmaa/package-summary.html">compbio.engine.cluster.drmaa</A> that throw <A HREF="../../../compbio/metadata/JobExecutionException.html" title="class in compbio.metadata">JobExecutionException</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;org.ggf.drmaa.JobInfo</CODE></FONT></TD>\r
-<TD><CODE><B>JobRunner.</B><B><A HREF="../../../compbio/engine/cluster/drmaa/JobRunner.html#getJobInfo()">getJobInfo</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;This method will block before the calculation has completed and then
- return the object containing a job execution statistics</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>JobRunner.</B><B><A HREF="../../../compbio/engine/cluster/drmaa/JobRunner.html#waitForResult()">waitForResult</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;org.ggf.drmaa.JobInfo</CODE></FONT></TD>\r
-<TD><CODE><B>ClusterUtil.</B><B><A HREF="../../../compbio/engine/cluster/drmaa/ClusterUtil.html#waitForResult(compbio.engine.cluster.drmaa.ClusterSession, java.lang.String)">waitForResult</A></B>(<A HREF="../../../compbio/engine/cluster/drmaa/ClusterSession.html" title="class in compbio.engine.cluster.drmaa">ClusterSession</A>&nbsp;csession,\r
-              java.lang.String&nbsp;jobId)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.engine.local"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../compbio/metadata/JobExecutionException.html" title="class in compbio.metadata">JobExecutionException</A> in <A HREF="../../../compbio/engine/local/package-summary.html">compbio.engine.local</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/engine/local/package-summary.html">compbio.engine.local</A> that throw <A HREF="../../../compbio/metadata/JobExecutionException.html" title="class in compbio.metadata">JobExecutionException</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>LocalRunner.</B><B><A HREF="../../../compbio/engine/local/LocalRunner.html#waitForResult()">waitForResult</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../compbio/metadata/JobExecutionException.html" title="class in compbio.metadata"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/metadata/\class-useJobExecutionException.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="JobExecutionException.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/metadata/class-use/JobStatus.html b/website/full_javadoc/compbio/metadata/class-use/JobStatus.html

deleted file mode 100644 (file)

index 227a5b0..0000000
--- a/website/full_javadoc/compbio/metadata/class-use/JobStatus.html
+++ /dev/null
@@ -1,501 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Uses of Class compbio.metadata.JobStatus\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Uses of Class compbio.metadata.JobStatus";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/metadata/\class-useJobStatus.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="JobStatus.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-<B>Uses of Class<br>compbio.metadata.JobStatus</B></H2>\r
-</CENTER>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Packages that use <A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.data.msa"><B>compbio.data.msa</B></A></TD>\r
-<TD>&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.data.msa.jaxws"><B>compbio.data.msa.jaxws</B></A></TD>\r
-<TD>&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.engine"><B>compbio.engine</B></A></TD>\r
-<TD>&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.engine.client"><B>compbio.engine.client</B></A></TD>\r
-<TD>Classes and interfaces representing an input for engines.&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.engine.cluster.drmaa"><B>compbio.engine.cluster.drmaa</B></A></TD>\r
-<TD>An cluster engine classes responsible for execution of Executables on the clusters.&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.engine.local"><B>compbio.engine.local</B></A></TD>\r
-<TD>An local engine classes responsible for execution of Executables on the local computer 
- (the same machine as JVM running these classes).&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.metadata"><B>compbio.metadata</B></A></TD>\r
-<TD>A meta-data model for multiple sequence alignment web services 
- Classes in this package have no dependencies to other sources in the project.&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.ws.server"><B>compbio.ws.server</B></A></TD>\r
-<TD>&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.data.msa"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A> in <A HREF="../../../compbio/data/msa/package-summary.html">compbio.data.msa</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/data/msa/package-summary.html">compbio.data.msa</A> that return <A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A></CODE></FONT></TD>\r
-<TD><CODE><B>MsaWS.</B><B><A HREF="../../../compbio/data/msa/MsaWS.html#getJobStatus(java.lang.String)">getJobStatus</A></B>(java.lang.String&nbsp;jobId)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Return the status of the job.</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.data.msa.jaxws"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A> in <A HREF="../../../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A> that return <A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A></CODE></FONT></TD>\r
-<TD><CODE><B>GetJobStatusResponse.</B><B><A HREF="../../../compbio/data/msa/jaxws/GetJobStatusResponse.html#getReturn()">getReturn</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A> with parameters of type <A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B>GetJobStatusResponse.</B><B><A HREF="../../../compbio/data/msa/jaxws/GetJobStatusResponse.html#setReturn(compbio.metadata.JobStatus)">setReturn</A></B>(<A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A>&nbsp;_return)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.engine"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A> in <A HREF="../../../compbio/engine/package-summary.html">compbio.engine</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/engine/package-summary.html">compbio.engine</A> that return <A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A></CODE></FONT></TD>\r
-<TD><CODE><B>SyncExecutor.</B><B><A HREF="../../../compbio/engine/SyncExecutor.html#getJobStatus()">getJobStatus</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Query the status of the job by its id.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A></CODE></FONT></TD>\r
-<TD><CODE><B>AsyncExecutor.</B><B><A HREF="../../../compbio/engine/AsyncExecutor.html#getJobStatus(java.lang.String)">getJobStatus</A></B>(java.lang.String&nbsp;jobId)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Query the status of the job</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.engine.client"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A> in <A HREF="../../../compbio/engine/client/package-summary.html">compbio.engine.client</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/engine/client/package-summary.html">compbio.engine.client</A> with parameters of type <A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;boolean</CODE></FONT></TD>\r
-<TD><CODE><B>Util.</B><B><A HREF="../../../compbio/engine/client/Util.html#isMarked(java.lang.String, compbio.metadata.JobStatus)">isMarked</A></B>(java.lang.String&nbsp;workDirectory,\r
-         <A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A>&nbsp;marker)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;boolean</CODE></FONT></TD>\r
-<TD><CODE><B>Util.</B><B><A HREF="../../../compbio/engine/client/Util.html#writeMarker(java.lang.String, compbio.metadata.JobStatus)">writeMarker</A></B>(java.lang.String&nbsp;workDirectory,\r
-            <A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A>&nbsp;fileType)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.engine.cluster.drmaa"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A> in <A HREF="../../../compbio/engine/cluster/drmaa/package-summary.html">compbio.engine.cluster.drmaa</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/engine/cluster/drmaa/package-summary.html">compbio.engine.cluster.drmaa</A> that return <A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A></CODE></FONT></TD>\r
-<TD><CODE><B>JobRunner.</B><B><A HREF="../../../compbio/engine/cluster/drmaa/JobRunner.html#getJobStatus()">getJobStatus</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A></CODE></FONT></TD>\r
-<TD><CODE><B>AsyncJobRunner.</B><B><A HREF="../../../compbio/engine/cluster/drmaa/AsyncJobRunner.html#getJobStatus(java.lang.String)">getJobStatus</A></B>(java.lang.String&nbsp;jobId)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;This will never return clust.engine.JobStatus.CANCELLED as for sun grid
- engine cancelled job is the same as failed.</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.engine.local"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A> in <A HREF="../../../compbio/engine/local/package-summary.html">compbio.engine.local</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/engine/local/package-summary.html">compbio.engine.local</A> that return <A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A></CODE></FONT></TD>\r
-<TD><CODE><B>LocalRunner.</B><B><A HREF="../../../compbio/engine/local/LocalRunner.html#getJobStatus()">getJobStatus</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A></CODE></FONT></TD>\r
-<TD><CODE><B>LocalEngineUtil.</B><B><A HREF="../../../compbio/engine/local/LocalEngineUtil.html#getJobStatus(java.util.concurrent.Future)">getJobStatus</A></B>(java.util.concurrent.Future&lt;<A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&gt;&nbsp;future)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A></CODE></FONT></TD>\r
-<TD><CODE><B>AsyncLocalRunner.</B><B><A HREF="../../../compbio/engine/local/AsyncLocalRunner.html#getJobStatus(java.lang.String)">getJobStatus</A></B>(java.lang.String&nbsp;jobId)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A></CODE></FONT></TD>\r
-<TD><CODE><B>LocalEngineUtil.</B><B><A HREF="../../../compbio/engine/local/LocalEngineUtil.html#getRecordedJobStatus(java.lang.String)">getRecordedJobStatus</A></B>(java.lang.String&nbsp;jobId)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.metadata"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A> in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A> that return <A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A></CODE></FONT></TD>\r
-<TD><CODE><B>JobStatus.</B><B><A HREF="../../../compbio/metadata/JobStatus.html#valueOf(java.lang.String)">valueOf</A></B>(java.lang.String&nbsp;name)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Returns the enum constant of this type with the specified name.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A>[]</CODE></FONT></TD>\r
-<TD><CODE><B>JobStatus.</B><B><A HREF="../../../compbio/metadata/JobStatus.html#values()">values</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Returns an array containing the constants of this enum type, in
-the order they are declared.</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.ws.server"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A> in <A HREF="../../../compbio/ws/server/package-summary.html">compbio.ws.server</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/ws/server/package-summary.html">compbio.ws.server</A> that return <A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A></CODE></FONT></TD>\r
-<TD><CODE><B>WSUtil.</B><B><A HREF="../../../compbio/ws/server/WSUtil.html#getJobStatus(java.lang.String)">getJobStatus</A></B>(java.lang.String&nbsp;jobId)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A></CODE></FONT></TD>\r
-<TD><CODE><B>TcoffeeWS.</B><B><A HREF="../../../compbio/ws/server/TcoffeeWS.html#getJobStatus(java.lang.String)">getJobStatus</A></B>(java.lang.String&nbsp;jobId)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A></CODE></FONT></TD>\r
-<TD><CODE><B>ProbconsWS.</B><B><A HREF="../../../compbio/ws/server/ProbconsWS.html#getJobStatus(java.lang.String)">getJobStatus</A></B>(java.lang.String&nbsp;jobId)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A></CODE></FONT></TD>\r
-<TD><CODE><B>MuscleWS.</B><B><A HREF="../../../compbio/ws/server/MuscleWS.html#getJobStatus(java.lang.String)">getJobStatus</A></B>(java.lang.String&nbsp;jobId)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A></CODE></FONT></TD>\r
-<TD><CODE><B>MafftWS.</B><B><A HREF="../../../compbio/ws/server/MafftWS.html#getJobStatus(java.lang.String)">getJobStatus</A></B>(java.lang.String&nbsp;jobId)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A></CODE></FONT></TD>\r
-<TD><CODE><B>ClustalWS.</B><B><A HREF="../../../compbio/ws/server/ClustalWS.html#getJobStatus(java.lang.String)">getJobStatus</A></B>(java.lang.String&nbsp;jobId)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/metadata/\class-useJobStatus.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="JobStatus.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/metadata/class-use/JobSubmissionException.html b/website/full_javadoc/compbio/metadata/class-use/JobSubmissionException.html

deleted file mode 100644 (file)

index 1e1329f..0000000
--- a/website/full_javadoc/compbio/metadata/class-use/JobSubmissionException.html
+++ /dev/null
@@ -1,651 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Uses of Class compbio.metadata.JobSubmissionException\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Uses of Class compbio.metadata.JobSubmissionException";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/metadata/\class-useJobSubmissionException.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="JobSubmissionException.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-<B>Uses of Class<br>compbio.metadata.JobSubmissionException</B></H2>\r
-</CENTER>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Packages that use <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.data.msa"><B>compbio.data.msa</B></A></TD>\r
-<TD>&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.engine"><B>compbio.engine</B></A></TD>\r
-<TD>&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.engine.client"><B>compbio.engine.client</B></A></TD>\r
-<TD>Classes and interfaces representing an input for engines.&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.engine.cluster.drmaa"><B>compbio.engine.cluster.drmaa</B></A></TD>\r
-<TD>An cluster engine classes responsible for execution of Executables on the clusters.&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.engine.local"><B>compbio.engine.local</B></A></TD>\r
-<TD>An local engine classes responsible for execution of Executables on the local computer 
- (the same machine as JVM running these classes).&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.metadata"><B>compbio.metadata</B></A></TD>\r
-<TD>A meta-data model for multiple sequence alignment web services 
- Classes in this package have no dependencies to other sources in the project.&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.ws.server"><B>compbio.ws.server</B></A></TD>\r
-<TD>&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.data.msa"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A> in <A HREF="../../../compbio/data/msa/package-summary.html">compbio.data.msa</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/data/msa/package-summary.html">compbio.data.msa</A> that throw <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B>MsaWS.</B><B><A HREF="../../../compbio/data/msa/MsaWS.html#align(java.util.List)">align</A></B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Align a list of sequences with default settings.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B>MsaWS.</B><B><A HREF="../../../compbio/data/msa/MsaWS.html#customAlign(java.util.List, java.util.List)">customAlign</A></B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-            java.util.List&lt;<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../compbio/data/msa/MsaWS.html" title="type parameter in MsaWS">T</A>&gt;&gt;&nbsp;options)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Align a list of sequences with options.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B>MsaWS.</B><B><A HREF="../../../compbio/data/msa/MsaWS.html#presetAlign(java.util.List, compbio.metadata.Preset)">presetAlign</A></B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-            <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>&lt;<A HREF="../../../compbio/data/msa/MsaWS.html" title="type parameter in MsaWS">T</A>&gt;&nbsp;preset)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Align a list of sequences with preset.</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.engine"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A> in <A HREF="../../../compbio/engine/package-summary.html">compbio.engine</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/engine/package-summary.html">compbio.engine</A> that throw <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
-<TR ALIGN="right" VALIGN="">\r
-<TD NOWRAP><FONT SIZE="-1">\r
-<CODE>&lt;T&gt; <A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;T&gt;</CODE></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-</CODE></FONT></TD>\r
-<TD><CODE><B>Configurator.</B><B><A HREF="../../../compbio/engine/Configurator.html#configureExecutable(compbio.engine.client.Executable)">configureExecutable</A></B>(<A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;T&gt;&nbsp;executable)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
-<TR ALIGN="right" VALIGN="">\r
-<TD NOWRAP><FONT SIZE="-1">\r
-<CODE>&lt;T&gt; <A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;T&gt;</CODE></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-</CODE></FONT></TD>\r
-<TD><CODE><B>Configurator.</B><B><A HREF="../../../compbio/engine/Configurator.html#configureExecutable(compbio.engine.client.Executable, compbio.engine.client.Executable.ExecProvider)">configureExecutable</A></B>(<A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;T&gt;&nbsp;executable,\r
-                    <A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
-<TR ALIGN="right" VALIGN="">\r
-<TD NOWRAP><FONT SIZE="-1">\r
-<CODE>&lt;T&gt; <A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;T&gt;</CODE></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-</CODE></FONT></TD>\r
-<TD><CODE><B>Configurator.</B><B><A HREF="../../../compbio/engine/Configurator.html#configureExecutable(compbio.engine.client.Executable, java.util.List)">configureExecutable</A></B>(<A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;T&gt;&nbsp;executable,\r
-                    java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;dataSet)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B>SyncExecutor.</B><B><A HREF="../../../compbio/engine/SyncExecutor.html#executeJob()">executeJob</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Execute the job</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../compbio/engine/SyncExecutor.html" title="interface in compbio.engine">SyncExecutor</A></CODE></FONT></TD>\r
-<TD><CODE><B>Configurator.</B><B><A HREF="../../../compbio/engine/Configurator.html#getSyncEngine(compbio.engine.client.ConfiguredExecutable)">getSyncEngine</A></B>(<A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;executable)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../compbio/engine/SyncExecutor.html" title="interface in compbio.engine">SyncExecutor</A></CODE></FONT></TD>\r
-<TD><CODE><B>Configurator.</B><B><A HREF="../../../compbio/engine/Configurator.html#getSyncEngine(compbio.engine.client.ConfiguredExecutable, compbio.engine.client.Executable.ExecProvider)">getSyncEngine</A></B>(<A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;executable,\r
-              <A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B>AsyncExecutor.</B><B><A HREF="../../../compbio/engine/AsyncExecutor.html#submitJob(compbio.engine.client.ConfiguredExecutable)">submitJob</A></B>(<A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;executable)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Submits job for the execution
- Immediate execution is not guaranteed, this method puts the job in the queue.</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.engine.client"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A> in <A HREF="../../../compbio/engine/client/package-summary.html">compbio.engine.client</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/engine/client/package-summary.html">compbio.engine.client</A> that throw <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B>ConfiguredExecutable.</B><B><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html#getCommand(compbio.engine.client.Executable.ExecProvider)">getCommand</A></B>(<A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.engine.cluster.drmaa"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A> in <A HREF="../../../compbio/engine/cluster/drmaa/package-summary.html">compbio.engine.cluster.drmaa</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/engine/cluster/drmaa/package-summary.html">compbio.engine.cluster.drmaa</A> that throw <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B>JobRunner.</B><B><A HREF="../../../compbio/engine/cluster/drmaa/JobRunner.html#executeJob()">executeJob</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../compbio/engine/cluster/drmaa/JobRunner.html" title="class in compbio.engine.cluster.drmaa">JobRunner</A></CODE></FONT></TD>\r
-<TD><CODE><B>JobRunner.</B><B><A HREF="../../../compbio/engine/cluster/drmaa/JobRunner.html#getInstance(compbio.engine.client.ConfiguredExecutable)">getInstance</A></B>(<A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;executable)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B>AsyncJobRunner.</B><B><A HREF="../../../compbio/engine/cluster/drmaa/AsyncJobRunner.html#submitJob(compbio.engine.client.ConfiguredExecutable)">submitJob</A></B>(<A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;executable)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Constructors in <A HREF="../../../compbio/engine/cluster/drmaa/package-summary.html">compbio.engine.cluster.drmaa</A> that throw <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/engine/cluster/drmaa/JobRunner.html#JobRunner(compbio.engine.client.ConfiguredExecutable)">JobRunner</A></B>(<A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;confExec)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.engine.local"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A> in <A HREF="../../../compbio/engine/local/package-summary.html">compbio.engine.local</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/engine/local/package-summary.html">compbio.engine.local</A> that throw <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B>LocalRunner.</B><B><A HREF="../../../compbio/engine/local/LocalRunner.html#executeJob()">executeJob</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B>AsyncLocalRunner.</B><B><A HREF="../../../compbio/engine/local/AsyncLocalRunner.html#submitJob(compbio.engine.client.ConfiguredExecutable)">submitJob</A></B>(<A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;executable)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Constructors in <A HREF="../../../compbio/engine/local/package-summary.html">compbio.engine.local</A> that throw <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/engine/local/ExecutableWrapper.html#ExecutableWrapper(compbio.engine.client.ConfiguredExecutable, java.lang.String)">ExecutableWrapper</A></B>(<A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;executable,\r
-                  java.lang.String&nbsp;workDirectory)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.metadata"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A> in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Subclasses of <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A> in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;class</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Thrown if the task larger in size that the limit that applies to the
- calculation.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;class</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Indicates that the server could not execute native executables.</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.ws.server"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A> in <A HREF="../../../compbio/ws/server/package-summary.html">compbio.ws.server</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/ws/server/package-summary.html">compbio.ws.server</A> that throw <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B>TcoffeeWS.</B><B><A HREF="../../../compbio/ws/server/TcoffeeWS.html#align(java.util.List)">align</A></B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B>ProbconsWS.</B><B><A HREF="../../../compbio/ws/server/ProbconsWS.html#align(java.util.List)">align</A></B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B>MuscleWS.</B><B><A HREF="../../../compbio/ws/server/MuscleWS.html#align(java.util.List)">align</A></B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B>MafftWS.</B><B><A HREF="../../../compbio/ws/server/MafftWS.html#align(java.util.List)">align</A></B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B>ClustalWS.</B><B><A HREF="../../../compbio/ws/server/ClustalWS.html#align(java.util.List)">align</A></B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
-<TR ALIGN="right" VALIGN="">\r
-<TD NOWRAP><FONT SIZE="-1">\r
-<CODE>&lt;T&gt; java.lang.String</CODE></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-</CODE></FONT></TD>\r
-<TD><CODE><B>WSUtil.</B><B><A HREF="../../../compbio/ws/server/WSUtil.html#align(java.util.List, compbio.engine.client.ConfiguredExecutable, org.apache.log4j.Logger, javax.xml.ws.WebServiceContext, java.lang.String, compbio.metadata.Limit)">align</A></B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-      <A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;T&gt;&nbsp;confExec,\r
-      org.apache.log4j.Logger&nbsp;statLog,\r
-      javax.xml.ws.WebServiceContext&nbsp;wsContext,\r
-      java.lang.String&nbsp;callingMethod,\r
-      <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;T&gt;&nbsp;limit)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B>ClustalWS.</B><B><A HREF="../../../compbio/ws/server/ClustalWS.html#customAlign(java.util.List, java.util.List)">customAlign</A></B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-            java.util.List&lt;<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>&gt;&gt;&nbsp;options)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B>MafftWS.</B><B><A HREF="../../../compbio/ws/server/MafftWS.html#customAlign(java.util.List, java.util.List)">customAlign</A></B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-            java.util.List&lt;<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>&gt;&gt;&nbsp;options)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B>MuscleWS.</B><B><A HREF="../../../compbio/ws/server/MuscleWS.html#customAlign(java.util.List, java.util.List)">customAlign</A></B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-            java.util.List&lt;<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>&gt;&gt;&nbsp;options)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B>ProbconsWS.</B><B><A HREF="../../../compbio/ws/server/ProbconsWS.html#customAlign(java.util.List, java.util.List)">customAlign</A></B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-            java.util.List&lt;<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>&gt;&gt;&nbsp;options)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B>TcoffeeWS.</B><B><A HREF="../../../compbio/ws/server/TcoffeeWS.html#customAlign(java.util.List, java.util.List)">customAlign</A></B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-            java.util.List&lt;<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>&gt;&gt;&nbsp;options)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B>ClustalWS.</B><B><A HREF="../../../compbio/ws/server/ClustalWS.html#presetAlign(java.util.List, compbio.metadata.Preset)">presetAlign</A></B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-            <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>&lt;<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>&gt;&nbsp;preset)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B>MafftWS.</B><B><A HREF="../../../compbio/ws/server/MafftWS.html#presetAlign(java.util.List, compbio.metadata.Preset)">presetAlign</A></B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-            <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>&lt;<A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>&gt;&nbsp;preset)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B>MuscleWS.</B><B><A HREF="../../../compbio/ws/server/MuscleWS.html#presetAlign(java.util.List, compbio.metadata.Preset)">presetAlign</A></B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-            <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>&lt;<A HREF="../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>&gt;&nbsp;preset)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B>ProbconsWS.</B><B><A HREF="../../../compbio/ws/server/ProbconsWS.html#presetAlign(java.util.List, compbio.metadata.Preset)">presetAlign</A></B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-            <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>&lt;<A HREF="../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>&gt;&nbsp;preset)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B>TcoffeeWS.</B><B><A HREF="../../../compbio/ws/server/TcoffeeWS.html#presetAlign(java.util.List, compbio.metadata.Preset)">presetAlign</A></B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-            <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>&lt;<A HREF="../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>&gt;&nbsp;preset)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/metadata/\class-useJobSubmissionException.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="JobSubmissionException.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/metadata/class-use/Limit.html b/website/full_javadoc/compbio/metadata/class-use/Limit.html

deleted file mode 100644 (file)

index fa7eced..0000000
--- a/website/full_javadoc/compbio/metadata/class-use/Limit.html
+++ /dev/null
@@ -1,570 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Uses of Class compbio.metadata.Limit\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Uses of Class compbio.metadata.Limit";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/metadata/\class-useLimit.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="Limit.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-<B>Uses of Class<br>compbio.metadata.Limit</B></H2>\r
-</CENTER>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Packages that use <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.data.msa"><B>compbio.data.msa</B></A></TD>\r
-<TD>&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.data.msa.jaxws"><B>compbio.data.msa.jaxws</B></A></TD>\r
-<TD>&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.engine.client"><B>compbio.engine.client</B></A></TD>\r
-<TD>Classes and interfaces representing an input for engines.&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.metadata"><B>compbio.metadata</B></A></TD>\r
-<TD>A meta-data model for multiple sequence alignment web services 
- Classes in this package have no dependencies to other sources in the project.&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.runner"><B>compbio.runner</B></A></TD>\r
-<TD>Utilities commonly used by all runners.&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.runner._impl"><B>compbio.runner._impl</B></A></TD>\r
-<TD>&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.runner.msa"><B>compbio.runner.msa</B></A></TD>\r
-<TD>Wrappers for native executables for multiple sequence alignment (msa)&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.runner.psiblast"><B>compbio.runner.psiblast</B></A></TD>\r
-<TD>&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.ws.server"><B>compbio.ws.server</B></A></TD>\r
-<TD>&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.data.msa"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A> in <A HREF="../../../compbio/data/msa/package-summary.html">compbio.data.msa</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/data/msa/package-summary.html">compbio.data.msa</A> that return <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;<A HREF="../../../compbio/data/msa/MsaWS.html" title="type parameter in MsaWS">T</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>MsaWS.</B><B><A HREF="../../../compbio/data/msa/MsaWS.html#getLimit(java.lang.String)">getLimit</A></B>(java.lang.String&nbsp;presetName)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Get a Limit for a preset.</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.data.msa.jaxws"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A> in <A HREF="../../../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A> that return <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A></CODE></FONT></TD>\r
-<TD><CODE><B>GetLimitResponse.</B><B><A HREF="../../../compbio/data/msa/jaxws/GetLimitResponse.html#getReturn()">getReturn</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A> with parameters of type <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B>GetLimitResponse.</B><B><A HREF="../../../compbio/data/msa/jaxws/GetLimitResponse.html#setReturn(compbio.metadata.Limit)">setReturn</A></B>(<A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&nbsp;_return)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.engine.client"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A> in <A HREF="../../../compbio/engine/client/package-summary.html">compbio.engine.client</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/engine/client/package-summary.html">compbio.engine.client</A> that return <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;<A HREF="../../../compbio/engine/client/Executable.html" title="type parameter in Executable">T</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>Executable.</B><B><A HREF="../../../compbio/engine/client/Executable.html#getLimit(java.lang.String)">getLimit</A></B>(java.lang.String&nbsp;presetName)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>ConfExecutable.</B><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getLimit(java.lang.String)">getLimit</A></B>(java.lang.String&nbsp;presetName)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.metadata"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A> in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A> that return <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;<A HREF="../../../compbio/metadata/LimitsManager.html" title="type parameter in LimitsManager">T</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>LimitsManager.</B><B><A HREF="../../../compbio/metadata/LimitsManager.html#getDefaultLimit()">getDefaultLimit</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;<A HREF="../../../compbio/metadata/LimitsManager.html" title="type parameter in LimitsManager">T</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>LimitsManager.</B><B><A HREF="../../../compbio/metadata/LimitsManager.html#getLimitByName(java.lang.String)">getLimitByName</A></B>(java.lang.String&nbsp;presetName)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A> that return types with arguments of type <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.util.List&lt;<A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;<A HREF="../../../compbio/metadata/LimitsManager.html" title="type parameter in LimitsManager">T</A>&gt;&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>LimitsManager.</B><B><A HREF="../../../compbio/metadata/LimitsManager.html#getLimits()">getLimits</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A> with parameters of type <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A></CODE></FONT></TD>\r
-<TD><CODE><B>LimitExceededException.</B><B><A HREF="../../../compbio/metadata/LimitExceededException.html#newLimitExceeded(compbio.metadata.Limit, java.util.List)">newLimitExceeded</A></B>(<A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;?&gt;&nbsp;limit,\r
-                 java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;seqs)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.runner"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A> in <A HREF="../../../compbio/runner/package-summary.html">compbio.runner</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/runner/package-summary.html">compbio.runner</A> that return <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;<A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>_SkeletalCommandBuilder.</B><B><A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#getLimit(java.lang.String)">getLimit</A></B>(java.lang.String&nbsp;presetName)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.runner._impl"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A> in <A HREF="../../../compbio/runner/_impl/package-summary.html">compbio.runner._impl</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/runner/_impl/package-summary.html">compbio.runner._impl</A> that return <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;<A HREF="../../../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>NetNglyc.</B><B><A HREF="../../../compbio/runner/_impl/NetNglyc.html#getLimit(java.lang.String)">getLimit</A></B>(java.lang.String&nbsp;presetName)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.runner.msa"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A> in <A HREF="../../../compbio/runner/msa/package-summary.html">compbio.runner.msa</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/runner/msa/package-summary.html">compbio.runner.msa</A> that return <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;<A HREF="../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>Tcoffee.</B><B><A HREF="../../../compbio/runner/msa/Tcoffee.html#getLimit(java.lang.String)">getLimit</A></B>(java.lang.String&nbsp;presetName)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>ClustalW.</B><B><A HREF="../../../compbio/runner/msa/ClustalW.html#getLimit(java.lang.String)">getLimit</A></B>(java.lang.String&nbsp;presetName)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;<A HREF="../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>Probcons.</B><B><A HREF="../../../compbio/runner/msa/Probcons.html#getLimit(java.lang.String)">getLimit</A></B>(java.lang.String&nbsp;presetName)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;<A HREF="../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>Muscle.</B><B><A HREF="../../../compbio/runner/msa/Muscle.html#getLimit(java.lang.String)">getLimit</A></B>(java.lang.String&nbsp;presetName)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;<A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>Mafft.</B><B><A HREF="../../../compbio/runner/msa/Mafft.html#getLimit(java.lang.String)">getLimit</A></B>(java.lang.String&nbsp;presetName)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.runner.psiblast"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A> in <A HREF="../../../compbio/runner/psiblast/package-summary.html">compbio.runner.psiblast</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/runner/psiblast/package-summary.html">compbio.runner.psiblast</A> that return <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;<A HREF="../../../compbio/runner/psiblast/PsiBlast.html" title="class in compbio.runner.psiblast">PsiBlast</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>PsiBlast.</B><B><A HREF="../../../compbio/runner/psiblast/PsiBlast.html#getLimit(java.lang.String)">getLimit</A></B>(java.lang.String&nbsp;presetName)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.ws.server"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A> in <A HREF="../../../compbio/ws/server/package-summary.html">compbio.ws.server</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/ws/server/package-summary.html">compbio.ws.server</A> that return <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;<A HREF="../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>TcoffeeWS.</B><B><A HREF="../../../compbio/ws/server/TcoffeeWS.html#getLimit(java.lang.String)">getLimit</A></B>(java.lang.String&nbsp;presetName)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;<A HREF="../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>ProbconsWS.</B><B><A HREF="../../../compbio/ws/server/ProbconsWS.html#getLimit(java.lang.String)">getLimit</A></B>(java.lang.String&nbsp;presetName)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;<A HREF="../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>MuscleWS.</B><B><A HREF="../../../compbio/ws/server/MuscleWS.html#getLimit(java.lang.String)">getLimit</A></B>(java.lang.String&nbsp;presetName)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;<A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>MafftWS.</B><B><A HREF="../../../compbio/ws/server/MafftWS.html#getLimit(java.lang.String)">getLimit</A></B>(java.lang.String&nbsp;presetName)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>ClustalWS.</B><B><A HREF="../../../compbio/ws/server/ClustalWS.html#getLimit(java.lang.String)">getLimit</A></B>(java.lang.String&nbsp;presetName)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/ws/server/package-summary.html">compbio.ws.server</A> with parameters of type <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
-<TR ALIGN="right" VALIGN="">\r
-<TD NOWRAP><FONT SIZE="-1">\r
-<CODE>&lt;T&gt; java.lang.String</CODE></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-</CODE></FONT></TD>\r
-<TD><CODE><B>WSUtil.</B><B><A HREF="../../../compbio/ws/server/WSUtil.html#align(java.util.List, compbio.engine.client.ConfiguredExecutable, org.apache.log4j.Logger, javax.xml.ws.WebServiceContext, java.lang.String, compbio.metadata.Limit)">align</A></B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-      <A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;T&gt;&nbsp;confExec,\r
-      org.apache.log4j.Logger&nbsp;statLog,\r
-      javax.xml.ws.WebServiceContext&nbsp;wsContext,\r
-      java.lang.String&nbsp;callingMethod,\r
-      <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;T&gt;&nbsp;limit)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/metadata/\class-useLimit.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="Limit.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/metadata/class-use/LimitExceededException.html b/website/full_javadoc/compbio/metadata/class-use/LimitExceededException.html

deleted file mode 100644 (file)

index 22163d6..0000000
--- a/website/full_javadoc/compbio/metadata/class-use/LimitExceededException.html
+++ /dev/null
@@ -1,270 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Uses of Class compbio.metadata.LimitExceededException\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Uses of Class compbio.metadata.LimitExceededException";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/metadata/\class-useLimitExceededException.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="LimitExceededException.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-<B>Uses of Class<br>compbio.metadata.LimitExceededException</B></H2>\r
-</CENTER>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Packages that use <A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.data.msa"><B>compbio.data.msa</B></A></TD>\r
-<TD>&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.metadata"><B>compbio.metadata</B></A></TD>\r
-<TD>A meta-data model for multiple sequence alignment web services 
- Classes in this package have no dependencies to other sources in the project.&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.ws.server"><B>compbio.ws.server</B></A></TD>\r
-<TD>&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.data.msa"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A> in <A HREF="../../../compbio/data/msa/package-summary.html">compbio.data.msa</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/data/msa/package-summary.html">compbio.data.msa</A> that throw <A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B>MsaWS.</B><B><A HREF="../../../compbio/data/msa/MsaWS.html#align(java.util.List)">align</A></B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Align a list of sequences with default settings.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B>MsaWS.</B><B><A HREF="../../../compbio/data/msa/MsaWS.html#customAlign(java.util.List, java.util.List)">customAlign</A></B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-            java.util.List&lt;<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../compbio/data/msa/MsaWS.html" title="type parameter in MsaWS">T</A>&gt;&gt;&nbsp;options)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Align a list of sequences with options.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B>MsaWS.</B><B><A HREF="../../../compbio/data/msa/MsaWS.html#presetAlign(java.util.List, compbio.metadata.Preset)">presetAlign</A></B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-            <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>&lt;<A HREF="../../../compbio/data/msa/MsaWS.html" title="type parameter in MsaWS">T</A>&gt;&nbsp;preset)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Align a list of sequences with preset.</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.metadata"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A> in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A> that return <A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A></CODE></FONT></TD>\r
-<TD><CODE><B>LimitExceededException.</B><B><A HREF="../../../compbio/metadata/LimitExceededException.html#newLimitExceeded(compbio.metadata.Limit, java.util.List)">newLimitExceeded</A></B>(<A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;?&gt;&nbsp;limit,\r
-                 java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;seqs)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.ws.server"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A> in <A HREF="../../../compbio/ws/server/package-summary.html">compbio.ws.server</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/ws/server/package-summary.html">compbio.ws.server</A> that throw <A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
-<TR ALIGN="right" VALIGN="">\r
-<TD NOWRAP><FONT SIZE="-1">\r
-<CODE>&lt;T&gt; java.lang.String</CODE></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-</CODE></FONT></TD>\r
-<TD><CODE><B>WSUtil.</B><B><A HREF="../../../compbio/ws/server/WSUtil.html#align(java.util.List, compbio.engine.client.ConfiguredExecutable, org.apache.log4j.Logger, javax.xml.ws.WebServiceContext, java.lang.String, compbio.metadata.Limit)">align</A></B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-      <A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;T&gt;&nbsp;confExec,\r
-      org.apache.log4j.Logger&nbsp;statLog,\r
-      javax.xml.ws.WebServiceContext&nbsp;wsContext,\r
-      java.lang.String&nbsp;callingMethod,\r
-      <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;T&gt;&nbsp;limit)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/metadata/\class-useLimitExceededException.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="LimitExceededException.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/metadata/class-use/LimitsManager.html b/website/full_javadoc/compbio/metadata/class-use/LimitsManager.html

deleted file mode 100644 (file)

index 1bbf5d5..0000000
--- a/website/full_javadoc/compbio/metadata/class-use/LimitsManager.html
+++ /dev/null
@@ -1,502 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Uses of Class compbio.metadata.LimitsManager\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Uses of Class compbio.metadata.LimitsManager";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/metadata/\class-useLimitsManager.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="LimitsManager.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-<B>Uses of Class<br>compbio.metadata.LimitsManager</B></H2>\r
-</CENTER>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Packages that use <A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.data.msa"><B>compbio.data.msa</B></A></TD>\r
-<TD>&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.data.msa.jaxws"><B>compbio.data.msa.jaxws</B></A></TD>\r
-<TD>&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.engine.client"><B>compbio.engine.client</B></A></TD>\r
-<TD>Classes and interfaces representing an input for engines.&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.runner"><B>compbio.runner</B></A></TD>\r
-<TD>Utilities commonly used by all runners.&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.runner._impl"><B>compbio.runner._impl</B></A></TD>\r
-<TD>&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.runner.msa"><B>compbio.runner.msa</B></A></TD>\r
-<TD>Wrappers for native executables for multiple sequence alignment (msa)&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.runner.psiblast"><B>compbio.runner.psiblast</B></A></TD>\r
-<TD>&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.ws.server"><B>compbio.ws.server</B></A></TD>\r
-<TD>&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.data.msa"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A> in <A HREF="../../../compbio/data/msa/package-summary.html">compbio.data.msa</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/data/msa/package-summary.html">compbio.data.msa</A> that return <A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;<A HREF="../../../compbio/data/msa/MsaWS.html" title="type parameter in MsaWS">T</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>MsaWS.</B><B><A HREF="../../../compbio/data/msa/MsaWS.html#getLimits()">getLimits</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;List Limits supported by a web service.</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.data.msa.jaxws"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A> in <A HREF="../../../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A> that return <A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A></CODE></FONT></TD>\r
-<TD><CODE><B>GetLimitsResponse.</B><B><A HREF="../../../compbio/data/msa/jaxws/GetLimitsResponse.html#getReturn()">getReturn</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A> with parameters of type <A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B>GetLimitsResponse.</B><B><A HREF="../../../compbio/data/msa/jaxws/GetLimitsResponse.html#setReturn(compbio.metadata.LimitsManager)">setReturn</A></B>(<A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&nbsp;_return)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.engine.client"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A> in <A HREF="../../../compbio/engine/client/package-summary.html">compbio.engine.client</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/engine/client/package-summary.html">compbio.engine.client</A> that return <A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;<A HREF="../../../compbio/engine/client/Executable.html" title="type parameter in Executable">T</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>Executable.</B><B><A HREF="../../../compbio/engine/client/Executable.html#getLimits()">getLimits</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>ConfExecutable.</B><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getLimits()">getLimits</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
-<TR ALIGN="right" VALIGN="">\r
-<TD NOWRAP><FONT SIZE="-1">\r
-<CODE>&lt;V&gt; <A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;V&gt;</CODE></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-</CODE></FONT></TD>\r
-<TD><CODE><B>ConfExecutable.</B><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getRunnerLimits(java.lang.Class)">getRunnerLimits</A></B>(java.lang.Class&lt;? extends <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;V&gt;&gt;&nbsp;clazz)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;This method should be executed once and result of its execution reused.</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.runner"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A> in <A HREF="../../../compbio/runner/package-summary.html">compbio.runner</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/runner/package-summary.html">compbio.runner</A> that return <A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;<A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>_SkeletalCommandBuilder.</B><B><A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#getLimits()">getLimits</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
-<TR ALIGN="right" VALIGN="">\r
-<TD NOWRAP><FONT SIZE="-1">\r
-<CODE>&lt;T&gt; <A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;T&gt;</CODE></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-</CODE></FONT></TD>\r
-<TD><CODE><B>Util.</B><B><A HREF="../../../compbio/runner/Util.html#getLimits(java.lang.Class)">getLimits</A></B>(java.lang.Class&lt;? extends <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;T&gt;&gt;&nbsp;clazz)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;For now just assume that all parameters which came in needs setting it
- will be a client responsibility to prepare RunnerConfig object then</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.runner._impl"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A> in <A HREF="../../../compbio/runner/_impl/package-summary.html">compbio.runner._impl</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/runner/_impl/package-summary.html">compbio.runner._impl</A> that return <A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;<A HREF="../../../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>NetNglyc.</B><B><A HREF="../../../compbio/runner/_impl/NetNglyc.html#getLimits()">getLimits</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.runner.msa"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A> in <A HREF="../../../compbio/runner/msa/package-summary.html">compbio.runner.msa</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/runner/msa/package-summary.html">compbio.runner.msa</A> that return <A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;<A HREF="../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>Tcoffee.</B><B><A HREF="../../../compbio/runner/msa/Tcoffee.html#getLimits()">getLimits</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>ClustalW.</B><B><A HREF="../../../compbio/runner/msa/ClustalW.html#getLimits()">getLimits</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;<A HREF="../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>Probcons.</B><B><A HREF="../../../compbio/runner/msa/Probcons.html#getLimits()">getLimits</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;<A HREF="../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>Muscle.</B><B><A HREF="../../../compbio/runner/msa/Muscle.html#getLimits()">getLimits</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;<A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>Mafft.</B><B><A HREF="../../../compbio/runner/msa/Mafft.html#getLimits()">getLimits</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.runner.psiblast"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A> in <A HREF="../../../compbio/runner/psiblast/package-summary.html">compbio.runner.psiblast</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/runner/psiblast/package-summary.html">compbio.runner.psiblast</A> that return <A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;<A HREF="../../../compbio/runner/psiblast/PsiBlast.html" title="class in compbio.runner.psiblast">PsiBlast</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>PsiBlast.</B><B><A HREF="../../../compbio/runner/psiblast/PsiBlast.html#getLimits()">getLimits</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.ws.server"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A> in <A HREF="../../../compbio/ws/server/package-summary.html">compbio.ws.server</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/ws/server/package-summary.html">compbio.ws.server</A> that return <A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;<A HREF="../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>TcoffeeWS.</B><B><A HREF="../../../compbio/ws/server/TcoffeeWS.html#getLimits()">getLimits</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;<A HREF="../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>ProbconsWS.</B><B><A HREF="../../../compbio/ws/server/ProbconsWS.html#getLimits()">getLimits</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;<A HREF="../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>MuscleWS.</B><B><A HREF="../../../compbio/ws/server/MuscleWS.html#getLimits()">getLimits</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;<A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>MafftWS.</B><B><A HREF="../../../compbio/ws/server/MafftWS.html#getLimits()">getLimits</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>ClustalWS.</B><B><A HREF="../../../compbio/ws/server/ClustalWS.html#getLimits()">getLimits</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/metadata/\class-useLimitsManager.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="LimitsManager.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/metadata/class-use/Option.html b/website/full_javadoc/compbio/metadata/class-use/Option.html

deleted file mode 100644 (file)

index 1defb5a..0000000
--- a/website/full_javadoc/compbio/metadata/class-use/Option.html
+++ /dev/null
@@ -1,539 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Uses of Class compbio.metadata.Option\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Uses of Class compbio.metadata.Option";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/metadata/\class-useOption.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="Option.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-<B>Uses of Class<br>compbio.metadata.Option</B></H2>\r
-</CENTER>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Packages that use <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.data.msa"><B>compbio.data.msa</B></A></TD>\r
-<TD>&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.data.msa.jaxws"><B>compbio.data.msa.jaxws</B></A></TD>\r
-<TD>&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.engine.client"><B>compbio.engine.client</B></A></TD>\r
-<TD>Classes and interfaces representing an input for engines.&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.metadata"><B>compbio.metadata</B></A></TD>\r
-<TD>A meta-data model for multiple sequence alignment web services 
- Classes in this package have no dependencies to other sources in the project.&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.runner"><B>compbio.runner</B></A></TD>\r
-<TD>Utilities commonly used by all runners.&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.ws.server"><B>compbio.ws.server</B></A></TD>\r
-<TD>&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.data.msa"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A> in <A HREF="../../../compbio/data/msa/package-summary.html">compbio.data.msa</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Method parameters in <A HREF="../../../compbio/data/msa/package-summary.html">compbio.data.msa</A> with type arguments of type <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B>MsaWS.</B><B><A HREF="../../../compbio/data/msa/MsaWS.html#customAlign(java.util.List, java.util.List)">customAlign</A></B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-            java.util.List&lt;<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../compbio/data/msa/MsaWS.html" title="type parameter in MsaWS">T</A>&gt;&gt;&nbsp;options)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Align a list of sequences with options.</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.data.msa.jaxws"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A> in <A HREF="../../../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A> that return types with arguments of type <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.util.List&lt;<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>CustomAlign.</B><B><A HREF="../../../compbio/data/msa/jaxws/CustomAlign.html#getOptions()">getOptions</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Method parameters in <A HREF="../../../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A> with type arguments of type <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B>CustomAlign.</B><B><A HREF="../../../compbio/data/msa/jaxws/CustomAlign.html#setOptions(java.util.List)">setOptions</A></B>(java.util.List&lt;<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&gt;&nbsp;options)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.engine.client"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A> in <A HREF="../../../compbio/engine/client/package-summary.html">compbio.engine.client</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Method parameters in <A HREF="../../../compbio/engine/client/package-summary.html">compbio.engine.client</A> with type arguments of type <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
-<TR ALIGN="right" VALIGN="">\r
-<TD NOWRAP><FONT SIZE="-1">\r
-<CODE>&lt;T&gt; <A HREF="../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>&lt;T&gt;</CODE></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-</CODE></FONT></TD>\r
-<TD><CODE><B>CommandBuilder.</B><B><A HREF="../../../compbio/engine/client/CommandBuilder.html#newCommandBuilder(java.util.List, java.lang.String)">newCommandBuilder</A></B>(java.util.List&lt;? extends <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;T&gt;&gt;&nbsp;arguments,\r
-                  java.lang.String&nbsp;nameValueSeparator)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;This produces the same result as getCommands method.</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.metadata"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A> in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Subclasses of <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A> in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;class</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter&lt;T&gt;</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;A single value containing option supported by the web service e.g.</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A> that return <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>RunnerConfig.</B><B><A HREF="../../../compbio/metadata/RunnerConfig.html#getArgument(java.lang.String)">getArgument</A></B>(java.lang.String&nbsp;name)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Returns the argument by its name if found, NULL otherwise</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>RunnerConfig.</B><B><A HREF="../../../compbio/metadata/RunnerConfig.html#getArgumentByOptionName(java.lang.String)">getArgumentByOptionName</A></B>(java.lang.String&nbsp;optionName)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Returns the argument by option name, NULL if the argument is not found</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A> that return types with arguments of type <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.util.List&lt;<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>&gt;&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>RunnerConfig.</B><B><A HREF="../../../compbio/metadata/RunnerConfig.html#getArguments()">getArguments</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.util.List&lt;<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../compbio/metadata/Preset.html" title="type parameter in Preset">T</A>&gt;&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>Preset.</B><B><A HREF="../../../compbio/metadata/Preset.html#getArguments(compbio.metadata.RunnerConfig)">getArguments</A></B>(<A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&lt;<A HREF="../../../compbio/metadata/Preset.html" title="type parameter in Preset">T</A>&gt;&nbsp;rconfig)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Converts list of options as String to type Option</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.util.List&lt;<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>&gt;&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>RunnerConfig.</B><B><A HREF="../../../compbio/metadata/RunnerConfig.html#getOptions()">getOptions</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A> with parameters of type <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B>RunnerConfig.</B><B><A HREF="../../../compbio/metadata/RunnerConfig.html#addOption(compbio.metadata.Option)">addOption</A></B>(<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>&gt;&nbsp;option)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Method parameters in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A> with type arguments of type <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B>RunnerConfig.</B><B><A HREF="../../../compbio/metadata/RunnerConfig.html#setOptions(java.util.List)">setOptions</A></B>(java.util.List&lt;<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>&gt;&gt;&nbsp;parameters)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Constructors in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A> with parameters of type <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/metadata/WrongParameterException.html#WrongParameterException(compbio.metadata.Option)">WrongParameterException</A></B>(<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;?&gt;&nbsp;option)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.runner"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A> in <A HREF="../../../compbio/runner/package-summary.html">compbio.runner</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/runner/package-summary.html">compbio.runner</A> that return types with arguments of type <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.util.List&lt;<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;?&gt;&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>OptionCombinator.</B><B><A HREF="../../../compbio/runner/OptionCombinator.html#getAllOptions()">getAllOptions</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Method parameters in <A HREF="../../../compbio/runner/package-summary.html">compbio.runner</A> with type arguments of type <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.util.List&lt;java.lang.String&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>OptionCombinator.</B><B><A HREF="../../../compbio/runner/OptionCombinator.html#argumentsToCommandString(java.util.List)">argumentsToCommandString</A></B>(java.util.List&lt;? extends <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;?&gt;&gt;&nbsp;arguments)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;java.util.List&lt;java.lang.String&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>OptionCombinator.</B><B><A HREF="../../../compbio/runner/OptionCombinator.html#argumentsToCommandString(java.util.List, compbio.metadata.RunnerConfig)">argumentsToCommandString</A></B>(java.util.List&lt;? extends <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;?&gt;&gt;&nbsp;arguments,\r
-                         <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&lt;? extends <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;?&gt;&gt;&nbsp;rconfig)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.util.List&lt;java.lang.String&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>OptionCombinator.</B><B><A HREF="../../../compbio/runner/OptionCombinator.html#optionsToCommandString(java.util.List)">optionsToCommandString</A></B>(java.util.List&lt;<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;?&gt;&gt;&nbsp;options)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.ws.server"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A> in <A HREF="../../../compbio/ws/server/package-summary.html">compbio.ws.server</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Method parameters in <A HREF="../../../compbio/ws/server/package-summary.html">compbio.ws.server</A> with type arguments of type <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B>ClustalWS.</B><B><A HREF="../../../compbio/ws/server/ClustalWS.html#customAlign(java.util.List, java.util.List)">customAlign</A></B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-            java.util.List&lt;<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>&gt;&gt;&nbsp;options)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B>MafftWS.</B><B><A HREF="../../../compbio/ws/server/MafftWS.html#customAlign(java.util.List, java.util.List)">customAlign</A></B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-            java.util.List&lt;<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>&gt;&gt;&nbsp;options)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B>MuscleWS.</B><B><A HREF="../../../compbio/ws/server/MuscleWS.html#customAlign(java.util.List, java.util.List)">customAlign</A></B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-            java.util.List&lt;<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>&gt;&gt;&nbsp;options)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B>ProbconsWS.</B><B><A HREF="../../../compbio/ws/server/ProbconsWS.html#customAlign(java.util.List, java.util.List)">customAlign</A></B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-            java.util.List&lt;<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>&gt;&gt;&nbsp;options)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B>TcoffeeWS.</B><B><A HREF="../../../compbio/ws/server/TcoffeeWS.html#customAlign(java.util.List, java.util.List)">customAlign</A></B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-            java.util.List&lt;<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>&gt;&gt;&nbsp;options)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
-<TR ALIGN="right" VALIGN="">\r
-<TD NOWRAP><FONT SIZE="-1">\r
-<CODE>&lt;T&gt; java.util.List&lt;java.lang.String&gt;</CODE></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-</CODE></FONT></TD>\r
-<TD><CODE><B>WSUtil.</B><B><A HREF="../../../compbio/ws/server/WSUtil.html#getCommands(java.util.List, java.lang.String)">getCommands</A></B>(java.util.List&lt;<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;T&gt;&gt;&nbsp;options,\r
-            java.lang.String&nbsp;keyValueSeparator)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/metadata/\class-useOption.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="Option.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/metadata/class-use/Parameter.html b/website/full_javadoc/compbio/metadata/class-use/Parameter.html

deleted file mode 100644 (file)

index 8038618..0000000
--- a/website/full_javadoc/compbio/metadata/class-use/Parameter.html
+++ /dev/null
@@ -1,284 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Uses of Class compbio.metadata.Parameter\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Uses of Class compbio.metadata.Parameter";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../compbio/metadata/Parameter.html" title="class in compbio.metadata"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/metadata/\class-useParameter.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="Parameter.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-<B>Uses of Class<br>compbio.metadata.Parameter</B></H2>\r
-</CENTER>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Packages that use <A HREF="../../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.metadata"><B>compbio.metadata</B></A></TD>\r
-<TD>A meta-data model for multiple sequence alignment web services 
- Classes in this package have no dependencies to other sources in the project.&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.runner"><B>compbio.runner</B></A></TD>\r
-<TD>Utilities commonly used by all runners.&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.metadata"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A> in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A> that return types with arguments of type <A HREF="../../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.util.List&lt;<A HREF="../../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>&lt;<A HREF="../../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>&gt;&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>RunnerConfig.</B><B><A HREF="../../../compbio/metadata/RunnerConfig.html#getParameters()">getParameters</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A> with parameters of type <A HREF="../../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B>RunnerConfig.</B><B><A HREF="../../../compbio/metadata/RunnerConfig.html#addParameter(compbio.metadata.Parameter)">addParameter</A></B>(<A HREF="../../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>&lt;<A HREF="../../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>&gt;&nbsp;param)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Method parameters in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A> with type arguments of type <A HREF="../../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B>RunnerConfig.</B><B><A HREF="../../../compbio/metadata/RunnerConfig.html#setParameters(java.util.List)">setParameters</A></B>(java.util.List&lt;<A HREF="../../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>&lt;<A HREF="../../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>&gt;&gt;&nbsp;parameters)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.runner"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A> in <A HREF="../../../compbio/runner/package-summary.html">compbio.runner</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/runner/package-summary.html">compbio.runner</A> that return types with arguments of type <A HREF="../../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.util.Map&lt;<A HREF="../../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>&lt;?&gt;,java.lang.String&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>OptionCombinator.</B><B><A HREF="../../../compbio/runner/OptionCombinator.html#getAllConstrainedParametersWithBorderValues(boolean)">getAllConstrainedParametersWithBorderValues</A></B>(boolean&nbsp;minValue)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.util.Map&lt;<A HREF="../../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>&lt;?&gt;,java.lang.String&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>OptionCombinator.</B><B><A HREF="../../../compbio/runner/OptionCombinator.html#getAllConstrainedParametersWithRandomValues()">getAllConstrainedParametersWithRandomValues</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.util.List&lt;<A HREF="../../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>&lt;?&gt;&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>OptionCombinator.</B><B><A HREF="../../../compbio/runner/OptionCombinator.html#getAllParameters()">getAllParameters</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Method parameters in <A HREF="../../../compbio/runner/package-summary.html">compbio.runner</A> with type arguments of type <A HREF="../../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.util.List&lt;java.lang.String&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>OptionCombinator.</B><B><A HREF="../../../compbio/runner/OptionCombinator.html#parametersToCommandString(java.util.List, java.util.Map)">parametersToCommandString</A></B>(java.util.List&lt;<A HREF="../../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>&lt;?&gt;&gt;&nbsp;orderedList,\r
-                          java.util.Map&lt;<A HREF="../../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>&lt;?&gt;,java.lang.String&gt;&nbsp;prmValue)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.util.List&lt;java.lang.String&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>OptionCombinator.</B><B><A HREF="../../../compbio/runner/OptionCombinator.html#parametersToCommandString(java.util.List, java.util.Map)">parametersToCommandString</A></B>(java.util.List&lt;<A HREF="../../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>&lt;?&gt;&gt;&nbsp;orderedList,\r
-                          java.util.Map&lt;<A HREF="../../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>&lt;?&gt;,java.lang.String&gt;&nbsp;prmValue)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../compbio/metadata/Parameter.html" title="class in compbio.metadata"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/metadata/\class-useParameter.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="Parameter.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/metadata/class-use/Preset.html b/website/full_javadoc/compbio/metadata/class-use/Preset.html

deleted file mode 100644 (file)

index e8f8abe..0000000
--- a/website/full_javadoc/compbio/metadata/class-use/Preset.html
+++ /dev/null
@@ -1,354 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Uses of Class compbio.metadata.Preset\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Uses of Class compbio.metadata.Preset";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/metadata/\class-usePreset.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="Preset.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-<B>Uses of Class<br>compbio.metadata.Preset</B></H2>\r
-</CENTER>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Packages that use <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.data.msa"><B>compbio.data.msa</B></A></TD>\r
-<TD>&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.data.msa.jaxws"><B>compbio.data.msa.jaxws</B></A></TD>\r
-<TD>&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.metadata"><B>compbio.metadata</B></A></TD>\r
-<TD>A meta-data model for multiple sequence alignment web services 
- Classes in this package have no dependencies to other sources in the project.&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.ws.server"><B>compbio.ws.server</B></A></TD>\r
-<TD>&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.data.msa"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A> in <A HREF="../../../compbio/data/msa/package-summary.html">compbio.data.msa</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/data/msa/package-summary.html">compbio.data.msa</A> with parameters of type <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B>MsaWS.</B><B><A HREF="../../../compbio/data/msa/MsaWS.html#presetAlign(java.util.List, compbio.metadata.Preset)">presetAlign</A></B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-            <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>&lt;<A HREF="../../../compbio/data/msa/MsaWS.html" title="type parameter in MsaWS">T</A>&gt;&nbsp;preset)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Align a list of sequences with preset.</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.data.msa.jaxws"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A> in <A HREF="../../../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A> that return <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A></CODE></FONT></TD>\r
-<TD><CODE><B>PresetAlign.</B><B><A HREF="../../../compbio/data/msa/jaxws/PresetAlign.html#getPreset()">getPreset</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A> with parameters of type <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B>PresetAlign.</B><B><A HREF="../../../compbio/data/msa/jaxws/PresetAlign.html#setPreset(compbio.metadata.Preset)">setPreset</A></B>(<A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>&nbsp;preset)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.metadata"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A> in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A> that return <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>&lt;<A HREF="../../../compbio/metadata/PresetManager.html" title="type parameter in PresetManager">T</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>PresetManager.</B><B><A HREF="../../../compbio/metadata/PresetManager.html#getPresetByName(java.lang.String)">getPresetByName</A></B>(java.lang.String&nbsp;presetName)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A> that return types with arguments of type <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.util.List&lt;<A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>&lt;<A HREF="../../../compbio/metadata/PresetManager.html" title="type parameter in PresetManager">T</A>&gt;&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>PresetManager.</B><B><A HREF="../../../compbio/metadata/PresetManager.html#getPresets()">getPresets</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Method parameters in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A> with type arguments of type <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B>PresetManager.</B><B><A HREF="../../../compbio/metadata/PresetManager.html#setPresets(java.util.List)">setPresets</A></B>(java.util.List&lt;<A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>&lt;<A HREF="../../../compbio/metadata/PresetManager.html" title="type parameter in PresetManager">T</A>&gt;&gt;&nbsp;presets)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.ws.server"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A> in <A HREF="../../../compbio/ws/server/package-summary.html">compbio.ws.server</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/ws/server/package-summary.html">compbio.ws.server</A> with parameters of type <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B>ClustalWS.</B><B><A HREF="../../../compbio/ws/server/ClustalWS.html#presetAlign(java.util.List, compbio.metadata.Preset)">presetAlign</A></B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-            <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>&lt;<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>&gt;&nbsp;preset)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B>MafftWS.</B><B><A HREF="../../../compbio/ws/server/MafftWS.html#presetAlign(java.util.List, compbio.metadata.Preset)">presetAlign</A></B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-            <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>&lt;<A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>&gt;&nbsp;preset)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B>MuscleWS.</B><B><A HREF="../../../compbio/ws/server/MuscleWS.html#presetAlign(java.util.List, compbio.metadata.Preset)">presetAlign</A></B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-            <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>&lt;<A HREF="../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>&gt;&nbsp;preset)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B>ProbconsWS.</B><B><A HREF="../../../compbio/ws/server/ProbconsWS.html#presetAlign(java.util.List, compbio.metadata.Preset)">presetAlign</A></B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-            <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>&lt;<A HREF="../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>&gt;&nbsp;preset)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B>TcoffeeWS.</B><B><A HREF="../../../compbio/ws/server/TcoffeeWS.html#presetAlign(java.util.List, compbio.metadata.Preset)">presetAlign</A></B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-            <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>&lt;<A HREF="../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>&gt;&nbsp;preset)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/metadata/\class-usePreset.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="Preset.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/metadata/class-use/PresetManager.html b/website/full_javadoc/compbio/metadata/class-use/PresetManager.html

deleted file mode 100644 (file)

index c6c458a..0000000
--- a/website/full_javadoc/compbio/metadata/class-use/PresetManager.html
+++ /dev/null
@@ -1,388 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Uses of Class compbio.metadata.PresetManager\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Uses of Class compbio.metadata.PresetManager";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../compbio/metadata/PresetManager.html" title="class in compbio.metadata"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/metadata/\class-usePresetManager.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="PresetManager.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-<B>Uses of Class<br>compbio.metadata.PresetManager</B></H2>\r
-</CENTER>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Packages that use <A HREF="../../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.data.msa"><B>compbio.data.msa</B></A></TD>\r
-<TD>&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.data.msa.jaxws"><B>compbio.data.msa.jaxws</B></A></TD>\r
-<TD>&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.engine.client"><B>compbio.engine.client</B></A></TD>\r
-<TD>Classes and interfaces representing an input for engines.&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.metadata"><B>compbio.metadata</B></A></TD>\r
-<TD>A meta-data model for multiple sequence alignment web services 
- Classes in this package have no dependencies to other sources in the project.&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.runner"><B>compbio.runner</B></A></TD>\r
-<TD>Utilities commonly used by all runners.&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.ws.server"><B>compbio.ws.server</B></A></TD>\r
-<TD>&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.data.msa"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A> in <A HREF="../../../compbio/data/msa/package-summary.html">compbio.data.msa</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/data/msa/package-summary.html">compbio.data.msa</A> that return <A HREF="../../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>&lt;<A HREF="../../../compbio/data/msa/MsaWS.html" title="type parameter in MsaWS">T</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>MsaWS.</B><B><A HREF="../../../compbio/data/msa/MsaWS.html#getPresets()">getPresets</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Get presets supported by a web service</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.data.msa.jaxws"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A> in <A HREF="../../../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A> that return <A HREF="../../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A></CODE></FONT></TD>\r
-<TD><CODE><B>GetPresetsResponse.</B><B><A HREF="../../../compbio/data/msa/jaxws/GetPresetsResponse.html#getReturn()">getReturn</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A> with parameters of type <A HREF="../../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B>GetPresetsResponse.</B><B><A HREF="../../../compbio/data/msa/jaxws/GetPresetsResponse.html#setReturn(compbio.metadata.PresetManager)">setReturn</A></B>(<A HREF="../../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>&nbsp;_return)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.engine.client"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A> in <A HREF="../../../compbio/engine/client/package-summary.html">compbio.engine.client</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/engine/client/package-summary.html">compbio.engine.client</A> that return <A HREF="../../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
-<TR ALIGN="right" VALIGN="">\r
-<TD NOWRAP><FONT SIZE="-1">\r
-<CODE>&lt;V&gt; <A HREF="../../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>&lt;V&gt;</CODE></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-</CODE></FONT></TD>\r
-<TD><CODE><B>ConfExecutable.</B><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getRunnerPresets(java.lang.Class)">getRunnerPresets</A></B>(java.lang.Class&lt;? extends <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;V&gt;&gt;&nbsp;clazz)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.metadata"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A> in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A> with parameters of type <A HREF="../../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B>LimitsManager.</B><B><A HREF="../../../compbio/metadata/LimitsManager.html#validate(compbio.metadata.PresetManager)">validate</A></B>(<A HREF="../../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>&lt;<A HREF="../../../compbio/metadata/LimitsManager.html" title="type parameter in LimitsManager">T</A>&gt;&nbsp;presets)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Validate Limits</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.runner"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A> in <A HREF="../../../compbio/runner/package-summary.html">compbio.runner</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/runner/package-summary.html">compbio.runner</A> that return <A HREF="../../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
-<TR ALIGN="right" VALIGN="">\r
-<TD NOWRAP><FONT SIZE="-1">\r
-<CODE>&lt;T&gt; <A HREF="../../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>&lt;T&gt;</CODE></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-</CODE></FONT></TD>\r
-<TD><CODE><B>Util.</B><B><A HREF="../../../compbio/runner/Util.html#getPresets(java.lang.Class)">getPresets</A></B>(java.lang.Class&lt;? extends <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;T&gt;&gt;&nbsp;clazz)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.ws.server"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A> in <A HREF="../../../compbio/ws/server/package-summary.html">compbio.ws.server</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/ws/server/package-summary.html">compbio.ws.server</A> that return <A HREF="../../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>&lt;<A HREF="../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>TcoffeeWS.</B><B><A HREF="../../../compbio/ws/server/TcoffeeWS.html#getPresets()">getPresets</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>&lt;<A HREF="../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>ProbconsWS.</B><B><A HREF="../../../compbio/ws/server/ProbconsWS.html#getPresets()">getPresets</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>&lt;<A HREF="../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>MuscleWS.</B><B><A HREF="../../../compbio/ws/server/MuscleWS.html#getPresets()">getPresets</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>&lt;<A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>MafftWS.</B><B><A HREF="../../../compbio/ws/server/MafftWS.html#getPresets()">getPresets</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>&lt;<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>ClustalWS.</B><B><A HREF="../../../compbio/ws/server/ClustalWS.html#getPresets()">getPresets</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
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-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
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-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/metadata/\class-usePresetManager.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="PresetManager.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/metadata/class-use/ResultNotAvailableException.html b/website/full_javadoc/compbio/metadata/class-use/ResultNotAvailableException.html

deleted file mode 100644 (file)

index 2be5ac6..0000000
--- a/website/full_javadoc/compbio/metadata/class-use/ResultNotAvailableException.html
+++ /dev/null
@@ -1,532 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Uses of Class compbio.metadata.ResultNotAvailableException\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Uses of Class compbio.metadata.ResultNotAvailableException";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
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-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/metadata/\class-useResultNotAvailableException.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="ResultNotAvailableException.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
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-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
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-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-<B>Uses of Class<br>compbio.metadata.ResultNotAvailableException</B></H2>\r
-</CENTER>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Packages that use <A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.data.msa"><B>compbio.data.msa</B></A></TD>\r
-<TD>&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.engine"><B>compbio.engine</B></A></TD>\r
-<TD>&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.engine.client"><B>compbio.engine.client</B></A></TD>\r
-<TD>Classes and interfaces representing an input for engines.&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.engine.cluster.drmaa"><B>compbio.engine.cluster.drmaa</B></A></TD>\r
-<TD>An cluster engine classes responsible for execution of Executables on the clusters.&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.engine.local"><B>compbio.engine.local</B></A></TD>\r
-<TD>An local engine classes responsible for execution of Executables on the local computer 
- (the same machine as JVM running these classes).&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.runner.msa"><B>compbio.runner.msa</B></A></TD>\r
-<TD>Wrappers for native executables for multiple sequence alignment (msa)&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.runner.psiblast"><B>compbio.runner.psiblast</B></A></TD>\r
-<TD>&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.ws.server"><B>compbio.ws.server</B></A></TD>\r
-<TD>&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.data.msa"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A> in <A HREF="../../../compbio/data/msa/package-summary.html">compbio.data.msa</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/data/msa/package-summary.html">compbio.data.msa</A> that throw <A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
-<TD><CODE><B>MsaWS.</B><B><A HREF="../../../compbio/data/msa/MsaWS.html#getResult(java.lang.String)">getResult</A></B>(java.lang.String&nbsp;jobId)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Return the result of the job.</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.engine"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A> in <A HREF="../../../compbio/engine/package-summary.html">compbio.engine</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/engine/package-summary.html">compbio.engine</A> that throw <A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>AsyncExecutor.</B><B><A HREF="../../../compbio/engine/AsyncExecutor.html#getResults(java.lang.String)">getResults</A></B>(java.lang.String&nbsp;jobId)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Retrieve the results of the job.</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.engine.client"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A> in <A HREF="../../../compbio/engine/client/package-summary.html">compbio.engine.client</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/engine/client/package-summary.html">compbio.engine.client</A> that throw <A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
-<TR ALIGN="right" VALIGN="">\r
-<TD NOWRAP><FONT SIZE="-1">\r
-<CODE>&lt;V&gt; V</CODE></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-</CODE></FONT></TD>\r
-<TD><CODE><B>ConfiguredExecutable.</B><B><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html#getResults()">getResults</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
-<TR ALIGN="right" VALIGN="">\r
-<TD NOWRAP><FONT SIZE="-1">\r
-<CODE>&lt;V&gt; V</CODE></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-</CODE></FONT></TD>\r
-<TD><CODE><B>ConfExecutable.</B><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getResults()">getResults</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
-<TR ALIGN="right" VALIGN="">\r
-<TD NOWRAP><FONT SIZE="-1">\r
-<CODE>&lt;V&gt; V</CODE></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-</CODE></FONT></TD>\r
-<TD><CODE><B>Executable.</B><B><A HREF="../../../compbio/engine/client/Executable.html#getResults(java.lang.String)">getResults</A></B>(java.lang.String&nbsp;directory)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
-<TR ALIGN="right" VALIGN="">\r
-<TD NOWRAP><FONT SIZE="-1">\r
-<CODE>&lt;V&gt; V</CODE></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-</CODE></FONT></TD>\r
-<TD><CODE><B>ConfExecutable.</B><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getResults(java.lang.String)">getResults</A></B>(java.lang.String&nbsp;directory)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>Util.</B><B><A HREF="../../../compbio/engine/client/Util.html#loadExecutable(java.lang.String)">loadExecutable</A></B>(java.lang.String&nbsp;taskId)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.engine.cluster.drmaa"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A> in <A HREF="../../../compbio/engine/cluster/drmaa/package-summary.html">compbio.engine.cluster.drmaa</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/engine/cluster/drmaa/package-summary.html">compbio.engine.cluster.drmaa</A> that throw <A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>ClusterSession.</B><B><A HREF="../../../compbio/engine/cluster/drmaa/ClusterSession.html#getResults(java.lang.String)">getResults</A></B>(java.lang.String&nbsp;taskId)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>AsyncJobRunner.</B><B><A HREF="../../../compbio/engine/cluster/drmaa/AsyncJobRunner.html#getResults(java.lang.String)">getResults</A></B>(java.lang.String&nbsp;jobId)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.engine.local"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A> in <A HREF="../../../compbio/engine/local/package-summary.html">compbio.engine.local</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/engine/local/package-summary.html">compbio.engine.local</A> that throw <A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>LocalEngineUtil.</B><B><A HREF="../../../compbio/engine/local/LocalEngineUtil.html#getResults(java.util.concurrent.Future, java.lang.String)">getResults</A></B>(java.util.concurrent.Future&lt;<A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&gt;&nbsp;future,\r
-           java.lang.String&nbsp;taskId)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>AsyncLocalRunner.</B><B><A HREF="../../../compbio/engine/local/AsyncLocalRunner.html#getResults(java.lang.String)">getResults</A></B>(java.lang.String&nbsp;taskId)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.runner.msa"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A> in <A HREF="../../../compbio/runner/msa/package-summary.html">compbio.runner.msa</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/runner/msa/package-summary.html">compbio.runner.msa</A> that throw <A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
-<TD><CODE><B>Tcoffee.</B><B><A HREF="../../../compbio/runner/msa/Tcoffee.html#getResults(java.lang.String)">getResults</A></B>(java.lang.String&nbsp;workDirectory)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
-<TD><CODE><B>ClustalW.</B><B><A HREF="../../../compbio/runner/msa/ClustalW.html#getResults(java.lang.String)">getResults</A></B>(java.lang.String&nbsp;workDirectory)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
-<TD><CODE><B>Probcons.</B><B><A HREF="../../../compbio/runner/msa/Probcons.html#getResults(java.lang.String)">getResults</A></B>(java.lang.String&nbsp;workDirectory)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
-<TD><CODE><B>Muscle.</B><B><A HREF="../../../compbio/runner/msa/Muscle.html#getResults(java.lang.String)">getResults</A></B>(java.lang.String&nbsp;workDirectory)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
-<TD><CODE><B>Mafft.</B><B><A HREF="../../../compbio/runner/msa/Mafft.html#getResults(java.lang.String)">getResults</A></B>(java.lang.String&nbsp;workDirectory)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.runner.psiblast"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A> in <A HREF="../../../compbio/runner/psiblast/package-summary.html">compbio.runner.psiblast</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/runner/psiblast/package-summary.html">compbio.runner.psiblast</A> that throw <A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
-<TR ALIGN="right" VALIGN="">\r
-<TD NOWRAP><FONT SIZE="-1">\r
-<CODE>&lt;V&gt; V</CODE></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-</CODE></FONT></TD>\r
-<TD><CODE><B>PsiBlast.</B><B><A HREF="../../../compbio/runner/psiblast/PsiBlast.html#getResults(java.lang.String)">getResults</A></B>(java.lang.String&nbsp;directory)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.ws.server"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A> in <A HREF="../../../compbio/ws/server/package-summary.html">compbio.ws.server</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/ws/server/package-summary.html">compbio.ws.server</A> that throw <A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
-<TD><CODE><B>TcoffeeWS.</B><B><A HREF="../../../compbio/ws/server/TcoffeeWS.html#getResult(java.lang.String)">getResult</A></B>(java.lang.String&nbsp;jobId)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
-<TD><CODE><B>ProbconsWS.</B><B><A HREF="../../../compbio/ws/server/ProbconsWS.html#getResult(java.lang.String)">getResult</A></B>(java.lang.String&nbsp;jobId)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
-<TD><CODE><B>MuscleWS.</B><B><A HREF="../../../compbio/ws/server/MuscleWS.html#getResult(java.lang.String)">getResult</A></B>(java.lang.String&nbsp;jobId)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
-<TD><CODE><B>MafftWS.</B><B><A HREF="../../../compbio/ws/server/MafftWS.html#getResult(java.lang.String)">getResult</A></B>(java.lang.String&nbsp;jobId)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
-<TD><CODE><B>ClustalWS.</B><B><A HREF="../../../compbio/ws/server/ClustalWS.html#getResult(java.lang.String)">getResult</A></B>(java.lang.String&nbsp;jobId)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/metadata/\class-useResultNotAvailableException.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="ResultNotAvailableException.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/metadata/class-use/RunnerConfig.html b/website/full_javadoc/compbio/metadata/class-use/RunnerConfig.html

deleted file mode 100644 (file)

index 26548ba..0000000
--- a/website/full_javadoc/compbio/metadata/class-use/RunnerConfig.html
+++ /dev/null
@@ -1,452 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Uses of Class compbio.metadata.RunnerConfig\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Uses of Class compbio.metadata.RunnerConfig";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/metadata/\class-useRunnerConfig.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="RunnerConfig.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-<B>Uses of Class<br>compbio.metadata.RunnerConfig</B></H2>\r
-</CENTER>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Packages that use <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.data.msa"><B>compbio.data.msa</B></A></TD>\r
-<TD>&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.data.msa.jaxws"><B>compbio.data.msa.jaxws</B></A></TD>\r
-<TD>&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.engine.client"><B>compbio.engine.client</B></A></TD>\r
-<TD>Classes and interfaces representing an input for engines.&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.metadata"><B>compbio.metadata</B></A></TD>\r
-<TD>A meta-data model for multiple sequence alignment web services 
- Classes in this package have no dependencies to other sources in the project.&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.runner"><B>compbio.runner</B></A></TD>\r
-<TD>Utilities commonly used by all runners.&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.ws.server"><B>compbio.ws.server</B></A></TD>\r
-<TD>&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.data.msa"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A> in <A HREF="../../../compbio/data/msa/package-summary.html">compbio.data.msa</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/data/msa/package-summary.html">compbio.data.msa</A> that return <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&lt;<A HREF="../../../compbio/data/msa/MsaWS.html" title="type parameter in MsaWS">T</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>MsaWS.</B><B><A HREF="../../../compbio/data/msa/MsaWS.html#getRunnerOptions()">getRunnerOptions</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Get options supported by a web service</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.data.msa.jaxws"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A> in <A HREF="../../../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A> that return <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A></CODE></FONT></TD>\r
-<TD><CODE><B>GetRunnerOptionsResponse.</B><B><A HREF="../../../compbio/data/msa/jaxws/GetRunnerOptionsResponse.html#getReturn()">getReturn</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A> with parameters of type <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B>GetRunnerOptionsResponse.</B><B><A HREF="../../../compbio/data/msa/jaxws/GetRunnerOptionsResponse.html#setReturn(compbio.metadata.RunnerConfig)">setReturn</A></B>(<A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&nbsp;_return)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.engine.client"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A> in <A HREF="../../../compbio/engine/client/package-summary.html">compbio.engine.client</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/engine/client/package-summary.html">compbio.engine.client</A> that return <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
-<TR ALIGN="right" VALIGN="">\r
-<TD NOWRAP><FONT SIZE="-1">\r
-<CODE>&lt;V&gt; <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&lt;V&gt;</CODE></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-</CODE></FONT></TD>\r
-<TD><CODE><B>ConfExecutable.</B><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getRunnerOptions(java.lang.Class)">getRunnerOptions</A></B>(java.lang.Class&lt;? extends <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;V&gt;&gt;&nbsp;clazz)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.metadata"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A> in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A> that return <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&lt;<A HREF="../../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>RunnerConfig.</B><B><A HREF="../../../compbio/metadata/RunnerConfig.html#copyAndValidateRConfig(compbio.metadata.RunnerConfig)">copyAndValidateRConfig</A></B>(<A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&lt;?&gt;&nbsp;runnerConf)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A> with parameters of type <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&lt;<A HREF="../../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>RunnerConfig.</B><B><A HREF="../../../compbio/metadata/RunnerConfig.html#copyAndValidateRConfig(compbio.metadata.RunnerConfig)">copyAndValidateRConfig</A></B>(<A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&lt;?&gt;&nbsp;runnerConf)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.util.List&lt;<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../compbio/metadata/Preset.html" title="type parameter in Preset">T</A>&gt;&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>Preset.</B><B><A HREF="../../../compbio/metadata/Preset.html#getArguments(compbio.metadata.RunnerConfig)">getArguments</A></B>(<A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&lt;<A HREF="../../../compbio/metadata/Preset.html" title="type parameter in Preset">T</A>&gt;&nbsp;rconfig)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Converts list of options as String to type Option</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B>PresetManager.</B><B><A HREF="../../../compbio/metadata/PresetManager.html#validate(compbio.metadata.RunnerConfig)">validate</A></B>(<A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&lt;<A HREF="../../../compbio/metadata/PresetManager.html" title="type parameter in PresetManager">T</A>&gt;&nbsp;options)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Checks whether preset option and parameter are defined in RunnerConfig
- object.</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.runner"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A> in <A HREF="../../../compbio/runner/package-summary.html">compbio.runner</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/runner/package-summary.html">compbio.runner</A> that return <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
-<TR ALIGN="right" VALIGN="">\r
-<TD NOWRAP><FONT SIZE="-1">\r
-<CODE>&lt;T&gt; <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&lt;T&gt;</CODE></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-</CODE></FONT></TD>\r
-<TD><CODE><B>Util.</B><B><A HREF="../../../compbio/runner/Util.html#getSupportedOptions(java.lang.Class)">getSupportedOptions</A></B>(java.lang.Class&lt;? extends <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;T&gt;&gt;&nbsp;clazz)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/runner/package-summary.html">compbio.runner</A> with parameters of type <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;java.util.List&lt;java.lang.String&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>OptionCombinator.</B><B><A HREF="../../../compbio/runner/OptionCombinator.html#argumentsToCommandString(java.util.List, compbio.metadata.RunnerConfig)">argumentsToCommandString</A></B>(java.util.List&lt;? extends <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;?&gt;&gt;&nbsp;arguments,\r
-                         <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&lt;? extends <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;?&gt;&gt;&nbsp;rconfig)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Constructors in <A HREF="../../../compbio/runner/package-summary.html">compbio.runner</A> with parameters of type <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/runner/OptionCombinator.html#OptionCombinator(compbio.metadata.RunnerConfig)">OptionCombinator</A></B>(<A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&lt;? extends <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;?&gt;&gt;&nbsp;rconfig)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.ws.server"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A> in <A HREF="../../../compbio/ws/server/package-summary.html">compbio.ws.server</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/ws/server/package-summary.html">compbio.ws.server</A> that return <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&lt;<A HREF="../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>TcoffeeWS.</B><B><A HREF="../../../compbio/ws/server/TcoffeeWS.html#getRunnerOptions()">getRunnerOptions</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&lt;<A HREF="../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>ProbconsWS.</B><B><A HREF="../../../compbio/ws/server/ProbconsWS.html#getRunnerOptions()">getRunnerOptions</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&lt;<A HREF="../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>MuscleWS.</B><B><A HREF="../../../compbio/ws/server/MuscleWS.html#getRunnerOptions()">getRunnerOptions</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&lt;<A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>MafftWS.</B><B><A HREF="../../../compbio/ws/server/MafftWS.html#getRunnerOptions()">getRunnerOptions</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&lt;<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>ClustalWS.</B><B><A HREF="../../../compbio/ws/server/ClustalWS.html#getRunnerOptions()">getRunnerOptions</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/metadata/\class-useRunnerConfig.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="RunnerConfig.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/metadata/class-use/UnsupportedRuntimeException.html b/website/full_javadoc/compbio/metadata/class-use/UnsupportedRuntimeException.html

deleted file mode 100644 (file)

index 5c58046..0000000
--- a/website/full_javadoc/compbio/metadata/class-use/UnsupportedRuntimeException.html
+++ /dev/null
@@ -1,227 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Uses of Class compbio.metadata.UnsupportedRuntimeException\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Uses of Class compbio.metadata.UnsupportedRuntimeException";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/metadata/\class-useUnsupportedRuntimeException.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="UnsupportedRuntimeException.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-<B>Uses of Class<br>compbio.metadata.UnsupportedRuntimeException</B></H2>\r
-</CENTER>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Packages that use <A HREF="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.data.msa"><B>compbio.data.msa</B></A></TD>\r
-<TD>&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.engine.client"><B>compbio.engine.client</B></A></TD>\r
-<TD>Classes and interfaces representing an input for engines.&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.data.msa"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A> in <A HREF="../../../compbio/data/msa/package-summary.html">compbio.data.msa</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/data/msa/package-summary.html">compbio.data.msa</A> that throw <A HREF="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B>MsaWS.</B><B><A HREF="../../../compbio/data/msa/MsaWS.html#align(java.util.List)">align</A></B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Align a list of sequences with default settings.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B>MsaWS.</B><B><A HREF="../../../compbio/data/msa/MsaWS.html#customAlign(java.util.List, java.util.List)">customAlign</A></B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-            java.util.List&lt;<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../compbio/data/msa/MsaWS.html" title="type parameter in MsaWS">T</A>&gt;&gt;&nbsp;options)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Align a list of sequences with options.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B>MsaWS.</B><B><A HREF="../../../compbio/data/msa/MsaWS.html#presetAlign(java.util.List, compbio.metadata.Preset)">presetAlign</A></B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-            <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>&lt;<A HREF="../../../compbio/data/msa/MsaWS.html" title="type parameter in MsaWS">T</A>&gt;&nbsp;preset)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Align a list of sequences with preset.</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.engine.client"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A> in <A HREF="../../../compbio/engine/client/package-summary.html">compbio.engine.client</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/engine/client/package-summary.html">compbio.engine.client</A> that throw <A HREF="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B>ConfExecutable.</B><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getCommand(compbio.engine.client.Executable.ExecProvider)">getCommand</A></B>(<A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/metadata/\class-useUnsupportedRuntimeException.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="UnsupportedRuntimeException.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/metadata/class-use/ValueConstrain.Type.html b/website/full_javadoc/compbio/metadata/class-use/ValueConstrain.Type.html

deleted file mode 100644 (file)

index 41624ef..0000000
--- a/website/full_javadoc/compbio/metadata/class-use/ValueConstrain.Type.html
+++ /dev/null
@@ -1,214 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Uses of Class compbio.metadata.ValueConstrain.Type\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Uses of Class compbio.metadata.ValueConstrain.Type";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../compbio/metadata/ValueConstrain.Type.html" title="enum in compbio.metadata"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
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-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/metadata/\class-useValueConstrain.Type.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="ValueConstrain.Type.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-<B>Uses of Class<br>compbio.metadata.ValueConstrain.Type</B></H2>\r
-</CENTER>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Packages that use <A HREF="../../../compbio/metadata/ValueConstrain.Type.html" title="enum in compbio.metadata">ValueConstrain.Type</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.metadata"><B>compbio.metadata</B></A></TD>\r
-<TD>A meta-data model for multiple sequence alignment web services 
- Classes in this package have no dependencies to other sources in the project.&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.metadata"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../compbio/metadata/ValueConstrain.Type.html" title="enum in compbio.metadata">ValueConstrain.Type</A> in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A> that return <A HREF="../../../compbio/metadata/ValueConstrain.Type.html" title="enum in compbio.metadata">ValueConstrain.Type</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/ValueConstrain.Type.html" title="enum in compbio.metadata">ValueConstrain.Type</A></CODE></FONT></TD>\r
-<TD><CODE><B>ValueConstrain.</B><B><A HREF="../../../compbio/metadata/ValueConstrain.html#getType()">getType</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../compbio/metadata/ValueConstrain.Type.html" title="enum in compbio.metadata">ValueConstrain.Type</A></CODE></FONT></TD>\r
-<TD><CODE><B>ValueConstrain.Type.</B><B><A HREF="../../../compbio/metadata/ValueConstrain.Type.html#valueOf(java.lang.String)">valueOf</A></B>(java.lang.String&nbsp;name)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Returns the enum constant of this type with the specified name.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../compbio/metadata/ValueConstrain.Type.html" title="enum in compbio.metadata">ValueConstrain.Type</A>[]</CODE></FONT></TD>\r
-<TD><CODE><B>ValueConstrain.Type.</B><B><A HREF="../../../compbio/metadata/ValueConstrain.Type.html#values()">values</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Returns an array containing the constants of this enum type, in
-the order they are declared.</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A> with parameters of type <A HREF="../../../compbio/metadata/ValueConstrain.Type.html" title="enum in compbio.metadata">ValueConstrain.Type</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B>ValueConstrain.</B><B><A HREF="../../../compbio/metadata/ValueConstrain.html#setType(compbio.metadata.ValueConstrain.Type)">setType</A></B>(<A HREF="../../../compbio/metadata/ValueConstrain.Type.html" title="enum in compbio.metadata">ValueConstrain.Type</A>&nbsp;type)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../compbio/metadata/ValueConstrain.Type.html" title="enum in compbio.metadata"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/metadata/\class-useValueConstrain.Type.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="ValueConstrain.Type.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/metadata/class-use/ValueConstrain.html b/website/full_javadoc/compbio/metadata/class-use/ValueConstrain.html

deleted file mode 100644 (file)

index 7c8825a..0000000
--- a/website/full_javadoc/compbio/metadata/class-use/ValueConstrain.html
+++ /dev/null
@@ -1,197 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Uses of Class compbio.metadata.ValueConstrain\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Uses of Class compbio.metadata.ValueConstrain";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/metadata/\class-useValueConstrain.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="ValueConstrain.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-<B>Uses of Class<br>compbio.metadata.ValueConstrain</B></H2>\r
-</CENTER>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Packages that use <A HREF="../../../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.metadata"><B>compbio.metadata</B></A></TD>\r
-<TD>A meta-data model for multiple sequence alignment web services 
- Classes in this package have no dependencies to other sources in the project.&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.metadata"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A> in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A> that return <A HREF="../../../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A></CODE></FONT></TD>\r
-<TD><CODE><B>Parameter.</B><B><A HREF="../../../compbio/metadata/Parameter.html#getValidValue()">getValidValue</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A> with parameters of type <A HREF="../../../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B>Parameter.</B><B><A HREF="../../../compbio/metadata/Parameter.html#setValidValue(compbio.metadata.ValueConstrain)">setValidValue</A></B>(<A HREF="../../../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A>&nbsp;validValue)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
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-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/metadata/\class-useValueConstrain.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="ValueConstrain.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
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-</FONT></TD>\r
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-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
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diff --git a/website/full_javadoc/compbio/metadata/class-use/WrongParameterException.html b/website/full_javadoc/compbio/metadata/class-use/WrongParameterException.html

deleted file mode 100644 (file)

index 72f6664..0000000
--- a/website/full_javadoc/compbio/metadata/class-use/WrongParameterException.html
+++ /dev/null
@@ -1,363 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Uses of Class compbio.metadata.WrongParameterException\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
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-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Uses of Class compbio.metadata.WrongParameterException";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
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-  </TR>\r
-</TABLE>\r
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-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
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-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/metadata/\class-useWrongParameterException.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="WrongParameterException.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
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-  if(window==top) {\r
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-  }\r
-  //-->\r
-</SCRIPT>\r
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-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
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-\r
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-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-<B>Uses of Class<br>compbio.metadata.WrongParameterException</B></H2>\r
-</CENTER>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Packages that use <A HREF="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.data.msa"><B>compbio.data.msa</B></A></TD>\r
-<TD>&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.metadata"><B>compbio.metadata</B></A></TD>\r
-<TD>A meta-data model for multiple sequence alignment web services 
- Classes in this package have no dependencies to other sources in the project.&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.ws.server"><B>compbio.ws.server</B></A></TD>\r
-<TD>&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.data.msa"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A> in <A HREF="../../../compbio/data/msa/package-summary.html">compbio.data.msa</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/data/msa/package-summary.html">compbio.data.msa</A> that throw <A HREF="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B>MsaWS.</B><B><A HREF="../../../compbio/data/msa/MsaWS.html#customAlign(java.util.List, java.util.List)">customAlign</A></B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-            java.util.List&lt;<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../compbio/data/msa/MsaWS.html" title="type parameter in MsaWS">T</A>&gt;&gt;&nbsp;options)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Align a list of sequences with options.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B>MsaWS.</B><B><A HREF="../../../compbio/data/msa/MsaWS.html#presetAlign(java.util.List, compbio.metadata.Preset)">presetAlign</A></B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-            <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>&lt;<A HREF="../../../compbio/data/msa/MsaWS.html" title="type parameter in MsaWS">T</A>&gt;&nbsp;preset)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Align a list of sequences with preset.</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.metadata"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A> in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A> that throw <A HREF="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.util.List&lt;<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../compbio/metadata/Preset.html" title="type parameter in Preset">T</A>&gt;&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>Preset.</B><B><A HREF="../../../compbio/metadata/Preset.html#getArguments(compbio.metadata.RunnerConfig)">getArguments</A></B>(<A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&lt;<A HREF="../../../compbio/metadata/Preset.html" title="type parameter in Preset">T</A>&gt;&nbsp;rconfig)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Converts list of options as String to type Option</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B>Parameter.</B><B><A HREF="../../../compbio/metadata/Parameter.html#setDefaultValue(java.lang.String)">setDefaultValue</A></B>(java.lang.String&nbsp;defaultVal)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B>Option.</B><B><A HREF="../../../compbio/metadata/Option.html#setDefaultValue(java.lang.String)">setDefaultValue</A></B>(java.lang.String&nbsp;defaultVal)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Sets one of the values defined in optionList as default.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B>Argument.</B><B><A HREF="../../../compbio/metadata/Argument.html#setValue(java.lang.String)">setValue</A></B>(java.lang.String&nbsp;defaultValue)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Set default values for the parameter or an option</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B>Option.</B><B><A HREF="../../../compbio/metadata/Option.html#setValue(java.lang.String)">setValue</A></B>(java.lang.String&nbsp;dValue)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.ws.server"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A> in <A HREF="../../../compbio/ws/server/package-summary.html">compbio.ws.server</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/ws/server/package-summary.html">compbio.ws.server</A> that throw <A HREF="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B>ClustalWS.</B><B><A HREF="../../../compbio/ws/server/ClustalWS.html#customAlign(java.util.List, java.util.List)">customAlign</A></B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-            java.util.List&lt;<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>&gt;&gt;&nbsp;options)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B>MafftWS.</B><B><A HREF="../../../compbio/ws/server/MafftWS.html#customAlign(java.util.List, java.util.List)">customAlign</A></B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-            java.util.List&lt;<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>&gt;&gt;&nbsp;options)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B>MuscleWS.</B><B><A HREF="../../../compbio/ws/server/MuscleWS.html#customAlign(java.util.List, java.util.List)">customAlign</A></B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-            java.util.List&lt;<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>&gt;&gt;&nbsp;options)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B>ProbconsWS.</B><B><A HREF="../../../compbio/ws/server/ProbconsWS.html#customAlign(java.util.List, java.util.List)">customAlign</A></B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-            java.util.List&lt;<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>&gt;&gt;&nbsp;options)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B>TcoffeeWS.</B><B><A HREF="../../../compbio/ws/server/TcoffeeWS.html#customAlign(java.util.List, java.util.List)">customAlign</A></B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-            java.util.List&lt;<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>&gt;&gt;&nbsp;options)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B>ClustalWS.</B><B><A HREF="../../../compbio/ws/server/ClustalWS.html#presetAlign(java.util.List, compbio.metadata.Preset)">presetAlign</A></B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-            <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>&lt;<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>&gt;&nbsp;preset)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B>MafftWS.</B><B><A HREF="../../../compbio/ws/server/MafftWS.html#presetAlign(java.util.List, compbio.metadata.Preset)">presetAlign</A></B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-            <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>&lt;<A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>&gt;&nbsp;preset)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B>MuscleWS.</B><B><A HREF="../../../compbio/ws/server/MuscleWS.html#presetAlign(java.util.List, compbio.metadata.Preset)">presetAlign</A></B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-            <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>&lt;<A HREF="../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>&gt;&nbsp;preset)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B>ProbconsWS.</B><B><A HREF="../../../compbio/ws/server/ProbconsWS.html#presetAlign(java.util.List, compbio.metadata.Preset)">presetAlign</A></B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-            <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>&lt;<A HREF="../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>&gt;&nbsp;preset)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B>TcoffeeWS.</B><B><A HREF="../../../compbio/ws/server/TcoffeeWS.html#presetAlign(java.util.List, compbio.metadata.Preset)">presetAlign</A></B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-            <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>&lt;<A HREF="../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>&gt;&nbsp;preset)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/metadata/\class-useWrongParameterException.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="WrongParameterException.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/metadata/package-frame.html b/website/full_javadoc/compbio/metadata/package-frame.html

deleted file mode 100644 (file)

index 1739396..0000000
--- a/website/full_javadoc/compbio/metadata/package-frame.html
+++ /dev/null
@@ -1,93 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-compbio.metadata\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../stylesheet.css" TITLE="Style">\r
-\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white">\r
-<FONT size="+1" CLASS="FrameTitleFont">\r
-<A HREF="../../compbio/metadata/package-summary.html" target="classFrame">compbio.metadata</A></FONT>\r
-<TABLE BORDER="0" WIDTH="100%" SUMMARY="">\r
-<TR>\r
-<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">\r
-Interfaces</FONT>&nbsp;\r
-<FONT CLASS="FrameItemFont">\r
-<BR>\r
-<A HREF="Argument.html" title="interface in compbio.metadata" target="classFrame"><I>Argument</I></A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-\r
-\r
-<TABLE BORDER="0" WIDTH="100%" SUMMARY="">\r
-<TR>\r
-<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">\r
-Classes</FONT>&nbsp;\r
-<FONT CLASS="FrameItemFont">\r
-<BR>\r
-<A HREF="ChunkHolder.html" title="class in compbio.metadata" target="classFrame">ChunkHolder</A>\r
-<BR>\r
-<A HREF="Limit.html" title="class in compbio.metadata" target="classFrame">Limit</A>\r
-<BR>\r
-<A HREF="LimitsManager.html" title="class in compbio.metadata" target="classFrame">LimitsManager</A>\r
-<BR>\r
-<A HREF="Option.html" title="class in compbio.metadata" target="classFrame">Option</A>\r
-<BR>\r
-<A HREF="Parameter.html" title="class in compbio.metadata" target="classFrame">Parameter</A>\r
-<BR>\r
-<A HREF="Preset.html" title="class in compbio.metadata" target="classFrame">Preset</A>\r
-<BR>\r
-<A HREF="PresetManager.html" title="class in compbio.metadata" target="classFrame">PresetManager</A>\r
-<BR>\r
-<A HREF="RunnerConfig.html" title="class in compbio.metadata" target="classFrame">RunnerConfig</A>\r
-<BR>\r
-<A HREF="ValueConstrain.html" title="class in compbio.metadata" target="classFrame">ValueConstrain</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-\r
-\r
-<TABLE BORDER="0" WIDTH="100%" SUMMARY="">\r
-<TR>\r
-<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">\r
-Enums</FONT>&nbsp;\r
-<FONT CLASS="FrameItemFont">\r
-<BR>\r
-<A HREF="JobStatus.html" title="enum in compbio.metadata" target="classFrame">JobStatus</A>\r
-<BR>\r
-<A HREF="ValueConstrain.Type.html" title="enum in compbio.metadata" target="classFrame">ValueConstrain.Type</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-\r
-\r
-<TABLE BORDER="0" WIDTH="100%" SUMMARY="">\r
-<TR>\r
-<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">\r
-Exceptions</FONT>&nbsp;\r
-<FONT CLASS="FrameItemFont">\r
-<BR>\r
-<A HREF="JobExecutionException.html" title="class in compbio.metadata" target="classFrame">JobExecutionException</A>\r
-<BR>\r
-<A HREF="JobSubmissionException.html" title="class in compbio.metadata" target="classFrame">JobSubmissionException</A>\r
-<BR>\r
-<A HREF="LimitExceededException.html" title="class in compbio.metadata" target="classFrame">LimitExceededException</A>\r
-<BR>\r
-<A HREF="ResultNotAvailableException.html" title="class in compbio.metadata" target="classFrame">ResultNotAvailableException</A>\r
-<BR>\r
-<A HREF="UnsupportedRuntimeException.html" title="class in compbio.metadata" target="classFrame">UnsupportedRuntimeException</A>\r
-<BR>\r
-<A HREF="WrongParameterException.html" title="class in compbio.metadata" target="classFrame">WrongParameterException</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/metadata/package-summary.html b/website/full_javadoc/compbio/metadata/package-summary.html

deleted file mode 100644 (file)

index 5f5b66b..0000000
--- a/website/full_javadoc/compbio/metadata/package-summary.html
+++ /dev/null
@@ -1,286 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-compbio.metadata\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="compbio.metadata";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Class</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-use.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../compbio/engine/local/package-summary.html"><B>PREV PACKAGE</B></A>&nbsp;\r
-&nbsp;<A HREF="../../compbio/pipeline/_jpred/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../index.html?compbio/metadata/package-summary.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="package-summary.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<H2>\r
-Package compbio.metadata\r
-</H2>\r
-A meta-data model for multiple sequence alignment web services 
- Classes in this package have no dependencies to other sources in the project.\r
-<P>\r
-<B>See:</B>\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<A HREF="#package_description"><B>Description</B></A>\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Interface Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument&lt;T&gt;</A></B></TD>\r
-<TD>An unmodifiable view for the options and parameters, with one exception - it
- allows to set a value</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Class Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A></B></TD>\r
-<TD>Represents a chunk of string data together with the position in a file from
- where corresponding to of the data.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit&lt;T&gt;</A></B></TD>\r
-<TD>A value object containing a maximum number of sequences and a maximum average
- sequence length for a preset.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager&lt;T&gt;</A></B></TD>\r
-<TD>A collection of Limits</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option&lt;T&gt;</A></B></TD>\r
-<TD>Command line option/flag or multiple exclusive options with no value.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter&lt;T&gt;</A></B></TD>\r
-<TD>A single value containing option supported by the web service e.g.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset&lt;T&gt;</A></B></TD>\r
-<TD>Collection of Options and Parameters with their values</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager&lt;T&gt;</A></B></TD>\r
-<TD>Collection of presets and methods to manipulate them @see <A HREF="../../compbio/metadata/Preset.html" title="class in compbio.metadata"><CODE>Preset</CODE></A></TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig&lt;T&gt;</A></B></TD>\r
-<TD>The list of <A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata"><CODE>Parameter</CODE></A>s and <A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata"><CODE>Option</CODE></A>s supported by executable.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A></B></TD>\r
-<TD>The type and the lower and upper boundaries for numerical value.</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Enum Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A></B></TD>\r
-<TD>The status of the job.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../compbio/metadata/ValueConstrain.Type.html" title="enum in compbio.metadata">ValueConstrain.Type</A></B></TD>\r
-<TD>&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Exception Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../compbio/metadata/JobExecutionException.html" title="class in compbio.metadata">JobExecutionException</A></B></TD>\r
-<TD>JobExecutionException is thrown wherever the results of the calculation
- cannot be obtained.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></B></TD>\r
-<TD>Exception for generic problems with JobSubmission it is often thrown as a
- wrapper for the lower level exceptions like IOException or DrmaaException.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A></B></TD>\r
-<TD>Thrown if the task larger in size that the limit that applies to the
- calculation.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></B></TD>\r
-<TD>ResultNotAvailableException is thrown wherever the results of the calculation
- cannot be obtained.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A></B></TD>\r
-<TD>Indicates that the server could not execute native executables.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></B></TD>\r
-<TD>WrongParameterException is thrown wherever the <A HREF="../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata"><CODE>RunnerConfig</CODE></A> object
- does not match the actual runnable or then attempting to set the value of
- <A HREF="../../compbio/metadata/Argument.html" title="interface in compbio.metadata"><CODE>Argument</CODE></A> to invalid value.</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-\r
-<P>\r
-<A NAME="package_description"><!-- --></A><H2>\r
-Package compbio.metadata Description\r
-</H2>\r
-\r
-<P>\r
-A meta-data model for multiple sequence alignment web services 
- Classes in this package have no dependencies to other sources in the project. 
- They form a base layer of Jalview Web Services v2.\r
-<P>\r
-\r
-<P>\r
-<DL>\r
-<DT><B>Author:</B></DT>\r
-  <DD>Petr Troshin 
- 
-        Date January 2010</DD>\r
-</DL>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
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-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
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-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
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-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
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-  <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>\r
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-\r
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-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
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diff --git a/website/full_javadoc/compbio/metadata/package-tree.html b/website/full_javadoc/compbio/metadata/package-tree.html

deleted file mode 100644 (file)

index 3d95bb3..0000000
--- a/website/full_javadoc/compbio/metadata/package-tree.html
+++ /dev/null
@@ -1,178 +0,0 @@
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-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-compbio.metadata Class Hierarchy\r
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-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
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-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
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-<NOSCRIPT>\r
-</NOSCRIPT>\r
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-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
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-\r
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-<!-- ========= START OF TOP NAVBAR ======= -->\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Class</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Use</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
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-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../compbio/engine/local/package-tree.html"><B>PREV</B></A>&nbsp;\r
-&nbsp;<A HREF="../../compbio/pipeline/_jpred/package-tree.html"><B>NEXT</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../index.html?compbio/metadata/package-tree.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="package-tree.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-Hierarchy For Package compbio.metadata\r
-</H2>\r
-</CENTER>\r
-<DL>\r
-<DT><B>Package Hierarchies:</B><DD><A HREF="../../overview-tree.html">All Packages</A></DL>\r
-<HR>\r
-<H2>\r
-Class Hierarchy\r
-</H2>\r
-<UL>\r
-<LI TYPE="circle">java.lang.Object<UL>\r
-<LI TYPE="circle">compbio.metadata.<A HREF="../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata"><B>ChunkHolder</B></A><LI TYPE="circle">compbio.metadata.<A HREF="../../compbio/metadata/Limit.html" title="class in compbio.metadata"><B>Limit</B></A>&lt;T&gt;<LI TYPE="circle">compbio.metadata.<A HREF="../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata"><B>LimitsManager</B></A>&lt;T&gt;<LI TYPE="circle">compbio.metadata.<A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata"><B>Option</B></A>&lt;T&gt; (implements compbio.metadata.<A HREF="../../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</A>&lt;T&gt;)\r
-<UL>\r
-<LI TYPE="circle">compbio.metadata.<A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata"><B>Parameter</B></A>&lt;T&gt;</UL>\r
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-<UL>\r
-<LI TYPE="circle">java.lang.Exception<UL>\r
-<LI TYPE="circle">compbio.metadata.<A HREF="../../compbio/metadata/JobExecutionException.html" title="class in compbio.metadata"><B>JobExecutionException</B></A><LI TYPE="circle">compbio.metadata.<A HREF="../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata"><B>JobSubmissionException</B></A><UL>\r
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-<LI TYPE="circle">compbio.metadata.<A HREF="../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata"><B>ResultNotAvailableException</B></A><LI TYPE="circle">compbio.metadata.<A HREF="../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata"><B>WrongParameterException</B></A></UL>\r
-</UL>\r
-<LI TYPE="circle">compbio.metadata.<A HREF="../../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata"><B>ValueConstrain</B></A></UL>\r
-</UL>\r
-<H2>\r
-Interface Hierarchy\r
-</H2>\r
-<UL>\r
-<LI TYPE="circle">compbio.metadata.<A HREF="../../compbio/metadata/Argument.html" title="interface in compbio.metadata"><B>Argument</B></A>&lt;T&gt;</UL>\r
-<H2>\r
-Enum Hierarchy\r
-</H2>\r
-<UL>\r
-<LI TYPE="circle">java.lang.Object<UL>\r
-<LI TYPE="circle">java.lang.Enum&lt;E&gt; (implements java.lang.Comparable&lt;T&gt;, java.io.Serializable)\r
-<UL>\r
-<LI TYPE="circle">compbio.metadata.<A HREF="../../compbio/metadata/ValueConstrain.Type.html" title="enum in compbio.metadata"><B>ValueConstrain.Type</B></A><LI TYPE="circle">compbio.metadata.<A HREF="../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata"><B>JobStatus</B></A></UL>\r
-</UL>\r
-</UL>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Class</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Use</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
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-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../compbio/engine/local/package-tree.html"><B>PREV</B></A>&nbsp;\r
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-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
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-  <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>\r
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-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/metadata/package-use.html b/website/full_javadoc/compbio/metadata/package-use.html

deleted file mode 100644 (file)

index 25708de..0000000
--- a/website/full_javadoc/compbio/metadata/package-use.html
+++ /dev/null
@@ -1,842 +0,0 @@
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-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Uses of Package compbio.metadata\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Uses of Package compbio.metadata";\r
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-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Class</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
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-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
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-&nbsp;<A HREF="package-use.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
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-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
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-<HR>\r
-<CENTER>\r
-<H2>\r
-<B>Uses of Package<br>compbio.metadata</B></H2>\r
-</CENTER>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Packages that use <A HREF="../../compbio/metadata/package-summary.html">compbio.metadata</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.data.msa"><B>compbio.data.msa</B></A></TD>\r
-<TD>&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.data.msa.jaxws"><B>compbio.data.msa.jaxws</B></A></TD>\r
-<TD>&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.engine"><B>compbio.engine</B></A></TD>\r
-<TD>&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.engine.client"><B>compbio.engine.client</B></A></TD>\r
-<TD>Classes and interfaces representing an input for engines.&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.engine.cluster.drmaa"><B>compbio.engine.cluster.drmaa</B></A></TD>\r
-<TD>An cluster engine classes responsible for execution of Executables on the clusters.&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.engine.local"><B>compbio.engine.local</B></A></TD>\r
-<TD>An local engine classes responsible for execution of Executables on the local computer 
- (the same machine as JVM running these classes).&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.metadata"><B>compbio.metadata</B></A></TD>\r
-<TD>A meta-data model for multiple sequence alignment web services 
- Classes in this package have no dependencies to other sources in the project.&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.runner"><B>compbio.runner</B></A></TD>\r
-<TD>Utilities commonly used by all runners.&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.runner._impl"><B>compbio.runner._impl</B></A></TD>\r
-<TD>&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.runner.msa"><B>compbio.runner.msa</B></A></TD>\r
-<TD>Wrappers for native executables for multiple sequence alignment (msa)&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.runner.psiblast"><B>compbio.runner.psiblast</B></A></TD>\r
-<TD>&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.ws.server"><B>compbio.ws.server</B></A></TD>\r
-<TD>&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.data.msa"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Classes in <A HREF="../../compbio/metadata/package-summary.html">compbio.metadata</A> used by <A HREF="../../compbio/data/msa/package-summary.html">compbio.data.msa</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/metadata/class-use/ChunkHolder.html#compbio.data.msa"><B>ChunkHolder</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Represents a chunk of string data together with the position in a file from
- where corresponding to of the data.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/metadata/class-use/JobStatus.html#compbio.data.msa"><B>JobStatus</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The status of the job.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/metadata/class-use/JobSubmissionException.html#compbio.data.msa"><B>JobSubmissionException</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Exception for generic problems with JobSubmission it is often thrown as a
- wrapper for the lower level exceptions like IOException or DrmaaException.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/metadata/class-use/Limit.html#compbio.data.msa"><B>Limit</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;A value object containing a maximum number of sequences and a maximum average
- sequence length for a preset.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/metadata/class-use/LimitExceededException.html#compbio.data.msa"><B>LimitExceededException</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Thrown if the task larger in size that the limit that applies to the
- calculation.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/metadata/class-use/LimitsManager.html#compbio.data.msa"><B>LimitsManager</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;A collection of Limits</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/metadata/class-use/Option.html#compbio.data.msa"><B>Option</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Command line option/flag or multiple exclusive options with no value.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/metadata/class-use/Preset.html#compbio.data.msa"><B>Preset</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Collection of Options and Parameters with their values</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/metadata/class-use/PresetManager.html#compbio.data.msa"><B>PresetManager</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Collection of presets and methods to manipulate them @see <A HREF="../../compbio/metadata/Preset.html" title="class in compbio.metadata"><CODE>Preset</CODE></A></TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/metadata/class-use/ResultNotAvailableException.html#compbio.data.msa"><B>ResultNotAvailableException</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;ResultNotAvailableException is thrown wherever the results of the calculation
- cannot be obtained.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/metadata/class-use/RunnerConfig.html#compbio.data.msa"><B>RunnerConfig</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The list of <A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata"><CODE>Parameter</CODE></A>s and <A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata"><CODE>Option</CODE></A>s supported by executable.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/metadata/class-use/UnsupportedRuntimeException.html#compbio.data.msa"><B>UnsupportedRuntimeException</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Indicates that the server could not execute native executables.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/metadata/class-use/WrongParameterException.html#compbio.data.msa"><B>WrongParameterException</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;WrongParameterException is thrown wherever the <A HREF="../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata"><CODE>RunnerConfig</CODE></A> object
- does not match the actual runnable or then attempting to set the value of
- <A HREF="../../compbio/metadata/Argument.html" title="interface in compbio.metadata"><CODE>Argument</CODE></A> to invalid value.</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.data.msa.jaxws"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Classes in <A HREF="../../compbio/metadata/package-summary.html">compbio.metadata</A> used by <A HREF="../../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/metadata/class-use/ChunkHolder.html#compbio.data.msa.jaxws"><B>ChunkHolder</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Represents a chunk of string data together with the position in a file from
- where corresponding to of the data.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/metadata/class-use/JobStatus.html#compbio.data.msa.jaxws"><B>JobStatus</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The status of the job.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/metadata/class-use/Limit.html#compbio.data.msa.jaxws"><B>Limit</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;A value object containing a maximum number of sequences and a maximum average
- sequence length for a preset.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/metadata/class-use/LimitsManager.html#compbio.data.msa.jaxws"><B>LimitsManager</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;A collection of Limits</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/metadata/class-use/Option.html#compbio.data.msa.jaxws"><B>Option</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Command line option/flag or multiple exclusive options with no value.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/metadata/class-use/Preset.html#compbio.data.msa.jaxws"><B>Preset</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Collection of Options and Parameters with their values</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/metadata/class-use/PresetManager.html#compbio.data.msa.jaxws"><B>PresetManager</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Collection of presets and methods to manipulate them @see <A HREF="../../compbio/metadata/Preset.html" title="class in compbio.metadata"><CODE>Preset</CODE></A></TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/metadata/class-use/RunnerConfig.html#compbio.data.msa.jaxws"><B>RunnerConfig</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The list of <A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata"><CODE>Parameter</CODE></A>s and <A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata"><CODE>Option</CODE></A>s supported by executable.</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.engine"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Classes in <A HREF="../../compbio/metadata/package-summary.html">compbio.metadata</A> used by <A HREF="../../compbio/engine/package-summary.html">compbio.engine</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/metadata/class-use/ChunkHolder.html#compbio.engine"><B>ChunkHolder</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Represents a chunk of string data together with the position in a file from
- where corresponding to of the data.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/metadata/class-use/JobExecutionException.html#compbio.engine"><B>JobExecutionException</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;JobExecutionException is thrown wherever the results of the calculation
- cannot be obtained.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/metadata/class-use/JobStatus.html#compbio.engine"><B>JobStatus</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The status of the job.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/metadata/class-use/JobSubmissionException.html#compbio.engine"><B>JobSubmissionException</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Exception for generic problems with JobSubmission it is often thrown as a
- wrapper for the lower level exceptions like IOException or DrmaaException.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/metadata/class-use/ResultNotAvailableException.html#compbio.engine"><B>ResultNotAvailableException</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;ResultNotAvailableException is thrown wherever the results of the calculation
- cannot be obtained.</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.engine.client"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Classes in <A HREF="../../compbio/metadata/package-summary.html">compbio.metadata</A> used by <A HREF="../../compbio/engine/client/package-summary.html">compbio.engine.client</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/metadata/class-use/JobStatus.html#compbio.engine.client"><B>JobStatus</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The status of the job.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/metadata/class-use/JobSubmissionException.html#compbio.engine.client"><B>JobSubmissionException</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Exception for generic problems with JobSubmission it is often thrown as a
- wrapper for the lower level exceptions like IOException or DrmaaException.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/metadata/class-use/Limit.html#compbio.engine.client"><B>Limit</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;A value object containing a maximum number of sequences and a maximum average
- sequence length for a preset.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/metadata/class-use/LimitsManager.html#compbio.engine.client"><B>LimitsManager</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;A collection of Limits</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/metadata/class-use/Option.html#compbio.engine.client"><B>Option</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Command line option/flag or multiple exclusive options with no value.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/metadata/class-use/PresetManager.html#compbio.engine.client"><B>PresetManager</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Collection of presets and methods to manipulate them @see <A HREF="../../compbio/metadata/Preset.html" title="class in compbio.metadata"><CODE>Preset</CODE></A></TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/metadata/class-use/ResultNotAvailableException.html#compbio.engine.client"><B>ResultNotAvailableException</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;ResultNotAvailableException is thrown wherever the results of the calculation
- cannot be obtained.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/metadata/class-use/RunnerConfig.html#compbio.engine.client"><B>RunnerConfig</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The list of <A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata"><CODE>Parameter</CODE></A>s and <A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata"><CODE>Option</CODE></A>s supported by executable.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/metadata/class-use/UnsupportedRuntimeException.html#compbio.engine.client"><B>UnsupportedRuntimeException</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Indicates that the server could not execute native executables.</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.engine.cluster.drmaa"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Classes in <A HREF="../../compbio/metadata/package-summary.html">compbio.metadata</A> used by <A HREF="../../compbio/engine/cluster/drmaa/package-summary.html">compbio.engine.cluster.drmaa</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/metadata/class-use/JobExecutionException.html#compbio.engine.cluster.drmaa"><B>JobExecutionException</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;JobExecutionException is thrown wherever the results of the calculation
- cannot be obtained.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/metadata/class-use/JobStatus.html#compbio.engine.cluster.drmaa"><B>JobStatus</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The status of the job.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/metadata/class-use/JobSubmissionException.html#compbio.engine.cluster.drmaa"><B>JobSubmissionException</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Exception for generic problems with JobSubmission it is often thrown as a
- wrapper for the lower level exceptions like IOException or DrmaaException.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/metadata/class-use/ResultNotAvailableException.html#compbio.engine.cluster.drmaa"><B>ResultNotAvailableException</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;ResultNotAvailableException is thrown wherever the results of the calculation
- cannot be obtained.</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.engine.local"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Classes in <A HREF="../../compbio/metadata/package-summary.html">compbio.metadata</A> used by <A HREF="../../compbio/engine/local/package-summary.html">compbio.engine.local</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/metadata/class-use/JobExecutionException.html#compbio.engine.local"><B>JobExecutionException</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;JobExecutionException is thrown wherever the results of the calculation
- cannot be obtained.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/metadata/class-use/JobStatus.html#compbio.engine.local"><B>JobStatus</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The status of the job.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/metadata/class-use/JobSubmissionException.html#compbio.engine.local"><B>JobSubmissionException</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Exception for generic problems with JobSubmission it is often thrown as a
- wrapper for the lower level exceptions like IOException or DrmaaException.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/metadata/class-use/ResultNotAvailableException.html#compbio.engine.local"><B>ResultNotAvailableException</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;ResultNotAvailableException is thrown wherever the results of the calculation
- cannot be obtained.</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.metadata"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Classes in <A HREF="../../compbio/metadata/package-summary.html">compbio.metadata</A> used by <A HREF="../../compbio/metadata/package-summary.html">compbio.metadata</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/metadata/class-use/Argument.html#compbio.metadata"><B>Argument</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;An unmodifiable view for the options and parameters, with one exception - it
- allows to set a value</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/metadata/class-use/JobStatus.html#compbio.metadata"><B>JobStatus</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The status of the job.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/metadata/class-use/JobSubmissionException.html#compbio.metadata"><B>JobSubmissionException</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Exception for generic problems with JobSubmission it is often thrown as a
- wrapper for the lower level exceptions like IOException or DrmaaException.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/metadata/class-use/Limit.html#compbio.metadata"><B>Limit</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;A value object containing a maximum number of sequences and a maximum average
- sequence length for a preset.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/metadata/class-use/LimitExceededException.html#compbio.metadata"><B>LimitExceededException</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Thrown if the task larger in size that the limit that applies to the
- calculation.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/metadata/class-use/Option.html#compbio.metadata"><B>Option</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Command line option/flag or multiple exclusive options with no value.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/metadata/class-use/Parameter.html#compbio.metadata"><B>Parameter</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;A single value containing option supported by the web service e.g.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/metadata/class-use/Preset.html#compbio.metadata"><B>Preset</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Collection of Options and Parameters with their values</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/metadata/class-use/PresetManager.html#compbio.metadata"><B>PresetManager</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Collection of presets and methods to manipulate them @see <A HREF="../../compbio/metadata/Preset.html" title="class in compbio.metadata"><CODE>Preset</CODE></A></TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/metadata/class-use/RunnerConfig.html#compbio.metadata"><B>RunnerConfig</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The list of <A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata"><CODE>Parameter</CODE></A>s and <A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata"><CODE>Option</CODE></A>s supported by executable.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/metadata/class-use/ValueConstrain.html#compbio.metadata"><B>ValueConstrain</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The type and the lower and upper boundaries for numerical value.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/metadata/class-use/ValueConstrain.Type.html#compbio.metadata"><B>ValueConstrain.Type</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/metadata/class-use/WrongParameterException.html#compbio.metadata"><B>WrongParameterException</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;WrongParameterException is thrown wherever the <A HREF="../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata"><CODE>RunnerConfig</CODE></A> object
- does not match the actual runnable or then attempting to set the value of
- <A HREF="../../compbio/metadata/Argument.html" title="interface in compbio.metadata"><CODE>Argument</CODE></A> to invalid value.</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.runner"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Classes in <A HREF="../../compbio/metadata/package-summary.html">compbio.metadata</A> used by <A HREF="../../compbio/runner/package-summary.html">compbio.runner</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/metadata/class-use/Limit.html#compbio.runner"><B>Limit</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;A value object containing a maximum number of sequences and a maximum average
- sequence length for a preset.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/metadata/class-use/LimitsManager.html#compbio.runner"><B>LimitsManager</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;A collection of Limits</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/metadata/class-use/Option.html#compbio.runner"><B>Option</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Command line option/flag or multiple exclusive options with no value.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/metadata/class-use/Parameter.html#compbio.runner"><B>Parameter</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;A single value containing option supported by the web service e.g.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/metadata/class-use/PresetManager.html#compbio.runner"><B>PresetManager</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Collection of presets and methods to manipulate them @see <A HREF="../../compbio/metadata/Preset.html" title="class in compbio.metadata"><CODE>Preset</CODE></A></TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/metadata/class-use/RunnerConfig.html#compbio.runner"><B>RunnerConfig</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The list of <A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata"><CODE>Parameter</CODE></A>s and <A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata"><CODE>Option</CODE></A>s supported by executable.</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.runner._impl"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Classes in <A HREF="../../compbio/metadata/package-summary.html">compbio.metadata</A> used by <A HREF="../../compbio/runner/_impl/package-summary.html">compbio.runner._impl</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/metadata/class-use/Limit.html#compbio.runner._impl"><B>Limit</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;A value object containing a maximum number of sequences and a maximum average
- sequence length for a preset.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/metadata/class-use/LimitsManager.html#compbio.runner._impl"><B>LimitsManager</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;A collection of Limits</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.runner.msa"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Classes in <A HREF="../../compbio/metadata/package-summary.html">compbio.metadata</A> used by <A HREF="../../compbio/runner/msa/package-summary.html">compbio.runner.msa</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/metadata/class-use/Limit.html#compbio.runner.msa"><B>Limit</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;A value object containing a maximum number of sequences and a maximum average
- sequence length for a preset.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/metadata/class-use/LimitsManager.html#compbio.runner.msa"><B>LimitsManager</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;A collection of Limits</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/metadata/class-use/ResultNotAvailableException.html#compbio.runner.msa"><B>ResultNotAvailableException</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;ResultNotAvailableException is thrown wherever the results of the calculation
- cannot be obtained.</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.runner.psiblast"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Classes in <A HREF="../../compbio/metadata/package-summary.html">compbio.metadata</A> used by <A HREF="../../compbio/runner/psiblast/package-summary.html">compbio.runner.psiblast</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/metadata/class-use/Limit.html#compbio.runner.psiblast"><B>Limit</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;A value object containing a maximum number of sequences and a maximum average
- sequence length for a preset.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/metadata/class-use/LimitsManager.html#compbio.runner.psiblast"><B>LimitsManager</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;A collection of Limits</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/metadata/class-use/ResultNotAvailableException.html#compbio.runner.psiblast"><B>ResultNotAvailableException</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;ResultNotAvailableException is thrown wherever the results of the calculation
- cannot be obtained.</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.ws.server"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Classes in <A HREF="../../compbio/metadata/package-summary.html">compbio.metadata</A> used by <A HREF="../../compbio/ws/server/package-summary.html">compbio.ws.server</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/metadata/class-use/ChunkHolder.html#compbio.ws.server"><B>ChunkHolder</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Represents a chunk of string data together with the position in a file from
- where corresponding to of the data.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/metadata/class-use/JobStatus.html#compbio.ws.server"><B>JobStatus</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The status of the job.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/metadata/class-use/JobSubmissionException.html#compbio.ws.server"><B>JobSubmissionException</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Exception for generic problems with JobSubmission it is often thrown as a
- wrapper for the lower level exceptions like IOException or DrmaaException.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/metadata/class-use/Limit.html#compbio.ws.server"><B>Limit</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;A value object containing a maximum number of sequences and a maximum average
- sequence length for a preset.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/metadata/class-use/LimitExceededException.html#compbio.ws.server"><B>LimitExceededException</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Thrown if the task larger in size that the limit that applies to the
- calculation.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/metadata/class-use/LimitsManager.html#compbio.ws.server"><B>LimitsManager</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;A collection of Limits</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/metadata/class-use/Option.html#compbio.ws.server"><B>Option</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Command line option/flag or multiple exclusive options with no value.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/metadata/class-use/Preset.html#compbio.ws.server"><B>Preset</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Collection of Options and Parameters with their values</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/metadata/class-use/PresetManager.html#compbio.ws.server"><B>PresetManager</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Collection of presets and methods to manipulate them @see <A HREF="../../compbio/metadata/Preset.html" title="class in compbio.metadata"><CODE>Preset</CODE></A></TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/metadata/class-use/ResultNotAvailableException.html#compbio.ws.server"><B>ResultNotAvailableException</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;ResultNotAvailableException is thrown wherever the results of the calculation
- cannot be obtained.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/metadata/class-use/RunnerConfig.html#compbio.ws.server"><B>RunnerConfig</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The list of <A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata"><CODE>Parameter</CODE></A>s and <A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata"><CODE>Option</CODE></A>s supported by executable.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/metadata/class-use/WrongParameterException.html#compbio.ws.server"><B>WrongParameterException</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;WrongParameterException is thrown wherever the <A HREF="../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata"><CODE>RunnerConfig</CODE></A> object
- does not match the actual runnable or then attempting to set the value of
- <A HREF="../../compbio/metadata/Argument.html" title="interface in compbio.metadata"><CODE>Argument</CODE></A> to invalid value.</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Class</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../index.html?compbio/metadata/package-use.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="package-use.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/pipeline/_jpred/BlastParser.html b/website/full_javadoc/compbio/pipeline/_jpred/BlastParser.html

deleted file mode 100644 (file)

index f15b429..0000000
--- a/website/full_javadoc/compbio/pipeline/_jpred/BlastParser.html
+++ /dev/null
@@ -1,259 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-BlastParser\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="BlastParser";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/BlastParser.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV CLASS&nbsp;\r
-&nbsp;<A HREF="../../../compbio/pipeline/_jpred/Jpred4.html" title="class in compbio.pipeline._jpred"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/pipeline/_jpred/BlastParser.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="BlastParser.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.pipeline._jpred</FONT>\r
-<BR>\r
-Class BlastParser</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.pipeline._jpred.BlastParser</B>\r
-</PRE>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public class <B>BlastParser</B><DT>extends java.lang.Object</DL>\r
-</PRE>\r
-\r
-<P>\r
-<HR>\r
-\r
-<P>\r
-\r
-<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
-\r
-<A NAME="constructor_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Constructor Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/pipeline/_jpred/BlastParser.html#BlastParser()">BlastParser</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/pipeline/_jpred/BlastParser.html#main(java.lang.String[])">main</A></B>(java.lang.String[]&nbsp;args)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;args[0] is assumed to be the name of a Blast output file</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
-\r
-<A NAME="constructor_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Constructor Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="BlastParser()"><!-- --></A><H3>\r
-BlastParser</H3>\r
-<PRE>\r
-public <B>BlastParser</B>()</PRE>\r
-<DL>\r
-</DL>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
-<A NAME="method_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="main(java.lang.String[])"><!-- --></A><H3>\r
-main</H3>\r
-<PRE>\r
-public static void <B>main</B>(java.lang.String[]&nbsp;args)\r
-                 throws java.io.FileNotFoundException,\r
-                        javax.xml.stream.XMLStreamException</PRE>\r
-<DL>\r
-<DD>args[0] is assumed to be the name of a Blast output file\r
-<P>\r
-<DD><DL>\r
-\r
-<DT><B>Throws:</B>\r
-<DD><CODE>javax.xml.stream.XMLStreamException</CODE>\r
-<DD><CODE>java.io.FileNotFoundException</CODE></DL>\r
-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/BlastParser.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV CLASS&nbsp;\r
-&nbsp;<A HREF="../../../compbio/pipeline/_jpred/Jpred4.html" title="class in compbio.pipeline._jpred"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/pipeline/_jpred/BlastParser.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="BlastParser.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/pipeline/_jpred/Jpred4.html b/website/full_javadoc/compbio/pipeline/_jpred/Jpred4.html

deleted file mode 100644 (file)

index 8669156..0000000
--- a/website/full_javadoc/compbio/pipeline/_jpred/Jpred4.html
+++ /dev/null
@@ -1,277 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Jpred4\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Jpred4";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/Jpred4.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/pipeline/_jpred/BlastParser.html" title="class in compbio.pipeline._jpred"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../compbio/pipeline/_jpred/Pairwise.html" title="class in compbio.pipeline._jpred"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/pipeline/_jpred/Jpred4.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="Jpred4.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.pipeline._jpred</FONT>\r
-<BR>\r
-Class Jpred4</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.pipeline._jpred.Jpred4</B>\r
-</PRE>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public class <B>Jpred4</B><DT>extends java.lang.Object</DL>\r
-</PRE>\r
-\r
-<P>\r
-jpred --sequence <fasta file> OR --alignment <clustalW alignment> [--db
- <database>] [--pred-nohits] [--logLevel=(ERROR|INFO|DEBUG)] [--help]
- 
- jpred4 --sequence <fasta file> The path to the sequence (in FASTA format) you
- want to predict OR
- 
- [--alignment <clustalW alignment>] The alignment which to use for prediction
- 
- [--profile=<path to HMM profile>]
- 
- [--db <database>] Database to use for PSI-BLAST querying. Default: uniref90 (
- /homes/www-jpred/databases/uniref90.filt) Please note that database must be
- psi-blast indexed
- 
- [--pred-nohits] Toggle allowing Jpred to make predictions even when there are
- no PSI-BLAST hits.
- 
- [--logLevel=(ERROR|INFO|DEBUG)] one of ERROR, INFO, DEBUG [--help]\r
-<P>\r
-\r
-<P>\r
-<DL>\r
-<DT><B>Author:</B></DT>\r
-  <DD>pvtroshin</DD>\r
-</DL>\r
-<HR>\r
-\r
-<P>\r
-\r
-<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
-\r
-<A NAME="constructor_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Constructor Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/pipeline/_jpred/Jpred4.html#Jpred4()">Jpred4</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/pipeline/_jpred/Jpred4.html#runPsiBlast()">runPsiBlast</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
-\r
-<A NAME="constructor_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Constructor Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="Jpred4()"><!-- --></A><H3>\r
-Jpred4</H3>\r
-<PRE>\r
-public <B>Jpred4</B>()</PRE>\r
-<DL>\r
-</DL>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
-<A NAME="method_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="runPsiBlast()"><!-- --></A><H3>\r
-runPsiBlast</H3>\r
-<PRE>\r
-public void <B>runPsiBlast</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/Jpred4.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/pipeline/_jpred/BlastParser.html" title="class in compbio.pipeline._jpred"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../compbio/pipeline/_jpred/Pairwise.html" title="class in compbio.pipeline._jpred"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/pipeline/_jpred/Jpred4.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="Jpred4.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/pipeline/_jpred/PScore.html b/website/full_javadoc/compbio/pipeline/_jpred/PScore.html

deleted file mode 100644 (file)

index 668b60b..0000000
--- a/website/full_javadoc/compbio/pipeline/_jpred/PScore.html
+++ /dev/null
@@ -1,299 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-PScore\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="PScore";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/PScore.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/pipeline/_jpred/Pairwise.html" title="class in compbio.pipeline._jpred"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;NEXT CLASS</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/pipeline/_jpred/PScore.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="PScore.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.pipeline._jpred</FONT>\r
-<BR>\r
-Class PScore</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.pipeline._jpred.PScore</B>\r
-</PRE>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public class <B>PScore</B><DT>extends java.lang.Object</DL>\r
-</PRE>\r
-\r
-<P>\r
-<HR>\r
-\r
-<P>\r
-\r
-<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
-\r
-<A NAME="constructor_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Constructor Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/pipeline/_jpred/PScore.html#PScore()">PScore</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/pipeline/_jpred/PScore.html#equals(java.lang.Object)">equals</A></B>(java.lang.Object&nbsp;obj)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;int</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/pipeline/_jpred/PScore.html#hashCode()">hashCode</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/pipeline/_jpred/PScore.html#toString()">toString</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>getClass, notify, notifyAll, wait, wait, wait</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
-\r
-<A NAME="constructor_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Constructor Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="PScore()"><!-- --></A><H3>\r
-PScore</H3>\r
-<PRE>\r
-public <B>PScore</B>()</PRE>\r
-<DL>\r
-</DL>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
-<A NAME="method_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="equals(java.lang.Object)"><!-- --></A><H3>\r
-equals</H3>\r
-<PRE>\r
-public boolean <B>equals</B>(java.lang.Object&nbsp;obj)</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Overrides:</B><DD><CODE>equals</CODE> in class <CODE>java.lang.Object</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="hashCode()"><!-- --></A><H3>\r
-hashCode</H3>\r
-<PRE>\r
-public int <B>hashCode</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Overrides:</B><DD><CODE>hashCode</CODE> in class <CODE>java.lang.Object</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="toString()"><!-- --></A><H3>\r
-toString</H3>\r
-<PRE>\r
-public java.lang.String <B>toString</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Overrides:</B><DD><CODE>toString</CODE> in class <CODE>java.lang.Object</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/PScore.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/pipeline/_jpred/Pairwise.html" title="class in compbio.pipeline._jpred"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;NEXT CLASS</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/pipeline/_jpred/PScore.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="PScore.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
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-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
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diff --git a/website/full_javadoc/compbio/pipeline/_jpred/Pairwise.html b/website/full_javadoc/compbio/pipeline/_jpred/Pairwise.html

deleted file mode 100644 (file)

index 3200264..0000000
--- a/website/full_javadoc/compbio/pipeline/_jpred/Pairwise.html
+++ /dev/null
@@ -1,257 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Pairwise\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Pairwise";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/Pairwise.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/pipeline/_jpred/Jpred4.html" title="class in compbio.pipeline._jpred"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../compbio/pipeline/_jpred/PScore.html" title="class in compbio.pipeline._jpred"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/pipeline/_jpred/Pairwise.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="Pairwise.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.pipeline._jpred</FONT>\r
-<BR>\r
-Class Pairwise</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.pipeline._jpred.Pairwise</B>\r
-</PRE>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public class <B>Pairwise</B><DT>extends java.lang.Object</DL>\r
-</PRE>\r
-\r
-<P>\r
-<HR>\r
-\r
-<P>\r
-\r
-<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
-\r
-<A NAME="constructor_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Constructor Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/pipeline/_jpred/Pairwise.html#Pairwise(java.util.List)">Pairwise</A></B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/pipeline/_jpred/Pairwise.html#main(java.lang.String[])">main</A></B>(java.lang.String[]&nbsp;args)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
-\r
-<A NAME="constructor_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Constructor Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="Pairwise(java.util.List)"><!-- --></A><H3>\r
-Pairwise</H3>\r
-<PRE>\r
-public <B>Pairwise</B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences)</PRE>\r
-<DL>\r
-</DL>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
-<A NAME="method_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="main(java.lang.String[])"><!-- --></A><H3>\r
-main</H3>\r
-<PRE>\r
-public static final void <B>main</B>(java.lang.String[]&nbsp;args)\r
-                       throws java.io.FileNotFoundException,\r
-                              java.io.IOException</PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Throws:</B>\r
-<DD><CODE>java.io.FileNotFoundException</CODE>\r
-<DD><CODE>java.io.IOException</CODE></DL>\r
-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/Pairwise.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/pipeline/_jpred/Jpred4.html" title="class in compbio.pipeline._jpred"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../compbio/pipeline/_jpred/PScore.html" title="class in compbio.pipeline._jpred"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/pipeline/_jpred/Pairwise.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="Pairwise.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/pipeline/_jpred/class-use/BlastParser.html b/website/full_javadoc/compbio/pipeline/_jpred/class-use/BlastParser.html

deleted file mode 100644 (file)

index 5380574..0000000
--- a/website/full_javadoc/compbio/pipeline/_jpred/class-use/BlastParser.html
+++ /dev/null
@@ -1,144 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Uses of Class compbio.pipeline._jpred.BlastParser\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Uses of Class compbio.pipeline._jpred.BlastParser";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../compbio/pipeline/_jpred/BlastParser.html" title="class in compbio.pipeline._jpred"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/pipeline/_jpred/\class-useBlastParser.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="BlastParser.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-<B>Uses of Class<br>compbio.pipeline._jpred.BlastParser</B></H2>\r
-</CENTER>\r
-No usage of compbio.pipeline._jpred.BlastParser\r
-<P>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../compbio/pipeline/_jpred/BlastParser.html" title="class in compbio.pipeline._jpred"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
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-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
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diff --git a/website/full_javadoc/compbio/pipeline/_jpred/class-use/Jpred4.html b/website/full_javadoc/compbio/pipeline/_jpred/class-use/Jpred4.html

deleted file mode 100644 (file)

index e70f570..0000000
--- a/website/full_javadoc/compbio/pipeline/_jpred/class-use/Jpred4.html
+++ /dev/null
@@ -1,144 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Uses of Class compbio.pipeline._jpred.Jpred4\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Uses of Class compbio.pipeline._jpred.Jpred4";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
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-<TR>\r
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-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../compbio/pipeline/_jpred/Jpred4.html" title="class in compbio.pipeline._jpred"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/pipeline/_jpred/\class-useJpred4.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="Jpred4.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-<B>Uses of Class<br>compbio.pipeline._jpred.Jpred4</B></H2>\r
-</CENTER>\r
-No usage of compbio.pipeline._jpred.Jpred4\r
-<P>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
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-<TR>\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
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-  <A HREF="../../../../index.html?compbio/pipeline/_jpred/\class-useJpred4.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
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-&nbsp;<SCRIPT type="text/javascript">\r
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-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/pipeline/_jpred/class-use/PScore.html b/website/full_javadoc/compbio/pipeline/_jpred/class-use/PScore.html

deleted file mode 100644 (file)

index 26263db..0000000
--- a/website/full_javadoc/compbio/pipeline/_jpred/class-use/PScore.html
+++ /dev/null
@@ -1,144 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Uses of Class compbio.pipeline._jpred.PScore\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Uses of Class compbio.pipeline._jpred.PScore";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
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-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/pipeline/_jpred/\class-usePScore.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="PScore.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
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-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-<B>Uses of Class<br>compbio.pipeline._jpred.PScore</B></H2>\r
-</CENTER>\r
-No usage of compbio.pipeline._jpred.PScore\r
-<P>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
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-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/pipeline/_jpred/\class-usePScore.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="PScore.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
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-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
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-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/pipeline/_jpred/class-use/Pairwise.html b/website/full_javadoc/compbio/pipeline/_jpred/class-use/Pairwise.html

deleted file mode 100644 (file)

index 754a87e..0000000
--- a/website/full_javadoc/compbio/pipeline/_jpred/class-use/Pairwise.html
+++ /dev/null
@@ -1,144 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Uses of Class compbio.pipeline._jpred.Pairwise\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Uses of Class compbio.pipeline._jpred.Pairwise";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../compbio/pipeline/_jpred/Pairwise.html" title="class in compbio.pipeline._jpred"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
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-\r
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-  <A HREF="../../../../index.html?compbio/pipeline/_jpred/\class-usePairwise.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="Pairwise.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
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-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
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-<B>Uses of Class<br>compbio.pipeline._jpred.Pairwise</B></H2>\r
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-No usage of compbio.pipeline._jpred.Pairwise\r
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diff --git a/website/full_javadoc/compbio/pipeline/_jpred/package-frame.html b/website/full_javadoc/compbio/pipeline/_jpred/package-frame.html

deleted file mode 100644 (file)

index f22d288..0000000
--- a/website/full_javadoc/compbio/pipeline/_jpred/package-frame.html
+++ /dev/null
@@ -1,38 +0,0 @@
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-<!--NewPage-->\r
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-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
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-<TR>\r
-<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">\r
-Classes</FONT>&nbsp;\r
-<FONT CLASS="FrameItemFont">\r
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-<A HREF="Pairwise.html" title="class in compbio.pipeline._jpred" target="classFrame">Pairwise</A>\r
-<BR>\r
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-</TR>\r
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diff --git a/website/full_javadoc/compbio/pipeline/_jpred/package-summary.html b/website/full_javadoc/compbio/pipeline/_jpred/package-summary.html

deleted file mode 100644 (file)

index 06bf2f8..0000000
--- a/website/full_javadoc/compbio/pipeline/_jpred/package-summary.html
+++ /dev/null
@@ -1,179 +0,0 @@
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-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
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-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
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-</SCRIPT>\r
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-\r
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-<H2>\r
-Package compbio.pipeline._jpred\r
-</H2>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Class Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../../compbio/pipeline/_jpred/BlastParser.html" title="class in compbio.pipeline._jpred">BlastParser</A></B></TD>\r
-<TD>&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../../compbio/pipeline/_jpred/Jpred4.html" title="class in compbio.pipeline._jpred">Jpred4</A></B></TD>\r
-<TD>jpred --sequence <fasta file> OR --alignment <clustalW alignment> [--db
- <database>] [--pred-nohits] [--logLevel=(ERROR|INFO|DEBUG)] [--help]
- 
- jpred4 --sequence <fasta file> The path to the sequence (in FASTA format) you
- want to predict OR
- 
- [--alignment <clustalW alignment>] The alignment which to use for prediction
- 
- [--profile=<path to HMM profile>]
- 
- [--db <database>] Database to use for PSI-BLAST querying.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../../compbio/pipeline/_jpred/Pairwise.html" title="class in compbio.pipeline._jpred">Pairwise</A></B></TD>\r
-<TD>&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../../compbio/pipeline/_jpred/PScore.html" title="class in compbio.pipeline._jpred">PScore</A></B></TD>\r
-<TD>&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-\r
-<P>\r
-<DL>\r
-</DL>\r
-<HR>\r
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diff --git a/website/full_javadoc/compbio/pipeline/_jpred/package-tree.html b/website/full_javadoc/compbio/pipeline/_jpred/package-tree.html

deleted file mode 100644 (file)

index e907ee7..0000000
--- a/website/full_javadoc/compbio/pipeline/_jpred/package-tree.html
+++ /dev/null
@@ -1,153 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
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-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
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-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="compbio.pipeline._jpred Class Hierarchy";\r
-    }\r
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-  </TR>\r
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-</TD>\r
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-  <!--\r
-  if(window==top) {\r
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-Hierarchy For Package compbio.pipeline._jpred\r
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deleted file mode 100644 (file)

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+++ /dev/null
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diff --git a/website/full_javadoc/compbio/runner/OptionCombinator.html b/website/full_javadoc/compbio/runner/OptionCombinator.html

deleted file mode 100644 (file)

index 69a5662..0000000
--- a/website/full_javadoc/compbio/runner/OptionCombinator.html
+++ /dev/null
@@ -1,421 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
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-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:49 GMT 2010 -->\r
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-    }\r
-}\r
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-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
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-<FONT SIZE="-1">\r
-compbio.runner</FONT>\r
-<BR>\r
-Class OptionCombinator</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../resources/inherit.gif" ALT="extended by "><B>compbio.runner.OptionCombinator</B>\r
-</PRE>\r
-<HR>\r
-<DL>\r
-<DT><PRE><FONT SIZE="-1">@Immutable\r
-</FONT>public final class <B>OptionCombinator</B><DT>extends java.lang.Object</DL>\r
-</PRE>\r
-\r
-<P>\r
-This class solve the following problems. Given the RunnerConfig
- 
- 1) generate a valid option string with all options and parameters in it
- 
- 2) Permute all possible combinations of options order and parameters values\r
-<P>\r
-\r
-<P>\r
-<DL>\r
-<DT><B>Author:</B></DT>\r
-  <DD>pvtroshin</DD>\r
-</DL>\r
-<HR>\r
-\r
-<P>\r
-\r
-<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
-\r
-<A NAME="constructor_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
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-<B>Constructor Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../compbio/runner/OptionCombinator.html#OptionCombinator(compbio.metadata.RunnerConfig)">OptionCombinator</A></B>(<A HREF="../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&lt;? extends <A HREF="../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;?&gt;&gt;&nbsp;rconfig)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
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-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
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-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.util.List&lt;java.lang.String&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/runner/OptionCombinator.html#argumentsToCommandString(java.util.List)">argumentsToCommandString</A></B>(java.util.List&lt;? extends <A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;?&gt;&gt;&nbsp;arguments)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;java.util.List&lt;java.lang.String&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/runner/OptionCombinator.html#argumentsToCommandString(java.util.List, compbio.metadata.RunnerConfig)">argumentsToCommandString</A></B>(java.util.List&lt;? extends <A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;?&gt;&gt;&nbsp;arguments,\r
-                         <A HREF="../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&lt;? extends <A HREF="../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;?&gt;&gt;&nbsp;rconfig)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.util.Map&lt;<A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>&lt;?&gt;,java.lang.String&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/runner/OptionCombinator.html#getAllConstrainedParametersWithBorderValues(boolean)">getAllConstrainedParametersWithBorderValues</A></B>(boolean&nbsp;minValue)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.util.Map&lt;<A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>&lt;?&gt;,java.lang.String&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/runner/OptionCombinator.html#getAllConstrainedParametersWithRandomValues()">getAllConstrainedParametersWithRandomValues</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
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-<TR BGCOLOR="white" CLASS="TableRowColor">\r
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-<TD><CODE><B><A HREF="../../compbio/runner/OptionCombinator.html#getAllOptions()">getAllOptions</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
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-<TD><CODE><B><A HREF="../../compbio/runner/OptionCombinator.html#getAllParameters()">getAllParameters</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
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-<TR BGCOLOR="white" CLASS="TableRowColor">\r
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-<CODE>&nbsp;java.util.List&lt;java.lang.String&gt;</CODE></FONT></TD>\r
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-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
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-<TR BGCOLOR="white" CLASS="TableRowColor">\r
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-\r
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-<TD><CODE><B><A HREF="../../compbio/runner/OptionCombinator.html#parametersToCommandString(java.util.List, java.util.Map)">parametersToCommandString</A></B>(java.util.List&lt;<A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>&lt;?&gt;&gt;&nbsp;orderedList,\r
-                          java.util.Map&lt;<A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>&lt;?&gt;,java.lang.String&gt;&nbsp;prmValue)</CODE>\r
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-<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
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-public java.util.List&lt;java.lang.String&gt; <B>optionsToCommandString</B>(java.util.List&lt;<A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;?&gt;&gt;&nbsp;options)</PRE>\r
-<DL>\r
-<DD><DL>\r
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-\r
-<A NAME="getOptionsAtRandom()"><!-- --></A><H3>\r
-getOptionsAtRandom</H3>\r
-<PRE>\r
-public java.util.List&lt;java.lang.String&gt; <B>getOptionsAtRandom</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
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-<A NAME="getAllOptions()"><!-- --></A><H3>\r
-getAllOptions</H3>\r
-<PRE>\r
-public java.util.List&lt;<A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;?&gt;&gt; <B>getAllOptions</B>()</PRE>\r
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-argumentsToCommandString</H3>\r
-<PRE>\r
-public static java.util.List&lt;java.lang.String&gt; <B>argumentsToCommandString</B>(java.util.List&lt;? extends <A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;?&gt;&gt;&nbsp;arguments,\r
-                                                                        <A HREF="../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&lt;? extends <A HREF="../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;?&gt;&gt;&nbsp;rconfig)</PRE>\r
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-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="parametersToCommandString(java.util.List, java.util.Map)"><!-- --></A><H3>\r
-parametersToCommandString</H3>\r
-<PRE>\r
-public java.util.List&lt;java.lang.String&gt; <B>parametersToCommandString</B>(java.util.List&lt;<A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>&lt;?&gt;&gt;&nbsp;orderedList,\r
-                                                                  java.util.Map&lt;<A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>&lt;?&gt;,java.lang.String&gt;&nbsp;prmValue)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getAllConstrainedParametersWithBorderValues(boolean)"><!-- --></A><H3>\r
-getAllConstrainedParametersWithBorderValues</H3>\r
-<PRE>\r
-public java.util.Map&lt;<A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>&lt;?&gt;,java.lang.String&gt; <B>getAllConstrainedParametersWithBorderValues</B>(boolean&nbsp;minValue)</PRE>\r
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-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
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-getAllConstrainedParametersWithRandomValues</H3>\r
-<PRE>\r
-public java.util.Map&lt;<A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>&lt;?&gt;,java.lang.String&gt; <B>getAllConstrainedParametersWithRandomValues</B>()</PRE>\r
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-&nbsp;<A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../compbio/runner/Util.html" title="class in compbio.runner"><B>NEXT CLASS</B></A></FONT></TD>\r
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diff --git a/website/full_javadoc/compbio/runner/Util.html b/website/full_javadoc/compbio/runner/Util.html

deleted file mode 100644 (file)

index d09afc7..0000000
--- a/website/full_javadoc/compbio/runner/Util.html
+++ /dev/null
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-<!-- =========== FIELD SUMMARY =========== -->\r
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-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
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-<TD><CODE><B><A HREF="../../compbio/runner/Util.html#Util()">Util</A></B>()</CODE>\r
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-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
-<TR ALIGN="right" VALIGN="">\r
-<TD NOWRAP><FONT SIZE="-1">\r
-<CODE>&lt;T&gt; <A HREF="../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;T&gt;</CODE></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/runner/Util.html#getLimits(java.lang.Class)">getLimits</A></B>(java.lang.Class&lt;? extends <A HREF="../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;T&gt;&gt;&nbsp;clazz)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;For now just assume that all parameters which came in needs setting it
- will be a client responsibility to prepare RunnerConfig object then</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
-<TR ALIGN="right" VALIGN="">\r
-<TD NOWRAP><FONT SIZE="-1">\r
-<CODE>&lt;T&gt; <A HREF="../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>&lt;T&gt;</CODE></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/runner/Util.html#getPresets(java.lang.Class)">getPresets</A></B>(java.lang.Class&lt;? extends <A HREF="../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;T&gt;&gt;&nbsp;clazz)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
-<TR ALIGN="right" VALIGN="">\r
-<TD NOWRAP><FONT SIZE="-1">\r
-<CODE>&lt;T&gt; <A HREF="../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&lt;T&gt;</CODE></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/runner/Util.html#getSupportedOptions(java.lang.Class)">getSupportedOptions</A></B>(java.lang.Class&lt;? extends <A HREF="../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;T&gt;&gt;&nbsp;clazz)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/runner/Util.html#readClustalFile(java.lang.String, java.lang.String)">readClustalFile</A></B>(java.lang.String&nbsp;workDirectory,\r
-                java.lang.String&nbsp;clustFile)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/runner/Util.html#writeInput(java.util.List, compbio.engine.client.ConfiguredExecutable)">writeInput</A></B>(java.util.List&lt;<A HREF="../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-           <A HREF="../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;exec)</CODE>\r
-\r
-<BR>\r
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-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>\r
-</TR>\r
-</TABLE>\r
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-\r
-<!-- ============ FIELD DETAIL =========== -->\r
-\r
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-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Field Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="SPACE"><!-- --></A><H3>\r
-SPACE</H3>\r
-<PRE>\r
-public static final java.lang.String <B>SPACE</B></PRE>\r
-<DL>\r
-<DL>\r
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-</DL>\r
-\r
-<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
-\r
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-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Constructor Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="Util()"><!-- --></A><H3>\r
-Util</H3>\r
-<PRE>\r
-public <B>Util</B>()</PRE>\r
-<DL>\r
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-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
-<A NAME="method_detail"><!-- --></A>\r
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-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="getLimits(java.lang.Class)"><!-- --></A><H3>\r
-getLimits</H3>\r
-<PRE>\r
-public static &lt;T&gt; <A HREF="../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;T&gt; <B>getLimits</B>(java.lang.Class&lt;? extends <A HREF="../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;T&gt;&gt;&nbsp;clazz)</PRE>\r
-<DL>\r
-<DD>For now just assume that all parameters which came in needs setting it
- will be a client responsibility to prepare RunnerConfig object then\r
-<P>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>rconfig</CODE> - \r
-<DT><B>Returns:</B><DD>public static List<String> toOptionString(RunnerConfig<?>
-         rconfig) { String option = ""; List<String> options = new
-         ArrayList<String>(); for (Parameter<?> par :
-         rconfig.getParameters()) { if (par.getPossibleValues().isEmpty())
-         { option = par.getOptionName(); } else { option =
-         par.getOptionName() + "=" + par.getPossibleValues().get(0); } //
-         separate options options.add(option); } return options; }</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getSupportedOptions(java.lang.Class)"><!-- --></A><H3>\r
-getSupportedOptions</H3>\r
-<PRE>\r
-public static &lt;T&gt; <A HREF="../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&lt;T&gt; <B>getSupportedOptions</B>(java.lang.Class&lt;? extends <A HREF="../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;T&gt;&gt;&nbsp;clazz)</PRE>\r
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-</DD>\r
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-\r
-<A NAME="getPresets(java.lang.Class)"><!-- --></A><H3>\r
-getPresets</H3>\r
-<PRE>\r
-public static &lt;T&gt; <A HREF="../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>&lt;T&gt; <B>getPresets</B>(java.lang.Class&lt;? extends <A HREF="../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;T&gt;&gt;&nbsp;clazz)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="readClustalFile(java.lang.String, java.lang.String)"><!-- --></A><H3>\r
-readClustalFile</H3>\r
-<PRE>\r
-public static final <A HREF="../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A> <B>readClustalFile</B>(java.lang.String&nbsp;workDirectory,\r
-                                              java.lang.String&nbsp;clustFile)\r
-                                       throws <A HREF="../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</A>,\r
-                                              java.io.IOException,\r
-                                              java.io.FileNotFoundException,\r
-                                              java.lang.NullPointerException</PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Throws:</B>\r
-<DD><CODE><A HREF="../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</A></CODE>\r
-<DD><CODE>java.io.IOException</CODE>\r
-<DD><CODE>java.io.FileNotFoundException</CODE>\r
-<DD><CODE>java.lang.NullPointerException</CODE></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="writeInput(java.util.List, compbio.engine.client.ConfiguredExecutable)"><!-- --></A><H3>\r
-writeInput</H3>\r
-<PRE>\r
-public static void <B>writeInput</B>(java.util.List&lt;<A HREF="../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-                              <A HREF="../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;exec)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/Util.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
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-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
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-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../compbio/runner/OptionCombinator.html" title="class in compbio.runner"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;NEXT CLASS</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../index.html?compbio/runner/Util.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
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-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
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-</SCRIPT>\r
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-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;<A HREF="#field_summary">FIELD</A>&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;<A HREF="#field_detail">FIELD</A>&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
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diff --git a/website/full_javadoc/compbio/runner/_NativeSpecHelper.html b/website/full_javadoc/compbio/runner/_NativeSpecHelper.html

deleted file mode 100644 (file)

index 05a5ca7..0000000
--- a/website/full_javadoc/compbio/runner/_NativeSpecHelper.html
+++ /dev/null
@@ -1,347 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:49 GMT 2010 -->\r
-<TITLE>\r
-_NativeSpecHelper\r
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-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="_NativeSpecHelper";\r
-    }\r
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-<!-- ========= START OF TOP NAVBAR ======= -->\r
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-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
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-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/_NativeSpecHelper.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
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-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
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-    document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');\r
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-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
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-Class _NativeSpecHelper</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../resources/inherit.gif" ALT="extended by "><B>compbio.runner._NativeSpecHelper</B>\r
-</PRE>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public class <B>_NativeSpecHelper</B><DT>extends java.lang.Object</DL>\r
-</PRE>\r
-\r
-<P>\r
-<HR>\r
-\r
-<P>\r
-\r
-<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
-\r
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-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Constructor Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../compbio/runner/_NativeSpecHelper.html#_NativeSpecHelper(int)">_NativeSpecHelper</A></B>(int&nbsp;requiredMemory)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../compbio/runner/_NativeSpecHelper.html#_NativeSpecHelper(int, int)">_NativeSpecHelper</A></B>(int&nbsp;requiredMemory,\r
-                  int&nbsp;maxCalculationTime)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
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-&nbsp;\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
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-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../compbio/engine/cluster/dundee/_Queue.html" title="enum in compbio.engine.cluster.dundee">_Queue</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/runner/_NativeSpecHelper.html#getApproprieteQueue()">getApproprieteQueue</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/runner/_NativeSpecHelper.html#getNativeSpec()">getNativeSpec</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/runner/_NativeSpecHelper.html#getQueue()">getQueue</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/runner/_NativeSpecHelper.html#setQueue(java.lang.String)">setQueue</A></B>(java.lang.String&nbsp;queue)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
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-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
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-\r
-<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
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-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Constructor Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="_NativeSpecHelper(int)"><!-- --></A><H3>\r
-_NativeSpecHelper</H3>\r
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-public <B>_NativeSpecHelper</B>(int&nbsp;requiredMemory)</PRE>\r
-<DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="_NativeSpecHelper(int, int)"><!-- --></A><H3>\r
-_NativeSpecHelper</H3>\r
-<PRE>\r
-public <B>_NativeSpecHelper</B>(int&nbsp;requiredMemory,\r
-                         int&nbsp;maxCalculationTime)</PRE>\r
-<DL>\r
-</DL>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
-<A NAME="method_detail"><!-- --></A>\r
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-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="setRequiredMemory(int)"><!-- --></A><H3>\r
-setRequiredMemory</H3>\r
-<PRE>\r
-public void <B>setRequiredMemory</B>(int&nbsp;memory)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="setQueue(java.lang.String)"><!-- --></A><H3>\r
-setQueue</H3>\r
-<PRE>\r
-public void <B>setQueue</B>(java.lang.String&nbsp;queue)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getQueue()"><!-- --></A><H3>\r
-getQueue</H3>\r
-<PRE>\r
-public java.lang.String <B>getQueue</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getNativeSpec()"><!-- --></A><H3>\r
-getNativeSpec</H3>\r
-<PRE>\r
-public java.lang.String <B>getNativeSpec</B>()\r
-                               throws java.net.UnknownServiceException</PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Throws:</B>\r
-<DD><CODE>java.net.UnknownServiceException</CODE></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getApproprieteQueue()"><!-- --></A><H3>\r
-getApproprieteQueue</H3>\r
-<PRE>\r
-public <A HREF="../../compbio/engine/cluster/dundee/_Queue.html" title="enum in compbio.engine.cluster.dundee">_Queue</A> <B>getApproprieteQueue</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
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-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV CLASS&nbsp;\r
-&nbsp;<A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../index.html?compbio/runner/_NativeSpecHelper.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="_NativeSpecHelper.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/runner/_SkeletalCommandBuilder.html b/website/full_javadoc/compbio/runner/_SkeletalCommandBuilder.html

deleted file mode 100644 (file)

index ff0efa8..0000000
--- a/website/full_javadoc/compbio/runner/_SkeletalCommandBuilder.html
+++ /dev/null
@@ -1,586 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:49 GMT 2010 -->\r
-<TITLE>\r
-_SkeletalCommandBuilder\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="_SkeletalCommandBuilder";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/_SkeletalCommandBuilder.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../compbio/runner/_NativeSpecHelper.html" title="class in compbio.runner"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../compbio/runner/OptionCombinator.html" title="class in compbio.runner"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../index.html?compbio/runner/_SkeletalCommandBuilder.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="_SkeletalCommandBuilder.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.runner</FONT>\r
-<BR>\r
-Class _SkeletalCommandBuilder</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../resources/inherit.gif" ALT="extended by "><B>compbio.runner._SkeletalCommandBuilder</B>\r
-</PRE>\r
-<DL>\r
-<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>&gt;</DD>\r
-</DL>\r
-<DL>\r
-<DT><B>Direct Known Subclasses:</B> <DD><A HREF="../../compbio/runner/_impl/BlastAll.html" title="class in compbio.runner._impl">BlastAll</A>, <A HREF="../../compbio/runner/_impl/Disembl.html" title="class in compbio.runner._impl">Disembl</A>, <A HREF="../../compbio/runner/_impl/Mcl.html" title="class in compbio.runner._impl">Mcl</A>, <A HREF="../../compbio/runner/_impl/OB.html" title="class in compbio.runner._impl">OB</A>, <A HREF="../../compbio/runner/_impl/PSIBlast.html" title="class in compbio.runner._impl">PSIBlast</A>, <A HREF="../../compbio/runner/_impl/Ronn.html" title="class in compbio.runner._impl">Ronn</A>, <A HREF="../../compbio/runner/_impl/RPSBlast.html" title="class in compbio.runner._impl">RPSBlast</A></DD>\r
-</DL>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public abstract class <B>_SkeletalCommandBuilder</B><DT>extends java.lang.Object<DT>implements <A HREF="../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>&gt;</DL>\r
-</PRE>\r
-\r
-<P>\r
-<HR>\r
-\r
-<P>\r
-<!-- ======== NESTED CLASS SUMMARY ======== -->\r
-\r
-<A NAME="nested_class_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Nested Class Summary</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="nested_classes_inherited_from_class_compbio.engine.client.Executable"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Nested classes/interfaces inherited from interface compbio.engine.client.<A HREF="../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><A HREF="../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A></CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-\r
-<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
-\r
-<A NAME="constructor_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Constructor Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../compbio/runner/_SkeletalCommandBuilder.html#_SkeletalCommandBuilder()">_SkeletalCommandBuilder</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/runner/_SkeletalCommandBuilder.html#addParameter(java.lang.String)">addParameter</A></B>(java.lang.String&nbsp;parameter)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/runner/_SkeletalCommandBuilder.html#addParameters(java.util.List)">addParameters</A></B>(java.util.List&lt;java.lang.String&gt;&nbsp;parameters)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Adds parameter to the list of parameters for a native executable</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/runner/_SkeletalCommandBuilder.html#addParameters(java.lang.String[])">addParameters</A></B>(java.lang.String[]&nbsp;parameters)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/runner/_SkeletalCommandBuilder.html#getEmail()">getEmail</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/runner/_SkeletalCommandBuilder.html#getError()">getError</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;<A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/runner/_SkeletalCommandBuilder.html#getLimit(java.lang.String)">getLimit</A></B>(java.lang.String&nbsp;presetName)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;<A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/runner/_SkeletalCommandBuilder.html#getLimits()">getLimits</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/runner/_SkeletalCommandBuilder.html#getName()">getName</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/runner/_SkeletalCommandBuilder.html#getOutput()">getOutput</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>&lt;<A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/runner/_SkeletalCommandBuilder.html#getParameters(compbio.engine.client.Executable.ExecProvider)">getParameters</A></B>(<A HREF="../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
-<TR ALIGN="right" VALIGN="">\r
-<TD NOWRAP><FONT SIZE="-1">\r
-<CODE>&lt;V&gt; V</CODE></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/runner/_SkeletalCommandBuilder.html#getResults(java.lang.String)">getResults</A></B>(java.lang.String&nbsp;directory)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;?&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/runner/_SkeletalCommandBuilder.html#loadRunConfiguration(compbio.engine.client.RunConfiguration)">loadRunConfiguration</A></B>(<A HREF="../../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>&nbsp;rconfig)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/runner/_SkeletalCommandBuilder.html#setEmail(java.lang.String)">setEmail</A></B>(java.lang.String&nbsp;email)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/runner/_SkeletalCommandBuilder.html#setName(java.lang.String)">setName</A></B>(java.lang.String&nbsp;name)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_compbio.engine.client.Executable"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from interface compbio.engine.client.<A HREF="../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><A HREF="../../compbio/engine/client/Executable.html#getCreatedFiles()">getCreatedFiles</A>, <A HREF="../../compbio/engine/client/Executable.html#getInput()">getInput</A></CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
-\r
-<A NAME="constructor_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Constructor Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="_SkeletalCommandBuilder()"><!-- --></A><H3>\r
-_SkeletalCommandBuilder</H3>\r
-<PRE>\r
-public <B>_SkeletalCommandBuilder</B>()</PRE>\r
-<DL>\r
-</DL>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
-<A NAME="method_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="setEmail(java.lang.String)"><!-- --></A><H3>\r
-setEmail</H3>\r
-<PRE>\r
-public <A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A> <B>setEmail</B>(java.lang.String&nbsp;email)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="setName(java.lang.String)"><!-- --></A><H3>\r
-setName</H3>\r
-<PRE>\r
-public <A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A> <B>setName</B>(java.lang.String&nbsp;name)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getName()"><!-- --></A><H3>\r
-getName</H3>\r
-<PRE>\r
-public java.lang.String <B>getName</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getEmail()"><!-- --></A><H3>\r
-getEmail</H3>\r
-<PRE>\r
-public java.lang.String <B>getEmail</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="addParameters(java.lang.String[])"><!-- --></A><H3>\r
-addParameters</H3>\r
-<PRE>\r
-public <A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A> <B>addParameters</B>(java.lang.String[]&nbsp;parameters)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="addParameters(java.util.List)"><!-- --></A><H3>\r
-addParameters</H3>\r
-<PRE>\r
-public <A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A> <B>addParameters</B>(java.util.List&lt;java.lang.String&gt;&nbsp;parameters)</PRE>\r
-<DL>\r
-<DD><B>Description copied from interface: <CODE><A HREF="../../compbio/engine/client/Executable.html#addParameters(java.util.List)">Executable</A></CODE></B></DD>\r
-<DD>Adds parameter to the list of parameters for a native executable\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../compbio/engine/client/Executable.html#addParameters(java.util.List)">addParameters</A></CODE> in interface <CODE><A HREF="../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>this Executable</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getParameters(compbio.engine.client.Executable.ExecProvider)"><!-- --></A><H3>\r
-getParameters</H3>\r
-<PRE>\r
-public <A HREF="../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>&lt;<A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>&gt; <B>getParameters</B>(<A HREF="../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider)</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../compbio/engine/client/Executable.html#getParameters(compbio.engine.client.Executable.ExecProvider)">getParameters</A></CODE> in interface <CODE><A HREF="../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="addParameter(java.lang.String)"><!-- --></A><H3>\r
-addParameter</H3>\r
-<PRE>\r
-public <A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A> <B>addParameter</B>(java.lang.String&nbsp;parameter)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getResults(java.lang.String)"><!-- --></A><H3>\r
-getResults</H3>\r
-<PRE>\r
-public &lt;V&gt; V <B>getResults</B>(java.lang.String&nbsp;directory)</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../compbio/engine/client/Executable.html#getResults(java.lang.String)">getResults</A></CODE> in interface <CODE><A HREF="../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="loadRunConfiguration(compbio.engine.client.RunConfiguration)"><!-- --></A><H3>\r
-loadRunConfiguration</H3>\r
-<PRE>\r
-public <A HREF="../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;?&gt; <B>loadRunConfiguration</B>(<A HREF="../../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>&nbsp;rconfig)</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../compbio/engine/client/Executable.html#loadRunConfiguration(compbio.engine.client.RunConfiguration)">loadRunConfiguration</A></CODE> in interface <CODE><A HREF="../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getOutput()"><!-- --></A><H3>\r
-getOutput</H3>\r
-<PRE>\r
-public java.lang.String <B>getOutput</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../compbio/engine/client/Executable.html#getOutput()">getOutput</A></CODE> in interface <CODE><A HREF="../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getError()"><!-- --></A><H3>\r
-getError</H3>\r
-<PRE>\r
-public java.lang.String <B>getError</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../compbio/engine/client/Executable.html#getError()">getError</A></CODE> in interface <CODE><A HREF="../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getLimit(java.lang.String)"><!-- --></A><H3>\r
-getLimit</H3>\r
-<PRE>\r
-public <A HREF="../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;<A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>&gt; <B>getLimit</B>(java.lang.String&nbsp;presetName)</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../compbio/engine/client/Executable.html#getLimit(java.lang.String)">getLimit</A></CODE> in interface <CODE><A HREF="../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getLimits()"><!-- --></A><H3>\r
-getLimits</H3>\r
-<PRE>\r
-public <A HREF="../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;<A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>&gt; <B>getLimits</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../compbio/engine/client/Executable.html#getLimits()">getLimits</A></CODE> in interface <CODE><A HREF="../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/_SkeletalCommandBuilder.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../compbio/runner/_NativeSpecHelper.html" title="class in compbio.runner"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../compbio/runner/OptionCombinator.html" title="class in compbio.runner"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../index.html?compbio/runner/_SkeletalCommandBuilder.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="_SkeletalCommandBuilder.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/runner/_impl/BlastAll.html b/website/full_javadoc/compbio/runner/_impl/BlastAll.html

deleted file mode 100644 (file)

index 2faddc5..0000000
--- a/website/full_javadoc/compbio/runner/_impl/BlastAll.html
+++ /dev/null
@@ -1,360 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:49 GMT 2010 -->\r
-<TITLE>\r
-BlastAll\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="BlastAll";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/BlastAll.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV CLASS&nbsp;\r
-&nbsp;<A HREF="../../../compbio/runner/_impl/BlastParameters.html" title="class in compbio.runner._impl"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/runner/_impl/BlastAll.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="BlastAll.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.runner._impl</FONT>\r
-<BR>\r
-Class BlastAll</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">compbio.runner._SkeletalCommandBuilder</A>\r
-      <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.runner._impl.BlastAll</B>\r
-</PRE>\r
-<DL>\r
-<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>&gt;</DD>\r
-</DL>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public class <B>BlastAll</B><DT>extends <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A></DL>\r
-</PRE>\r
-\r
-<P>\r
-<HR>\r
-\r
-<P>\r
-<!-- ======== NESTED CLASS SUMMARY ======== -->\r
-\r
-<A NAME="nested_class_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Nested Class Summary</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="nested_classes_inherited_from_class_compbio.engine.client.Executable"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Nested classes/interfaces inherited from interface compbio.engine.client.<A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A></CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-\r
-<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
-\r
-<A NAME="constructor_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Constructor Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/runner/_impl/BlastAll.html#BlastAll(java.lang.String)">BlastAll</A></B>(java.lang.String&nbsp;workDirectory)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/_impl/BlastAll.html#getCommand(compbio.engine.client.Executable.ExecProvider)">getCommand</A></B>(<A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/_impl/BlastAll.html#getCommandName()">getCommandName</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.util.List&lt;java.lang.String&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/_impl/BlastAll.html#getCreatedFiles()">getCreatedFiles</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/_impl/BlastAll.html#getInput()">getInput</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/_impl/BlastAll.html#removeOutput(java.lang.String)">removeOutput</A></B>(java.lang.String&nbsp;outfile)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_compbio.runner._SkeletalCommandBuilder"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class compbio.runner.<A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A></B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#addParameter(java.lang.String)">addParameter</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#addParameters(java.util.List)">addParameters</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#addParameters(java.lang.String[])">addParameters</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#getEmail()">getEmail</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#getError()">getError</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#getLimit(java.lang.String)">getLimit</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#getLimits()">getLimits</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#getName()">getName</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#getOutput()">getOutput</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#getParameters(compbio.engine.client.Executable.ExecProvider)">getParameters</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#getResults(java.lang.String)">getResults</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#loadRunConfiguration(compbio.engine.client.RunConfiguration)">loadRunConfiguration</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#setEmail(java.lang.String)">setEmail</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#setName(java.lang.String)">setName</A></CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
-\r
-<A NAME="constructor_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Constructor Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="BlastAll(java.lang.String)"><!-- --></A><H3>\r
-BlastAll</H3>\r
-<PRE>\r
-public <B>BlastAll</B>(java.lang.String&nbsp;workDirectory)</PRE>\r
-<DL>\r
-</DL>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
-<A NAME="method_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="removeOutput(java.lang.String)"><!-- --></A><H3>\r
-removeOutput</H3>\r
-<PRE>\r
-public boolean <B>removeOutput</B>(java.lang.String&nbsp;outfile)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getCommand(compbio.engine.client.Executable.ExecProvider)"><!-- --></A><H3>\r
-getCommand</H3>\r
-<PRE>\r
-public java.lang.String <B>getCommand</B>(<A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getCommandName()"><!-- --></A><H3>\r
-getCommandName</H3>\r
-<PRE>\r
-public java.lang.String <B>getCommandName</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getCreatedFiles()"><!-- --></A><H3>\r
-getCreatedFiles</H3>\r
-<PRE>\r
-public java.util.List&lt;java.lang.String&gt; <B>getCreatedFiles</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getInput()"><!-- --></A><H3>\r
-getInput</H3>\r
-<PRE>\r
-public java.lang.String <B>getInput</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/BlastAll.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV CLASS&nbsp;\r
-&nbsp;<A HREF="../../../compbio/runner/_impl/BlastParameters.html" title="class in compbio.runner._impl"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/runner/_impl/BlastAll.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="BlastAll.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/runner/_impl/BlastParameters.html b/website/full_javadoc/compbio/runner/_impl/BlastParameters.html

deleted file mode 100644 (file)

index 0dfb3cf..0000000
--- a/website/full_javadoc/compbio/runner/_impl/BlastParameters.html
+++ /dev/null
@@ -1,200 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:49 GMT 2010 -->\r
-<TITLE>\r
-BlastParameters\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="BlastParameters";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/BlastParameters.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/runner/_impl/BlastAll.html" title="class in compbio.runner._impl"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../compbio/runner/_impl/Disembl.html" title="class in compbio.runner._impl"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/runner/_impl/BlastParameters.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="BlastParameters.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;CONSTR&nbsp;|&nbsp;<A HREF="#methods_inherited_from_class_java.lang.Object">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;CONSTR&nbsp;|&nbsp;METHOD</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.runner._impl</FONT>\r
-<BR>\r
-Class BlastParameters</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.runner._impl.BlastParameters</B>\r
-</PRE>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public class <B>BlastParameters</B><DT>extends java.lang.Object</DL>\r
-</PRE>\r
-\r
-<P>\r
-Utility class for common Blast parameters\r
-<P>\r
-\r
-<P>\r
-<DL>\r
-<DT><B>Author:</B></DT>\r
-  <DD>pvtroshin
- TODO</DD>\r
-</DL>\r
-<HR>\r
-\r
-<P>\r
-\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/BlastParameters.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/runner/_impl/BlastAll.html" title="class in compbio.runner._impl"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../compbio/runner/_impl/Disembl.html" title="class in compbio.runner._impl"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/runner/_impl/BlastParameters.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="BlastParameters.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;CONSTR&nbsp;|&nbsp;<A HREF="#methods_inherited_from_class_java.lang.Object">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;CONSTR&nbsp;|&nbsp;METHOD</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/runner/_impl/Disembl.html b/website/full_javadoc/compbio/runner/_impl/Disembl.html

deleted file mode 100644 (file)

index 9c5d600..0000000
--- a/website/full_javadoc/compbio/runner/_impl/Disembl.html
+++ /dev/null
@@ -1,379 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:49 GMT 2010 -->\r
-<TITLE>\r
-Disembl\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Disembl";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/Disembl.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/runner/_impl/BlastParameters.html" title="class in compbio.runner._impl"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../compbio/runner/_impl/Environment.html" title="class in compbio.runner._impl"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/runner/_impl/Disembl.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="Disembl.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.runner._impl</FONT>\r
-<BR>\r
-Class Disembl</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">compbio.runner._SkeletalCommandBuilder</A>\r
-      <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.runner._impl.Disembl</B>\r
-</PRE>\r
-<DL>\r
-<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>&gt;</DD>\r
-</DL>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public class <B>Disembl</B><DT>extends <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A></DL>\r
-</PRE>\r
-\r
-<P>\r
-<HR>\r
-\r
-<P>\r
-<!-- ======== NESTED CLASS SUMMARY ======== -->\r
-\r
-<A NAME="nested_class_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Nested Class Summary</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="nested_classes_inherited_from_class_compbio.engine.client.Executable"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Nested classes/interfaces inherited from interface compbio.engine.client.<A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A></CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-\r
-<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
-\r
-<A NAME="constructor_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Constructor Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/runner/_impl/Disembl.html#Disembl(java.lang.String)">Disembl</A></B>(java.lang.String&nbsp;workDirectory)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/_impl/Disembl.html#getCommand(compbio.engine.client.Executable.ExecProvider)">getCommand</A></B>(<A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/_impl/Disembl.html#getCommandName()">getCommandName</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.util.List&lt;java.lang.String&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/_impl/Disembl.html#getCreatedFiles()">getCreatedFiles</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/_impl/Disembl.html#getInput()">getInput</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;java.util.List&lt;java.lang.String&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/_impl/Disembl.html#getTestArgs()">getTestArgs</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/_impl/Disembl.html#getTestCommand()">getTestCommand</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_compbio.runner._SkeletalCommandBuilder"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class compbio.runner.<A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A></B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#addParameter(java.lang.String)">addParameter</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#addParameters(java.util.List)">addParameters</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#addParameters(java.lang.String[])">addParameters</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#getEmail()">getEmail</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#getError()">getError</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#getLimit(java.lang.String)">getLimit</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#getLimits()">getLimits</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#getName()">getName</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#getOutput()">getOutput</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#getParameters(compbio.engine.client.Executable.ExecProvider)">getParameters</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#getResults(java.lang.String)">getResults</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#loadRunConfiguration(compbio.engine.client.RunConfiguration)">loadRunConfiguration</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#setEmail(java.lang.String)">setEmail</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#setName(java.lang.String)">setName</A></CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
-\r
-<A NAME="constructor_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Constructor Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="Disembl(java.lang.String)"><!-- --></A><H3>\r
-Disembl</H3>\r
-<PRE>\r
-public <B>Disembl</B>(java.lang.String&nbsp;workDirectory)</PRE>\r
-<DL>\r
-</DL>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
-<A NAME="method_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="getTestArgs()"><!-- --></A><H3>\r
-getTestArgs</H3>\r
-<PRE>\r
-public static java.util.List&lt;java.lang.String&gt; <B>getTestArgs</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getCommand(compbio.engine.client.Executable.ExecProvider)"><!-- --></A><H3>\r
-getCommand</H3>\r
-<PRE>\r
-public java.lang.String <B>getCommand</B>(<A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getTestCommand()"><!-- --></A><H3>\r
-getTestCommand</H3>\r
-<PRE>\r
-public static java.lang.String <B>getTestCommand</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getCommandName()"><!-- --></A><H3>\r
-getCommandName</H3>\r
-<PRE>\r
-public java.lang.String <B>getCommandName</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getCreatedFiles()"><!-- --></A><H3>\r
-getCreatedFiles</H3>\r
-<PRE>\r
-public java.util.List&lt;java.lang.String&gt; <B>getCreatedFiles</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getInput()"><!-- --></A><H3>\r
-getInput</H3>\r
-<PRE>\r
-public java.lang.String <B>getInput</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/Disembl.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/runner/_impl/BlastParameters.html" title="class in compbio.runner._impl"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../compbio/runner/_impl/Environment.html" title="class in compbio.runner._impl"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/runner/_impl/Disembl.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="Disembl.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/runner/_impl/Environment.html b/website/full_javadoc/compbio/runner/_impl/Environment.html

deleted file mode 100644 (file)

index bc7399c..0000000
--- a/website/full_javadoc/compbio/runner/_impl/Environment.html
+++ /dev/null
@@ -1,265 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:49 GMT 2010 -->\r
-<TITLE>\r
-Environment\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Environment";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/Environment.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/runner/_impl/Disembl.html" title="class in compbio.runner._impl"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../compbio/runner/_impl/Mcl.html" title="class in compbio.runner._impl"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/runner/_impl/Environment.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="Environment.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;CONSTR&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;CONSTR&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.runner._impl</FONT>\r
-<BR>\r
-Class Environment</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.runner._impl.Environment</B>\r
-</PRE>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public final class <B>Environment</B><DT>extends java.lang.Object</DL>\r
-</PRE>\r
-\r
-<P>\r
-This is utility class to encapsulate environmental variables like directory paths\r
-<P>\r
-\r
-<P>\r
-<DL>\r
-<DT><B>Author:</B></DT>\r
-  <DD>pvtroshin</DD>\r
-</DL>\r
-<HR>\r
-\r
-<P>\r
-\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/_impl/Environment.html#getBlastBinDir()">getBlastBinDir</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/_impl/Environment.html#getBlastDatabasesDir()">getBlastDatabasesDir</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/_impl/Environment.html#getRPSBlastDatabasesDir()">getRPSBlastDatabasesDir</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
-<A NAME="method_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="getBlastBinDir()"><!-- --></A><H3>\r
-getBlastBinDir</H3>\r
-<PRE>\r
-public static java.lang.String <B>getBlastBinDir</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getBlastDatabasesDir()"><!-- --></A><H3>\r
-getBlastDatabasesDir</H3>\r
-<PRE>\r
-public static final java.lang.String <B>getBlastDatabasesDir</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getRPSBlastDatabasesDir()"><!-- --></A><H3>\r
-getRPSBlastDatabasesDir</H3>\r
-<PRE>\r
-public static final java.lang.String <B>getRPSBlastDatabasesDir</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/Environment.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/runner/_impl/Disembl.html" title="class in compbio.runner._impl"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../compbio/runner/_impl/Mcl.html" title="class in compbio.runner._impl"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/runner/_impl/Environment.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="Environment.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;CONSTR&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;CONSTR&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/runner/_impl/Mcl.html b/website/full_javadoc/compbio/runner/_impl/Mcl.html

deleted file mode 100644 (file)

index c5c546f..0000000
--- a/website/full_javadoc/compbio/runner/_impl/Mcl.html
+++ /dev/null
@@ -1,379 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:49 GMT 2010 -->\r
-<TITLE>\r
-Mcl\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Mcl";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/Mcl.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/runner/_impl/Environment.html" title="class in compbio.runner._impl"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/runner/_impl/Mcl.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="Mcl.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.runner._impl</FONT>\r
-<BR>\r
-Class Mcl</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">compbio.runner._SkeletalCommandBuilder</A>\r
-      <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.runner._impl.Mcl</B>\r
-</PRE>\r
-<DL>\r
-<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>&gt;</DD>\r
-</DL>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public class <B>Mcl</B><DT>extends <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A></DL>\r
-</PRE>\r
-\r
-<P>\r
-<HR>\r
-\r
-<P>\r
-<!-- ======== NESTED CLASS SUMMARY ======== -->\r
-\r
-<A NAME="nested_class_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Nested Class Summary</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="nested_classes_inherited_from_class_compbio.engine.client.Executable"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Nested classes/interfaces inherited from interface compbio.engine.client.<A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A></CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-\r
-<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
-\r
-<A NAME="constructor_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Constructor Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/runner/_impl/Mcl.html#Mcl(java.lang.String)">Mcl</A></B>(java.lang.String&nbsp;workDirectory)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/_impl/Mcl.html#getCommand(compbio.engine.client.Executable.ExecProvider)">getCommand</A></B>(<A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/_impl/Mcl.html#getCommandName()">getCommandName</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.util.List&lt;java.lang.String&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/_impl/Mcl.html#getCreatedFiles()">getCreatedFiles</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/_impl/Mcl.html#getInput()">getInput</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/_impl/Mcl.html#getTestCommand()">getTestCommand</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;java.util.List&lt;java.lang.String&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/_impl/Mcl.html#getTestParams()">getTestParams</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_compbio.runner._SkeletalCommandBuilder"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class compbio.runner.<A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A></B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#addParameter(java.lang.String)">addParameter</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#addParameters(java.util.List)">addParameters</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#addParameters(java.lang.String[])">addParameters</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#getEmail()">getEmail</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#getError()">getError</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#getLimit(java.lang.String)">getLimit</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#getLimits()">getLimits</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#getName()">getName</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#getOutput()">getOutput</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#getParameters(compbio.engine.client.Executable.ExecProvider)">getParameters</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#getResults(java.lang.String)">getResults</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#loadRunConfiguration(compbio.engine.client.RunConfiguration)">loadRunConfiguration</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#setEmail(java.lang.String)">setEmail</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#setName(java.lang.String)">setName</A></CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
-\r
-<A NAME="constructor_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Constructor Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="Mcl(java.lang.String)"><!-- --></A><H3>\r
-Mcl</H3>\r
-<PRE>\r
-public <B>Mcl</B>(java.lang.String&nbsp;workDirectory)</PRE>\r
-<DL>\r
-</DL>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
-<A NAME="method_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="getTestParams()"><!-- --></A><H3>\r
-getTestParams</H3>\r
-<PRE>\r
-public static java.util.List&lt;java.lang.String&gt; <B>getTestParams</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getCommand(compbio.engine.client.Executable.ExecProvider)"><!-- --></A><H3>\r
-getCommand</H3>\r
-<PRE>\r
-public java.lang.String <B>getCommand</B>(<A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getTestCommand()"><!-- --></A><H3>\r
-getTestCommand</H3>\r
-<PRE>\r
-public static java.lang.String <B>getTestCommand</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getCommandName()"><!-- --></A><H3>\r
-getCommandName</H3>\r
-<PRE>\r
-public java.lang.String <B>getCommandName</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getCreatedFiles()"><!-- --></A><H3>\r
-getCreatedFiles</H3>\r
-<PRE>\r
-public java.util.List&lt;java.lang.String&gt; <B>getCreatedFiles</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getInput()"><!-- --></A><H3>\r
-getInput</H3>\r
-<PRE>\r
-public java.lang.String <B>getInput</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/Mcl.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/runner/_impl/Environment.html" title="class in compbio.runner._impl"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/runner/_impl/Mcl.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="Mcl.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
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-\r
-<HR>\r
-\r
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diff --git a/website/full_javadoc/compbio/runner/_impl/NetNglyc.html b/website/full_javadoc/compbio/runner/_impl/NetNglyc.html

deleted file mode 100644 (file)

index 418085d..0000000
--- a/website/full_javadoc/compbio/runner/_impl/NetNglyc.html
+++ /dev/null
@@ -1,552 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:49 GMT 2010 -->\r
-<TITLE>\r
-NetNglyc\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="NetNglyc";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/NetNglyc.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/runner/_impl/Mcl.html" title="class in compbio.runner._impl"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../compbio/runner/_impl/OB.html" title="class in compbio.runner._impl"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/runner/_impl/NetNglyc.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="NetNglyc.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
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-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.runner._impl</FONT>\r
-<BR>\r
-Class NetNglyc</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.runner._impl.NetNglyc</B>\r
-</PRE>\r
-<DL>\r
-<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>&gt;</DD>\r
-</DL>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public class <B>NetNglyc</B><DT>extends java.lang.Object<DT>implements <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>&gt;</DL>\r
-</PRE>\r
-\r
-<P>\r
-<HR>\r
-\r
-<P>\r
-<!-- ======== NESTED CLASS SUMMARY ======== -->\r
-\r
-<A NAME="nested_class_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Nested Class Summary</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="nested_classes_inherited_from_class_compbio.engine.client.Executable"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Nested classes/interfaces inherited from interface compbio.engine.client.<A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A></CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-\r
-<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
-\r
-<A NAME="constructor_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Constructor Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/runner/_impl/NetNglyc.html#NetNglyc()">NetNglyc</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/_impl/NetNglyc.html#addParameters(java.util.List)">addParameters</A></B>(java.util.List&lt;java.lang.String&gt;&nbsp;parameters)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Adds parameter to the list of parameters for a native executable</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/_impl/NetNglyc.html#getCommandName()">getCommandName</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.util.List&lt;java.lang.String&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/_impl/NetNglyc.html#getCreatedFiles()">getCreatedFiles</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/_impl/NetNglyc.html#getError()">getError</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/_impl/NetNglyc.html#getInput()">getInput</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;<A HREF="../../../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/_impl/NetNglyc.html#getLimit(java.lang.String)">getLimit</A></B>(java.lang.String&nbsp;presetName)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;<A HREF="../../../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/_impl/NetNglyc.html#getLimits()">getLimits</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/_impl/NetNglyc.html#getOutput()">getOutput</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>&lt;<A HREF="../../../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/_impl/NetNglyc.html#getParameters(compbio.engine.client.Executable.ExecProvider)">getParameters</A></B>(<A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
-<TR ALIGN="right" VALIGN="">\r
-<TD NOWRAP><FONT SIZE="-1">\r
-<CODE>&lt;V&gt; V</CODE></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/_impl/NetNglyc.html#getResults(java.lang.String)">getResults</A></B>(java.lang.String&nbsp;directory)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;java.util.List&lt;java.lang.String&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/_impl/NetNglyc.html#getTestArgs()">getTestArgs</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/_impl/NetNglyc.html#getTestCommand()">getTestCommand</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;?&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/_impl/NetNglyc.html#loadRunConfiguration(compbio.engine.client.RunConfiguration)">loadRunConfiguration</A></B>(<A HREF="../../../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>&nbsp;rconfig)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
-\r
-<A NAME="constructor_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Constructor Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="NetNglyc()"><!-- --></A><H3>\r
-NetNglyc</H3>\r
-<PRE>\r
-public <B>NetNglyc</B>()</PRE>\r
-<DL>\r
-</DL>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
-<A NAME="method_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="getParameters(compbio.engine.client.Executable.ExecProvider)"><!-- --></A><H3>\r
-getParameters</H3>\r
-<PRE>\r
-public <A HREF="../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>&lt;<A HREF="../../../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>&gt; <B>getParameters</B>(<A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider)</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#getParameters(compbio.engine.client.Executable.ExecProvider)">getParameters</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getTestArgs()"><!-- --></A><H3>\r
-getTestArgs</H3>\r
-<PRE>\r
-public static java.util.List&lt;java.lang.String&gt; <B>getTestArgs</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="addParameters(java.util.List)"><!-- --></A><H3>\r
-addParameters</H3>\r
-<PRE>\r
-public <A HREF="../../../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A> <B>addParameters</B>(java.util.List&lt;java.lang.String&gt;&nbsp;parameters)</PRE>\r
-<DL>\r
-<DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/engine/client/Executable.html#addParameters(java.util.List)">Executable</A></CODE></B></DD>\r
-<DD>Adds parameter to the list of parameters for a native executable\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#addParameters(java.util.List)">addParameters</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>this Executable</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getTestCommand()"><!-- --></A><H3>\r
-getTestCommand</H3>\r
-<PRE>\r
-public static java.lang.String <B>getTestCommand</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getCommandName()"><!-- --></A><H3>\r
-getCommandName</H3>\r
-<PRE>\r
-public java.lang.String <B>getCommandName</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getCreatedFiles()"><!-- --></A><H3>\r
-getCreatedFiles</H3>\r
-<PRE>\r
-public java.util.List&lt;java.lang.String&gt; <B>getCreatedFiles</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#getCreatedFiles()">getCreatedFiles</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getInput()"><!-- --></A><H3>\r
-getInput</H3>\r
-<PRE>\r
-public java.lang.String <B>getInput</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#getInput()">getInput</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getResults(java.lang.String)"><!-- --></A><H3>\r
-getResults</H3>\r
-<PRE>\r
-public &lt;V&gt; V <B>getResults</B>(java.lang.String&nbsp;directory)</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#getResults(java.lang.String)">getResults</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="loadRunConfiguration(compbio.engine.client.RunConfiguration)"><!-- --></A><H3>\r
-loadRunConfiguration</H3>\r
-<PRE>\r
-public <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;?&gt; <B>loadRunConfiguration</B>(<A HREF="../../../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>&nbsp;rconfig)</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#loadRunConfiguration(compbio.engine.client.RunConfiguration)">loadRunConfiguration</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getOutput()"><!-- --></A><H3>\r
-getOutput</H3>\r
-<PRE>\r
-public java.lang.String <B>getOutput</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#getOutput()">getOutput</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getError()"><!-- --></A><H3>\r
-getError</H3>\r
-<PRE>\r
-public java.lang.String <B>getError</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#getError()">getError</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getLimit(java.lang.String)"><!-- --></A><H3>\r
-getLimit</H3>\r
-<PRE>\r
-public <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;<A HREF="../../../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>&gt; <B>getLimit</B>(java.lang.String&nbsp;presetName)</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#getLimit(java.lang.String)">getLimit</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getLimits()"><!-- --></A><H3>\r
-getLimits</H3>\r
-<PRE>\r
-public <A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;<A HREF="../../../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>&gt; <B>getLimits</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#getLimits()">getLimits</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/NetNglyc.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/runner/_impl/Mcl.html" title="class in compbio.runner._impl"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../compbio/runner/_impl/OB.html" title="class in compbio.runner._impl"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/runner/_impl/NetNglyc.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="NetNglyc.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/runner/_impl/OB.html b/website/full_javadoc/compbio/runner/_impl/OB.html

deleted file mode 100644 (file)

index 55d1730..0000000
--- a/website/full_javadoc/compbio/runner/_impl/OB.html
+++ /dev/null
@@ -1,382 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:49 GMT 2010 -->\r
-<TITLE>\r
-OB\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="OB";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/OB.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../compbio/runner/_impl/PSIBlast.html" title="class in compbio.runner._impl"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/runner/_impl/OB.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="OB.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.runner._impl</FONT>\r
-<BR>\r
-Class OB</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">compbio.runner._SkeletalCommandBuilder</A>\r
-      <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.runner._impl.OB</B>\r
-</PRE>\r
-<DL>\r
-<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>&gt;</DD>\r
-</DL>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public class <B>OB</B><DT>extends <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A></DL>\r
-</PRE>\r
-\r
-<P>\r
-TODO this needs fixing! Executable does not work\r
-<P>\r
-\r
-<P>\r
-<DL>\r
-<DT><B>Author:</B></DT>\r
-  <DD>pvtroshin</DD>\r
-</DL>\r
-<HR>\r
-\r
-<P>\r
-<!-- ======== NESTED CLASS SUMMARY ======== -->\r
-\r
-<A NAME="nested_class_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Nested Class Summary</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="nested_classes_inherited_from_class_compbio.engine.client.Executable"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Nested classes/interfaces inherited from interface compbio.engine.client.<A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A></CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-\r
-<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
-\r
-<A NAME="constructor_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Constructor Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/runner/_impl/OB.html#OB()">OB</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/runner/_impl/OB.html#OB(java.lang.String)">OB</A></B>(java.lang.String&nbsp;workDirectory)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.util.List&lt;java.lang.String&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/_impl/OB.html#getCreatedFiles()">getCreatedFiles</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/_impl/OB.html#getInput()">getInput</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.util.List&lt;java.lang.String&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/_impl/OB.html#getTestArgs()">getTestArgs</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/_impl/OB.html#getTestCommand()">getTestCommand</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/_impl/OB.html#main(java.lang.String[])">main</A></B>(java.lang.String[]&nbsp;args)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_compbio.runner._SkeletalCommandBuilder"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class compbio.runner.<A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A></B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#addParameter(java.lang.String)">addParameter</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#addParameters(java.util.List)">addParameters</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#addParameters(java.lang.String[])">addParameters</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#getEmail()">getEmail</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#getError()">getError</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#getLimit(java.lang.String)">getLimit</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#getLimits()">getLimits</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#getName()">getName</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#getOutput()">getOutput</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#getParameters(compbio.engine.client.Executable.ExecProvider)">getParameters</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#getResults(java.lang.String)">getResults</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#loadRunConfiguration(compbio.engine.client.RunConfiguration)">loadRunConfiguration</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#setEmail(java.lang.String)">setEmail</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#setName(java.lang.String)">setName</A></CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
-\r
-<A NAME="constructor_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Constructor Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="OB()"><!-- --></A><H3>\r
-OB</H3>\r
-<PRE>\r
-public <B>OB</B>()</PRE>\r
-<DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="OB(java.lang.String)"><!-- --></A><H3>\r
-OB</H3>\r
-<PRE>\r
-public <B>OB</B>(java.lang.String&nbsp;workDirectory)</PRE>\r
-<DL>\r
-</DL>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
-<A NAME="method_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="getTestCommand()"><!-- --></A><H3>\r
-getTestCommand</H3>\r
-<PRE>\r
-public static java.lang.String <B>getTestCommand</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getTestArgs()"><!-- --></A><H3>\r
-getTestArgs</H3>\r
-<PRE>\r
-public java.util.List&lt;java.lang.String&gt; <B>getTestArgs</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="main(java.lang.String[])"><!-- --></A><H3>\r
-main</H3>\r
-<PRE>\r
-public static void <B>main</B>(java.lang.String[]&nbsp;args)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getCreatedFiles()"><!-- --></A><H3>\r
-getCreatedFiles</H3>\r
-<PRE>\r
-public java.util.List&lt;java.lang.String&gt; <B>getCreatedFiles</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getInput()"><!-- --></A><H3>\r
-getInput</H3>\r
-<PRE>\r
-public java.lang.String <B>getInput</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/OB.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../compbio/runner/_impl/PSIBlast.html" title="class in compbio.runner._impl"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/runner/_impl/OB.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="OB.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/runner/_impl/PSIBlast.html b/website/full_javadoc/compbio/runner/_impl/PSIBlast.html

deleted file mode 100644 (file)

index b14bdb4..0000000
--- a/website/full_javadoc/compbio/runner/_impl/PSIBlast.html
+++ /dev/null
@@ -1,360 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:49 GMT 2010 -->\r
-<TITLE>\r
-PSIBlast\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="PSIBlast";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/PSIBlast.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/runner/_impl/OB.html" title="class in compbio.runner._impl"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../compbio/runner/_impl/Ronn.html" title="class in compbio.runner._impl"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/runner/_impl/PSIBlast.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="PSIBlast.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.runner._impl</FONT>\r
-<BR>\r
-Class PSIBlast</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">compbio.runner._SkeletalCommandBuilder</A>\r
-      <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.runner._impl.PSIBlast</B>\r
-</PRE>\r
-<DL>\r
-<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>&gt;</DD>\r
-</DL>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public class <B>PSIBlast</B><DT>extends <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A></DL>\r
-</PRE>\r
-\r
-<P>\r
-<HR>\r
-\r
-<P>\r
-<!-- ======== NESTED CLASS SUMMARY ======== -->\r
-\r
-<A NAME="nested_class_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Nested Class Summary</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="nested_classes_inherited_from_class_compbio.engine.client.Executable"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Nested classes/interfaces inherited from interface compbio.engine.client.<A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A></CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-\r
-<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
-\r
-<A NAME="constructor_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Constructor Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/runner/_impl/PSIBlast.html#PSIBlast(java.lang.String)">PSIBlast</A></B>(java.lang.String&nbsp;workDirectory)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/_impl/PSIBlast.html#getCommand(compbio.engine.client.Executable.ExecProvider)">getCommand</A></B>(<A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/_impl/PSIBlast.html#getCommandName()">getCommandName</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.util.List&lt;java.lang.String&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/_impl/PSIBlast.html#getCreatedFiles()">getCreatedFiles</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/_impl/PSIBlast.html#getInput()">getInput</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/_impl/PSIBlast.html#removeOutput(java.lang.String)">removeOutput</A></B>(java.lang.String&nbsp;outfile)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_compbio.runner._SkeletalCommandBuilder"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class compbio.runner.<A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A></B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#addParameter(java.lang.String)">addParameter</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#addParameters(java.util.List)">addParameters</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#addParameters(java.lang.String[])">addParameters</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#getEmail()">getEmail</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#getError()">getError</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#getLimit(java.lang.String)">getLimit</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#getLimits()">getLimits</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#getName()">getName</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#getOutput()">getOutput</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#getParameters(compbio.engine.client.Executable.ExecProvider)">getParameters</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#getResults(java.lang.String)">getResults</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#loadRunConfiguration(compbio.engine.client.RunConfiguration)">loadRunConfiguration</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#setEmail(java.lang.String)">setEmail</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#setName(java.lang.String)">setName</A></CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
-\r
-<A NAME="constructor_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Constructor Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="PSIBlast(java.lang.String)"><!-- --></A><H3>\r
-PSIBlast</H3>\r
-<PRE>\r
-public <B>PSIBlast</B>(java.lang.String&nbsp;workDirectory)</PRE>\r
-<DL>\r
-</DL>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
-<A NAME="method_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="removeOutput(java.lang.String)"><!-- --></A><H3>\r
-removeOutput</H3>\r
-<PRE>\r
-public boolean <B>removeOutput</B>(java.lang.String&nbsp;outfile)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getCommand(compbio.engine.client.Executable.ExecProvider)"><!-- --></A><H3>\r
-getCommand</H3>\r
-<PRE>\r
-public java.lang.String <B>getCommand</B>(<A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getCommandName()"><!-- --></A><H3>\r
-getCommandName</H3>\r
-<PRE>\r
-public java.lang.String <B>getCommandName</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getCreatedFiles()"><!-- --></A><H3>\r
-getCreatedFiles</H3>\r
-<PRE>\r
-public java.util.List&lt;java.lang.String&gt; <B>getCreatedFiles</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getInput()"><!-- --></A><H3>\r
-getInput</H3>\r
-<PRE>\r
-public java.lang.String <B>getInput</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/PSIBlast.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/runner/_impl/OB.html" title="class in compbio.runner._impl"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../compbio/runner/_impl/Ronn.html" title="class in compbio.runner._impl"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/runner/_impl/PSIBlast.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="PSIBlast.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/runner/_impl/RPSBlast.html b/website/full_javadoc/compbio/runner/_impl/RPSBlast.html

deleted file mode 100644 (file)

index 64cecfd..0000000
--- a/website/full_javadoc/compbio/runner/_impl/RPSBlast.html
+++ /dev/null
@@ -1,360 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:49 GMT 2010 -->\r
-<TITLE>\r
-RPSBlast\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="RPSBlast";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/RPSBlast.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/runner/_impl/Ronn.html" title="class in compbio.runner._impl"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../compbio/runner/_impl/Runners.html" title="class in compbio.runner._impl"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/runner/_impl/RPSBlast.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="RPSBlast.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.runner._impl</FONT>\r
-<BR>\r
-Class RPSBlast</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">compbio.runner._SkeletalCommandBuilder</A>\r
-      <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.runner._impl.RPSBlast</B>\r
-</PRE>\r
-<DL>\r
-<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>&gt;</DD>\r
-</DL>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public class <B>RPSBlast</B><DT>extends <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A></DL>\r
-</PRE>\r
-\r
-<P>\r
-<HR>\r
-\r
-<P>\r
-<!-- ======== NESTED CLASS SUMMARY ======== -->\r
-\r
-<A NAME="nested_class_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Nested Class Summary</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="nested_classes_inherited_from_class_compbio.engine.client.Executable"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Nested classes/interfaces inherited from interface compbio.engine.client.<A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A></CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-\r
-<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
-\r
-<A NAME="constructor_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Constructor Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/runner/_impl/RPSBlast.html#RPSBlast(java.lang.String)">RPSBlast</A></B>(java.lang.String&nbsp;workDirectory)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/_impl/RPSBlast.html#getCommand(compbio.engine.client.Executable.ExecProvider)">getCommand</A></B>(<A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/_impl/RPSBlast.html#getCommandName()">getCommandName</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.util.List&lt;java.lang.String&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/_impl/RPSBlast.html#getCreatedFiles()">getCreatedFiles</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/_impl/RPSBlast.html#getInput()">getInput</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/_impl/RPSBlast.html#getTestCommand()">getTestCommand</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_compbio.runner._SkeletalCommandBuilder"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class compbio.runner.<A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A></B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#addParameter(java.lang.String)">addParameter</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#addParameters(java.util.List)">addParameters</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#addParameters(java.lang.String[])">addParameters</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#getEmail()">getEmail</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#getError()">getError</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#getLimit(java.lang.String)">getLimit</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#getLimits()">getLimits</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#getName()">getName</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#getOutput()">getOutput</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#getParameters(compbio.engine.client.Executable.ExecProvider)">getParameters</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#getResults(java.lang.String)">getResults</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#loadRunConfiguration(compbio.engine.client.RunConfiguration)">loadRunConfiguration</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#setEmail(java.lang.String)">setEmail</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#setName(java.lang.String)">setName</A></CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
-\r
-<A NAME="constructor_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Constructor Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="RPSBlast(java.lang.String)"><!-- --></A><H3>\r
-RPSBlast</H3>\r
-<PRE>\r
-public <B>RPSBlast</B>(java.lang.String&nbsp;workDirectory)</PRE>\r
-<DL>\r
-</DL>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
-<A NAME="method_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="getCommand(compbio.engine.client.Executable.ExecProvider)"><!-- --></A><H3>\r
-getCommand</H3>\r
-<PRE>\r
-public java.lang.String <B>getCommand</B>(<A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getTestCommand()"><!-- --></A><H3>\r
-getTestCommand</H3>\r
-<PRE>\r
-public static java.lang.String <B>getTestCommand</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getCommandName()"><!-- --></A><H3>\r
-getCommandName</H3>\r
-<PRE>\r
-public static java.lang.String <B>getCommandName</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getCreatedFiles()"><!-- --></A><H3>\r
-getCreatedFiles</H3>\r
-<PRE>\r
-public java.util.List&lt;java.lang.String&gt; <B>getCreatedFiles</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getInput()"><!-- --></A><H3>\r
-getInput</H3>\r
-<PRE>\r
-public java.lang.String <B>getInput</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/RPSBlast.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/runner/_impl/Ronn.html" title="class in compbio.runner._impl"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../compbio/runner/_impl/Runners.html" title="class in compbio.runner._impl"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/runner/_impl/RPSBlast.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="RPSBlast.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/runner/_impl/Ronn.html b/website/full_javadoc/compbio/runner/_impl/Ronn.html

deleted file mode 100644 (file)

index d5f9998..0000000
--- a/website/full_javadoc/compbio/runner/_impl/Ronn.html
+++ /dev/null
@@ -1,360 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:49 GMT 2010 -->\r
-<TITLE>\r
-Ronn\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Ronn";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/Ronn.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/runner/_impl/PSIBlast.html" title="class in compbio.runner._impl"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../compbio/runner/_impl/RPSBlast.html" title="class in compbio.runner._impl"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/runner/_impl/Ronn.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="Ronn.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.runner._impl</FONT>\r
-<BR>\r
-Class Ronn</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">compbio.runner._SkeletalCommandBuilder</A>\r
-      <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.runner._impl.Ronn</B>\r
-</PRE>\r
-<DL>\r
-<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>&gt;</DD>\r
-</DL>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public class <B>Ronn</B><DT>extends <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A></DL>\r
-</PRE>\r
-\r
-<P>\r
-<HR>\r
-\r
-<P>\r
-<!-- ======== NESTED CLASS SUMMARY ======== -->\r
-\r
-<A NAME="nested_class_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Nested Class Summary</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="nested_classes_inherited_from_class_compbio.engine.client.Executable"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Nested classes/interfaces inherited from interface compbio.engine.client.<A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A></CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-\r
-<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
-\r
-<A NAME="constructor_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Constructor Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/runner/_impl/Ronn.html#Ronn(java.lang.String)">Ronn</A></B>(java.lang.String&nbsp;workDirectory)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/_impl/Ronn.html#getCommand(compbio.engine.client.Executable.ExecProvider)">getCommand</A></B>(<A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/_impl/Ronn.html#getCommandName()">getCommandName</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.util.List&lt;java.lang.String&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/_impl/Ronn.html#getCreatedFiles()">getCreatedFiles</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/_impl/Ronn.html#getInput()">getInput</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/_impl/Ronn.html#getTestCommand()">getTestCommand</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_compbio.runner._SkeletalCommandBuilder"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class compbio.runner.<A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A></B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#addParameter(java.lang.String)">addParameter</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#addParameters(java.util.List)">addParameters</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#addParameters(java.lang.String[])">addParameters</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#getEmail()">getEmail</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#getError()">getError</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#getLimit(java.lang.String)">getLimit</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#getLimits()">getLimits</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#getName()">getName</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#getOutput()">getOutput</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#getParameters(compbio.engine.client.Executable.ExecProvider)">getParameters</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#getResults(java.lang.String)">getResults</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#loadRunConfiguration(compbio.engine.client.RunConfiguration)">loadRunConfiguration</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#setEmail(java.lang.String)">setEmail</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#setName(java.lang.String)">setName</A></CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
-\r
-<A NAME="constructor_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Constructor Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="Ronn(java.lang.String)"><!-- --></A><H3>\r
-Ronn</H3>\r
-<PRE>\r
-public <B>Ronn</B>(java.lang.String&nbsp;workDirectory)</PRE>\r
-<DL>\r
-</DL>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
-<A NAME="method_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="getCommand(compbio.engine.client.Executable.ExecProvider)"><!-- --></A><H3>\r
-getCommand</H3>\r
-<PRE>\r
-public java.lang.String <B>getCommand</B>(<A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getTestCommand()"><!-- --></A><H3>\r
-getTestCommand</H3>\r
-<PRE>\r
-public static java.lang.String <B>getTestCommand</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getCommandName()"><!-- --></A><H3>\r
-getCommandName</H3>\r
-<PRE>\r
-public java.lang.String <B>getCommandName</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getCreatedFiles()"><!-- --></A><H3>\r
-getCreatedFiles</H3>\r
-<PRE>\r
-public java.util.List&lt;java.lang.String&gt; <B>getCreatedFiles</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getInput()"><!-- --></A><H3>\r
-getInput</H3>\r
-<PRE>\r
-public java.lang.String <B>getInput</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/Ronn.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/runner/_impl/PSIBlast.html" title="class in compbio.runner._impl"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../compbio/runner/_impl/RPSBlast.html" title="class in compbio.runner._impl"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/runner/_impl/Ronn.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="Ronn.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/runner/_impl/Runners.html b/website/full_javadoc/compbio/runner/_impl/Runners.html

deleted file mode 100644 (file)

index 3a3978d..0000000
--- a/website/full_javadoc/compbio/runner/_impl/Runners.html
+++ /dev/null
@@ -1,371 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:49 GMT 2010 -->\r
-<TITLE>\r
-Runners\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Runners";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/Runners.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/runner/_impl/RPSBlast.html" title="class in compbio.runner._impl"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;NEXT CLASS</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/runner/_impl/Runners.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="Runners.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;CONSTR&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;CONSTR&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.runner._impl</FONT>\r
-<BR>\r
-Class Runners</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.runner._impl.Runners</B>\r
-</PRE>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public final class <B>Runners</B><DT>extends java.lang.Object</DL>\r
-</PRE>\r
-\r
-<P>\r
-<HR>\r
-\r
-<P>\r
-\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../compbio/runner/_impl/BlastAll.html" title="class in compbio.runner._impl">BlastAll</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/_impl/Runners.html#getBlastAllRunnable(java.lang.String)">getBlastAllRunnable</A></B>(java.lang.String&nbsp;workDirectory)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../compbio/runner/_impl/Disembl.html" title="class in compbio.runner._impl">Disembl</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/_impl/Runners.html#getDisemblRunnable(java.lang.String)">getDisemblRunnable</A></B>(java.lang.String&nbsp;workDirectory)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../compbio/runner/_impl/Mcl.html" title="class in compbio.runner._impl">Mcl</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/_impl/Runners.html#getMclRunnable(java.lang.String)">getMclRunnable</A></B>(java.lang.String&nbsp;workDirectory)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/_impl/Runners.html#getNetNglycRunnable(java.lang.String)">getNetNglycRunnable</A></B>(java.lang.String&nbsp;workDirectory)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../compbio/runner/_impl/OB.html" title="class in compbio.runner._impl">OB</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/_impl/Runners.html#getOBRunnable(java.lang.String)">getOBRunnable</A></B>(java.lang.String&nbsp;workDirectory)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../compbio/runner/_impl/PSIBlast.html" title="class in compbio.runner._impl">PSIBlast</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/_impl/Runners.html#getPSIBlastRunnable(java.lang.String)">getPSIBlastRunnable</A></B>(java.lang.String&nbsp;workDirectory)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../compbio/runner/_impl/Ronn.html" title="class in compbio.runner._impl">Ronn</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/_impl/Runners.html#getRonnRunnable(java.lang.String)">getRonnRunnable</A></B>(java.lang.String&nbsp;workDirectory)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../compbio/runner/_impl/RPSBlast.html" title="class in compbio.runner._impl">RPSBlast</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/_impl/Runners.html#getRPSBlastRunnable(java.lang.String)">getRPSBlastRunnable</A></B>(java.lang.String&nbsp;workDirectory)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;compbio.runner._impl.Tmhmm2</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/_impl/Runners.html#getTmhmm2Runnable(java.lang.String)">getTmhmm2Runnable</A></B>(java.lang.String&nbsp;workDirectory)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
-<A NAME="method_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="getMclRunnable(java.lang.String)"><!-- --></A><H3>\r
-getMclRunnable</H3>\r
-<PRE>\r
-public static <A HREF="../../../compbio/runner/_impl/Mcl.html" title="class in compbio.runner._impl">Mcl</A> <B>getMclRunnable</B>(java.lang.String&nbsp;workDirectory)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getOBRunnable(java.lang.String)"><!-- --></A><H3>\r
-getOBRunnable</H3>\r
-<PRE>\r
-public static <A HREF="../../../compbio/runner/_impl/OB.html" title="class in compbio.runner._impl">OB</A> <B>getOBRunnable</B>(java.lang.String&nbsp;workDirectory)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getDisemblRunnable(java.lang.String)"><!-- --></A><H3>\r
-getDisemblRunnable</H3>\r
-<PRE>\r
-public static <A HREF="../../../compbio/runner/_impl/Disembl.html" title="class in compbio.runner._impl">Disembl</A> <B>getDisemblRunnable</B>(java.lang.String&nbsp;workDirectory)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getNetNglycRunnable(java.lang.String)"><!-- --></A><H3>\r
-getNetNglycRunnable</H3>\r
-<PRE>\r
-public static <A HREF="../../../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A> <B>getNetNglycRunnable</B>(java.lang.String&nbsp;workDirectory)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getRonnRunnable(java.lang.String)"><!-- --></A><H3>\r
-getRonnRunnable</H3>\r
-<PRE>\r
-public static <A HREF="../../../compbio/runner/_impl/Ronn.html" title="class in compbio.runner._impl">Ronn</A> <B>getRonnRunnable</B>(java.lang.String&nbsp;workDirectory)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getTmhmm2Runnable(java.lang.String)"><!-- --></A><H3>\r
-getTmhmm2Runnable</H3>\r
-<PRE>\r
-public static compbio.runner._impl.Tmhmm2 <B>getTmhmm2Runnable</B>(java.lang.String&nbsp;workDirectory)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getRPSBlastRunnable(java.lang.String)"><!-- --></A><H3>\r
-getRPSBlastRunnable</H3>\r
-<PRE>\r
-public static <A HREF="../../../compbio/runner/_impl/RPSBlast.html" title="class in compbio.runner._impl">RPSBlast</A> <B>getRPSBlastRunnable</B>(java.lang.String&nbsp;workDirectory)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getBlastAllRunnable(java.lang.String)"><!-- --></A><H3>\r
-getBlastAllRunnable</H3>\r
-<PRE>\r
-public static <A HREF="../../../compbio/runner/_impl/BlastAll.html" title="class in compbio.runner._impl">BlastAll</A> <B>getBlastAllRunnable</B>(java.lang.String&nbsp;workDirectory)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getPSIBlastRunnable(java.lang.String)"><!-- --></A><H3>\r
-getPSIBlastRunnable</H3>\r
-<PRE>\r
-public static <A HREF="../../../compbio/runner/_impl/PSIBlast.html" title="class in compbio.runner._impl">PSIBlast</A> <B>getPSIBlastRunnable</B>(java.lang.String&nbsp;workDirectory)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/Runners.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/runner/_impl/RPSBlast.html" title="class in compbio.runner._impl"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;NEXT CLASS</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/runner/_impl/Runners.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="Runners.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;CONSTR&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;CONSTR&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/runner/_impl/class-use/BlastAll.html b/website/full_javadoc/compbio/runner/_impl/class-use/BlastAll.html

deleted file mode 100644 (file)

index 6389cd6..0000000
--- a/website/full_javadoc/compbio/runner/_impl/class-use/BlastAll.html
+++ /dev/null
@@ -1,180 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Uses of Class compbio.runner._impl.BlastAll\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Uses of Class compbio.runner._impl.BlastAll";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../compbio/runner/_impl/BlastAll.html" title="class in compbio.runner._impl"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/runner/_impl/\class-useBlastAll.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="BlastAll.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-<B>Uses of Class<br>compbio.runner._impl.BlastAll</B></H2>\r
-</CENTER>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Packages that use <A HREF="../../../../compbio/runner/_impl/BlastAll.html" title="class in compbio.runner._impl">BlastAll</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.runner._impl"><B>compbio.runner._impl</B></A></TD>\r
-<TD>&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.runner._impl"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../../compbio/runner/_impl/BlastAll.html" title="class in compbio.runner._impl">BlastAll</A> in <A HREF="../../../../compbio/runner/_impl/package-summary.html">compbio.runner._impl</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/runner/_impl/package-summary.html">compbio.runner._impl</A> that return <A HREF="../../../../compbio/runner/_impl/BlastAll.html" title="class in compbio.runner._impl">BlastAll</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../../compbio/runner/_impl/BlastAll.html" title="class in compbio.runner._impl">BlastAll</A></CODE></FONT></TD>\r
-<TD><CODE><B>Runners.</B><B><A HREF="../../../../compbio/runner/_impl/Runners.html#getBlastAllRunnable(java.lang.String)">getBlastAllRunnable</A></B>(java.lang.String&nbsp;workDirectory)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../compbio/runner/_impl/BlastAll.html" title="class in compbio.runner._impl"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/runner/_impl/\class-useBlastAll.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="BlastAll.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/runner/_impl/class-use/BlastParameters.html b/website/full_javadoc/compbio/runner/_impl/class-use/BlastParameters.html

deleted file mode 100644 (file)

index 8ebcce6..0000000
--- a/website/full_javadoc/compbio/runner/_impl/class-use/BlastParameters.html
+++ /dev/null
@@ -1,144 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Uses of Class compbio.runner._impl.BlastParameters\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Uses of Class compbio.runner._impl.BlastParameters";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../compbio/runner/_impl/BlastParameters.html" title="class in compbio.runner._impl"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/runner/_impl/\class-useBlastParameters.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="BlastParameters.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-<B>Uses of Class<br>compbio.runner._impl.BlastParameters</B></H2>\r
-</CENTER>\r
-No usage of compbio.runner._impl.BlastParameters\r
-<P>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../compbio/runner/_impl/BlastParameters.html" title="class in compbio.runner._impl"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/runner/_impl/\class-useBlastParameters.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="BlastParameters.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/runner/_impl/class-use/Disembl.html b/website/full_javadoc/compbio/runner/_impl/class-use/Disembl.html

deleted file mode 100644 (file)

index 005572a..0000000
--- a/website/full_javadoc/compbio/runner/_impl/class-use/Disembl.html
+++ /dev/null
@@ -1,180 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Uses of Class compbio.runner._impl.Disembl\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Uses of Class compbio.runner._impl.Disembl";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../compbio/runner/_impl/Disembl.html" title="class in compbio.runner._impl"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/runner/_impl/\class-useDisembl.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="Disembl.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-<B>Uses of Class<br>compbio.runner._impl.Disembl</B></H2>\r
-</CENTER>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Packages that use <A HREF="../../../../compbio/runner/_impl/Disembl.html" title="class in compbio.runner._impl">Disembl</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.runner._impl"><B>compbio.runner._impl</B></A></TD>\r
-<TD>&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.runner._impl"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../../compbio/runner/_impl/Disembl.html" title="class in compbio.runner._impl">Disembl</A> in <A HREF="../../../../compbio/runner/_impl/package-summary.html">compbio.runner._impl</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/runner/_impl/package-summary.html">compbio.runner._impl</A> that return <A HREF="../../../../compbio/runner/_impl/Disembl.html" title="class in compbio.runner._impl">Disembl</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../../compbio/runner/_impl/Disembl.html" title="class in compbio.runner._impl">Disembl</A></CODE></FONT></TD>\r
-<TD><CODE><B>Runners.</B><B><A HREF="../../../../compbio/runner/_impl/Runners.html#getDisemblRunnable(java.lang.String)">getDisemblRunnable</A></B>(java.lang.String&nbsp;workDirectory)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../compbio/runner/_impl/Disembl.html" title="class in compbio.runner._impl"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
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-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/runner/_impl/\class-useDisembl.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="Disembl.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/runner/_impl/class-use/Environment.html b/website/full_javadoc/compbio/runner/_impl/class-use/Environment.html

deleted file mode 100644 (file)

index 243aeae..0000000
--- a/website/full_javadoc/compbio/runner/_impl/class-use/Environment.html
+++ /dev/null
@@ -1,144 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Uses of Class compbio.runner._impl.Environment\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Uses of Class compbio.runner._impl.Environment";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../compbio/runner/_impl/Environment.html" title="class in compbio.runner._impl"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/runner/_impl/\class-useEnvironment.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="Environment.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-<B>Uses of Class<br>compbio.runner._impl.Environment</B></H2>\r
-</CENTER>\r
-No usage of compbio.runner._impl.Environment\r
-<P>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../compbio/runner/_impl/Environment.html" title="class in compbio.runner._impl"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/runner/_impl/\class-useEnvironment.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="Environment.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/runner/_impl/class-use/Mcl.html b/website/full_javadoc/compbio/runner/_impl/class-use/Mcl.html

deleted file mode 100644 (file)

index d08bb98..0000000
--- a/website/full_javadoc/compbio/runner/_impl/class-use/Mcl.html
+++ /dev/null
@@ -1,180 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Uses of Class compbio.runner._impl.Mcl\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Uses of Class compbio.runner._impl.Mcl";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../compbio/runner/_impl/Mcl.html" title="class in compbio.runner._impl"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
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-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/runner/_impl/\class-useMcl.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
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-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
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-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
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-\r
-\r
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-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-<B>Uses of Class<br>compbio.runner._impl.Mcl</B></H2>\r
-</CENTER>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Packages that use <A HREF="../../../../compbio/runner/_impl/Mcl.html" title="class in compbio.runner._impl">Mcl</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.runner._impl"><B>compbio.runner._impl</B></A></TD>\r
-<TD>&nbsp;&nbsp;</TD>\r
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-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.runner._impl"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../../compbio/runner/_impl/Mcl.html" title="class in compbio.runner._impl">Mcl</A> in <A HREF="../../../../compbio/runner/_impl/package-summary.html">compbio.runner._impl</A></FONT></TH>\r
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-&nbsp;\r
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-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/runner/_impl/package-summary.html">compbio.runner._impl</A> that return <A HREF="../../../../compbio/runner/_impl/Mcl.html" title="class in compbio.runner._impl">Mcl</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../../compbio/runner/_impl/Mcl.html" title="class in compbio.runner._impl">Mcl</A></CODE></FONT></TD>\r
-<TD><CODE><B>Runners.</B><B><A HREF="../../../../compbio/runner/_impl/Runners.html#getMclRunnable(java.lang.String)">getMclRunnable</A></B>(java.lang.String&nbsp;workDirectory)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
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-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
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-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
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-\r
-\r
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diff --git a/website/full_javadoc/compbio/runner/_impl/class-use/NetNglyc.html b/website/full_javadoc/compbio/runner/_impl/class-use/NetNglyc.html

deleted file mode 100644 (file)

index ecd9ab5..0000000
--- a/website/full_javadoc/compbio/runner/_impl/class-use/NetNglyc.html
+++ /dev/null
@@ -1,220 +0,0 @@
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-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Uses of Class compbio.runner._impl.NetNglyc\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Uses of Class compbio.runner._impl.NetNglyc";\r
-    }\r
-}\r
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-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
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-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
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-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/runner/_impl/\class-useNetNglyc.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="NetNglyc.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
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-\r
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-<CENTER>\r
-<H2>\r
-<B>Uses of Class<br>compbio.runner._impl.NetNglyc</B></H2>\r
-</CENTER>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
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-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Packages that use <A HREF="../../../../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.runner._impl"><B>compbio.runner._impl</B></A></TD>\r
-<TD>&nbsp;&nbsp;</TD>\r
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-<P>\r
-<A NAME="compbio.runner._impl"><!-- --></A>\r
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-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A> in <A HREF="../../../../compbio/runner/_impl/package-summary.html">compbio.runner._impl</A></FONT></TH>\r
-</TR>\r
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-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/runner/_impl/package-summary.html">compbio.runner._impl</A> that return <A HREF="../../../../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A></CODE></FONT></TD>\r
-<TD><CODE><B>NetNglyc.</B><B><A HREF="../../../../compbio/runner/_impl/NetNglyc.html#addParameters(java.util.List)">addParameters</A></B>(java.util.List&lt;java.lang.String&gt;&nbsp;parameters)</CODE>\r
-\r
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-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
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-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A></CODE></FONT></TD>\r
-<TD><CODE><B>Runners.</B><B><A HREF="../../../../compbio/runner/_impl/Runners.html#getNetNglycRunnable(java.lang.String)">getNetNglycRunnable</A></B>(java.lang.String&nbsp;workDirectory)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
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-&nbsp;\r
-<P>\r
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-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/runner/_impl/package-summary.html">compbio.runner._impl</A> that return types with arguments of type <A HREF="../../../../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;<A HREF="../../../../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>NetNglyc.</B><B><A HREF="../../../../compbio/runner/_impl/NetNglyc.html#getLimit(java.lang.String)">getLimit</A></B>(java.lang.String&nbsp;presetName)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
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-<TD><CODE><B>NetNglyc.</B><B><A HREF="../../../../compbio/runner/_impl/NetNglyc.html#getLimits()">getLimits</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>&lt;<A HREF="../../../../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>NetNglyc.</B><B><A HREF="../../../../compbio/runner/_impl/NetNglyc.html#getParameters(compbio.engine.client.Executable.ExecProvider)">getParameters</A></B>(<A HREF="../../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider)</CODE>\r
-\r
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-</TR>\r
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-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
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-</TR>\r
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-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/runner/_impl/\class-useNetNglyc.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="NetNglyc.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
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-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/runner/_impl/class-use/OB.html b/website/full_javadoc/compbio/runner/_impl/class-use/OB.html

deleted file mode 100644 (file)

index ce2519a..0000000
--- a/website/full_javadoc/compbio/runner/_impl/class-use/OB.html
+++ /dev/null
@@ -1,180 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Uses of Class compbio.runner._impl.OB\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Uses of Class compbio.runner._impl.OB";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../compbio/runner/_impl/OB.html" title="class in compbio.runner._impl"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/runner/_impl/\class-useOB.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="OB.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-<B>Uses of Class<br>compbio.runner._impl.OB</B></H2>\r
-</CENTER>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Packages that use <A HREF="../../../../compbio/runner/_impl/OB.html" title="class in compbio.runner._impl">OB</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.runner._impl"><B>compbio.runner._impl</B></A></TD>\r
-<TD>&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.runner._impl"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../../compbio/runner/_impl/OB.html" title="class in compbio.runner._impl">OB</A> in <A HREF="../../../../compbio/runner/_impl/package-summary.html">compbio.runner._impl</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/runner/_impl/package-summary.html">compbio.runner._impl</A> that return <A HREF="../../../../compbio/runner/_impl/OB.html" title="class in compbio.runner._impl">OB</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../../compbio/runner/_impl/OB.html" title="class in compbio.runner._impl">OB</A></CODE></FONT></TD>\r
-<TD><CODE><B>Runners.</B><B><A HREF="../../../../compbio/runner/_impl/Runners.html#getOBRunnable(java.lang.String)">getOBRunnable</A></B>(java.lang.String&nbsp;workDirectory)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../compbio/runner/_impl/OB.html" title="class in compbio.runner._impl"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/runner/_impl/\class-useOB.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="OB.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/runner/_impl/class-use/PSIBlast.html b/website/full_javadoc/compbio/runner/_impl/class-use/PSIBlast.html

deleted file mode 100644 (file)

index 8bc9956..0000000
--- a/website/full_javadoc/compbio/runner/_impl/class-use/PSIBlast.html
+++ /dev/null
@@ -1,180 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Uses of Class compbio.runner._impl.PSIBlast\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Uses of Class compbio.runner._impl.PSIBlast";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../compbio/runner/_impl/PSIBlast.html" title="class in compbio.runner._impl"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/runner/_impl/\class-usePSIBlast.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="PSIBlast.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-<B>Uses of Class<br>compbio.runner._impl.PSIBlast</B></H2>\r
-</CENTER>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Packages that use <A HREF="../../../../compbio/runner/_impl/PSIBlast.html" title="class in compbio.runner._impl">PSIBlast</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.runner._impl"><B>compbio.runner._impl</B></A></TD>\r
-<TD>&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.runner._impl"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../../compbio/runner/_impl/PSIBlast.html" title="class in compbio.runner._impl">PSIBlast</A> in <A HREF="../../../../compbio/runner/_impl/package-summary.html">compbio.runner._impl</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/runner/_impl/package-summary.html">compbio.runner._impl</A> that return <A HREF="../../../../compbio/runner/_impl/PSIBlast.html" title="class in compbio.runner._impl">PSIBlast</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../../compbio/runner/_impl/PSIBlast.html" title="class in compbio.runner._impl">PSIBlast</A></CODE></FONT></TD>\r
-<TD><CODE><B>Runners.</B><B><A HREF="../../../../compbio/runner/_impl/Runners.html#getPSIBlastRunnable(java.lang.String)">getPSIBlastRunnable</A></B>(java.lang.String&nbsp;workDirectory)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../compbio/runner/_impl/PSIBlast.html" title="class in compbio.runner._impl"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/runner/_impl/\class-usePSIBlast.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="PSIBlast.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/runner/_impl/class-use/RPSBlast.html b/website/full_javadoc/compbio/runner/_impl/class-use/RPSBlast.html

deleted file mode 100644 (file)

index a1f52e3..0000000
--- a/website/full_javadoc/compbio/runner/_impl/class-use/RPSBlast.html
+++ /dev/null
@@ -1,180 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Uses of Class compbio.runner._impl.RPSBlast\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Uses of Class compbio.runner._impl.RPSBlast";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../compbio/runner/_impl/RPSBlast.html" title="class in compbio.runner._impl"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/runner/_impl/\class-useRPSBlast.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="RPSBlast.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-<B>Uses of Class<br>compbio.runner._impl.RPSBlast</B></H2>\r
-</CENTER>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Packages that use <A HREF="../../../../compbio/runner/_impl/RPSBlast.html" title="class in compbio.runner._impl">RPSBlast</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.runner._impl"><B>compbio.runner._impl</B></A></TD>\r
-<TD>&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.runner._impl"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../../compbio/runner/_impl/RPSBlast.html" title="class in compbio.runner._impl">RPSBlast</A> in <A HREF="../../../../compbio/runner/_impl/package-summary.html">compbio.runner._impl</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/runner/_impl/package-summary.html">compbio.runner._impl</A> that return <A HREF="../../../../compbio/runner/_impl/RPSBlast.html" title="class in compbio.runner._impl">RPSBlast</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../../compbio/runner/_impl/RPSBlast.html" title="class in compbio.runner._impl">RPSBlast</A></CODE></FONT></TD>\r
-<TD><CODE><B>Runners.</B><B><A HREF="../../../../compbio/runner/_impl/Runners.html#getRPSBlastRunnable(java.lang.String)">getRPSBlastRunnable</A></B>(java.lang.String&nbsp;workDirectory)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../compbio/runner/_impl/RPSBlast.html" title="class in compbio.runner._impl"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/runner/_impl/\class-useRPSBlast.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="RPSBlast.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/runner/_impl/class-use/Ronn.html b/website/full_javadoc/compbio/runner/_impl/class-use/Ronn.html

deleted file mode 100644 (file)

index cc6975e..0000000
--- a/website/full_javadoc/compbio/runner/_impl/class-use/Ronn.html
+++ /dev/null
@@ -1,180 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Uses of Class compbio.runner._impl.Ronn\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Uses of Class compbio.runner._impl.Ronn";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../compbio/runner/_impl/Ronn.html" title="class in compbio.runner._impl"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/runner/_impl/\class-useRonn.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="Ronn.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-<B>Uses of Class<br>compbio.runner._impl.Ronn</B></H2>\r
-</CENTER>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Packages that use <A HREF="../../../../compbio/runner/_impl/Ronn.html" title="class in compbio.runner._impl">Ronn</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.runner._impl"><B>compbio.runner._impl</B></A></TD>\r
-<TD>&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.runner._impl"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../../compbio/runner/_impl/Ronn.html" title="class in compbio.runner._impl">Ronn</A> in <A HREF="../../../../compbio/runner/_impl/package-summary.html">compbio.runner._impl</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/runner/_impl/package-summary.html">compbio.runner._impl</A> that return <A HREF="../../../../compbio/runner/_impl/Ronn.html" title="class in compbio.runner._impl">Ronn</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../../compbio/runner/_impl/Ronn.html" title="class in compbio.runner._impl">Ronn</A></CODE></FONT></TD>\r
-<TD><CODE><B>Runners.</B><B><A HREF="../../../../compbio/runner/_impl/Runners.html#getRonnRunnable(java.lang.String)">getRonnRunnable</A></B>(java.lang.String&nbsp;workDirectory)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../compbio/runner/_impl/Ronn.html" title="class in compbio.runner._impl"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/runner/_impl/\class-useRonn.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="Ronn.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/runner/_impl/class-use/Runners.html b/website/full_javadoc/compbio/runner/_impl/class-use/Runners.html

deleted file mode 100644 (file)

index af87076..0000000
--- a/website/full_javadoc/compbio/runner/_impl/class-use/Runners.html
+++ /dev/null
@@ -1,144 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Uses of Class compbio.runner._impl.Runners\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Uses of Class compbio.runner._impl.Runners";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../compbio/runner/_impl/Runners.html" title="class in compbio.runner._impl"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/runner/_impl/\class-useRunners.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="Runners.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-<B>Uses of Class<br>compbio.runner._impl.Runners</B></H2>\r
-</CENTER>\r
-No usage of compbio.runner._impl.Runners\r
-<P>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../compbio/runner/_impl/Runners.html" title="class in compbio.runner._impl"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/runner/_impl/\class-useRunners.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="Runners.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/runner/_impl/package-frame.html b/website/full_javadoc/compbio/runner/_impl/package-frame.html

deleted file mode 100644 (file)

index 55be9ff..0000000
--- a/website/full_javadoc/compbio/runner/_impl/package-frame.html
+++ /dev/null
@@ -1,52 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-compbio.runner._impl\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white">\r
-<FONT size="+1" CLASS="FrameTitleFont">\r
-<A HREF="../../../compbio/runner/_impl/package-summary.html" target="classFrame">compbio.runner._impl</A></FONT>\r
-<TABLE BORDER="0" WIDTH="100%" SUMMARY="">\r
-<TR>\r
-<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">\r
-Classes</FONT>&nbsp;\r
-<FONT CLASS="FrameItemFont">\r
-<BR>\r
-<A HREF="BlastAll.html" title="class in compbio.runner._impl" target="classFrame">BlastAll</A>\r
-<BR>\r
-<A HREF="BlastParameters.html" title="class in compbio.runner._impl" target="classFrame">BlastParameters</A>\r
-<BR>\r
-<A HREF="Disembl.html" title="class in compbio.runner._impl" target="classFrame">Disembl</A>\r
-<BR>\r
-<A HREF="Environment.html" title="class in compbio.runner._impl" target="classFrame">Environment</A>\r
-<BR>\r
-<A HREF="Mcl.html" title="class in compbio.runner._impl" target="classFrame">Mcl</A>\r
-<BR>\r
-<A HREF="NetNglyc.html" title="class in compbio.runner._impl" target="classFrame">NetNglyc</A>\r
-<BR>\r
-<A HREF="OB.html" title="class in compbio.runner._impl" target="classFrame">OB</A>\r
-<BR>\r
-<A HREF="PSIBlast.html" title="class in compbio.runner._impl" target="classFrame">PSIBlast</A>\r
-<BR>\r
-<A HREF="Ronn.html" title="class in compbio.runner._impl" target="classFrame">Ronn</A>\r
-<BR>\r
-<A HREF="RPSBlast.html" title="class in compbio.runner._impl" target="classFrame">RPSBlast</A>\r
-<BR>\r
-<A HREF="Runners.html" title="class in compbio.runner._impl" target="classFrame">Runners</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/runner/_impl/package-summary.html b/website/full_javadoc/compbio/runner/_impl/package-summary.html

deleted file mode 100644 (file)

index c985bf0..0000000
--- a/website/full_javadoc/compbio/runner/_impl/package-summary.html
+++ /dev/null
@@ -1,197 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-compbio.runner._impl\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="compbio.runner._impl";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Class</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-use.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/runner/package-summary.html"><B>PREV PACKAGE</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../compbio/runner/_jpred/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/runner/_impl/package-summary.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="package-summary.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<H2>\r
-Package compbio.runner._impl\r
-</H2>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Class Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../../compbio/runner/_impl/BlastAll.html" title="class in compbio.runner._impl">BlastAll</A></B></TD>\r
-<TD>&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../../compbio/runner/_impl/BlastParameters.html" title="class in compbio.runner._impl">BlastParameters</A></B></TD>\r
-<TD>Utility class for common Blast parameters</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../../compbio/runner/_impl/Disembl.html" title="class in compbio.runner._impl">Disembl</A></B></TD>\r
-<TD>&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../../compbio/runner/_impl/Environment.html" title="class in compbio.runner._impl">Environment</A></B></TD>\r
-<TD>This is utility class to encapsulate environmental variables like directory paths</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../../compbio/runner/_impl/Mcl.html" title="class in compbio.runner._impl">Mcl</A></B></TD>\r
-<TD>&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A></B></TD>\r
-<TD>&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../../compbio/runner/_impl/OB.html" title="class in compbio.runner._impl">OB</A></B></TD>\r
-<TD>TODO this needs fixing! Executable does not work</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../../compbio/runner/_impl/PSIBlast.html" title="class in compbio.runner._impl">PSIBlast</A></B></TD>\r
-<TD>&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../../compbio/runner/_impl/Ronn.html" title="class in compbio.runner._impl">Ronn</A></B></TD>\r
-<TD>&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../../compbio/runner/_impl/RPSBlast.html" title="class in compbio.runner._impl">RPSBlast</A></B></TD>\r
-<TD>&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../../compbio/runner/_impl/Runners.html" title="class in compbio.runner._impl">Runners</A></B></TD>\r
-<TD>&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-\r
-<P>\r
-<DL>\r
-</DL>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Class</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-use.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/runner/package-summary.html"><B>PREV PACKAGE</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../compbio/runner/_jpred/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/runner/_impl/package-summary.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="package-summary.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/runner/_impl/package-tree.html b/website/full_javadoc/compbio/runner/_impl/package-tree.html

deleted file mode 100644 (file)

index 3f894d8..0000000
--- a/website/full_javadoc/compbio/runner/_impl/package-tree.html
+++ /dev/null
@@ -1,157 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-compbio.runner._impl Class Hierarchy\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="compbio.runner._impl Class Hierarchy";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Class</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Use</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/runner/package-tree.html"><B>PREV</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../compbio/runner/_jpred/package-tree.html"><B>NEXT</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/runner/_impl/package-tree.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="package-tree.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-Hierarchy For Package compbio.runner._impl\r
-</H2>\r
-</CENTER>\r
-<DL>\r
-<DT><B>Package Hierarchies:</B><DD><A HREF="../../../overview-tree.html">All Packages</A></DL>\r
-<HR>\r
-<H2>\r
-Class Hierarchy\r
-</H2>\r
-<UL>\r
-<LI TYPE="circle">java.lang.Object<UL>\r
-<LI TYPE="circle">compbio.runner.<A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner"><B>_SkeletalCommandBuilder</B></A> (implements compbio.engine.client.<A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;T&gt;)\r
-<UL>\r
-<LI TYPE="circle">compbio.runner._impl.<A HREF="../../../compbio/runner/_impl/BlastAll.html" title="class in compbio.runner._impl"><B>BlastAll</B></A><LI TYPE="circle">compbio.runner._impl.<A HREF="../../../compbio/runner/_impl/Disembl.html" title="class in compbio.runner._impl"><B>Disembl</B></A><LI TYPE="circle">compbio.runner._impl.<A HREF="../../../compbio/runner/_impl/Mcl.html" title="class in compbio.runner._impl"><B>Mcl</B></A><LI TYPE="circle">compbio.runner._impl.<A HREF="../../../compbio/runner/_impl/OB.html" title="class in compbio.runner._impl"><B>OB</B></A><LI TYPE="circle">compbio.runner._impl.<A HREF="../../../compbio/runner/_impl/PSIBlast.html" title="class in compbio.runner._impl"><B>PSIBlast</B></A><LI TYPE="circle">compbio.runner._impl.<A HREF="../../../compbio/runner/_impl/Ronn.html" title="class in compbio.runner._impl"><B>Ronn</B></A><LI TYPE="circle">compbio.runner._impl.<A HREF="../../../compbio/runner/_impl/RPSBlast.html" title="class in compbio.runner._impl"><B>RPSBlast</B></A></UL>\r
-<LI TYPE="circle">compbio.runner._impl.<A HREF="../../../compbio/runner/_impl/BlastParameters.html" title="class in compbio.runner._impl"><B>BlastParameters</B></A><LI TYPE="circle">compbio.runner._impl.<A HREF="../../../compbio/runner/_impl/Environment.html" title="class in compbio.runner._impl"><B>Environment</B></A><LI TYPE="circle">compbio.runner._impl.<A HREF="../../../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl"><B>NetNglyc</B></A> (implements compbio.engine.client.<A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;T&gt;)\r
-<LI TYPE="circle">compbio.runner._impl.<A HREF="../../../compbio/runner/_impl/Runners.html" title="class in compbio.runner._impl"><B>Runners</B></A></UL>\r
-</UL>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Class</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Use</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/runner/package-tree.html"><B>PREV</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../compbio/runner/_jpred/package-tree.html"><B>NEXT</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/runner/_impl/package-tree.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="package-tree.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/runner/_impl/package-use.html b/website/full_javadoc/compbio/runner/_impl/package-use.html

deleted file mode 100644 (file)

index 5ada742..0000000
--- a/website/full_javadoc/compbio/runner/_impl/package-use.html
+++ /dev/null
@@ -1,212 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Uses of Package compbio.runner._impl\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Uses of Package compbio.runner._impl";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Class</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/runner/_impl/package-use.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="package-use.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-<B>Uses of Package<br>compbio.runner._impl</B></H2>\r
-</CENTER>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Packages that use <A HREF="../../../compbio/runner/_impl/package-summary.html">compbio.runner._impl</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.runner._impl"><B>compbio.runner._impl</B></A></TD>\r
-<TD>&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.runner._impl"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Classes in <A HREF="../../../compbio/runner/_impl/package-summary.html">compbio.runner._impl</A> used by <A HREF="../../../compbio/runner/_impl/package-summary.html">compbio.runner._impl</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../../compbio/runner/_impl/class-use/BlastAll.html#compbio.runner._impl"><B>BlastAll</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../../compbio/runner/_impl/class-use/Disembl.html#compbio.runner._impl"><B>Disembl</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../../compbio/runner/_impl/class-use/Mcl.html#compbio.runner._impl"><B>Mcl</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../../compbio/runner/_impl/class-use/NetNglyc.html#compbio.runner._impl"><B>NetNglyc</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../../compbio/runner/_impl/class-use/OB.html#compbio.runner._impl"><B>OB</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;TODO this needs fixing! Executable does not work</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../../compbio/runner/_impl/class-use/PSIBlast.html#compbio.runner._impl"><B>PSIBlast</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../../compbio/runner/_impl/class-use/Ronn.html#compbio.runner._impl"><B>Ronn</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../../compbio/runner/_impl/class-use/RPSBlast.html#compbio.runner._impl"><B>RPSBlast</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Class</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/runner/_impl/package-use.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="package-use.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/runner/_jpred/_Jpred.html b/website/full_javadoc/compbio/runner/_jpred/_Jpred.html

deleted file mode 100644 (file)

index 4eee1a7..0000000
--- a/website/full_javadoc/compbio/runner/_jpred/_Jpred.html
+++ /dev/null
@@ -1,224 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-_Jpred\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="_Jpred";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/_Jpred.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
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-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV CLASS&nbsp;\r
-&nbsp;NEXT CLASS</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/runner/_jpred/_Jpred.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="_Jpred.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#methods_inherited_from_class_java.lang.Object">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;METHOD</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.runner._jpred</FONT>\r
-<BR>\r
-Class _Jpred</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.runner._jpred._Jpred</B>\r
-</PRE>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public class <B>_Jpred</B><DT>extends java.lang.Object</DL>\r
-</PRE>\r
-\r
-<P>\r
-<HR>\r
-\r
-<P>\r
-\r
-<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
-\r
-<A NAME="constructor_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Constructor Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/runner/_jpred/_Jpred.html#_Jpred()">_Jpred</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
-\r
-<A NAME="constructor_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Constructor Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="_Jpred()"><!-- --></A><H3>\r
-_Jpred</H3>\r
-<PRE>\r
-public <B>_Jpred</B>()</PRE>\r
-<DL>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/_Jpred.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV CLASS&nbsp;\r
-&nbsp;NEXT CLASS</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/runner/_jpred/_Jpred.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="_Jpred.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#methods_inherited_from_class_java.lang.Object">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;METHOD</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/runner/_jpred/class-use/_Jpred.html b/website/full_javadoc/compbio/runner/_jpred/class-use/_Jpred.html

deleted file mode 100644 (file)

index fd98536..0000000
--- a/website/full_javadoc/compbio/runner/_jpred/class-use/_Jpred.html
+++ /dev/null
@@ -1,144 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Uses of Class compbio.runner._jpred._Jpred\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Uses of Class compbio.runner._jpred._Jpred";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../compbio/runner/_jpred/_Jpred.html" title="class in compbio.runner._jpred"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/runner/_jpred/\class-use_Jpred.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="_Jpred.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-<B>Uses of Class<br>compbio.runner._jpred._Jpred</B></H2>\r
-</CENTER>\r
-No usage of compbio.runner._jpred._Jpred\r
-<P>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../compbio/runner/_jpred/_Jpred.html" title="class in compbio.runner._jpred"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/runner/_jpred/\class-use_Jpred.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="_Jpred.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/runner/_jpred/package-frame.html b/website/full_javadoc/compbio/runner/_jpred/package-frame.html

deleted file mode 100644 (file)

index 2640f34..0000000
--- a/website/full_javadoc/compbio/runner/_jpred/package-frame.html
+++ /dev/null
@@ -1,32 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-compbio.runner._jpred\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white">\r
-<FONT size="+1" CLASS="FrameTitleFont">\r
-<A HREF="../../../compbio/runner/_jpred/package-summary.html" target="classFrame">compbio.runner._jpred</A></FONT>\r
-<TABLE BORDER="0" WIDTH="100%" SUMMARY="">\r
-<TR>\r
-<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">\r
-Classes</FONT>&nbsp;\r
-<FONT CLASS="FrameItemFont">\r
-<BR>\r
-<A HREF="_Jpred.html" title="class in compbio.runner._jpred" target="classFrame">_Jpred</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/runner/_jpred/package-summary.html b/website/full_javadoc/compbio/runner/_jpred/package-summary.html

deleted file mode 100644 (file)

index f375d9f..0000000
--- a/website/full_javadoc/compbio/runner/_jpred/package-summary.html
+++ /dev/null
@@ -1,157 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-compbio.runner._jpred\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="compbio.runner._jpred";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
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diff --git a/website/full_javadoc/compbio/runner/_jpred/package-tree.html b/website/full_javadoc/compbio/runner/_jpred/package-tree.html

deleted file mode 100644 (file)

index e9e4095..0000000
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diff --git a/website/full_javadoc/compbio/runner/_jpred/package-use.html b/website/full_javadoc/compbio/runner/_jpred/package-use.html

deleted file mode 100644 (file)

index dd3eac5..0000000
--- a/website/full_javadoc/compbio/runner/_jpred/package-use.html
+++ /dev/null
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-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
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-<B>Uses of Package<br>compbio.runner._jpred</B></H2>\r
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-<HR>\r
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-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/runner/_jpred/package-use.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="package-use.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/runner/class-use/OptionCombinator.html b/website/full_javadoc/compbio/runner/class-use/OptionCombinator.html

deleted file mode 100644 (file)

index 82f1f31..0000000
--- a/website/full_javadoc/compbio/runner/class-use/OptionCombinator.html
+++ /dev/null
@@ -1,144 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Uses of Class compbio.runner.OptionCombinator\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Uses of Class compbio.runner.OptionCombinator";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../compbio/runner/OptionCombinator.html" title="class in compbio.runner"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/runner/\class-useOptionCombinator.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="OptionCombinator.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-<B>Uses of Class<br>compbio.runner.OptionCombinator</B></H2>\r
-</CENTER>\r
-No usage of compbio.runner.OptionCombinator\r
-<P>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../compbio/runner/OptionCombinator.html" title="class in compbio.runner"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/runner/\class-useOptionCombinator.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="OptionCombinator.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/runner/class-use/Util.html b/website/full_javadoc/compbio/runner/class-use/Util.html

deleted file mode 100644 (file)

index 7d1eef5..0000000
--- a/website/full_javadoc/compbio/runner/class-use/Util.html
+++ /dev/null
@@ -1,144 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Uses of Class compbio.runner.Util\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Uses of Class compbio.runner.Util";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../compbio/runner/Util.html" title="class in compbio.runner"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/runner/\class-useUtil.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="Util.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-<B>Uses of Class<br>compbio.runner.Util</B></H2>\r
-</CENTER>\r
-No usage of compbio.runner.Util\r
-<P>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../compbio/runner/Util.html" title="class in compbio.runner"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/runner/\class-useUtil.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="Util.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/runner/class-use/_NativeSpecHelper.html b/website/full_javadoc/compbio/runner/class-use/_NativeSpecHelper.html

deleted file mode 100644 (file)

index cbcc70d..0000000
--- a/website/full_javadoc/compbio/runner/class-use/_NativeSpecHelper.html
+++ /dev/null
@@ -1,144 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Uses of Class compbio.runner._NativeSpecHelper\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Uses of Class compbio.runner._NativeSpecHelper";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../compbio/runner/_NativeSpecHelper.html" title="class in compbio.runner"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/runner/\class-use_NativeSpecHelper.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="_NativeSpecHelper.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-<B>Uses of Class<br>compbio.runner._NativeSpecHelper</B></H2>\r
-</CENTER>\r
-No usage of compbio.runner._NativeSpecHelper\r
-<P>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../compbio/runner/_NativeSpecHelper.html" title="class in compbio.runner"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/runner/\class-use_NativeSpecHelper.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="_NativeSpecHelper.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/runner/class-use/_SkeletalCommandBuilder.html b/website/full_javadoc/compbio/runner/class-use/_SkeletalCommandBuilder.html

deleted file mode 100644 (file)

index 46aa6c4..0000000
--- a/website/full_javadoc/compbio/runner/class-use/_SkeletalCommandBuilder.html
+++ /dev/null
@@ -1,321 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Uses of Class compbio.runner._SkeletalCommandBuilder\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Uses of Class compbio.runner._SkeletalCommandBuilder";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/runner/\class-use_SkeletalCommandBuilder.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="_SkeletalCommandBuilder.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-<B>Uses of Class<br>compbio.runner._SkeletalCommandBuilder</B></H2>\r
-</CENTER>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Packages that use <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.runner"><B>compbio.runner</B></A></TD>\r
-<TD>Utilities commonly used by all runners.&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.runner._impl"><B>compbio.runner._impl</B></A></TD>\r
-<TD>&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.runner"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A> in <A HREF="../../../compbio/runner/package-summary.html">compbio.runner</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/runner/package-summary.html">compbio.runner</A> that return <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A></CODE></FONT></TD>\r
-<TD><CODE><B>_SkeletalCommandBuilder.</B><B><A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#addParameter(java.lang.String)">addParameter</A></B>(java.lang.String&nbsp;parameter)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A></CODE></FONT></TD>\r
-<TD><CODE><B>_SkeletalCommandBuilder.</B><B><A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#addParameters(java.util.List)">addParameters</A></B>(java.util.List&lt;java.lang.String&gt;&nbsp;parameters)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A></CODE></FONT></TD>\r
-<TD><CODE><B>_SkeletalCommandBuilder.</B><B><A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#addParameters(java.lang.String[])">addParameters</A></B>(java.lang.String[]&nbsp;parameters)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A></CODE></FONT></TD>\r
-<TD><CODE><B>_SkeletalCommandBuilder.</B><B><A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#setEmail(java.lang.String)">setEmail</A></B>(java.lang.String&nbsp;email)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A></CODE></FONT></TD>\r
-<TD><CODE><B>_SkeletalCommandBuilder.</B><B><A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#setName(java.lang.String)">setName</A></B>(java.lang.String&nbsp;name)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/runner/package-summary.html">compbio.runner</A> that return types with arguments of type <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;<A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>_SkeletalCommandBuilder.</B><B><A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#getLimit(java.lang.String)">getLimit</A></B>(java.lang.String&nbsp;presetName)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;<A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>_SkeletalCommandBuilder.</B><B><A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#getLimits()">getLimits</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>&lt;<A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>_SkeletalCommandBuilder.</B><B><A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#getParameters(compbio.engine.client.Executable.ExecProvider)">getParameters</A></B>(<A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.runner._impl"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A> in <A HREF="../../../compbio/runner/_impl/package-summary.html">compbio.runner._impl</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Subclasses of <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A> in <A HREF="../../../compbio/runner/_impl/package-summary.html">compbio.runner._impl</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;class</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/_impl/BlastAll.html" title="class in compbio.runner._impl">BlastAll</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;class</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/_impl/Disembl.html" title="class in compbio.runner._impl">Disembl</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;class</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/_impl/Mcl.html" title="class in compbio.runner._impl">Mcl</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;class</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/_impl/OB.html" title="class in compbio.runner._impl">OB</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;TODO this needs fixing! Executable does not work</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;class</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/_impl/PSIBlast.html" title="class in compbio.runner._impl">PSIBlast</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;class</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/_impl/Ronn.html" title="class in compbio.runner._impl">Ronn</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;class</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/_impl/RPSBlast.html" title="class in compbio.runner._impl">RPSBlast</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/runner/\class-use_SkeletalCommandBuilder.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="_SkeletalCommandBuilder.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/runner/msa/ClustalW.html b/website/full_javadoc/compbio/runner/msa/ClustalW.html

deleted file mode 100644 (file)

index e2cbdb5..0000000
--- a/website/full_javadoc/compbio/runner/msa/ClustalW.html
+++ /dev/null
@@ -1,473 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:49 GMT 2010 -->\r
-<TITLE>\r
-ClustalW\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="ClustalW";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/ClustalW.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV CLASS&nbsp;\r
-&nbsp;<A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/runner/msa/ClustalW.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="ClustalW.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;<A HREF="#field_summary">FIELD</A>&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;<A HREF="#field_detail">FIELD</A>&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.runner.msa</FONT>\r
-<BR>\r
-Class ClustalW</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">compbio.engine.client.SkeletalExecutable</A>&lt;<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>&gt;\r
-      <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.runner.msa.ClustalW</B>\r
-</PRE>\r
-<DL>\r
-<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>&gt;</DD>\r
-</DL>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public class <B>ClustalW</B><DT>extends <A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>&lt;<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>&gt;</DL>\r
-</PRE>\r
-\r
-<P>\r
-<HR>\r
-\r
-<P>\r
-<!-- ======== NESTED CLASS SUMMARY ======== -->\r
-\r
-<A NAME="nested_class_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Nested Class Summary</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="nested_classes_inherited_from_class_compbio.engine.client.Executable"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Nested classes/interfaces inherited from interface compbio.engine.client.<A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A></CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- =========== FIELD SUMMARY =========== -->\r
-\r
-<A NAME="field_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Field Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/msa/ClustalW.html#KEY_VALUE_SEPARATOR">KEY_VALUE_SEPARATOR</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
-\r
-<A NAME="constructor_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Constructor Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/runner/msa/ClustalW.html#ClustalW()">ClustalW</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.util.List&lt;java.lang.String&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/msa/ClustalW.html#getCreatedFiles()">getCreatedFiles</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;This method cannot really tell whether the files has actually been
- created or not.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/msa/ClustalW.html#getLimit(java.lang.String)">getLimit</A></B>(java.lang.String&nbsp;presetName)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/msa/ClustalW.html#getLimits()">getLimits</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/msa/ClustalW.html#getResults(java.lang.String)">getResults</A></B>(java.lang.String&nbsp;workDirectory)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/msa/ClustalW.html#getStatFile()">getStatFile</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.Class&lt;? extends <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;?&gt;&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/msa/ClustalW.html#getType()">getType</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/msa/ClustalW.html#setInput(java.lang.String)">setInput</A></B>(java.lang.String&nbsp;inFile)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/msa/ClustalW.html#setOutput(java.lang.String)">setOutput</A></B>(java.lang.String&nbsp;outFile)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_compbio.engine.client.SkeletalExecutable"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class compbio.engine.client.<A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A></B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#addParameters(java.util.List)">addParameters</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#equals(java.lang.Object)">equals</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getClusterSettings()">getClusterSettings</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getError()">getError</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getInput()">getInput</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getOutput()">getOutput</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getParameters(compbio.engine.client.Executable.ExecProvider)">getParameters</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#hashCode()">hashCode</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#loadRunConfiguration(compbio.engine.client.RunConfiguration)">loadRunConfiguration</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#setError(java.lang.String)">setError</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#setParameter(java.lang.String)">setParameter</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#toString()">toString</A></CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>getClass, notify, notifyAll, wait, wait, wait</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ============ FIELD DETAIL =========== -->\r
-\r
-<A NAME="field_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Field Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="KEY_VALUE_SEPARATOR"><!-- --></A><H3>\r
-KEY_VALUE_SEPARATOR</H3>\r
-<PRE>\r
-public static final java.lang.String <B>KEY_VALUE_SEPARATOR</B></PRE>\r
-<DL>\r
-<DL>\r
-<DT><B>See Also:</B><DD><A HREF="../../../constant-values.html#compbio.runner.msa.ClustalW.KEY_VALUE_SEPARATOR">Constant Field Values</A></DL>\r
-</DL>\r
-\r
-<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
-\r
-<A NAME="constructor_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Constructor Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="ClustalW()"><!-- --></A><H3>\r
-ClustalW</H3>\r
-<PRE>\r
-public <B>ClustalW</B>()</PRE>\r
-<DL>\r
-</DL>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
-<A NAME="method_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="setOutput(java.lang.String)"><!-- --></A><H3>\r
-setOutput</H3>\r
-<PRE>\r
-public <A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A> <B>setOutput</B>(java.lang.String&nbsp;outFile)</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Overrides:</B><DD><CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#setOutput(java.lang.String)">setOutput</A></CODE> in class <CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>&lt;<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="setInput(java.lang.String)"><!-- --></A><H3>\r
-setInput</H3>\r
-<PRE>\r
-public <A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A> <B>setInput</B>(java.lang.String&nbsp;inFile)</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Overrides:</B><DD><CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#setInput(java.lang.String)">setInput</A></CODE> in class <CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>&lt;<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getResults(java.lang.String)"><!-- --></A><H3>\r
-getResults</H3>\r
-<PRE>\r
-public <A HREF="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A> <B>getResults</B>(java.lang.String&nbsp;workDirectory)\r
-                     throws <A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Throws:</B>\r
-<DD><CODE><A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></CODE></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getCreatedFiles()"><!-- --></A><H3>\r
-getCreatedFiles</H3>\r
-<PRE>\r
-public java.util.List&lt;java.lang.String&gt; <B>getCreatedFiles</B>()</PRE>\r
-<DL>\r
-<DD><B>Description copied from class: <CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getCreatedFiles()">SkeletalExecutable</A></CODE></B></DD>\r
-<DD>This method cannot really tell whether the files has actually been
- created or not. It must be overridden as required.\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#getCreatedFiles()">getCreatedFiles</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>&gt;</CODE><DT><B>Overrides:</B><DD><CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getCreatedFiles()">getCreatedFiles</A></CODE> in class <CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>&lt;<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-<DT><B>See Also:</B><DD><A HREF="../../../compbio/engine/client/Executable.html#getCreatedFiles()"><CODE>Executable.getCreatedFiles()</CODE></A></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getStatFile()"><!-- --></A><H3>\r
-getStatFile</H3>\r
-<PRE>\r
-public static java.lang.String <B>getStatFile</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getLimit(java.lang.String)"><!-- --></A><H3>\r
-getLimit</H3>\r
-<PRE>\r
-public <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>&gt; <B>getLimit</B>(java.lang.String&nbsp;presetName)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getLimits()"><!-- --></A><H3>\r
-getLimits</H3>\r
-<PRE>\r
-public <A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>&gt; <B>getLimits</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getType()"><!-- --></A><H3>\r
-getType</H3>\r
-<PRE>\r
-public java.lang.Class&lt;? extends <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;?&gt;&gt; <B>getType</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getType()">getType</A></CODE> in class <CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>&lt;<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/ClustalW.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV CLASS&nbsp;\r
-&nbsp;<A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/runner/msa/ClustalW.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="ClustalW.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;<A HREF="#field_summary">FIELD</A>&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;<A HREF="#field_detail">FIELD</A>&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/runner/msa/Mafft.html b/website/full_javadoc/compbio/runner/msa/Mafft.html

deleted file mode 100644 (file)

index 0a6d12c..0000000
--- a/website/full_javadoc/compbio/runner/msa/Mafft.html
+++ /dev/null
@@ -1,448 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Mafft\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Mafft";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/Mafft.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/runner/msa/Mafft.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="Mafft.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;<A HREF="#field_summary">FIELD</A>&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;<A HREF="#field_detail">FIELD</A>&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.runner.msa</FONT>\r
-<BR>\r
-Class Mafft</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">compbio.engine.client.SkeletalExecutable</A>&lt;<A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>&gt;\r
-      <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.runner.msa.Mafft</B>\r
-</PRE>\r
-<DL>\r
-<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>&gt;, <A HREF="../../../compbio/engine/client/PipedExecutable.html" title="interface in compbio.engine.client">PipedExecutable</A>&lt;<A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>&gt;</DD>\r
-</DL>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public class <B>Mafft</B><DT>extends <A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>&lt;<A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>&gt;<DT>implements <A HREF="../../../compbio/engine/client/PipedExecutable.html" title="interface in compbio.engine.client">PipedExecutable</A>&lt;<A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>&gt;</DL>\r
-</PRE>\r
-\r
-<P>\r
-<HR>\r
-\r
-<P>\r
-<!-- ======== NESTED CLASS SUMMARY ======== -->\r
-\r
-<A NAME="nested_class_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Nested Class Summary</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="nested_classes_inherited_from_class_compbio.engine.client.Executable"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Nested classes/interfaces inherited from interface compbio.engine.client.<A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A></CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- =========== FIELD SUMMARY =========== -->\r
-\r
-<A NAME="field_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Field Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/msa/Mafft.html#KEY_VALUE_SEPARATOR">KEY_VALUE_SEPARATOR</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
-\r
-<A NAME="constructor_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Constructor Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/runner/msa/Mafft.html#Mafft()">Mafft</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/msa/Mafft.html#addParameters(java.util.List)">addParameters</A></B>(java.util.List&lt;java.lang.String&gt;&nbsp;parameters)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Mafft input must always be the last parameter!</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;<A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/msa/Mafft.html#getLimit(java.lang.String)">getLimit</A></B>(java.lang.String&nbsp;presetName)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;<A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/msa/Mafft.html#getLimits()">getLimits</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/msa/Mafft.html#getResults(java.lang.String)">getResults</A></B>(java.lang.String&nbsp;workDirectory)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.Class&lt;? extends <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;?&gt;&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/msa/Mafft.html#getType()">getType</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/msa/Mafft.html#setInput(java.lang.String)">setInput</A></B>(java.lang.String&nbsp;inFile)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_compbio.engine.client.SkeletalExecutable"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class compbio.engine.client.<A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A></B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#equals(java.lang.Object)">equals</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getClusterSettings()">getClusterSettings</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getCreatedFiles()">getCreatedFiles</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getError()">getError</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getInput()">getInput</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getOutput()">getOutput</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getParameters(compbio.engine.client.Executable.ExecProvider)">getParameters</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#hashCode()">hashCode</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#loadRunConfiguration(compbio.engine.client.RunConfiguration)">loadRunConfiguration</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#setError(java.lang.String)">setError</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#setOutput(java.lang.String)">setOutput</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#setParameter(java.lang.String)">setParameter</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#toString()">toString</A></CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>getClass, notify, notifyAll, wait, wait, wait</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_compbio.engine.client.Executable"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from interface compbio.engine.client.<A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><A HREF="../../../compbio/engine/client/Executable.html#getCreatedFiles()">getCreatedFiles</A>, <A HREF="../../../compbio/engine/client/Executable.html#getError()">getError</A>, <A HREF="../../../compbio/engine/client/Executable.html#getInput()">getInput</A>, <A HREF="../../../compbio/engine/client/Executable.html#getOutput()">getOutput</A>, <A HREF="../../../compbio/engine/client/Executable.html#getParameters(compbio.engine.client.Executable.ExecProvider)">getParameters</A>, <A HREF="../../../compbio/engine/client/Executable.html#loadRunConfiguration(compbio.engine.client.RunConfiguration)">loadRunConfiguration</A></CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ============ FIELD DETAIL =========== -->\r
-\r
-<A NAME="field_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Field Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="KEY_VALUE_SEPARATOR"><!-- --></A><H3>\r
-KEY_VALUE_SEPARATOR</H3>\r
-<PRE>\r
-public static final java.lang.String <B>KEY_VALUE_SEPARATOR</B></PRE>\r
-<DL>\r
-<DL>\r
-<DT><B>See Also:</B><DD><A HREF="../../../constant-values.html#compbio.runner.msa.Mafft.KEY_VALUE_SEPARATOR">Constant Field Values</A></DL>\r
-</DL>\r
-\r
-<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
-\r
-<A NAME="constructor_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Constructor Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="Mafft()"><!-- --></A><H3>\r
-Mafft</H3>\r
-<PRE>\r
-public <B>Mafft</B>()</PRE>\r
-<DL>\r
-</DL>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
-<A NAME="method_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="getResults(java.lang.String)"><!-- --></A><H3>\r
-getResults</H3>\r
-<PRE>\r
-public <A HREF="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A> <B>getResults</B>(java.lang.String&nbsp;workDirectory)\r
-                     throws <A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#getResults(java.lang.String)">getResults</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-\r
-<DT><B>Throws:</B>\r
-<DD><CODE><A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></CODE></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="setInput(java.lang.String)"><!-- --></A><H3>\r
-setInput</H3>\r
-<PRE>\r
-public <A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A> <B>setInput</B>(java.lang.String&nbsp;inFile)</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Overrides:</B><DD><CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#setInput(java.lang.String)">setInput</A></CODE> in class <CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>&lt;<A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="addParameters(java.util.List)"><!-- --></A><H3>\r
-addParameters</H3>\r
-<PRE>\r
-public <A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A> <B>addParameters</B>(java.util.List&lt;java.lang.String&gt;&nbsp;parameters)</PRE>\r
-<DL>\r
-<DD>Mafft input must always be the last parameter!\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#addParameters(java.util.List)">addParameters</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>&gt;</CODE><DT><B>Overrides:</B><DD><CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#addParameters(java.util.List)">addParameters</A></CODE> in class <CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>&lt;<A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>this Executable</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getLimit(java.lang.String)"><!-- --></A><H3>\r
-getLimit</H3>\r
-<PRE>\r
-public <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;<A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>&gt; <B>getLimit</B>(java.lang.String&nbsp;presetName)</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#getLimit(java.lang.String)">getLimit</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getLimits()"><!-- --></A><H3>\r
-getLimits</H3>\r
-<PRE>\r
-public <A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;<A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>&gt; <B>getLimits</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#getLimits()">getLimits</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getType()"><!-- --></A><H3>\r
-getType</H3>\r
-<PRE>\r
-public java.lang.Class&lt;? extends <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;?&gt;&gt; <B>getType</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getType()">getType</A></CODE> in class <CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>&lt;<A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/Mafft.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/runner/msa/Mafft.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="Mafft.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;<A HREF="#field_summary">FIELD</A>&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;<A HREF="#field_detail">FIELD</A>&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/runner/msa/Muscle.html b/website/full_javadoc/compbio/runner/msa/Muscle.html

deleted file mode 100644 (file)

index 479eb57..0000000
--- a/website/full_javadoc/compbio/runner/msa/Muscle.html
+++ /dev/null
@@ -1,481 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Muscle\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Muscle";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/Muscle.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/runner/msa/Muscle.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="Muscle.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;<A HREF="#field_summary">FIELD</A>&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;<A HREF="#field_detail">FIELD</A>&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.runner.msa</FONT>\r
-<BR>\r
-Class Muscle</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">compbio.engine.client.SkeletalExecutable</A>&lt;<A HREF="../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>&gt;\r
-      <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.runner.msa.Muscle</B>\r
-</PRE>\r
-<DL>\r
-<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>&gt;</DD>\r
-</DL>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public class <B>Muscle</B><DT>extends <A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>&lt;<A HREF="../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>&gt;</DL>\r
-</PRE>\r
-\r
-<P>\r
-<HR>\r
-\r
-<P>\r
-<!-- ======== NESTED CLASS SUMMARY ======== -->\r
-\r
-<A NAME="nested_class_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Nested Class Summary</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="nested_classes_inherited_from_class_compbio.engine.client.Executable"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Nested classes/interfaces inherited from interface compbio.engine.client.<A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A></CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- =========== FIELD SUMMARY =========== -->\r
-\r
-<A NAME="field_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Field Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/msa/Muscle.html#KEY_VALUE_SEPARATOR">KEY_VALUE_SEPARATOR</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
-\r
-<A NAME="constructor_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Constructor Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/runner/msa/Muscle.html#Muscle()">Muscle</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Default options are
- 
- -clwstrict - write output in clustal format</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.util.List&lt;java.lang.String&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/msa/Muscle.html#getCreatedFiles()">getCreatedFiles</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;This method cannot really tell whether the files has actually been
- created or not.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;<A HREF="../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/msa/Muscle.html#getLimit(java.lang.String)">getLimit</A></B>(java.lang.String&nbsp;presetName)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;<A HREF="../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/msa/Muscle.html#getLimits()">getLimits</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/msa/Muscle.html#getResults(java.lang.String)">getResults</A></B>(java.lang.String&nbsp;workDirectory)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/msa/Muscle.html#getStatFile()">getStatFile</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.Class&lt;? extends <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;?&gt;&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/msa/Muscle.html#getType()">getType</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/msa/Muscle.html#setInput(java.lang.String)">setInput</A></B>(java.lang.String&nbsp;inFile)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/msa/Muscle.html#setOutput(java.lang.String)">setOutput</A></B>(java.lang.String&nbsp;outFile)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_compbio.engine.client.SkeletalExecutable"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class compbio.engine.client.<A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A></B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#addParameters(java.util.List)">addParameters</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#equals(java.lang.Object)">equals</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getClusterSettings()">getClusterSettings</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getError()">getError</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getInput()">getInput</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getOutput()">getOutput</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getParameters(compbio.engine.client.Executable.ExecProvider)">getParameters</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#hashCode()">hashCode</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#loadRunConfiguration(compbio.engine.client.RunConfiguration)">loadRunConfiguration</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#setError(java.lang.String)">setError</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#setParameter(java.lang.String)">setParameter</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#toString()">toString</A></CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>getClass, notify, notifyAll, wait, wait, wait</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ============ FIELD DETAIL =========== -->\r
-\r
-<A NAME="field_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Field Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="KEY_VALUE_SEPARATOR"><!-- --></A><H3>\r
-KEY_VALUE_SEPARATOR</H3>\r
-<PRE>\r
-public static final java.lang.String <B>KEY_VALUE_SEPARATOR</B></PRE>\r
-<DL>\r
-<DL>\r
-<DT><B>See Also:</B><DD><A HREF="../../../constant-values.html#compbio.runner.msa.Muscle.KEY_VALUE_SEPARATOR">Constant Field Values</A></DL>\r
-</DL>\r
-\r
-<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
-\r
-<A NAME="constructor_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Constructor Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="Muscle()"><!-- --></A><H3>\r
-Muscle</H3>\r
-<PRE>\r
-public <B>Muscle</B>()</PRE>\r
-<DL>\r
-<DD>Default options are
- 
- -clwstrict - write output in clustal format\r
-<P>\r
-<DL>\r
-<DT><B>Parameters:</B><DD><CODE>workDirectory</CODE> - </DL>\r
-</DL>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
-<A NAME="method_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="setOutput(java.lang.String)"><!-- --></A><H3>\r
-setOutput</H3>\r
-<PRE>\r
-public <A HREF="../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A> <B>setOutput</B>(java.lang.String&nbsp;outFile)</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Overrides:</B><DD><CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#setOutput(java.lang.String)">setOutput</A></CODE> in class <CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>&lt;<A HREF="../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="setInput(java.lang.String)"><!-- --></A><H3>\r
-setInput</H3>\r
-<PRE>\r
-public <A HREF="../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A> <B>setInput</B>(java.lang.String&nbsp;inFile)</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Overrides:</B><DD><CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#setInput(java.lang.String)">setInput</A></CODE> in class <CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>&lt;<A HREF="../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getResults(java.lang.String)"><!-- --></A><H3>\r
-getResults</H3>\r
-<PRE>\r
-public <A HREF="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A> <B>getResults</B>(java.lang.String&nbsp;workDirectory)\r
-                     throws <A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Throws:</B>\r
-<DD><CODE><A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></CODE></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getCreatedFiles()"><!-- --></A><H3>\r
-getCreatedFiles</H3>\r
-<PRE>\r
-public java.util.List&lt;java.lang.String&gt; <B>getCreatedFiles</B>()</PRE>\r
-<DL>\r
-<DD><B>Description copied from class: <CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getCreatedFiles()">SkeletalExecutable</A></CODE></B></DD>\r
-<DD>This method cannot really tell whether the files has actually been
- created or not. It must be overridden as required.\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#getCreatedFiles()">getCreatedFiles</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>&gt;</CODE><DT><B>Overrides:</B><DD><CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getCreatedFiles()">getCreatedFiles</A></CODE> in class <CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>&lt;<A HREF="../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-<DT><B>See Also:</B><DD><A HREF="../../../compbio/engine/client/Executable.html#getCreatedFiles()"><CODE>Executable.getCreatedFiles()</CODE></A></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getStatFile()"><!-- --></A><H3>\r
-getStatFile</H3>\r
-<PRE>\r
-public static java.lang.String <B>getStatFile</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getLimit(java.lang.String)"><!-- --></A><H3>\r
-getLimit</H3>\r
-<PRE>\r
-public <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;<A HREF="../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>&gt; <B>getLimit</B>(java.lang.String&nbsp;presetName)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getLimits()"><!-- --></A><H3>\r
-getLimits</H3>\r
-<PRE>\r
-public <A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;<A HREF="../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>&gt; <B>getLimits</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getType()"><!-- --></A><H3>\r
-getType</H3>\r
-<PRE>\r
-public java.lang.Class&lt;? extends <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;?&gt;&gt; <B>getType</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getType()">getType</A></CODE> in class <CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>&lt;<A HREF="../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/Muscle.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/runner/msa/Muscle.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="Muscle.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;<A HREF="#field_summary">FIELD</A>&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;<A HREF="#field_detail">FIELD</A>&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/runner/msa/Probcons.html b/website/full_javadoc/compbio/runner/msa/Probcons.html

deleted file mode 100644 (file)

index 74a2d6a..0000000
--- a/website/full_javadoc/compbio/runner/msa/Probcons.html
+++ /dev/null
@@ -1,452 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Probcons\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Probcons";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/Probcons.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/runner/msa/Probcons.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="Probcons.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;<A HREF="#field_summary">FIELD</A>&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;<A HREF="#field_detail">FIELD</A>&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.runner.msa</FONT>\r
-<BR>\r
-Class Probcons</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">compbio.engine.client.SkeletalExecutable</A>&lt;<A HREF="../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>&gt;\r
-      <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.runner.msa.Probcons</B>\r
-</PRE>\r
-<DL>\r
-<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>&gt;, <A HREF="../../../compbio/engine/client/PipedExecutable.html" title="interface in compbio.engine.client">PipedExecutable</A>&lt;<A HREF="../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>&gt;</DD>\r
-</DL>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public class <B>Probcons</B><DT>extends <A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>&lt;<A HREF="../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>&gt;<DT>implements <A HREF="../../../compbio/engine/client/PipedExecutable.html" title="interface in compbio.engine.client">PipedExecutable</A>&lt;<A HREF="../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>&gt;</DL>\r
-</PRE>\r
-\r
-<P>\r
-<HR>\r
-\r
-<P>\r
-<!-- ======== NESTED CLASS SUMMARY ======== -->\r
-\r
-<A NAME="nested_class_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Nested Class Summary</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="nested_classes_inherited_from_class_compbio.engine.client.Executable"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Nested classes/interfaces inherited from interface compbio.engine.client.<A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A></CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- =========== FIELD SUMMARY =========== -->\r
-\r
-<A NAME="field_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Field Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/msa/Probcons.html#KEY_VALUE_SEPARATOR">KEY_VALUE_SEPARATOR</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
-\r
-<A NAME="constructor_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Constructor Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/runner/msa/Probcons.html#Probcons()">Probcons</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.util.List&lt;java.lang.String&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/msa/Probcons.html#getCreatedFiles()">getCreatedFiles</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;This method cannot really tell whether the files has actually been
- created or not.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;<A HREF="../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/msa/Probcons.html#getLimit(java.lang.String)">getLimit</A></B>(java.lang.String&nbsp;presetName)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;<A HREF="../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/msa/Probcons.html#getLimits()">getLimits</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/msa/Probcons.html#getResults(java.lang.String)">getResults</A></B>(java.lang.String&nbsp;workDirectory)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.Class&lt;? extends <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;?&gt;&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/msa/Probcons.html#getType()">getType</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/msa/Probcons.html#setInput(java.lang.String)">setInput</A></B>(java.lang.String&nbsp;inFile)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_compbio.engine.client.SkeletalExecutable"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class compbio.engine.client.<A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A></B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#addParameters(java.util.List)">addParameters</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#equals(java.lang.Object)">equals</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getClusterSettings()">getClusterSettings</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getError()">getError</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getInput()">getInput</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getOutput()">getOutput</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getParameters(compbio.engine.client.Executable.ExecProvider)">getParameters</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#hashCode()">hashCode</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#loadRunConfiguration(compbio.engine.client.RunConfiguration)">loadRunConfiguration</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#setError(java.lang.String)">setError</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#setOutput(java.lang.String)">setOutput</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#setParameter(java.lang.String)">setParameter</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#toString()">toString</A></CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>getClass, notify, notifyAll, wait, wait, wait</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_compbio.engine.client.Executable"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from interface compbio.engine.client.<A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><A HREF="../../../compbio/engine/client/Executable.html#addParameters(java.util.List)">addParameters</A>, <A HREF="../../../compbio/engine/client/Executable.html#getError()">getError</A>, <A HREF="../../../compbio/engine/client/Executable.html#getInput()">getInput</A>, <A HREF="../../../compbio/engine/client/Executable.html#getOutput()">getOutput</A>, <A HREF="../../../compbio/engine/client/Executable.html#getParameters(compbio.engine.client.Executable.ExecProvider)">getParameters</A>, <A HREF="../../../compbio/engine/client/Executable.html#loadRunConfiguration(compbio.engine.client.RunConfiguration)">loadRunConfiguration</A></CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ============ FIELD DETAIL =========== -->\r
-\r
-<A NAME="field_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Field Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="KEY_VALUE_SEPARATOR"><!-- --></A><H3>\r
-KEY_VALUE_SEPARATOR</H3>\r
-<PRE>\r
-public static final java.lang.String <B>KEY_VALUE_SEPARATOR</B></PRE>\r
-<DL>\r
-<DL>\r
-<DT><B>See Also:</B><DD><A HREF="../../../constant-values.html#compbio.runner.msa.Probcons.KEY_VALUE_SEPARATOR">Constant Field Values</A></DL>\r
-</DL>\r
-\r
-<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
-\r
-<A NAME="constructor_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Constructor Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="Probcons()"><!-- --></A><H3>\r
-Probcons</H3>\r
-<PRE>\r
-public <B>Probcons</B>()</PRE>\r
-<DL>\r
-<DL>\r
-<DT><B>Parameters:</B><DD><CODE>workDirectory</CODE> - </DL>\r
-</DL>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
-<A NAME="method_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="getResults(java.lang.String)"><!-- --></A><H3>\r
-getResults</H3>\r
-<PRE>\r
-public <A HREF="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A> <B>getResults</B>(java.lang.String&nbsp;workDirectory)\r
-                     throws <A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#getResults(java.lang.String)">getResults</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-\r
-<DT><B>Throws:</B>\r
-<DD><CODE><A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></CODE></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getCreatedFiles()"><!-- --></A><H3>\r
-getCreatedFiles</H3>\r
-<PRE>\r
-public java.util.List&lt;java.lang.String&gt; <B>getCreatedFiles</B>()</PRE>\r
-<DL>\r
-<DD><B>Description copied from class: <CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getCreatedFiles()">SkeletalExecutable</A></CODE></B></DD>\r
-<DD>This method cannot really tell whether the files has actually been
- created or not. It must be overridden as required.\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#getCreatedFiles()">getCreatedFiles</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>&gt;</CODE><DT><B>Overrides:</B><DD><CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getCreatedFiles()">getCreatedFiles</A></CODE> in class <CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>&lt;<A HREF="../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-<DT><B>See Also:</B><DD><A HREF="../../../compbio/engine/client/Executable.html#getCreatedFiles()"><CODE>Executable.getCreatedFiles()</CODE></A></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="setInput(java.lang.String)"><!-- --></A><H3>\r
-setInput</H3>\r
-<PRE>\r
-public <A HREF="../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A> <B>setInput</B>(java.lang.String&nbsp;inFile)</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Overrides:</B><DD><CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#setInput(java.lang.String)">setInput</A></CODE> in class <CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>&lt;<A HREF="../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getLimit(java.lang.String)"><!-- --></A><H3>\r
-getLimit</H3>\r
-<PRE>\r
-public <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;<A HREF="../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>&gt; <B>getLimit</B>(java.lang.String&nbsp;presetName)</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#getLimit(java.lang.String)">getLimit</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getLimits()"><!-- --></A><H3>\r
-getLimits</H3>\r
-<PRE>\r
-public <A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;<A HREF="../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>&gt; <B>getLimits</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#getLimits()">getLimits</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getType()"><!-- --></A><H3>\r
-getType</H3>\r
-<PRE>\r
-public java.lang.Class&lt;? extends <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;?&gt;&gt; <B>getType</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getType()">getType</A></CODE> in class <CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>&lt;<A HREF="../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/Probcons.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/runner/msa/Probcons.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="Probcons.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;<A HREF="#field_summary">FIELD</A>&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;<A HREF="#field_detail">FIELD</A>&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/runner/msa/Tcoffee.html b/website/full_javadoc/compbio/runner/msa/Tcoffee.html

deleted file mode 100644 (file)

index b35bcc1..0000000
--- a/website/full_javadoc/compbio/runner/msa/Tcoffee.html
+++ /dev/null
@@ -1,542 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Tcoffee\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Tcoffee";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/Tcoffee.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;NEXT CLASS</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/runner/msa/Tcoffee.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="Tcoffee.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;<A HREF="#field_summary">FIELD</A>&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;<A HREF="#field_detail">FIELD</A>&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.runner.msa</FONT>\r
-<BR>\r
-Class Tcoffee</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">compbio.engine.client.SkeletalExecutable</A>&lt;<A HREF="../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>&gt;\r
-      <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.runner.msa.Tcoffee</B>\r
-</PRE>\r
-<DL>\r
-<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../compbio/engine/client/ClusterNativeSpecExecutable.html" title="interface in compbio.engine.client">ClusterNativeSpecExecutable</A>&lt;<A HREF="../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>&gt;, <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>&gt;, <A HREF="../../../compbio/engine/client/PipedExecutable.html" title="interface in compbio.engine.client">PipedExecutable</A>&lt;<A HREF="../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>&gt;</DD>\r
-</DL>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public class <B>Tcoffee</B><DT>extends <A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>&lt;<A HREF="../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>&gt;<DT>implements <A HREF="../../../compbio/engine/client/PipedExecutable.html" title="interface in compbio.engine.client">PipedExecutable</A>&lt;<A HREF="../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>&gt;, <A HREF="../../../compbio/engine/client/ClusterNativeSpecExecutable.html" title="interface in compbio.engine.client">ClusterNativeSpecExecutable</A>&lt;<A HREF="../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>&gt;</DL>\r
-</PRE>\r
-\r
-<P>\r
-<HR>\r
-\r
-<P>\r
-<!-- ======== NESTED CLASS SUMMARY ======== -->\r
-\r
-<A NAME="nested_class_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Nested Class Summary</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="nested_classes_inherited_from_class_compbio.engine.client.Executable"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Nested classes/interfaces inherited from interface compbio.engine.client.<A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A></CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- =========== FIELD SUMMARY =========== -->\r
-\r
-<A NAME="field_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Field Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/msa/Tcoffee.html#KEY_VALUE_SEPARATOR">KEY_VALUE_SEPARATOR</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
-\r
-<A NAME="constructor_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Constructor Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/runner/msa/Tcoffee.html#Tcoffee()">Tcoffee</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;int</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/msa/Tcoffee.html#getClusterCpuNum()">getClusterCpuNum</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.util.List&lt;java.lang.String&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/msa/Tcoffee.html#getCreatedFiles()">getCreatedFiles</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;This method cannot really tell whether the files has actually been
- created or not.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;<A HREF="../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/msa/Tcoffee.html#getLimit(java.lang.String)">getLimit</A></B>(java.lang.String&nbsp;presetName)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;<A HREF="../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/msa/Tcoffee.html#getLimits()">getLimits</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/msa/Tcoffee.html#getNativeSpecs()">getNativeSpecs</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>&lt;<A HREF="../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/msa/Tcoffee.html#getParameters(compbio.engine.client.Executable.ExecProvider)">getParameters</A></B>(<A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/msa/Tcoffee.html#getResults(java.lang.String)">getResults</A></B>(java.lang.String&nbsp;workDirectory)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.Class&lt;? extends <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;?&gt;&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/msa/Tcoffee.html#getType()">getType</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/msa/Tcoffee.html#setInput(java.lang.String)">setInput</A></B>(java.lang.String&nbsp;inFile)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/msa/Tcoffee.html#setNCore(int)">setNCore</A></B>(int&nbsp;ncoreNumber)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_compbio.engine.client.SkeletalExecutable"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class compbio.engine.client.<A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A></B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#addParameters(java.util.List)">addParameters</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#equals(java.lang.Object)">equals</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getClusterSettings()">getClusterSettings</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getError()">getError</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getInput()">getInput</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getOutput()">getOutput</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#hashCode()">hashCode</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#loadRunConfiguration(compbio.engine.client.RunConfiguration)">loadRunConfiguration</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#setError(java.lang.String)">setError</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#setOutput(java.lang.String)">setOutput</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#setParameter(java.lang.String)">setParameter</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#toString()">toString</A></CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>getClass, notify, notifyAll, wait, wait, wait</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_compbio.engine.client.Executable"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from interface compbio.engine.client.<A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><A HREF="../../../compbio/engine/client/Executable.html#addParameters(java.util.List)">addParameters</A>, <A HREF="../../../compbio/engine/client/Executable.html#getError()">getError</A>, <A HREF="../../../compbio/engine/client/Executable.html#getInput()">getInput</A>, <A HREF="../../../compbio/engine/client/Executable.html#getOutput()">getOutput</A>, <A HREF="../../../compbio/engine/client/Executable.html#loadRunConfiguration(compbio.engine.client.RunConfiguration)">loadRunConfiguration</A></CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ============ FIELD DETAIL =========== -->\r
-\r
-<A NAME="field_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Field Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="KEY_VALUE_SEPARATOR"><!-- --></A><H3>\r
-KEY_VALUE_SEPARATOR</H3>\r
-<PRE>\r
-public static final java.lang.String <B>KEY_VALUE_SEPARATOR</B></PRE>\r
-<DL>\r
-<DL>\r
-<DT><B>See Also:</B><DD><A HREF="../../../constant-values.html#compbio.runner.msa.Tcoffee.KEY_VALUE_SEPARATOR">Constant Field Values</A></DL>\r
-</DL>\r
-\r
-<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
-\r
-<A NAME="constructor_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Constructor Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="Tcoffee()"><!-- --></A><H3>\r
-Tcoffee</H3>\r
-<PRE>\r
-public <B>Tcoffee</B>()</PRE>\r
-<DL>\r
-<DL>\r
-<DT><B>Parameters:</B><DD><CODE>workDirectory</CODE> - </DL>\r
-</DL>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
-<A NAME="method_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="setInput(java.lang.String)"><!-- --></A><H3>\r
-setInput</H3>\r
-<PRE>\r
-public <A HREF="../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A> <B>setInput</B>(java.lang.String&nbsp;inFile)</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Overrides:</B><DD><CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#setInput(java.lang.String)">setInput</A></CODE> in class <CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>&lt;<A HREF="../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getResults(java.lang.String)"><!-- --></A><H3>\r
-getResults</H3>\r
-<PRE>\r
-public <A HREF="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A> <B>getResults</B>(java.lang.String&nbsp;workDirectory)\r
-                     throws <A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#getResults(java.lang.String)">getResults</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-\r
-<DT><B>Throws:</B>\r
-<DD><CODE><A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></CODE></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getCreatedFiles()"><!-- --></A><H3>\r
-getCreatedFiles</H3>\r
-<PRE>\r
-public java.util.List&lt;java.lang.String&gt; <B>getCreatedFiles</B>()</PRE>\r
-<DL>\r
-<DD><B>Description copied from class: <CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getCreatedFiles()">SkeletalExecutable</A></CODE></B></DD>\r
-<DD>This method cannot really tell whether the files has actually been
- created or not. It must be overridden as required.\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#getCreatedFiles()">getCreatedFiles</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>&gt;</CODE><DT><B>Overrides:</B><DD><CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getCreatedFiles()">getCreatedFiles</A></CODE> in class <CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>&lt;<A HREF="../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-<DT><B>See Also:</B><DD><A HREF="../../../compbio/engine/client/Executable.html#getCreatedFiles()"><CODE>Executable.getCreatedFiles()</CODE></A></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="setNCore(int)"><!-- --></A><H3>\r
-setNCore</H3>\r
-<PRE>\r
-public void <B>setNCore</B>(int&nbsp;ncoreNumber)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getParameters(compbio.engine.client.Executable.ExecProvider)"><!-- --></A><H3>\r
-getParameters</H3>\r
-<PRE>\r
-public <A HREF="../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>&lt;<A HREF="../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>&gt; <B>getParameters</B>(<A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider)</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#getParameters(compbio.engine.client.Executable.ExecProvider)">getParameters</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>&gt;</CODE><DT><B>Overrides:</B><DD><CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getParameters(compbio.engine.client.Executable.ExecProvider)">getParameters</A></CODE> in class <CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>&lt;<A HREF="../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getLimit(java.lang.String)"><!-- --></A><H3>\r
-getLimit</H3>\r
-<PRE>\r
-public <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;<A HREF="../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>&gt; <B>getLimit</B>(java.lang.String&nbsp;presetName)</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#getLimit(java.lang.String)">getLimit</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getLimits()"><!-- --></A><H3>\r
-getLimits</H3>\r
-<PRE>\r
-public <A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;<A HREF="../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>&gt; <B>getLimits</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#getLimits()">getLimits</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getNativeSpecs()"><!-- --></A><H3>\r
-getNativeSpecs</H3>\r
-<PRE>\r
-public java.lang.String <B>getNativeSpecs</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/ClusterNativeSpecExecutable.html#getNativeSpecs()">getNativeSpecs</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/ClusterNativeSpecExecutable.html" title="interface in compbio.engine.client">ClusterNativeSpecExecutable</A>&lt;<A HREF="../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getClusterCpuNum()"><!-- --></A><H3>\r
-getClusterCpuNum</H3>\r
-<PRE>\r
-public static int <B>getClusterCpuNum</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>number of cpus to use on the cluster or 0 if the value is
-         undefined</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getType()"><!-- --></A><H3>\r
-getType</H3>\r
-<PRE>\r
-public java.lang.Class&lt;? extends <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;?&gt;&gt; <B>getType</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getType()">getType</A></CODE> in class <CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>&lt;<A HREF="../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/Tcoffee.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;NEXT CLASS</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/runner/msa/Tcoffee.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="Tcoffee.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;<A HREF="#field_summary">FIELD</A>&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;<A HREF="#field_detail">FIELD</A>&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/runner/msa/class-use/ClustalW.html b/website/full_javadoc/compbio/runner/msa/class-use/ClustalW.html

deleted file mode 100644 (file)

index 5d5eecf..0000000
--- a/website/full_javadoc/compbio/runner/msa/class-use/ClustalW.html
+++ /dev/null
@@ -1,291 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Uses of Class compbio.runner.msa.ClustalW\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Uses of Class compbio.runner.msa.ClustalW";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/runner/msa/\class-useClustalW.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="ClustalW.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-<B>Uses of Class<br>compbio.runner.msa.ClustalW</B></H2>\r
-</CENTER>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Packages that use <A HREF="../../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.runner.msa"><B>compbio.runner.msa</B></A></TD>\r
-<TD>Wrappers for native executables for multiple sequence alignment (msa)&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.ws.server"><B>compbio.ws.server</B></A></TD>\r
-<TD>&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.runner.msa"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A> in <A HREF="../../../../compbio/runner/msa/package-summary.html">compbio.runner.msa</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/runner/msa/package-summary.html">compbio.runner.msa</A> that return <A HREF="../../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A></CODE></FONT></TD>\r
-<TD><CODE><B>ClustalW.</B><B><A HREF="../../../../compbio/runner/msa/ClustalW.html#setInput(java.lang.String)">setInput</A></B>(java.lang.String&nbsp;inFile)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A></CODE></FONT></TD>\r
-<TD><CODE><B>ClustalW.</B><B><A HREF="../../../../compbio/runner/msa/ClustalW.html#setOutput(java.lang.String)">setOutput</A></B>(java.lang.String&nbsp;outFile)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/runner/msa/package-summary.html">compbio.runner.msa</A> that return types with arguments of type <A HREF="../../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;<A HREF="../../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>ClustalW.</B><B><A HREF="../../../../compbio/runner/msa/ClustalW.html#getLimit(java.lang.String)">getLimit</A></B>(java.lang.String&nbsp;presetName)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;<A HREF="../../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>ClustalW.</B><B><A HREF="../../../../compbio/runner/msa/ClustalW.html#getLimits()">getLimits</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.ws.server"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A> in <A HREF="../../../../compbio/ws/server/package-summary.html">compbio.ws.server</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/ws/server/package-summary.html">compbio.ws.server</A> that return types with arguments of type <A HREF="../../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;<A HREF="../../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>ClustalWS.</B><B><A HREF="../../../../compbio/ws/server/ClustalWS.html#getLimit(java.lang.String)">getLimit</A></B>(java.lang.String&nbsp;presetName)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;<A HREF="../../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>ClustalWS.</B><B><A HREF="../../../../compbio/ws/server/ClustalWS.html#getLimits()">getLimits</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>&lt;<A HREF="../../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>ClustalWS.</B><B><A HREF="../../../../compbio/ws/server/ClustalWS.html#getPresets()">getPresets</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&lt;<A HREF="../../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>ClustalWS.</B><B><A HREF="../../../../compbio/ws/server/ClustalWS.html#getRunnerOptions()">getRunnerOptions</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Method parameters in <A HREF="../../../../compbio/ws/server/package-summary.html">compbio.ws.server</A> with type arguments of type <A HREF="../../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B>ClustalWS.</B><B><A HREF="../../../../compbio/ws/server/ClustalWS.html#customAlign(java.util.List, java.util.List)">customAlign</A></B>(java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-            java.util.List&lt;<A HREF="../../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>&gt;&gt;&nbsp;options)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B>ClustalWS.</B><B><A HREF="../../../../compbio/ws/server/ClustalWS.html#presetAlign(java.util.List, compbio.metadata.Preset)">presetAlign</A></B>(java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-            <A HREF="../../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>&lt;<A HREF="../../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>&gt;&nbsp;preset)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
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-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/runner/msa/\class-useClustalW.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="ClustalW.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
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-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/runner/msa/class-use/Mafft.html b/website/full_javadoc/compbio/runner/msa/class-use/Mafft.html

deleted file mode 100644 (file)

index 65e6512..0000000
--- a/website/full_javadoc/compbio/runner/msa/class-use/Mafft.html
+++ /dev/null
@@ -1,291 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Uses of Class compbio.runner.msa.Mafft\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Uses of Class compbio.runner.msa.Mafft";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/runner/msa/\class-useMafft.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="Mafft.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-<B>Uses of Class<br>compbio.runner.msa.Mafft</B></H2>\r
-</CENTER>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Packages that use <A HREF="../../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.runner.msa"><B>compbio.runner.msa</B></A></TD>\r
-<TD>Wrappers for native executables for multiple sequence alignment (msa)&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.ws.server"><B>compbio.ws.server</B></A></TD>\r
-<TD>&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.runner.msa"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A> in <A HREF="../../../../compbio/runner/msa/package-summary.html">compbio.runner.msa</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/runner/msa/package-summary.html">compbio.runner.msa</A> that return <A HREF="../../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A></CODE></FONT></TD>\r
-<TD><CODE><B>Mafft.</B><B><A HREF="../../../../compbio/runner/msa/Mafft.html#addParameters(java.util.List)">addParameters</A></B>(java.util.List&lt;java.lang.String&gt;&nbsp;parameters)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Mafft input must always be the last parameter!</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A></CODE></FONT></TD>\r
-<TD><CODE><B>Mafft.</B><B><A HREF="../../../../compbio/runner/msa/Mafft.html#setInput(java.lang.String)">setInput</A></B>(java.lang.String&nbsp;inFile)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/runner/msa/package-summary.html">compbio.runner.msa</A> that return types with arguments of type <A HREF="../../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;<A HREF="../../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>Mafft.</B><B><A HREF="../../../../compbio/runner/msa/Mafft.html#getLimit(java.lang.String)">getLimit</A></B>(java.lang.String&nbsp;presetName)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;<A HREF="../../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>Mafft.</B><B><A HREF="../../../../compbio/runner/msa/Mafft.html#getLimits()">getLimits</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.ws.server"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A> in <A HREF="../../../../compbio/ws/server/package-summary.html">compbio.ws.server</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/ws/server/package-summary.html">compbio.ws.server</A> that return types with arguments of type <A HREF="../../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;<A HREF="../../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>MafftWS.</B><B><A HREF="../../../../compbio/ws/server/MafftWS.html#getLimit(java.lang.String)">getLimit</A></B>(java.lang.String&nbsp;presetName)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;<A HREF="../../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>MafftWS.</B><B><A HREF="../../../../compbio/ws/server/MafftWS.html#getLimits()">getLimits</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>&lt;<A HREF="../../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>MafftWS.</B><B><A HREF="../../../../compbio/ws/server/MafftWS.html#getPresets()">getPresets</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&lt;<A HREF="../../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>MafftWS.</B><B><A HREF="../../../../compbio/ws/server/MafftWS.html#getRunnerOptions()">getRunnerOptions</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Method parameters in <A HREF="../../../../compbio/ws/server/package-summary.html">compbio.ws.server</A> with type arguments of type <A HREF="../../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B>MafftWS.</B><B><A HREF="../../../../compbio/ws/server/MafftWS.html#customAlign(java.util.List, java.util.List)">customAlign</A></B>(java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-            java.util.List&lt;<A HREF="../../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>&gt;&gt;&nbsp;options)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B>MafftWS.</B><B><A HREF="../../../../compbio/ws/server/MafftWS.html#presetAlign(java.util.List, compbio.metadata.Preset)">presetAlign</A></B>(java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-            <A HREF="../../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>&lt;<A HREF="../../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>&gt;&nbsp;preset)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/runner/msa/\class-useMafft.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="Mafft.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/runner/msa/class-use/Muscle.html b/website/full_javadoc/compbio/runner/msa/class-use/Muscle.html

deleted file mode 100644 (file)

index 2621067..0000000
--- a/website/full_javadoc/compbio/runner/msa/class-use/Muscle.html
+++ /dev/null
@@ -1,291 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Uses of Class compbio.runner.msa.Muscle\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Uses of Class compbio.runner.msa.Muscle";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/runner/msa/\class-useMuscle.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="Muscle.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-<B>Uses of Class<br>compbio.runner.msa.Muscle</B></H2>\r
-</CENTER>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Packages that use <A HREF="../../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.runner.msa"><B>compbio.runner.msa</B></A></TD>\r
-<TD>Wrappers for native executables for multiple sequence alignment (msa)&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.ws.server"><B>compbio.ws.server</B></A></TD>\r
-<TD>&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.runner.msa"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A> in <A HREF="../../../../compbio/runner/msa/package-summary.html">compbio.runner.msa</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/runner/msa/package-summary.html">compbio.runner.msa</A> that return <A HREF="../../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A></CODE></FONT></TD>\r
-<TD><CODE><B>Muscle.</B><B><A HREF="../../../../compbio/runner/msa/Muscle.html#setInput(java.lang.String)">setInput</A></B>(java.lang.String&nbsp;inFile)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A></CODE></FONT></TD>\r
-<TD><CODE><B>Muscle.</B><B><A HREF="../../../../compbio/runner/msa/Muscle.html#setOutput(java.lang.String)">setOutput</A></B>(java.lang.String&nbsp;outFile)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/runner/msa/package-summary.html">compbio.runner.msa</A> that return types with arguments of type <A HREF="../../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;<A HREF="../../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>Muscle.</B><B><A HREF="../../../../compbio/runner/msa/Muscle.html#getLimit(java.lang.String)">getLimit</A></B>(java.lang.String&nbsp;presetName)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;<A HREF="../../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>Muscle.</B><B><A HREF="../../../../compbio/runner/msa/Muscle.html#getLimits()">getLimits</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.ws.server"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A> in <A HREF="../../../../compbio/ws/server/package-summary.html">compbio.ws.server</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/ws/server/package-summary.html">compbio.ws.server</A> that return types with arguments of type <A HREF="../../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;<A HREF="../../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>MuscleWS.</B><B><A HREF="../../../../compbio/ws/server/MuscleWS.html#getLimit(java.lang.String)">getLimit</A></B>(java.lang.String&nbsp;presetName)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;<A HREF="../../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>MuscleWS.</B><B><A HREF="../../../../compbio/ws/server/MuscleWS.html#getLimits()">getLimits</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>&lt;<A HREF="../../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>MuscleWS.</B><B><A HREF="../../../../compbio/ws/server/MuscleWS.html#getPresets()">getPresets</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&lt;<A HREF="../../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>MuscleWS.</B><B><A HREF="../../../../compbio/ws/server/MuscleWS.html#getRunnerOptions()">getRunnerOptions</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Method parameters in <A HREF="../../../../compbio/ws/server/package-summary.html">compbio.ws.server</A> with type arguments of type <A HREF="../../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B>MuscleWS.</B><B><A HREF="../../../../compbio/ws/server/MuscleWS.html#customAlign(java.util.List, java.util.List)">customAlign</A></B>(java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-            java.util.List&lt;<A HREF="../../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>&gt;&gt;&nbsp;options)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B>MuscleWS.</B><B><A HREF="../../../../compbio/ws/server/MuscleWS.html#presetAlign(java.util.List, compbio.metadata.Preset)">presetAlign</A></B>(java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-            <A HREF="../../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>&lt;<A HREF="../../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>&gt;&nbsp;preset)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/runner/msa/\class-useMuscle.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="Muscle.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/runner/msa/class-use/Probcons.html b/website/full_javadoc/compbio/runner/msa/class-use/Probcons.html

deleted file mode 100644 (file)

index 3ffa0e0..0000000
--- a/website/full_javadoc/compbio/runner/msa/class-use/Probcons.html
+++ /dev/null
@@ -1,283 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Uses of Class compbio.runner.msa.Probcons\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Uses of Class compbio.runner.msa.Probcons";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/runner/msa/\class-useProbcons.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="Probcons.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-<B>Uses of Class<br>compbio.runner.msa.Probcons</B></H2>\r
-</CENTER>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Packages that use <A HREF="../../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.runner.msa"><B>compbio.runner.msa</B></A></TD>\r
-<TD>Wrappers for native executables for multiple sequence alignment (msa)&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.ws.server"><B>compbio.ws.server</B></A></TD>\r
-<TD>&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.runner.msa"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A> in <A HREF="../../../../compbio/runner/msa/package-summary.html">compbio.runner.msa</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/runner/msa/package-summary.html">compbio.runner.msa</A> that return <A HREF="../../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A></CODE></FONT></TD>\r
-<TD><CODE><B>Probcons.</B><B><A HREF="../../../../compbio/runner/msa/Probcons.html#setInput(java.lang.String)">setInput</A></B>(java.lang.String&nbsp;inFile)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/runner/msa/package-summary.html">compbio.runner.msa</A> that return types with arguments of type <A HREF="../../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;<A HREF="../../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>Probcons.</B><B><A HREF="../../../../compbio/runner/msa/Probcons.html#getLimit(java.lang.String)">getLimit</A></B>(java.lang.String&nbsp;presetName)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;<A HREF="../../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>Probcons.</B><B><A HREF="../../../../compbio/runner/msa/Probcons.html#getLimits()">getLimits</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.ws.server"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A> in <A HREF="../../../../compbio/ws/server/package-summary.html">compbio.ws.server</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/ws/server/package-summary.html">compbio.ws.server</A> that return types with arguments of type <A HREF="../../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;<A HREF="../../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>ProbconsWS.</B><B><A HREF="../../../../compbio/ws/server/ProbconsWS.html#getLimit(java.lang.String)">getLimit</A></B>(java.lang.String&nbsp;presetName)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;<A HREF="../../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>ProbconsWS.</B><B><A HREF="../../../../compbio/ws/server/ProbconsWS.html#getLimits()">getLimits</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>&lt;<A HREF="../../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>ProbconsWS.</B><B><A HREF="../../../../compbio/ws/server/ProbconsWS.html#getPresets()">getPresets</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&lt;<A HREF="../../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>ProbconsWS.</B><B><A HREF="../../../../compbio/ws/server/ProbconsWS.html#getRunnerOptions()">getRunnerOptions</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Method parameters in <A HREF="../../../../compbio/ws/server/package-summary.html">compbio.ws.server</A> with type arguments of type <A HREF="../../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B>ProbconsWS.</B><B><A HREF="../../../../compbio/ws/server/ProbconsWS.html#customAlign(java.util.List, java.util.List)">customAlign</A></B>(java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-            java.util.List&lt;<A HREF="../../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>&gt;&gt;&nbsp;options)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B>ProbconsWS.</B><B><A HREF="../../../../compbio/ws/server/ProbconsWS.html#presetAlign(java.util.List, compbio.metadata.Preset)">presetAlign</A></B>(java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-            <A HREF="../../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>&lt;<A HREF="../../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>&gt;&nbsp;preset)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/runner/msa/\class-useProbcons.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="Probcons.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/runner/msa/class-use/Tcoffee.html b/website/full_javadoc/compbio/runner/msa/class-use/Tcoffee.html

deleted file mode 100644 (file)

index 243fcd9..0000000
--- a/website/full_javadoc/compbio/runner/msa/class-use/Tcoffee.html
+++ /dev/null
@@ -1,291 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Uses of Class compbio.runner.msa.Tcoffee\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Uses of Class compbio.runner.msa.Tcoffee";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/runner/msa/\class-useTcoffee.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="Tcoffee.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-<B>Uses of Class<br>compbio.runner.msa.Tcoffee</B></H2>\r
-</CENTER>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Packages that use <A HREF="../../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.runner.msa"><B>compbio.runner.msa</B></A></TD>\r
-<TD>Wrappers for native executables for multiple sequence alignment (msa)&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.ws.server"><B>compbio.ws.server</B></A></TD>\r
-<TD>&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.runner.msa"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A> in <A HREF="../../../../compbio/runner/msa/package-summary.html">compbio.runner.msa</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/runner/msa/package-summary.html">compbio.runner.msa</A> that return <A HREF="../../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A></CODE></FONT></TD>\r
-<TD><CODE><B>Tcoffee.</B><B><A HREF="../../../../compbio/runner/msa/Tcoffee.html#setInput(java.lang.String)">setInput</A></B>(java.lang.String&nbsp;inFile)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/runner/msa/package-summary.html">compbio.runner.msa</A> that return types with arguments of type <A HREF="../../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;<A HREF="../../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>Tcoffee.</B><B><A HREF="../../../../compbio/runner/msa/Tcoffee.html#getLimit(java.lang.String)">getLimit</A></B>(java.lang.String&nbsp;presetName)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;<A HREF="../../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>Tcoffee.</B><B><A HREF="../../../../compbio/runner/msa/Tcoffee.html#getLimits()">getLimits</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>&lt;<A HREF="../../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>Tcoffee.</B><B><A HREF="../../../../compbio/runner/msa/Tcoffee.html#getParameters(compbio.engine.client.Executable.ExecProvider)">getParameters</A></B>(<A HREF="../../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.ws.server"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A> in <A HREF="../../../../compbio/ws/server/package-summary.html">compbio.ws.server</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/ws/server/package-summary.html">compbio.ws.server</A> that return types with arguments of type <A HREF="../../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;<A HREF="../../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>TcoffeeWS.</B><B><A HREF="../../../../compbio/ws/server/TcoffeeWS.html#getLimit(java.lang.String)">getLimit</A></B>(java.lang.String&nbsp;presetName)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;<A HREF="../../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>TcoffeeWS.</B><B><A HREF="../../../../compbio/ws/server/TcoffeeWS.html#getLimits()">getLimits</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>&lt;<A HREF="../../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>TcoffeeWS.</B><B><A HREF="../../../../compbio/ws/server/TcoffeeWS.html#getPresets()">getPresets</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&lt;<A HREF="../../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>TcoffeeWS.</B><B><A HREF="../../../../compbio/ws/server/TcoffeeWS.html#getRunnerOptions()">getRunnerOptions</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Method parameters in <A HREF="../../../../compbio/ws/server/package-summary.html">compbio.ws.server</A> with type arguments of type <A HREF="../../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B>TcoffeeWS.</B><B><A HREF="../../../../compbio/ws/server/TcoffeeWS.html#customAlign(java.util.List, java.util.List)">customAlign</A></B>(java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-            java.util.List&lt;<A HREF="../../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>&gt;&gt;&nbsp;options)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B>TcoffeeWS.</B><B><A HREF="../../../../compbio/ws/server/TcoffeeWS.html#presetAlign(java.util.List, compbio.metadata.Preset)">presetAlign</A></B>(java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-            <A HREF="../../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>&lt;<A HREF="../../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>&gt;&nbsp;preset)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/runner/msa/\class-useTcoffee.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="Tcoffee.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/runner/msa/package-frame.html b/website/full_javadoc/compbio/runner/msa/package-frame.html

deleted file mode 100644 (file)

index eddc97b..0000000
--- a/website/full_javadoc/compbio/runner/msa/package-frame.html
+++ /dev/null
@@ -1,40 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-compbio.runner.msa\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white">\r
-<FONT size="+1" CLASS="FrameTitleFont">\r
-<A HREF="../../../compbio/runner/msa/package-summary.html" target="classFrame">compbio.runner.msa</A></FONT>\r
-<TABLE BORDER="0" WIDTH="100%" SUMMARY="">\r
-<TR>\r
-<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">\r
-Classes</FONT>&nbsp;\r
-<FONT CLASS="FrameItemFont">\r
-<BR>\r
-<A HREF="ClustalW.html" title="class in compbio.runner.msa" target="classFrame">ClustalW</A>\r
-<BR>\r
-<A HREF="Mafft.html" title="class in compbio.runner.msa" target="classFrame">Mafft</A>\r
-<BR>\r
-<A HREF="Muscle.html" title="class in compbio.runner.msa" target="classFrame">Muscle</A>\r
-<BR>\r
-<A HREF="Probcons.html" title="class in compbio.runner.msa" target="classFrame">Probcons</A>\r
-<BR>\r
-<A HREF="Tcoffee.html" title="class in compbio.runner.msa" target="classFrame">Tcoffee</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/runner/msa/package-summary.html b/website/full_javadoc/compbio/runner/msa/package-summary.html

deleted file mode 100644 (file)

index 82e1c12..0000000
--- a/website/full_javadoc/compbio/runner/msa/package-summary.html
+++ /dev/null
@@ -1,192 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-compbio.runner.msa\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="compbio.runner.msa";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Class</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-use.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/runner/_jpred/package-summary.html"><B>PREV PACKAGE</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../compbio/runner/psiblast/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/runner/msa/package-summary.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="package-summary.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<H2>\r
-Package compbio.runner.msa\r
-</H2>\r
-Wrappers for native executables for multiple sequence alignment (msa)\r
-<P>\r
-<B>See:</B>\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<A HREF="#package_description"><B>Description</B></A>\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Class Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A></B></TD>\r
-<TD>&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A></B></TD>\r
-<TD>&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A></B></TD>\r
-<TD>&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A></B></TD>\r
-<TD>&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A></B></TD>\r
-<TD>&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-\r
-<P>\r
-<A NAME="package_description"><!-- --></A><H2>\r
-Package compbio.runner.msa Description\r
-</H2>\r
-\r
-<P>\r
-Wrappers for native executables for multiple sequence alignment (msa)\r
-<P>\r
-\r
-<P>\r
-<DL>\r
-<DT><B>Author:</B></DT>\r
-  <DD>Petr Troshin 
- 
-        Date January 2010</DD>\r
-</DL>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT>&nbsp;</TD>\r
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diff --git a/website/full_javadoc/compbio/runner/msa/package-tree.html b/website/full_javadoc/compbio/runner/msa/package-tree.html

deleted file mode 100644 (file)

index d790016..0000000
--- a/website/full_javadoc/compbio/runner/msa/package-tree.html
+++ /dev/null
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-<!-- ========= END OF TOP NAVBAR ========= -->\r
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diff --git a/website/full_javadoc/compbio/runner/msa/package-use.html b/website/full_javadoc/compbio/runner/msa/package-use.html

deleted file mode 100644 (file)

index 9650cc0..0000000
--- a/website/full_javadoc/compbio/runner/msa/package-use.html
+++ /dev/null
@@ -1,237 +0,0 @@
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-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
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-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
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-  <A HREF="../../../index.html?compbio/runner/msa/package-use.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
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-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
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-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
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-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-<B>Uses of Package<br>compbio.runner.msa</B></H2>\r
-</CENTER>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Packages that use <A HREF="../../../compbio/runner/msa/package-summary.html">compbio.runner.msa</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.runner.msa"><B>compbio.runner.msa</B></A></TD>\r
-<TD>Wrappers for native executables for multiple sequence alignment (msa)&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.ws.server"><B>compbio.ws.server</B></A></TD>\r
-<TD>&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.runner.msa"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Classes in <A HREF="../../../compbio/runner/msa/package-summary.html">compbio.runner.msa</A> used by <A HREF="../../../compbio/runner/msa/package-summary.html">compbio.runner.msa</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../../compbio/runner/msa/class-use/ClustalW.html#compbio.runner.msa"><B>ClustalW</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
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-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
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-<TR BGCOLOR="white" CLASS="TableRowColor">\r
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-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
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-<TR BGCOLOR="white" CLASS="TableRowColor">\r
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-\r
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-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
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-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../../compbio/runner/msa/class-use/Tcoffee.html#compbio.runner.msa"><B>Tcoffee</B></A></B>\r
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-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
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-&nbsp;\r
-<P>\r
-<A NAME="compbio.ws.server"><!-- --></A>\r
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-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Classes in <A HREF="../../../compbio/runner/msa/package-summary.html">compbio.runner.msa</A> used by <A HREF="../../../compbio/ws/server/package-summary.html">compbio.ws.server</A></FONT></TH>\r
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-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../../compbio/runner/msa/class-use/ClustalW.html#compbio.ws.server"><B>ClustalW</B></A></B>\r
-\r
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-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
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-<TR BGCOLOR="white" CLASS="TableRowColor">\r
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-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
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-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../../compbio/runner/msa/class-use/Muscle.html#compbio.ws.server"><B>Muscle</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
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deleted file mode 100644 (file)

index 6fd25a9..0000000
--- a/website/full_javadoc/compbio/runner/package-frame.html
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diff --git a/website/full_javadoc/compbio/runner/package-summary.html b/website/full_javadoc/compbio/runner/package-summary.html

deleted file mode 100644 (file)

index e5f3a22..0000000
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-  <!--\r
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-\r
-\r
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-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<H2>\r
-Package compbio.runner\r
-</H2>\r
-Utilities commonly used by all runners.\r
-<P>\r
-<B>See:</B>\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<A HREF="#package_description"><B>Description</B></A>\r
-<P>\r
-\r
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-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
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-<B>Class Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../compbio/runner/_NativeSpecHelper.html" title="class in compbio.runner">_NativeSpecHelper</A></B></TD>\r
-<TD>&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A></B></TD>\r
-<TD>&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../compbio/runner/OptionCombinator.html" title="class in compbio.runner">OptionCombinator</A></B></TD>\r
-<TD>This class solve the following problems.</TD>\r
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-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../compbio/runner/Util.html" title="class in compbio.runner">Util</A></B></TD>\r
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-&nbsp;\r
-\r
-<P>\r
-<A NAME="package_description"><!-- --></A><H2>\r
-Package compbio.runner Description\r
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-\r
-<P>\r
-Utilities commonly used by all runners.\r
-<P>\r
-\r
-<P>\r
-<DL>\r
-<DT><B>Author:</B></DT>\r
-  <DD>Petr Troshin 
- 
-        Date January 2010</DD>\r
-</DL>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
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-  <!--\r
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diff --git a/website/full_javadoc/compbio/runner/package-tree.html b/website/full_javadoc/compbio/runner/package-tree.html

deleted file mode 100644 (file)

index 05b744b..0000000
--- a/website/full_javadoc/compbio/runner/package-tree.html
+++ /dev/null
@@ -1,154 +0,0 @@
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-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
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-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
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-\r
-\r
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-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-Hierarchy For Package compbio.runner\r
-</H2>\r
-</CENTER>\r
-<DL>\r
-<DT><B>Package Hierarchies:</B><DD><A HREF="../../overview-tree.html">All Packages</A></DL>\r
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-Class Hierarchy\r
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-<UL>\r
-<LI TYPE="circle">java.lang.Object<UL>\r
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-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
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-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
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-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Use</FONT>&nbsp;</TD>\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
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-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../compbio/pipeline/_jpred/package-tree.html"><B>PREV</B></A>&nbsp;\r
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-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../index.html?compbio/runner/package-tree.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="package-tree.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
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-  <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>\r
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-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/runner/package-use.html b/website/full_javadoc/compbio/runner/package-use.html

deleted file mode 100644 (file)

index ea6e047..0000000
--- a/website/full_javadoc/compbio/runner/package-use.html
+++ /dev/null
@@ -1,189 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Uses of Package compbio.runner\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Uses of Package compbio.runner";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
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-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
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-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../index.html?compbio/runner/package-use.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="package-use.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-<B>Uses of Package<br>compbio.runner</B></H2>\r
-</CENTER>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Packages that use <A HREF="../../compbio/runner/package-summary.html">compbio.runner</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.runner"><B>compbio.runner</B></A></TD>\r
-<TD>Utilities commonly used by all runners.&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.runner._impl"><B>compbio.runner._impl</B></A></TD>\r
-<TD>&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.runner"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Classes in <A HREF="../../compbio/runner/package-summary.html">compbio.runner</A> used by <A HREF="../../compbio/runner/package-summary.html">compbio.runner</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/runner/class-use/_SkeletalCommandBuilder.html#compbio.runner"><B>_SkeletalCommandBuilder</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.runner._impl"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Classes in <A HREF="../../compbio/runner/package-summary.html">compbio.runner</A> used by <A HREF="../../compbio/runner/_impl/package-summary.html">compbio.runner._impl</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/runner/class-use/_SkeletalCommandBuilder.html#compbio.runner._impl"><B>_SkeletalCommandBuilder</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
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-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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-  </TR>\r
-</TABLE>\r
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-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
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-&nbsp;<A HREF="package-use.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
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-\r
-\r
-</FONT></TD>\r
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-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/runner/psiblast/PsiBlast.html b/website/full_javadoc/compbio/runner/psiblast/PsiBlast.html

deleted file mode 100644 (file)

index 072dda7..0000000
--- a/website/full_javadoc/compbio/runner/psiblast/PsiBlast.html
+++ /dev/null
@@ -1,354 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-PsiBlast\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="PsiBlast";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/PsiBlast.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV CLASS&nbsp;\r
-&nbsp;NEXT CLASS</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/runner/psiblast/PsiBlast.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="PsiBlast.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.runner.psiblast</FONT>\r
-<BR>\r
-Class PsiBlast</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">compbio.engine.client.SkeletalExecutable</A>&lt;<A HREF="../../../compbio/runner/psiblast/PsiBlast.html" title="class in compbio.runner.psiblast">PsiBlast</A>&gt;\r
-      <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.runner.psiblast.PsiBlast</B>\r
-</PRE>\r
-<DL>\r
-<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/runner/psiblast/PsiBlast.html" title="class in compbio.runner.psiblast">PsiBlast</A>&gt;</DD>\r
-</DL>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public class <B>PsiBlast</B><DT>extends <A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>&lt;<A HREF="../../../compbio/runner/psiblast/PsiBlast.html" title="class in compbio.runner.psiblast">PsiBlast</A>&gt;</DL>\r
-</PRE>\r
-\r
-<P>\r
-<HR>\r
-\r
-<P>\r
-<!-- ======== NESTED CLASS SUMMARY ======== -->\r
-\r
-<A NAME="nested_class_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Nested Class Summary</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="nested_classes_inherited_from_class_compbio.engine.client.Executable"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Nested classes/interfaces inherited from interface compbio.engine.client.<A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A></CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-\r
-<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
-\r
-<A NAME="constructor_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Constructor Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/runner/psiblast/PsiBlast.html#PsiBlast()">PsiBlast</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;<A HREF="../../../compbio/runner/psiblast/PsiBlast.html" title="class in compbio.runner.psiblast">PsiBlast</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/psiblast/PsiBlast.html#getLimit(java.lang.String)">getLimit</A></B>(java.lang.String&nbsp;presetName)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;<A HREF="../../../compbio/runner/psiblast/PsiBlast.html" title="class in compbio.runner.psiblast">PsiBlast</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/psiblast/PsiBlast.html#getLimits()">getLimits</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
-<TR ALIGN="right" VALIGN="">\r
-<TD NOWRAP><FONT SIZE="-1">\r
-<CODE>&lt;V&gt; V</CODE></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/psiblast/PsiBlast.html#getResults(java.lang.String)">getResults</A></B>(java.lang.String&nbsp;directory)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.Class&lt;? extends <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;?&gt;&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/psiblast/PsiBlast.html#getType()">getType</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_compbio.engine.client.SkeletalExecutable"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class compbio.engine.client.<A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A></B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#addParameters(java.util.List)">addParameters</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#equals(java.lang.Object)">equals</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getClusterSettings()">getClusterSettings</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getCreatedFiles()">getCreatedFiles</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getError()">getError</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getInput()">getInput</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getOutput()">getOutput</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getParameters(compbio.engine.client.Executable.ExecProvider)">getParameters</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#hashCode()">hashCode</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#loadRunConfiguration(compbio.engine.client.RunConfiguration)">loadRunConfiguration</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#setError(java.lang.String)">setError</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#setInput(java.lang.String)">setInput</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#setOutput(java.lang.String)">setOutput</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#setParameter(java.lang.String)">setParameter</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#toString()">toString</A></CODE></TD>\r
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-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
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-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>getClass, notify, notifyAll, wait, wait, wait</CODE></TD>\r
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-\r
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-PsiBlast</H3>\r
-<PRE>\r
-public <B>PsiBlast</B>()</PRE>\r
-<DL>\r
-</DL>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
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-<B>Method Detail</B></FONT></TH>\r
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-\r
-<A NAME="getResults(java.lang.String)"><!-- --></A><H3>\r
-getResults</H3>\r
-<PRE>\r
-public &lt;V&gt; V <B>getResults</B>(java.lang.String&nbsp;directory)\r
-             throws <A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Throws:</B>\r
-<DD><CODE><A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></CODE></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getLimit(java.lang.String)"><!-- --></A><H3>\r
-getLimit</H3>\r
-<PRE>\r
-public <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;<A HREF="../../../compbio/runner/psiblast/PsiBlast.html" title="class in compbio.runner.psiblast">PsiBlast</A>&gt; <B>getLimit</B>(java.lang.String&nbsp;presetName)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getLimits()"><!-- --></A><H3>\r
-getLimits</H3>\r
-<PRE>\r
-public <A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;<A HREF="../../../compbio/runner/psiblast/PsiBlast.html" title="class in compbio.runner.psiblast">PsiBlast</A>&gt; <B>getLimits</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getType()"><!-- --></A><H3>\r
-getType</H3>\r
-<PRE>\r
-public java.lang.Class&lt;? extends <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;?&gt;&gt; <B>getType</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getType()">getType</A></CODE> in class <CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>&lt;<A HREF="../../../compbio/runner/psiblast/PsiBlast.html" title="class in compbio.runner.psiblast">PsiBlast</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
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-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
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-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV CLASS&nbsp;\r
-&nbsp;NEXT CLASS</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/runner/psiblast/PsiBlast.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="PsiBlast.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
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-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
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diff --git a/website/full_javadoc/compbio/runner/psiblast/class-use/PsiBlast.html b/website/full_javadoc/compbio/runner/psiblast/class-use/PsiBlast.html

deleted file mode 100644 (file)

index 278d08b..0000000
--- a/website/full_javadoc/compbio/runner/psiblast/class-use/PsiBlast.html
+++ /dev/null
@@ -1,188 +0,0 @@
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-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Uses of Class compbio.runner.psiblast.PsiBlast\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Uses of Class compbio.runner.psiblast.PsiBlast";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
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-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
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-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../compbio/runner/psiblast/PsiBlast.html" title="class in compbio.runner.psiblast"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
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-</TABLE>\r
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-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
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-</TD>\r
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-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/runner/psiblast/\class-usePsiBlast.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="PsiBlast.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
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-<H2>\r
-<B>Uses of Class<br>compbio.runner.psiblast.PsiBlast</B></H2>\r
-</CENTER>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
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-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Packages that use <A HREF="../../../../compbio/runner/psiblast/PsiBlast.html" title="class in compbio.runner.psiblast">PsiBlast</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.runner.psiblast"><B>compbio.runner.psiblast</B></A></TD>\r
-<TD>&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.runner.psiblast"><!-- --></A>\r
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-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../../compbio/runner/psiblast/PsiBlast.html" title="class in compbio.runner.psiblast">PsiBlast</A> in <A HREF="../../../../compbio/runner/psiblast/package-summary.html">compbio.runner.psiblast</A></FONT></TH>\r
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-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/runner/psiblast/package-summary.html">compbio.runner.psiblast</A> that return types with arguments of type <A HREF="../../../../compbio/runner/psiblast/PsiBlast.html" title="class in compbio.runner.psiblast">PsiBlast</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;<A HREF="../../../../compbio/runner/psiblast/PsiBlast.html" title="class in compbio.runner.psiblast">PsiBlast</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>PsiBlast.</B><B><A HREF="../../../../compbio/runner/psiblast/PsiBlast.html#getLimit(java.lang.String)">getLimit</A></B>(java.lang.String&nbsp;presetName)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;<A HREF="../../../../compbio/runner/psiblast/PsiBlast.html" title="class in compbio.runner.psiblast">PsiBlast</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>PsiBlast.</B><B><A HREF="../../../../compbio/runner/psiblast/PsiBlast.html#getLimits()">getLimits</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
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-<HR>\r
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-\r
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-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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deleted file mode 100644 (file)

index 0397a2b..0000000
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diff --git a/website/full_javadoc/compbio/runner/psiblast/package-summary.html b/website/full_javadoc/compbio/runner/psiblast/package-summary.html

deleted file mode 100644 (file)

index 869c38b..0000000
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diff --git a/website/full_javadoc/compbio/runner/psiblast/package-tree.html b/website/full_javadoc/compbio/runner/psiblast/package-tree.html

deleted file mode 100644 (file)

index 3af50a4..0000000
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diff --git a/website/full_javadoc/compbio/runner/psiblast/package-use.html b/website/full_javadoc/compbio/runner/psiblast/package-use.html

deleted file mode 100644 (file)

index 3db6d4a..0000000
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+++ /dev/null
@@ -1,170 +0,0 @@
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-Packages that use <A HREF="../../../compbio/runner/psiblast/package-summary.html">compbio.runner.psiblast</A></FONT></TH>\r
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-<TD><A HREF="#compbio.runner.psiblast"><B>compbio.runner.psiblast</B></A></TD>\r
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-<P>\r
-<A NAME="compbio.runner.psiblast"><!-- --></A>\r
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-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Classes in <A HREF="../../../compbio/runner/psiblast/package-summary.html">compbio.runner.psiblast</A> used by <A HREF="../../../compbio/runner/psiblast/package-summary.html">compbio.runner.psiblast</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../../compbio/runner/psiblast/class-use/PsiBlast.html#compbio.runner.psiblast"><B>PsiBlast</B></A></B>\r
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-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
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-&nbsp;<SCRIPT type="text/javascript">\r
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diff --git a/website/full_javadoc/compbio/ws/client/Jws2Client.Services.html b/website/full_javadoc/compbio/ws/client/Jws2Client.Services.html

deleted file mode 100644 (file)

index 35584df..0000000
--- a/website/full_javadoc/compbio/ws/client/Jws2Client.Services.html
+++ /dev/null
@@ -1,377 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Jws2Client.Services\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Jws2Client.Services";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
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-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/Jws2Client.Services.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
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-  </TR>\r
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-</TD>\r
-</TR>\r
-\r
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-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/ws/client/Jws2Client.html" title="class in compbio.ws.client"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../compbio/ws/client/WSTester.html" title="class in compbio.ws.client"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/ws/client/Jws2Client.Services.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
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-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
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-  }\r
-  //-->\r
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-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
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-\r
-\r
-</FONT></TD>\r
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-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;<A HREF="#enum_constant_summary">ENUM CONSTANTS</A>&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;<A HREF="#enum_constant_detail">ENUM CONSTANTS</A>&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.ws.client</FONT>\r
-<BR>\r
-Enum Jws2Client.Services</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../../resources/inherit.gif" ALT="extended by ">java.lang.Enum&lt;<A HREF="../../../compbio/ws/client/Jws2Client.Services.html" title="enum in compbio.ws.client">Jws2Client.Services</A>&gt;\r
-      <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.ws.client.Jws2Client.Services</B>\r
-</PRE>\r
-<DL>\r
-<DT><B>All Implemented Interfaces:</B> <DD>java.io.Serializable, java.lang.Comparable&lt;<A HREF="../../../compbio/ws/client/Jws2Client.Services.html" title="enum in compbio.ws.client">Jws2Client.Services</A>&gt;</DD>\r
-</DL>\r
-<DL>\r
-<DT><B>Enclosing class:</B><DD><A HREF="../../../compbio/ws/client/Jws2Client.html" title="class in compbio.ws.client">Jws2Client</A></DD>\r
-</DL>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public static enum <B>Jws2Client.Services</B><DT>extends java.lang.Enum&lt;<A HREF="../../../compbio/ws/client/Jws2Client.Services.html" title="enum in compbio.ws.client">Jws2Client.Services</A>&gt;</DL>\r
-</PRE>\r
-\r
-<P>\r
-List of web services currently supported by JWS2\r
-<P>\r
-\r
-<P>\r
-<HR>\r
-\r
-<P>\r
-<!-- =========== ENUM CONSTANT SUMMARY =========== -->\r
-\r
-<A NAME="enum_constant_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Enum Constant Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/ws/client/Jws2Client.Services.html#ClustalWS">ClustalWS</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/ws/client/Jws2Client.Services.html#MafftWS">MafftWS</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/ws/client/Jws2Client.Services.html#MuscleWS">MuscleWS</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/ws/client/Jws2Client.Services.html#ProbconsWS">ProbconsWS</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/ws/client/Jws2Client.Services.html#TcoffeeWS">TcoffeeWS</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../compbio/ws/client/Jws2Client.Services.html" title="enum in compbio.ws.client">Jws2Client.Services</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/ws/client/Jws2Client.Services.html#valueOf(java.lang.String)">valueOf</A></B>(java.lang.String&nbsp;name)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Returns the enum constant of this type with the specified name.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../compbio/ws/client/Jws2Client.Services.html" title="enum in compbio.ws.client">Jws2Client.Services</A>[]</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/ws/client/Jws2Client.Services.html#values()">values</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Returns an array containing the constants of this enum type, in
-the order they are declared.</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Enum"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Enum</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>compareTo, equals, getDeclaringClass, hashCode, name, ordinal, toString, valueOf</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>getClass, notify, notifyAll, wait, wait, wait</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ============ ENUM CONSTANT DETAIL =========== -->\r
-\r
-<A NAME="enum_constant_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Enum Constant Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="MafftWS"><!-- --></A><H3>\r
-MafftWS</H3>\r
-<PRE>\r
-public static final <A HREF="../../../compbio/ws/client/Jws2Client.Services.html" title="enum in compbio.ws.client">Jws2Client.Services</A> <B>MafftWS</B></PRE>\r
-<DL>\r
-<DL>\r
-</DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="MuscleWS"><!-- --></A><H3>\r
-MuscleWS</H3>\r
-<PRE>\r
-public static final <A HREF="../../../compbio/ws/client/Jws2Client.Services.html" title="enum in compbio.ws.client">Jws2Client.Services</A> <B>MuscleWS</B></PRE>\r
-<DL>\r
-<DL>\r
-</DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="ClustalWS"><!-- --></A><H3>\r
-ClustalWS</H3>\r
-<PRE>\r
-public static final <A HREF="../../../compbio/ws/client/Jws2Client.Services.html" title="enum in compbio.ws.client">Jws2Client.Services</A> <B>ClustalWS</B></PRE>\r
-<DL>\r
-<DL>\r
-</DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="TcoffeeWS"><!-- --></A><H3>\r
-TcoffeeWS</H3>\r
-<PRE>\r
-public static final <A HREF="../../../compbio/ws/client/Jws2Client.Services.html" title="enum in compbio.ws.client">Jws2Client.Services</A> <B>TcoffeeWS</B></PRE>\r
-<DL>\r
-<DL>\r
-</DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="ProbconsWS"><!-- --></A><H3>\r
-ProbconsWS</H3>\r
-<PRE>\r
-public static final <A HREF="../../../compbio/ws/client/Jws2Client.Services.html" title="enum in compbio.ws.client">Jws2Client.Services</A> <B>ProbconsWS</B></PRE>\r
-<DL>\r
-<DL>\r
-</DL>\r
-</DL>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
-<A NAME="method_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="values()"><!-- --></A><H3>\r
-values</H3>\r
-<PRE>\r
-public static <A HREF="../../../compbio/ws/client/Jws2Client.Services.html" title="enum in compbio.ws.client">Jws2Client.Services</A>[] <B>values</B>()</PRE>\r
-<DL>\r
-<DD>Returns an array containing the constants of this enum type, in
-the order they are declared.  This method may be used to iterate
-over the constants as follows:
-<pre>
-for (Jws2Client.Services c : Jws2Client.Services.values())
-&nbsp;   System.out.println(c);
-</pre>\r
-<P>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>an array containing the constants of this enum type, in
-the order they are declared</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="valueOf(java.lang.String)"><!-- --></A><H3>\r
-valueOf</H3>\r
-<PRE>\r
-public static <A HREF="../../../compbio/ws/client/Jws2Client.Services.html" title="enum in compbio.ws.client">Jws2Client.Services</A> <B>valueOf</B>(java.lang.String&nbsp;name)</PRE>\r
-<DL>\r
-<DD>Returns the enum constant of this type with the specified name.
-The string must match <I>exactly</I> an identifier used to declare an
-enum constant in this type.  (Extraneous whitespace characters are 
-not permitted.)\r
-<P>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>name</CODE> - the name of the enum constant to be returned.\r
-<DT><B>Returns:</B><DD>the enum constant with the specified name\r
-<DT><B>Throws:</B>\r
-<DD><CODE>java.lang.IllegalArgumentException</CODE> - if this enum type has no constant
-with the specified name\r
-<DD><CODE>java.lang.NullPointerException</CODE> - if the argument is null</DL>\r
-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/Jws2Client.Services.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/ws/client/Jws2Client.html" title="class in compbio.ws.client"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../compbio/ws/client/WSTester.html" title="class in compbio.ws.client"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/ws/client/Jws2Client.Services.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="Jws2Client.Services.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;<A HREF="#enum_constant_summary">ENUM CONSTANTS</A>&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;<A HREF="#enum_constant_detail">ENUM CONSTANTS</A>&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/ws/client/Jws2Client.html b/website/full_javadoc/compbio/ws/client/Jws2Client.html

deleted file mode 100644 (file)

index 97c55bf..0000000
--- a/website/full_javadoc/compbio/ws/client/Jws2Client.html
+++ /dev/null
@@ -1,375 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Jws2Client\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Jws2Client";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/Jws2Client.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV CLASS&nbsp;\r
-&nbsp;<A HREF="../../../compbio/ws/client/Jws2Client.Services.html" title="enum in compbio.ws.client"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/ws/client/Jws2Client.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="Jws2Client.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;<A HREF="#nested_class_summary">NESTED</A>&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;CONSTR&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;CONSTR&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.ws.client</FONT>\r
-<BR>\r
-Class Jws2Client</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.ws.client.Jws2Client</B>\r
-</PRE>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public class <B>Jws2Client</B><DT>extends java.lang.Object</DL>\r
-</PRE>\r
-\r
-<P>\r
-A command line client for Jalview Web Services version 2\r
-<P>\r
-\r
-<P>\r
-<DL>\r
-<DT><B>Author:</B></DT>\r
-  <DD>pvtroshin</DD>\r
-</DL>\r
-<HR>\r
-\r
-<P>\r
-<!-- ======== NESTED CLASS SUMMARY ======== -->\r
-\r
-<A NAME="nested_class_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Nested Class Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;class</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/ws/client/Jws2Client.Services.html" title="enum in compbio.ws.client">Jws2Client.Services</A></B></CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;List of web services currently supported by JWS2</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
-<TR ALIGN="right" VALIGN="">\r
-<TD NOWRAP><FONT SIZE="-1">\r
-<CODE>&lt;T&gt; <A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>&lt;T&gt;</CODE></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/ws/client/Jws2Client.html#connect(java.lang.String, compbio.ws.client.Jws2Client.Services)">connect</A></B>(java.lang.String&nbsp;host,\r
-        <A HREF="../../../compbio/ws/client/Jws2Client.Services.html" title="enum in compbio.ws.client">Jws2Client.Services</A>&nbsp;service)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Connects to a web service by the host and the service name</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/ws/client/Jws2Client.html#getHost(java.lang.String[])">getHost</A></B>(java.lang.String[]&nbsp;cmd)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Extracts host name from the command line</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/ws/client/Jws2Client.html#getServiceName(java.lang.String[])">getServiceName</A></B>(java.lang.String[]&nbsp;cmd)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Extracts service name from the command line</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/ws/client/Jws2Client.html#main(java.lang.String[])">main</A></B>(java.lang.String[]&nbsp;args)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Starts command line client, if no parameter are supported print help.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/ws/client/Jws2Client.html#validURL(java.lang.String)">validURL</A></B>(java.lang.String&nbsp;urlstr)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Attempt to construct the URL object from the string</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
-<A NAME="method_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="validURL(java.lang.String)"><!-- --></A><H3>\r
-validURL</H3>\r
-<PRE>\r
-public static boolean <B>validURL</B>(java.lang.String&nbsp;urlstr)</PRE>\r
-<DL>\r
-<DD>Attempt to construct the URL object from the string\r
-<P>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>urlstr</CODE> - \r
-<DT><B>Returns:</B><DD>true if it succeed false otherwise</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getServiceName(java.lang.String[])"><!-- --></A><H3>\r
-getServiceName</H3>\r
-<PRE>\r
-public static java.lang.String <B>getServiceName</B>(java.lang.String[]&nbsp;cmd)</PRE>\r
-<DL>\r
-<DD>Extracts service name from the command line\r
-<P>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>cmd</CODE> - command line options\r
-<DT><B>Returns:</B><DD>service name or null if it is not defined</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getHost(java.lang.String[])"><!-- --></A><H3>\r
-getHost</H3>\r
-<PRE>\r
-public static java.lang.String <B>getHost</B>(java.lang.String[]&nbsp;cmd)</PRE>\r
-<DL>\r
-<DD>Extracts host name from the command line\r
-<P>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>cmd</CODE> - command line options\r
-<DT><B>Returns:</B><DD>host name or null if it is not defined</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="connect(java.lang.String, compbio.ws.client.Jws2Client.Services)"><!-- --></A><H3>\r
-connect</H3>\r
-<PRE>\r
-public static &lt;T&gt; <A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>&lt;T&gt; <B>connect</B>(java.lang.String&nbsp;host,\r
-                                   <A HREF="../../../compbio/ws/client/Jws2Client.Services.html" title="enum in compbio.ws.client">Jws2Client.Services</A>&nbsp;service)\r
-                        throws javax.xml.ws.WebServiceException</PRE>\r
-<DL>\r
-<DD>Connects to a web service by the host and the service name\r
-<P>\r
-<DD><DL>\r
-<DT><B>Type Parameters:</B><DD><CODE>T</CODE> - web service type<DT><B>Parameters:</B><DD><CODE>host</CODE> - <DD><CODE>service</CODE> - \r
-<DT><B>Returns:</B><DD>MsaWS<T>\r
-<DT><B>Throws:</B>\r
-<DD><CODE>javax.xml.ws.WebServiceException</CODE></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="main(java.lang.String[])"><!-- --></A><H3>\r
-main</H3>\r
-<PRE>\r
-public static void <B>main</B>(java.lang.String[]&nbsp;args)</PRE>\r
-<DL>\r
-<DD>Starts command line client, if no parameter are supported print help. Two
- parameters are required for successfull call the JWS2 host name and a
- service name.\r
-<P>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>args</CODE> - Usage: <Class or Jar file name> -h=host_and_context
-            -s=serviceName ACTION [OPTIONS]
- 
-            -h=<host_and_context> - a full URL to the JWS2 web server
-            including context path e.g. http://10.31.1.159:8080/ws
- 
-            -s=<ServiceName> - one of [MafftWS, MuscleWS, ClustalWS,
-            TcoffeeWS, ProbconsWS] ACTIONS:
- 
-            -i=<inputFile> - full path to fasta formatted sequence file,
-            from which to align sequences
- 
-            -parameters - lists parameters supported by web service
- 
-            -presets - lists presets supported by web service
- 
-            -limits - lists web services limits Please note that if input
-            file is specified other actions are ignored
- 
-            OPTIONS: (only for use with -i action):
- 
-            -r=<presetName> - name of the preset to use
- 
-            -o=<outputFile> - full path to the file where to write an
-            alignment -f=<parameterInputFile> - the name of the file with
-            the list of parameters to use. Please note that -r and -f
-            options cannot be used together. Alignment is done with either
-            preset or a parameters from the file, but not both!</DL>\r
-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/Jws2Client.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV CLASS&nbsp;\r
-&nbsp;<A HREF="../../../compbio/ws/client/Jws2Client.Services.html" title="enum in compbio.ws.client"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/ws/client/Jws2Client.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="Jws2Client.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;<A HREF="#nested_class_summary">NESTED</A>&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;CONSTR&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;CONSTR&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/ws/client/SimpleWSClient.html b/website/full_javadoc/compbio/ws/client/SimpleWSClient.html

deleted file mode 100644 (file)

index 724fc81..0000000
--- a/website/full_javadoc/compbio/ws/client/SimpleWSClient.html
+++ /dev/null
@@ -1,263 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 03 14:31:49 GMT 2010 -->\r
-<TITLE>\r
-SimpleWSClient\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-03">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="SimpleWSClient";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/SimpleWSClient.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV CLASS&nbsp;\r
-&nbsp;NEXT CLASS</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/ws/client/SimpleWSClient.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="SimpleWSClient.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.ws.client</FONT>\r
-<BR>\r
-Class SimpleWSClient</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.ws.client.SimpleWSClient</B>\r
-</PRE>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public class <B>SimpleWSClient</B><DT>extends java.lang.Object</DL>\r
-</PRE>\r
-\r
-<P>\r
-<HR>\r
-\r
-<P>\r
-\r
-<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
-\r
-<A NAME="constructor_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Constructor Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/ws/client/SimpleWSClient.html#SimpleWSClient()">SimpleWSClient</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/ws/client/SimpleWSClient.html#main(java.lang.String[])">main</A></B>(java.lang.String[]&nbsp;args)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
-\r
-<A NAME="constructor_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Constructor Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="SimpleWSClient()"><!-- --></A><H3>\r
-SimpleWSClient</H3>\r
-<PRE>\r
-public <B>SimpleWSClient</B>()</PRE>\r
-<DL>\r
-</DL>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
-<A NAME="method_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="main(java.lang.String[])"><!-- --></A><H3>\r
-main</H3>\r
-<PRE>\r
-public static void <B>main</B>(java.lang.String[]&nbsp;args)\r
-                 throws java.io.FileNotFoundException,\r
-                        java.io.IOException,\r
-                        <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A>,\r
-                        java.lang.InterruptedException,\r
-                        <A HREF="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Throws:</B>\r
-<DD><CODE>java.io.FileNotFoundException</CODE>\r
-<DD><CODE>java.io.IOException</CODE>\r
-<DD><CODE><A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></CODE>\r
-<DD><CODE>java.lang.InterruptedException</CODE>\r
-<DD><CODE><A HREF="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></CODE></DL>\r
-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/SimpleWSClient.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV CLASS&nbsp;\r
-&nbsp;NEXT CLASS</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/ws/client/SimpleWSClient.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="SimpleWSClient.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/ws/client/WSTester.html b/website/full_javadoc/compbio/ws/client/WSTester.html

deleted file mode 100644 (file)

index f138ed2..0000000
--- a/website/full_javadoc/compbio/ws/client/WSTester.html
+++ /dev/null
@@ -1,275 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-WSTester\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="WSTester";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
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-\r
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-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/ws/client/Jws2Client.Services.html" title="enum in compbio.ws.client"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;NEXT CLASS</FONT></TD>\r
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-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
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-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
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-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.ws.client</FONT>\r
-<BR>\r
-Class WSTester</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.ws.client.WSTester</B>\r
-</PRE>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public class <B>WSTester</B><DT>extends java.lang.Object</DL>\r
-</PRE>\r
-\r
-<P>\r
-Class for testing web services\r
-<P>\r
-\r
-<P>\r
-<DL>\r
-<DT><B>Author:</B></DT>\r
-  <DD>pvtroshin
- 
-         Date February 2010</DD>\r
-</DL>\r
-<HR>\r
-\r
-<P>\r
-\r
-<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
-\r
-<A NAME="constructor_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Constructor Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/ws/client/WSTester.html#WSTester()">WSTester</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
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-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
-<TR ALIGN="right" VALIGN="">\r
-<TD NOWRAP><FONT SIZE="-1">\r
-<CODE>&lt;T&gt; void</CODE></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/ws/client/WSTester.html#main(java.lang.String[])">main</A></B>(java.lang.String[]&nbsp;args)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Test JWS2 web services</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
-\r
-<A NAME="constructor_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Constructor Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="WSTester()"><!-- --></A><H3>\r
-WSTester</H3>\r
-<PRE>\r
-public <B>WSTester</B>()</PRE>\r
-<DL>\r
-</DL>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
-<A NAME="method_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="main(java.lang.String[])"><!-- --></A><H3>\r
-main</H3>\r
-<PRE>\r
-public static &lt;T&gt; void <B>main</B>(java.lang.String[]&nbsp;args)</PRE>\r
-<DL>\r
-<DD>Test JWS2 web services\r
-<P>\r
-<DD><DL>\r
-<DT><B>Type Parameters:</B><DD><CODE>T</CODE> - web service type<DT><B>Parameters:</B><DD><CODE>args</CODE> - -h=<Your web application server host name, port and JWS2
-            context path>
- 
-            -s=<ServiceName> which is optional. If service name is not
-            provided then all known JWS2 web services are tested</DL>\r
-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/WSTester.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
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-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/ws/client/Jws2Client.Services.html" title="enum in compbio.ws.client"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;NEXT CLASS</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/ws/client/WSTester.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="WSTester.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
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diff --git a/website/full_javadoc/compbio/ws/client/class-use/Jws2Client.Services.html b/website/full_javadoc/compbio/ws/client/class-use/Jws2Client.Services.html

deleted file mode 100644 (file)

index 7e5b0d6..0000000
--- a/website/full_javadoc/compbio/ws/client/class-use/Jws2Client.Services.html
+++ /dev/null
@@ -1,213 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Uses of Class compbio.ws.client.Jws2Client.Services\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Uses of Class compbio.ws.client.Jws2Client.Services";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../compbio/ws/client/Jws2Client.Services.html" title="enum in compbio.ws.client"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
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-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/ws/client/\class-useJws2Client.Services.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="Jws2Client.Services.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-<B>Uses of Class<br>compbio.ws.client.Jws2Client.Services</B></H2>\r
-</CENTER>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Packages that use <A HREF="../../../../compbio/ws/client/Jws2Client.Services.html" title="enum in compbio.ws.client">Jws2Client.Services</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.ws.client"><B>compbio.ws.client</B></A></TD>\r
-<TD>&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.ws.client"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../../compbio/ws/client/Jws2Client.Services.html" title="enum in compbio.ws.client">Jws2Client.Services</A> in <A HREF="../../../../compbio/ws/client/package-summary.html">compbio.ws.client</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/ws/client/package-summary.html">compbio.ws.client</A> that return <A HREF="../../../../compbio/ws/client/Jws2Client.Services.html" title="enum in compbio.ws.client">Jws2Client.Services</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../../compbio/ws/client/Jws2Client.Services.html" title="enum in compbio.ws.client">Jws2Client.Services</A></CODE></FONT></TD>\r
-<TD><CODE><B>Jws2Client.Services.</B><B><A HREF="../../../../compbio/ws/client/Jws2Client.Services.html#valueOf(java.lang.String)">valueOf</A></B>(java.lang.String&nbsp;name)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Returns the enum constant of this type with the specified name.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../../compbio/ws/client/Jws2Client.Services.html" title="enum in compbio.ws.client">Jws2Client.Services</A>[]</CODE></FONT></TD>\r
-<TD><CODE><B>Jws2Client.Services.</B><B><A HREF="../../../../compbio/ws/client/Jws2Client.Services.html#values()">values</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Returns an array containing the constants of this enum type, in
-the order they are declared.</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/ws/client/package-summary.html">compbio.ws.client</A> with parameters of type <A HREF="../../../../compbio/ws/client/Jws2Client.Services.html" title="enum in compbio.ws.client">Jws2Client.Services</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
-<TR ALIGN="right" VALIGN="">\r
-<TD NOWRAP><FONT SIZE="-1">\r
-<CODE>&lt;T&gt; <A HREF="../../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>&lt;T&gt;</CODE></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-</CODE></FONT></TD>\r
-<TD><CODE><B>Jws2Client.</B><B><A HREF="../../../../compbio/ws/client/Jws2Client.html#connect(java.lang.String, compbio.ws.client.Jws2Client.Services)">connect</A></B>(java.lang.String&nbsp;host,\r
-        <A HREF="../../../../compbio/ws/client/Jws2Client.Services.html" title="enum in compbio.ws.client">Jws2Client.Services</A>&nbsp;service)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Connects to a web service by the host and the service name</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
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-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
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-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
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-  <A HREF="../../../../index.html?compbio/ws/client/\class-useJws2Client.Services.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="Jws2Client.Services.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/ws/client/class-use/Jws2Client.html b/website/full_javadoc/compbio/ws/client/class-use/Jws2Client.html

deleted file mode 100644 (file)

index 5b7e832..0000000
--- a/website/full_javadoc/compbio/ws/client/class-use/Jws2Client.html
+++ /dev/null
@@ -1,144 +0,0 @@
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-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Uses of Class compbio.ws.client.Jws2Client\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Uses of Class compbio.ws.client.Jws2Client";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
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-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
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-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../compbio/ws/client/Jws2Client.html" title="class in compbio.ws.client"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/ws/client/\class-useJws2Client.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="Jws2Client.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-<B>Uses of Class<br>compbio.ws.client.Jws2Client</B></H2>\r
-</CENTER>\r
-No usage of compbio.ws.client.Jws2Client\r
-<P>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../compbio/ws/client/Jws2Client.html" title="class in compbio.ws.client"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/ws/client/\class-useJws2Client.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="Jws2Client.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/ws/client/class-use/SimpleWSClient.html b/website/full_javadoc/compbio/ws/client/class-use/SimpleWSClient.html

deleted file mode 100644 (file)

index 21628f6..0000000
--- a/website/full_javadoc/compbio/ws/client/class-use/SimpleWSClient.html
+++ /dev/null
@@ -1,144 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 03 14:31:50 GMT 2010 -->\r
-<TITLE>\r
-Uses of Class compbio.ws.client.SimpleWSClient\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-03">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Uses of Class compbio.ws.client.SimpleWSClient";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../compbio/ws/client/SimpleWSClient.html" title="class in compbio.ws.client"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/ws/client/\class-useSimpleWSClient.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="SimpleWSClient.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-<B>Uses of Class<br>compbio.ws.client.SimpleWSClient</B></H2>\r
-</CENTER>\r
-No usage of compbio.ws.client.SimpleWSClient\r
-<P>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
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-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/ws/client/\class-useSimpleWSClient.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="SimpleWSClient.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/ws/client/class-use/WSTester.html b/website/full_javadoc/compbio/ws/client/class-use/WSTester.html

deleted file mode 100644 (file)

index 3c10d3a..0000000
--- a/website/full_javadoc/compbio/ws/client/class-use/WSTester.html
+++ /dev/null
@@ -1,144 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Uses of Class compbio.ws.client.WSTester\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Uses of Class compbio.ws.client.WSTester";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../compbio/ws/client/WSTester.html" title="class in compbio.ws.client"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/ws/client/\class-useWSTester.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="WSTester.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-<B>Uses of Class<br>compbio.ws.client.WSTester</B></H2>\r
-</CENTER>\r
-No usage of compbio.ws.client.WSTester\r
-<P>\r
-<HR>\r
-\r
-\r
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-&nbsp;<SCRIPT type="text/javascript">\r
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-  if(window==top) {\r
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-\r
-\r
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-\r
-<HR>\r
-\r
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diff --git a/website/full_javadoc/compbio/ws/client/package-frame.html b/website/full_javadoc/compbio/ws/client/package-frame.html

deleted file mode 100644 (file)

index 3b26d63..0000000
--- a/website/full_javadoc/compbio/ws/client/package-frame.html
+++ /dev/null
@@ -1,45 +0,0 @@
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-\r
-\r
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diff --git a/website/full_javadoc/compbio/ws/client/package-summary.html b/website/full_javadoc/compbio/ws/client/package-summary.html

deleted file mode 100644 (file)

index bd6a63a..0000000
--- a/website/full_javadoc/compbio/ws/client/package-summary.html
+++ /dev/null
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-&nbsp;<A HREF="../../../compbio/runner/psiblast/package-summary.html"><B>PREV PACKAGE</B></A>&nbsp;\r
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-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
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-\r
-\r
-</FONT></TD>\r
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-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
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-\r
-<HR>\r
-<H2>\r
-Package compbio.ws.client\r
-</H2>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Class Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../../compbio/ws/client/Jws2Client.html" title="class in compbio.ws.client">Jws2Client</A></B></TD>\r
-<TD>A command line client for Jalview Web Services version 2</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../../compbio/ws/client/WSTester.html" title="class in compbio.ws.client">WSTester</A></B></TD>\r
-<TD>Class for testing web services</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
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-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Enum Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../../compbio/ws/client/Jws2Client.Services.html" title="enum in compbio.ws.client">Jws2Client.Services</A></B></TD>\r
-<TD>List of web services currently supported by JWS2</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-\r
-<P>\r
-<DL>\r
-</DL>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
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-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
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-  </TR>\r
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-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
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-\r
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-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/ws/client/package-tree.html b/website/full_javadoc/compbio/ws/client/package-tree.html

deleted file mode 100644 (file)

index 9a8e96a..0000000
--- a/website/full_javadoc/compbio/ws/client/package-tree.html
+++ /dev/null
@@ -1,163 +0,0 @@
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-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-compbio.ws.client Class Hierarchy\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="compbio.ws.client Class Hierarchy";\r
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-<NOSCRIPT>\r
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-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
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-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Class</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Use</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
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-&nbsp;<A HREF="../../../compbio/ws/server/package-tree.html"><B>NEXT</B></A></FONT></TD>\r
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-  <A HREF="../../../index.html?compbio/ws/client/package-tree.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
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-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
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-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
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-Hierarchy For Package compbio.ws.client\r
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-Enum Hierarchy\r
-</H2>\r
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-</UL>\r
-</UL>\r
-<HR>\r
-\r
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-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
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-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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-  </TR>\r
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-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
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-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/runner/psiblast/package-tree.html"><B>PREV</B></A>&nbsp;\r
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-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
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-</HTML>\r
diff --git a/website/full_javadoc/compbio/ws/client/package-use.html b/website/full_javadoc/compbio/ws/client/package-use.html

deleted file mode 100644 (file)

index bafcd7e..0000000
--- a/website/full_javadoc/compbio/ws/client/package-use.html
+++ /dev/null
@@ -1,170 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
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-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Uses of Package compbio.ws.client\r
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-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
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-\r
-<SCRIPT type="text/javascript">\r
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-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
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-<A NAME="navbar_top_firstrow"><!-- --></A>\r
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-  </TR>\r
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-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
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-&nbsp;NEXT</FONT></TD>\r
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-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
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-</SCRIPT>\r
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-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
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-\r
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-</FONT></TD>\r
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-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
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-<H2>\r
-<B>Uses of Package<br>compbio.ws.client</B></H2>\r
-</CENTER>\r
-\r
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-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Packages that use <A HREF="../../../compbio/ws/client/package-summary.html">compbio.ws.client</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.ws.client"><B>compbio.ws.client</B></A></TD>\r
-<TD>&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-<A NAME="compbio.ws.client"><!-- --></A>\r
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-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Classes in <A HREF="../../../compbio/ws/client/package-summary.html">compbio.ws.client</A> used by <A HREF="../../../compbio/ws/client/package-summary.html">compbio.ws.client</A></FONT></TH>\r
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-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../../compbio/ws/client/class-use/Jws2Client.Services.html#compbio.ws.client"><B>Jws2Client.Services</B></A></B>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;List of web services currently supported by JWS2</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
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-<HR>\r
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-\r
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-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
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-\r
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-\r
-<HR>\r
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diff --git a/website/full_javadoc/compbio/ws/server/ClustalWS.html b/website/full_javadoc/compbio/ws/server/ClustalWS.html

deleted file mode 100644 (file)

index 09d7072..0000000
--- a/website/full_javadoc/compbio/ws/server/ClustalWS.html
+++ /dev/null
@@ -1,599 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-ClustalWS\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="ClustalWS";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/ClustalWS.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
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-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV CLASS&nbsp;\r
-&nbsp;<A HREF="../../../compbio/ws/server/MafftWS.html" title="class in compbio.ws.server"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/ws/server/ClustalWS.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="ClustalWS.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.ws.server</FONT>\r
-<BR>\r
-Class ClustalWS</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.ws.server.ClustalWS</B>\r
-</PRE>\r
-<DL>\r
-<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>&lt;<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>&gt;</DD>\r
-</DL>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public class <B>ClustalWS</B><DT>extends java.lang.Object<DT>implements <A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>&lt;<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>&gt;</DL>\r
-</PRE>\r
-\r
-<P>\r
-<HR>\r
-\r
-<P>\r
-\r
-<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
-\r
-<A NAME="constructor_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Constructor Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/ws/server/ClustalWS.html#ClustalWS()">ClustalWS</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/ws/server/ClustalWS.html#align(java.util.List)">align</A></B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Align a list of sequences with default settings.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/ws/server/ClustalWS.html#cancelJob(java.lang.String)">cancelJob</A></B>(java.lang.String&nbsp;jobId)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Stop running job but leave its output untouched</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/ws/server/ClustalWS.html#customAlign(java.util.List, java.util.List)">customAlign</A></B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-            java.util.List&lt;<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>&gt;&gt;&nbsp;options)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Align a list of sequences with options.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/ws/server/ClustalWS.html#getJobStatus(java.lang.String)">getJobStatus</A></B>(java.lang.String&nbsp;jobId)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Return the status of the job.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/ws/server/ClustalWS.html#getLimit(java.lang.String)">getLimit</A></B>(java.lang.String&nbsp;presetName)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Get a Limit for a preset.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/ws/server/ClustalWS.html#getLimits()">getLimits</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;List Limits supported by a web service.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>&lt;<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/ws/server/ClustalWS.html#getPresets()">getPresets</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Get presets supported by a web service</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/ws/server/ClustalWS.html#getResult(java.lang.String)">getResult</A></B>(java.lang.String&nbsp;jobId)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Return the result of the job.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&lt;<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/ws/server/ClustalWS.html#getRunnerOptions()">getRunnerOptions</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Get options supported by a web service</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/ws/server/ClustalWS.html#presetAlign(java.util.List, compbio.metadata.Preset)">presetAlign</A></B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-            <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>&lt;<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>&gt;&nbsp;preset)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Align a list of sequences with preset.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/ws/server/ClustalWS.html#pullExecStatistics(java.lang.String, long)">pullExecStatistics</A></B>(java.lang.String&nbsp;jobId,\r
-                   long&nbsp;position)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Reads 1kb chunk from the statistics file which is specific to a given web
- service from the position.</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
-\r
-<A NAME="constructor_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Constructor Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="ClustalWS()"><!-- --></A><H3>\r
-ClustalWS</H3>\r
-<PRE>\r
-public <B>ClustalWS</B>()</PRE>\r
-<DL>\r
-</DL>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
-<A NAME="method_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="align(java.util.List)"><!-- --></A><H3>\r
-align</H3>\r
-<PRE>\r
-public java.lang.String <B>align</B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences)\r
-                       throws <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></PRE>\r
-<DL>\r
-<DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/data/msa/MsaWS.html#align(java.util.List)">MsaWS</A></CODE></B></DD>\r
-<DD>Align a list of sequences with default settings.
- 
- Any dataset containing a greater number of sequences or the average
- length of the sequences are greater then defined in the default Limit
- will not be accepted for an alignment operation and
- JobSubmissionException will be thrown.\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/data/msa/MsaWS.html#align(java.util.List)">align</A></CODE> in interface <CODE><A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>&lt;<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>sequences</CODE> - List of FastaSequence objects. The programme does not perform
-            any sequence validity checks. Nor does it checks whether the
-            sequences names are unique. It is responsibility of the caller
-            to validate this information\r
-<DT><B>Returns:</B><DD>jobId - unique identifier for the job\r
-<DT><B>Throws:</B>\r
-<DD><CODE><A HREF="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A></CODE> - thrown if server OS does not support native executables for a
-             given web service, e.g. JWS2 is deployed on Windows and Mafft
-             service is called\r
-<DD><CODE><A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A></CODE> - is throw if the input sequences number or average length
-             exceeds what is defined by the limit\r
-<DD><CODE><A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></CODE></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="presetAlign(java.util.List, compbio.metadata.Preset)"><!-- --></A><H3>\r
-presetAlign</H3>\r
-<PRE>\r
-public java.lang.String <B>presetAlign</B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-                                    <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>&lt;<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>&gt;&nbsp;preset)\r
-                             throws <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A>,\r
-                                    <A HREF="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></PRE>\r
-<DL>\r
-<DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/data/msa/MsaWS.html#presetAlign(java.util.List, compbio.metadata.Preset)">MsaWS</A></CODE></B></DD>\r
-<DD>Align a list of sequences with preset. @see Preset
- 
- Limit for a presetName is used whether the calculation will be permitted
- or denied. If no Limit was defined for a presetName, than default limit
- is used.\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/data/msa/MsaWS.html#presetAlign(java.util.List, compbio.metadata.Preset)">presetAlign</A></CODE> in interface <CODE><A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>&lt;<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>sequences</CODE> - List of FastaSequence objects. The programme does not perform
-            any sequence validity checks. Nor does it checks whether the
-            sequences names are unique. It is responsibility of the caller
-            to validate this information<DD><CODE>preset</CODE> - A list of Options\r
-<DT><B>Returns:</B><DD>String - jobId - unique identifier for the job\r
-<DT><B>Throws:</B>\r
-<DD><CODE><A HREF="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A></CODE> - thrown if server OS does not support native executables for a
-             given web service, e.g. JWS2 is deployed on Windows and Mafft
-             service is called\r
-<DD><CODE><A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A></CODE> - is throw if the input sequences number or average length
-             exceeds what is defined by the limit\r
-<DD><CODE><A HREF="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></CODE> - is throws when 1) One of the Options provided is not
-             supported, 2) The value of the option is defined outside the
-             boundaries. In both cases exception object contain the
-             information on the violating Option.\r
-<DD><CODE><A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></CODE></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="customAlign(java.util.List, java.util.List)"><!-- --></A><H3>\r
-customAlign</H3>\r
-<PRE>\r
-public java.lang.String <B>customAlign</B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-                                    java.util.List&lt;<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>&gt;&gt;&nbsp;options)\r
-                             throws <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A>,\r
-                                    <A HREF="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></PRE>\r
-<DL>\r
-<DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/data/msa/MsaWS.html#customAlign(java.util.List, java.util.List)">MsaWS</A></CODE></B></DD>\r
-<DD>Align a list of sequences with options.\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/data/msa/MsaWS.html#customAlign(java.util.List, java.util.List)">customAlign</A></CODE> in interface <CODE><A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>&lt;<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>sequences</CODE> - List of FastaSequence objects. The programme does not perform
-            any sequence validity checks. Nor does it checks whether the
-            sequences names are unique. It is responsibility of the caller
-            to validate this information<DD><CODE>options</CODE> - A list of Options\r
-<DT><B>Returns:</B><DD>jobId - unique identifier for the job\r
-<DT><B>Throws:</B>\r
-<DD><CODE><A HREF="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A></CODE> - thrown if server OS does not support native executables for a
-             given web service, e.g. JWS2 is deployed on Windows and Mafft
-             service is called\r
-<DD><CODE><A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A></CODE> - is throw if the input sequences number or average length
-             exceeds what is defined by the limit\r
-<DD><CODE><A HREF="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></CODE> - is throws when 1) One of the Options provided is not
-             supported, 2) The value of the option is defined outside the
-             boundaries. In both cases exception object contain the
-             information on the violating Option.\r
-<DD><CODE><A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></CODE><DT><B>See Also:</B><DD><A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata"><CODE>Default Limit is used to decide whether the calculation will be
-      permitted or denied</CODE></A></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getRunnerOptions()"><!-- --></A><H3>\r
-getRunnerOptions</H3>\r
-<PRE>\r
-public <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&lt;<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>&gt; <B>getRunnerOptions</B>()</PRE>\r
-<DL>\r
-<DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/data/msa/MsaWS.html#getRunnerOptions()">MsaWS</A></CODE></B></DD>\r
-<DD>Get options supported by a web service\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/data/msa/MsaWS.html#getRunnerOptions()">getRunnerOptions</A></CODE> in interface <CODE><A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>&lt;<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>RunnerConfig the list of options and parameters supported by a
-         web service.</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getResult(java.lang.String)"><!-- --></A><H3>\r
-getResult</H3>\r
-<PRE>\r
-public <A HREF="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A> <B>getResult</B>(java.lang.String&nbsp;jobId)\r
-                    throws <A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></PRE>\r
-<DL>\r
-<DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/data/msa/MsaWS.html#getResult(java.lang.String)">MsaWS</A></CODE></B></DD>\r
-<DD>Return the result of the job.\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/data/msa/MsaWS.html#getResult(java.lang.String)">getResult</A></CODE> in interface <CODE><A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>&lt;<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>jobId</CODE> - a unique job identifier\r
-<DT><B>Returns:</B><DD>Alignment\r
-<DT><B>Throws:</B>\r
-<DD><CODE><A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></CODE> - this exception is throw if the job execution was not
-             successful or the result of the execution could not be found.
-             (e.g. removed). Exception could also be thrown is dues to the
-             lower level problems on the server i.e. IOException,
-             FileNotFoundException problems as well as
-             UnknownFileFormatException.</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getLimit(java.lang.String)"><!-- --></A><H3>\r
-getLimit</H3>\r
-<PRE>\r
-public <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>&gt; <B>getLimit</B>(java.lang.String&nbsp;presetName)</PRE>\r
-<DL>\r
-<DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/data/msa/MsaWS.html#getLimit(java.lang.String)">MsaWS</A></CODE></B></DD>\r
-<DD>Get a Limit for a preset.\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/data/msa/MsaWS.html#getLimit(java.lang.String)">getLimit</A></CODE> in interface <CODE><A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>&lt;<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>presetName</CODE> - the name of the preset. if no name is provided, then the
-            default preset is returned. If no limit for a particular
-            preset is defined then the default preset is returned\r
-<DT><B>Returns:</B><DD>Limit</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getLimits()"><!-- --></A><H3>\r
-getLimits</H3>\r
-<PRE>\r
-public <A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>&gt; <B>getLimits</B>()</PRE>\r
-<DL>\r
-<DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/data/msa/MsaWS.html#getLimits()">MsaWS</A></CODE></B></DD>\r
-<DD>List Limits supported by a web service.\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/data/msa/MsaWS.html#getLimits()">getLimits</A></CODE> in interface <CODE><A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>&lt;<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>LimitManager</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="cancelJob(java.lang.String)"><!-- --></A><H3>\r
-cancelJob</H3>\r
-<PRE>\r
-public boolean <B>cancelJob</B>(java.lang.String&nbsp;jobId)</PRE>\r
-<DL>\r
-<DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/data/msa/MsaWS.html#cancelJob(java.lang.String)">MsaWS</A></CODE></B></DD>\r
-<DD>Stop running job but leave its output untouched\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/data/msa/MsaWS.html#cancelJob(java.lang.String)">cancelJob</A></CODE> in interface <CODE><A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>&lt;<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>true if job was cancelled successfully, false otherwise</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getJobStatus(java.lang.String)"><!-- --></A><H3>\r
-getJobStatus</H3>\r
-<PRE>\r
-public <A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A> <B>getJobStatus</B>(java.lang.String&nbsp;jobId)</PRE>\r
-<DL>\r
-<DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/data/msa/MsaWS.html#getJobStatus(java.lang.String)">MsaWS</A></CODE></B></DD>\r
-<DD>Return the status of the job. @see JobStatus\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/data/msa/MsaWS.html#getJobStatus(java.lang.String)">getJobStatus</A></CODE> in interface <CODE><A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>&lt;<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>jobId</CODE> - - unique job identifier\r
-<DT><B>Returns:</B><DD>JobStatus - status of the job</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getPresets()"><!-- --></A><H3>\r
-getPresets</H3>\r
-<PRE>\r
-public <A HREF="../../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>&lt;<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>&gt; <B>getPresets</B>()</PRE>\r
-<DL>\r
-<DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/data/msa/MsaWS.html#getPresets()">MsaWS</A></CODE></B></DD>\r
-<DD>Get presets supported by a web service\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/data/msa/MsaWS.html#getPresets()">getPresets</A></CODE> in interface <CODE><A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>&lt;<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>PresetManager the object contains information about presets
-         supported by a web service</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="pullExecStatistics(java.lang.String, long)"><!-- --></A><H3>\r
-pullExecStatistics</H3>\r
-<PRE>\r
-public <A HREF="../../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A> <B>pullExecStatistics</B>(java.lang.String&nbsp;jobId,\r
-                                      long&nbsp;position)</PRE>\r
-<DL>\r
-<DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/data/msa/MsaWS.html#pullExecStatistics(java.lang.String, long)">MsaWS</A></CODE></B></DD>\r
-<DD>Reads 1kb chunk from the statistics file which is specific to a given web
- service from the position. If in time of a request less then 1kb data is
- available from the position to the end of the file, then it returns all
- the data available from the position to the end of the file.\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/data/msa/MsaWS.html#pullExecStatistics(java.lang.String, long)">pullExecStatistics</A></CODE> in interface <CODE><A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>&lt;<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>jobId</CODE> - - unique job identifier<DD><CODE>position</CODE> - - next position within the file to read\r
-<DT><B>Returns:</B><DD>ChunkHolder - @see ChunkHolder which contains a chuink of data
-         and a next position within the file from which no data has been
-         read</DL>\r
-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/ClustalWS.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV CLASS&nbsp;\r
-&nbsp;<A HREF="../../../compbio/ws/server/MafftWS.html" title="class in compbio.ws.server"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/ws/server/ClustalWS.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="ClustalWS.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/ws/server/MafftWS.html b/website/full_javadoc/compbio/ws/server/MafftWS.html

deleted file mode 100644 (file)

index d419846..0000000
--- a/website/full_javadoc/compbio/ws/server/MafftWS.html
+++ /dev/null
@@ -1,599 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-MafftWS\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="MafftWS";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/MafftWS.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/ws/server/ClustalWS.html" title="class in compbio.ws.server"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../compbio/ws/server/MuscleWS.html" title="class in compbio.ws.server"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/ws/server/MafftWS.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="MafftWS.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.ws.server</FONT>\r
-<BR>\r
-Class MafftWS</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.ws.server.MafftWS</B>\r
-</PRE>\r
-<DL>\r
-<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>&lt;<A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>&gt;</DD>\r
-</DL>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public class <B>MafftWS</B><DT>extends java.lang.Object<DT>implements <A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>&lt;<A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>&gt;</DL>\r
-</PRE>\r
-\r
-<P>\r
-<HR>\r
-\r
-<P>\r
-\r
-<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
-\r
-<A NAME="constructor_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Constructor Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/ws/server/MafftWS.html#MafftWS()">MafftWS</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/ws/server/MafftWS.html#align(java.util.List)">align</A></B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Align a list of sequences with default settings.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/ws/server/MafftWS.html#cancelJob(java.lang.String)">cancelJob</A></B>(java.lang.String&nbsp;jobId)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Stop running job but leave its output untouched</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/ws/server/MafftWS.html#customAlign(java.util.List, java.util.List)">customAlign</A></B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-            java.util.List&lt;<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>&gt;&gt;&nbsp;options)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Align a list of sequences with options.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/ws/server/MafftWS.html#getJobStatus(java.lang.String)">getJobStatus</A></B>(java.lang.String&nbsp;jobId)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Return the status of the job.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;<A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/ws/server/MafftWS.html#getLimit(java.lang.String)">getLimit</A></B>(java.lang.String&nbsp;presetName)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Get a Limit for a preset.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;<A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/ws/server/MafftWS.html#getLimits()">getLimits</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;List Limits supported by a web service.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>&lt;<A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/ws/server/MafftWS.html#getPresets()">getPresets</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Get presets supported by a web service</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/ws/server/MafftWS.html#getResult(java.lang.String)">getResult</A></B>(java.lang.String&nbsp;jobId)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Return the result of the job.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&lt;<A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/ws/server/MafftWS.html#getRunnerOptions()">getRunnerOptions</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Get options supported by a web service</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/ws/server/MafftWS.html#presetAlign(java.util.List, compbio.metadata.Preset)">presetAlign</A></B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-            <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>&lt;<A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>&gt;&nbsp;preset)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Align a list of sequences with preset.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/ws/server/MafftWS.html#pullExecStatistics(java.lang.String, long)">pullExecStatistics</A></B>(java.lang.String&nbsp;jobId,\r
-                   long&nbsp;position)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Reads 1kb chunk from the statistics file which is specific to a given web
- service from the position.</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
-\r
-<A NAME="constructor_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Constructor Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="MafftWS()"><!-- --></A><H3>\r
-MafftWS</H3>\r
-<PRE>\r
-public <B>MafftWS</B>()</PRE>\r
-<DL>\r
-</DL>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
-<A NAME="method_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="align(java.util.List)"><!-- --></A><H3>\r
-align</H3>\r
-<PRE>\r
-public java.lang.String <B>align</B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences)\r
-                       throws <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></PRE>\r
-<DL>\r
-<DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/data/msa/MsaWS.html#align(java.util.List)">MsaWS</A></CODE></B></DD>\r
-<DD>Align a list of sequences with default settings.
- 
- Any dataset containing a greater number of sequences or the average
- length of the sequences are greater then defined in the default Limit
- will not be accepted for an alignment operation and
- JobSubmissionException will be thrown.\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/data/msa/MsaWS.html#align(java.util.List)">align</A></CODE> in interface <CODE><A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>&lt;<A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>sequences</CODE> - List of FastaSequence objects. The programme does not perform
-            any sequence validity checks. Nor does it checks whether the
-            sequences names are unique. It is responsibility of the caller
-            to validate this information\r
-<DT><B>Returns:</B><DD>jobId - unique identifier for the job\r
-<DT><B>Throws:</B>\r
-<DD><CODE><A HREF="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A></CODE> - thrown if server OS does not support native executables for a
-             given web service, e.g. JWS2 is deployed on Windows and Mafft
-             service is called\r
-<DD><CODE><A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A></CODE> - is throw if the input sequences number or average length
-             exceeds what is defined by the limit\r
-<DD><CODE><A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></CODE></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="customAlign(java.util.List, java.util.List)"><!-- --></A><H3>\r
-customAlign</H3>\r
-<PRE>\r
-public java.lang.String <B>customAlign</B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-                                    java.util.List&lt;<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>&gt;&gt;&nbsp;options)\r
-                             throws <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A>,\r
-                                    <A HREF="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></PRE>\r
-<DL>\r
-<DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/data/msa/MsaWS.html#customAlign(java.util.List, java.util.List)">MsaWS</A></CODE></B></DD>\r
-<DD>Align a list of sequences with options.\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/data/msa/MsaWS.html#customAlign(java.util.List, java.util.List)">customAlign</A></CODE> in interface <CODE><A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>&lt;<A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>sequences</CODE> - List of FastaSequence objects. The programme does not perform
-            any sequence validity checks. Nor does it checks whether the
-            sequences names are unique. It is responsibility of the caller
-            to validate this information<DD><CODE>options</CODE> - A list of Options\r
-<DT><B>Returns:</B><DD>jobId - unique identifier for the job\r
-<DT><B>Throws:</B>\r
-<DD><CODE><A HREF="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A></CODE> - thrown if server OS does not support native executables for a
-             given web service, e.g. JWS2 is deployed on Windows and Mafft
-             service is called\r
-<DD><CODE><A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A></CODE> - is throw if the input sequences number or average length
-             exceeds what is defined by the limit\r
-<DD><CODE><A HREF="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></CODE> - is throws when 1) One of the Options provided is not
-             supported, 2) The value of the option is defined outside the
-             boundaries. In both cases exception object contain the
-             information on the violating Option.\r
-<DD><CODE><A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></CODE><DT><B>See Also:</B><DD><A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata"><CODE>Default Limit is used to decide whether the calculation will be
-      permitted or denied</CODE></A></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="presetAlign(java.util.List, compbio.metadata.Preset)"><!-- --></A><H3>\r
-presetAlign</H3>\r
-<PRE>\r
-public java.lang.String <B>presetAlign</B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-                                    <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>&lt;<A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>&gt;&nbsp;preset)\r
-                             throws <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A>,\r
-                                    <A HREF="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></PRE>\r
-<DL>\r
-<DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/data/msa/MsaWS.html#presetAlign(java.util.List, compbio.metadata.Preset)">MsaWS</A></CODE></B></DD>\r
-<DD>Align a list of sequences with preset. @see Preset
- 
- Limit for a presetName is used whether the calculation will be permitted
- or denied. If no Limit was defined for a presetName, than default limit
- is used.\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/data/msa/MsaWS.html#presetAlign(java.util.List, compbio.metadata.Preset)">presetAlign</A></CODE> in interface <CODE><A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>&lt;<A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>sequences</CODE> - List of FastaSequence objects. The programme does not perform
-            any sequence validity checks. Nor does it checks whether the
-            sequences names are unique. It is responsibility of the caller
-            to validate this information<DD><CODE>preset</CODE> - A list of Options\r
-<DT><B>Returns:</B><DD>String - jobId - unique identifier for the job\r
-<DT><B>Throws:</B>\r
-<DD><CODE><A HREF="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A></CODE> - thrown if server OS does not support native executables for a
-             given web service, e.g. JWS2 is deployed on Windows and Mafft
-             service is called\r
-<DD><CODE><A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A></CODE> - is throw if the input sequences number or average length
-             exceeds what is defined by the limit\r
-<DD><CODE><A HREF="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></CODE> - is throws when 1) One of the Options provided is not
-             supported, 2) The value of the option is defined outside the
-             boundaries. In both cases exception object contain the
-             information on the violating Option.\r
-<DD><CODE><A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></CODE></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getResult(java.lang.String)"><!-- --></A><H3>\r
-getResult</H3>\r
-<PRE>\r
-public <A HREF="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A> <B>getResult</B>(java.lang.String&nbsp;jobId)\r
-                    throws <A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></PRE>\r
-<DL>\r
-<DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/data/msa/MsaWS.html#getResult(java.lang.String)">MsaWS</A></CODE></B></DD>\r
-<DD>Return the result of the job.\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/data/msa/MsaWS.html#getResult(java.lang.String)">getResult</A></CODE> in interface <CODE><A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>&lt;<A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>jobId</CODE> - a unique job identifier\r
-<DT><B>Returns:</B><DD>Alignment\r
-<DT><B>Throws:</B>\r
-<DD><CODE><A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></CODE> - this exception is throw if the job execution was not
-             successful or the result of the execution could not be found.
-             (e.g. removed). Exception could also be thrown is dues to the
-             lower level problems on the server i.e. IOException,
-             FileNotFoundException problems as well as
-             UnknownFileFormatException.</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getLimit(java.lang.String)"><!-- --></A><H3>\r
-getLimit</H3>\r
-<PRE>\r
-public <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;<A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>&gt; <B>getLimit</B>(java.lang.String&nbsp;presetName)</PRE>\r
-<DL>\r
-<DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/data/msa/MsaWS.html#getLimit(java.lang.String)">MsaWS</A></CODE></B></DD>\r
-<DD>Get a Limit for a preset.\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/data/msa/MsaWS.html#getLimit(java.lang.String)">getLimit</A></CODE> in interface <CODE><A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>&lt;<A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>presetName</CODE> - the name of the preset. if no name is provided, then the
-            default preset is returned. If no limit for a particular
-            preset is defined then the default preset is returned\r
-<DT><B>Returns:</B><DD>Limit</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getLimits()"><!-- --></A><H3>\r
-getLimits</H3>\r
-<PRE>\r
-public <A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;<A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>&gt; <B>getLimits</B>()</PRE>\r
-<DL>\r
-<DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/data/msa/MsaWS.html#getLimits()">MsaWS</A></CODE></B></DD>\r
-<DD>List Limits supported by a web service.\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/data/msa/MsaWS.html#getLimits()">getLimits</A></CODE> in interface <CODE><A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>&lt;<A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>LimitManager</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="pullExecStatistics(java.lang.String, long)"><!-- --></A><H3>\r
-pullExecStatistics</H3>\r
-<PRE>\r
-public <A HREF="../../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A> <B>pullExecStatistics</B>(java.lang.String&nbsp;jobId,\r
-                                      long&nbsp;position)</PRE>\r
-<DL>\r
-<DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/data/msa/MsaWS.html#pullExecStatistics(java.lang.String, long)">MsaWS</A></CODE></B></DD>\r
-<DD>Reads 1kb chunk from the statistics file which is specific to a given web
- service from the position. If in time of a request less then 1kb data is
- available from the position to the end of the file, then it returns all
- the data available from the position to the end of the file.\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/data/msa/MsaWS.html#pullExecStatistics(java.lang.String, long)">pullExecStatistics</A></CODE> in interface <CODE><A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>&lt;<A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>jobId</CODE> - - unique job identifier<DD><CODE>position</CODE> - - next position within the file to read\r
-<DT><B>Returns:</B><DD>ChunkHolder - @see ChunkHolder which contains a chuink of data
-         and a next position within the file from which no data has been
-         read</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="cancelJob(java.lang.String)"><!-- --></A><H3>\r
-cancelJob</H3>\r
-<PRE>\r
-public boolean <B>cancelJob</B>(java.lang.String&nbsp;jobId)</PRE>\r
-<DL>\r
-<DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/data/msa/MsaWS.html#cancelJob(java.lang.String)">MsaWS</A></CODE></B></DD>\r
-<DD>Stop running job but leave its output untouched\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/data/msa/MsaWS.html#cancelJob(java.lang.String)">cancelJob</A></CODE> in interface <CODE><A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>&lt;<A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>true if job was cancelled successfully, false otherwise</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getJobStatus(java.lang.String)"><!-- --></A><H3>\r
-getJobStatus</H3>\r
-<PRE>\r
-public <A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A> <B>getJobStatus</B>(java.lang.String&nbsp;jobId)</PRE>\r
-<DL>\r
-<DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/data/msa/MsaWS.html#getJobStatus(java.lang.String)">MsaWS</A></CODE></B></DD>\r
-<DD>Return the status of the job. @see JobStatus\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/data/msa/MsaWS.html#getJobStatus(java.lang.String)">getJobStatus</A></CODE> in interface <CODE><A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>&lt;<A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>jobId</CODE> - - unique job identifier\r
-<DT><B>Returns:</B><DD>JobStatus - status of the job</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getPresets()"><!-- --></A><H3>\r
-getPresets</H3>\r
-<PRE>\r
-public <A HREF="../../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>&lt;<A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>&gt; <B>getPresets</B>()</PRE>\r
-<DL>\r
-<DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/data/msa/MsaWS.html#getPresets()">MsaWS</A></CODE></B></DD>\r
-<DD>Get presets supported by a web service\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/data/msa/MsaWS.html#getPresets()">getPresets</A></CODE> in interface <CODE><A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>&lt;<A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>PresetManager the object contains information about presets
-         supported by a web service</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getRunnerOptions()"><!-- --></A><H3>\r
-getRunnerOptions</H3>\r
-<PRE>\r
-public <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&lt;<A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>&gt; <B>getRunnerOptions</B>()</PRE>\r
-<DL>\r
-<DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/data/msa/MsaWS.html#getRunnerOptions()">MsaWS</A></CODE></B></DD>\r
-<DD>Get options supported by a web service\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/data/msa/MsaWS.html#getRunnerOptions()">getRunnerOptions</A></CODE> in interface <CODE><A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>&lt;<A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>RunnerConfig the list of options and parameters supported by a
-         web service.</DL>\r
-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/MafftWS.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/ws/server/ClustalWS.html" title="class in compbio.ws.server"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../compbio/ws/server/MuscleWS.html" title="class in compbio.ws.server"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/ws/server/MafftWS.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="MafftWS.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/ws/server/MuscleWS.html b/website/full_javadoc/compbio/ws/server/MuscleWS.html

deleted file mode 100644 (file)

index 0d9ec95..0000000
--- a/website/full_javadoc/compbio/ws/server/MuscleWS.html
+++ /dev/null
@@ -1,599 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-MuscleWS\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="MuscleWS";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/MuscleWS.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/ws/server/MafftWS.html" title="class in compbio.ws.server"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../compbio/ws/server/ProbconsWS.html" title="class in compbio.ws.server"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/ws/server/MuscleWS.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="MuscleWS.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.ws.server</FONT>\r
-<BR>\r
-Class MuscleWS</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.ws.server.MuscleWS</B>\r
-</PRE>\r
-<DL>\r
-<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>&lt;<A HREF="../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>&gt;</DD>\r
-</DL>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public class <B>MuscleWS</B><DT>extends java.lang.Object<DT>implements <A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>&lt;<A HREF="../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>&gt;</DL>\r
-</PRE>\r
-\r
-<P>\r
-<HR>\r
-\r
-<P>\r
-\r
-<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
-\r
-<A NAME="constructor_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Constructor Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/ws/server/MuscleWS.html#MuscleWS()">MuscleWS</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/ws/server/MuscleWS.html#align(java.util.List)">align</A></B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Align a list of sequences with default settings.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/ws/server/MuscleWS.html#cancelJob(java.lang.String)">cancelJob</A></B>(java.lang.String&nbsp;jobId)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Stop running job but leave its output untouched</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/ws/server/MuscleWS.html#customAlign(java.util.List, java.util.List)">customAlign</A></B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-            java.util.List&lt;<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>&gt;&gt;&nbsp;options)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Align a list of sequences with options.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/ws/server/MuscleWS.html#getJobStatus(java.lang.String)">getJobStatus</A></B>(java.lang.String&nbsp;jobId)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Return the status of the job.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;<A HREF="../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/ws/server/MuscleWS.html#getLimit(java.lang.String)">getLimit</A></B>(java.lang.String&nbsp;presetName)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Get a Limit for a preset.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;<A HREF="../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/ws/server/MuscleWS.html#getLimits()">getLimits</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;List Limits supported by a web service.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>&lt;<A HREF="../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/ws/server/MuscleWS.html#getPresets()">getPresets</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Get presets supported by a web service</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/ws/server/MuscleWS.html#getResult(java.lang.String)">getResult</A></B>(java.lang.String&nbsp;jobId)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Return the result of the job.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&lt;<A HREF="../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/ws/server/MuscleWS.html#getRunnerOptions()">getRunnerOptions</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Get options supported by a web service</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/ws/server/MuscleWS.html#presetAlign(java.util.List, compbio.metadata.Preset)">presetAlign</A></B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-            <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>&lt;<A HREF="../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>&gt;&nbsp;preset)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Align a list of sequences with preset.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/ws/server/MuscleWS.html#pullExecStatistics(java.lang.String, long)">pullExecStatistics</A></B>(java.lang.String&nbsp;jobId,\r
-                   long&nbsp;position)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Reads 1kb chunk from the statistics file which is specific to a given web
- service from the position.</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
-\r
-<A NAME="constructor_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Constructor Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="MuscleWS()"><!-- --></A><H3>\r
-MuscleWS</H3>\r
-<PRE>\r
-public <B>MuscleWS</B>()</PRE>\r
-<DL>\r
-</DL>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
-<A NAME="method_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="align(java.util.List)"><!-- --></A><H3>\r
-align</H3>\r
-<PRE>\r
-public java.lang.String <B>align</B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences)\r
-                       throws <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></PRE>\r
-<DL>\r
-<DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/data/msa/MsaWS.html#align(java.util.List)">MsaWS</A></CODE></B></DD>\r
-<DD>Align a list of sequences with default settings.
- 
- Any dataset containing a greater number of sequences or the average
- length of the sequences are greater then defined in the default Limit
- will not be accepted for an alignment operation and
- JobSubmissionException will be thrown.\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/data/msa/MsaWS.html#align(java.util.List)">align</A></CODE> in interface <CODE><A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>&lt;<A HREF="../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>sequences</CODE> - List of FastaSequence objects. The programme does not perform
-            any sequence validity checks. Nor does it checks whether the
-            sequences names are unique. It is responsibility of the caller
-            to validate this information\r
-<DT><B>Returns:</B><DD>jobId - unique identifier for the job\r
-<DT><B>Throws:</B>\r
-<DD><CODE><A HREF="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A></CODE> - thrown if server OS does not support native executables for a
-             given web service, e.g. JWS2 is deployed on Windows and Mafft
-             service is called\r
-<DD><CODE><A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A></CODE> - is throw if the input sequences number or average length
-             exceeds what is defined by the limit\r
-<DD><CODE><A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></CODE></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="customAlign(java.util.List, java.util.List)"><!-- --></A><H3>\r
-customAlign</H3>\r
-<PRE>\r
-public java.lang.String <B>customAlign</B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-                                    java.util.List&lt;<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>&gt;&gt;&nbsp;options)\r
-                             throws <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A>,\r
-                                    <A HREF="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></PRE>\r
-<DL>\r
-<DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/data/msa/MsaWS.html#customAlign(java.util.List, java.util.List)">MsaWS</A></CODE></B></DD>\r
-<DD>Align a list of sequences with options.\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/data/msa/MsaWS.html#customAlign(java.util.List, java.util.List)">customAlign</A></CODE> in interface <CODE><A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>&lt;<A HREF="../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>sequences</CODE> - List of FastaSequence objects. The programme does not perform
-            any sequence validity checks. Nor does it checks whether the
-            sequences names are unique. It is responsibility of the caller
-            to validate this information<DD><CODE>options</CODE> - A list of Options\r
-<DT><B>Returns:</B><DD>jobId - unique identifier for the job\r
-<DT><B>Throws:</B>\r
-<DD><CODE><A HREF="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A></CODE> - thrown if server OS does not support native executables for a
-             given web service, e.g. JWS2 is deployed on Windows and Mafft
-             service is called\r
-<DD><CODE><A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A></CODE> - is throw if the input sequences number or average length
-             exceeds what is defined by the limit\r
-<DD><CODE><A HREF="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></CODE> - is throws when 1) One of the Options provided is not
-             supported, 2) The value of the option is defined outside the
-             boundaries. In both cases exception object contain the
-             information on the violating Option.\r
-<DD><CODE><A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></CODE><DT><B>See Also:</B><DD><A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata"><CODE>Default Limit is used to decide whether the calculation will be
-      permitted or denied</CODE></A></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="presetAlign(java.util.List, compbio.metadata.Preset)"><!-- --></A><H3>\r
-presetAlign</H3>\r
-<PRE>\r
-public java.lang.String <B>presetAlign</B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-                                    <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>&lt;<A HREF="../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>&gt;&nbsp;preset)\r
-                             throws <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A>,\r
-                                    <A HREF="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></PRE>\r
-<DL>\r
-<DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/data/msa/MsaWS.html#presetAlign(java.util.List, compbio.metadata.Preset)">MsaWS</A></CODE></B></DD>\r
-<DD>Align a list of sequences with preset. @see Preset
- 
- Limit for a presetName is used whether the calculation will be permitted
- or denied. If no Limit was defined for a presetName, than default limit
- is used.\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/data/msa/MsaWS.html#presetAlign(java.util.List, compbio.metadata.Preset)">presetAlign</A></CODE> in interface <CODE><A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>&lt;<A HREF="../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>sequences</CODE> - List of FastaSequence objects. The programme does not perform
-            any sequence validity checks. Nor does it checks whether the
-            sequences names are unique. It is responsibility of the caller
-            to validate this information<DD><CODE>preset</CODE> - A list of Options\r
-<DT><B>Returns:</B><DD>String - jobId - unique identifier for the job\r
-<DT><B>Throws:</B>\r
-<DD><CODE><A HREF="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A></CODE> - thrown if server OS does not support native executables for a
-             given web service, e.g. JWS2 is deployed on Windows and Mafft
-             service is called\r
-<DD><CODE><A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A></CODE> - is throw if the input sequences number or average length
-             exceeds what is defined by the limit\r
-<DD><CODE><A HREF="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></CODE> - is throws when 1) One of the Options provided is not
-             supported, 2) The value of the option is defined outside the
-             boundaries. In both cases exception object contain the
-             information on the violating Option.\r
-<DD><CODE><A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></CODE></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getResult(java.lang.String)"><!-- --></A><H3>\r
-getResult</H3>\r
-<PRE>\r
-public <A HREF="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A> <B>getResult</B>(java.lang.String&nbsp;jobId)\r
-                    throws <A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></PRE>\r
-<DL>\r
-<DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/data/msa/MsaWS.html#getResult(java.lang.String)">MsaWS</A></CODE></B></DD>\r
-<DD>Return the result of the job.\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/data/msa/MsaWS.html#getResult(java.lang.String)">getResult</A></CODE> in interface <CODE><A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>&lt;<A HREF="../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>jobId</CODE> - a unique job identifier\r
-<DT><B>Returns:</B><DD>Alignment\r
-<DT><B>Throws:</B>\r
-<DD><CODE><A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></CODE> - this exception is throw if the job execution was not
-             successful or the result of the execution could not be found.
-             (e.g. removed). Exception could also be thrown is dues to the
-             lower level problems on the server i.e. IOException,
-             FileNotFoundException problems as well as
-             UnknownFileFormatException.</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getLimit(java.lang.String)"><!-- --></A><H3>\r
-getLimit</H3>\r
-<PRE>\r
-public <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;<A HREF="../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>&gt; <B>getLimit</B>(java.lang.String&nbsp;presetName)</PRE>\r
-<DL>\r
-<DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/data/msa/MsaWS.html#getLimit(java.lang.String)">MsaWS</A></CODE></B></DD>\r
-<DD>Get a Limit for a preset.\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/data/msa/MsaWS.html#getLimit(java.lang.String)">getLimit</A></CODE> in interface <CODE><A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>&lt;<A HREF="../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>presetName</CODE> - the name of the preset. if no name is provided, then the
-            default preset is returned. If no limit for a particular
-            preset is defined then the default preset is returned\r
-<DT><B>Returns:</B><DD>Limit</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getLimits()"><!-- --></A><H3>\r
-getLimits</H3>\r
-<PRE>\r
-public <A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;<A HREF="../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>&gt; <B>getLimits</B>()</PRE>\r
-<DL>\r
-<DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/data/msa/MsaWS.html#getLimits()">MsaWS</A></CODE></B></DD>\r
-<DD>List Limits supported by a web service.\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/data/msa/MsaWS.html#getLimits()">getLimits</A></CODE> in interface <CODE><A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>&lt;<A HREF="../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>LimitManager</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="pullExecStatistics(java.lang.String, long)"><!-- --></A><H3>\r
-pullExecStatistics</H3>\r
-<PRE>\r
-public <A HREF="../../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A> <B>pullExecStatistics</B>(java.lang.String&nbsp;jobId,\r
-                                      long&nbsp;position)</PRE>\r
-<DL>\r
-<DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/data/msa/MsaWS.html#pullExecStatistics(java.lang.String, long)">MsaWS</A></CODE></B></DD>\r
-<DD>Reads 1kb chunk from the statistics file which is specific to a given web
- service from the position. If in time of a request less then 1kb data is
- available from the position to the end of the file, then it returns all
- the data available from the position to the end of the file.\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/data/msa/MsaWS.html#pullExecStatistics(java.lang.String, long)">pullExecStatistics</A></CODE> in interface <CODE><A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>&lt;<A HREF="../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>jobId</CODE> - - unique job identifier<DD><CODE>position</CODE> - - next position within the file to read\r
-<DT><B>Returns:</B><DD>ChunkHolder - @see ChunkHolder which contains a chuink of data
-         and a next position within the file from which no data has been
-         read</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="cancelJob(java.lang.String)"><!-- --></A><H3>\r
-cancelJob</H3>\r
-<PRE>\r
-public boolean <B>cancelJob</B>(java.lang.String&nbsp;jobId)</PRE>\r
-<DL>\r
-<DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/data/msa/MsaWS.html#cancelJob(java.lang.String)">MsaWS</A></CODE></B></DD>\r
-<DD>Stop running job but leave its output untouched\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/data/msa/MsaWS.html#cancelJob(java.lang.String)">cancelJob</A></CODE> in interface <CODE><A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>&lt;<A HREF="../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>true if job was cancelled successfully, false otherwise</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getJobStatus(java.lang.String)"><!-- --></A><H3>\r
-getJobStatus</H3>\r
-<PRE>\r
-public <A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A> <B>getJobStatus</B>(java.lang.String&nbsp;jobId)</PRE>\r
-<DL>\r
-<DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/data/msa/MsaWS.html#getJobStatus(java.lang.String)">MsaWS</A></CODE></B></DD>\r
-<DD>Return the status of the job. @see JobStatus\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/data/msa/MsaWS.html#getJobStatus(java.lang.String)">getJobStatus</A></CODE> in interface <CODE><A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>&lt;<A HREF="../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>jobId</CODE> - - unique job identifier\r
-<DT><B>Returns:</B><DD>JobStatus - status of the job</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getPresets()"><!-- --></A><H3>\r
-getPresets</H3>\r
-<PRE>\r
-public <A HREF="../../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>&lt;<A HREF="../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>&gt; <B>getPresets</B>()</PRE>\r
-<DL>\r
-<DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/data/msa/MsaWS.html#getPresets()">MsaWS</A></CODE></B></DD>\r
-<DD>Get presets supported by a web service\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/data/msa/MsaWS.html#getPresets()">getPresets</A></CODE> in interface <CODE><A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>&lt;<A HREF="../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>PresetManager the object contains information about presets
-         supported by a web service</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getRunnerOptions()"><!-- --></A><H3>\r
-getRunnerOptions</H3>\r
-<PRE>\r
-public <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&lt;<A HREF="../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>&gt; <B>getRunnerOptions</B>()</PRE>\r
-<DL>\r
-<DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/data/msa/MsaWS.html#getRunnerOptions()">MsaWS</A></CODE></B></DD>\r
-<DD>Get options supported by a web service\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/data/msa/MsaWS.html#getRunnerOptions()">getRunnerOptions</A></CODE> in interface <CODE><A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>&lt;<A HREF="../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>RunnerConfig the list of options and parameters supported by a
-         web service.</DL>\r
-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/MuscleWS.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/ws/server/MafftWS.html" title="class in compbio.ws.server"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../compbio/ws/server/ProbconsWS.html" title="class in compbio.ws.server"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/ws/server/MuscleWS.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="MuscleWS.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/ws/server/ProbconsWS.html b/website/full_javadoc/compbio/ws/server/ProbconsWS.html

deleted file mode 100644 (file)

index a97b8eb..0000000
--- a/website/full_javadoc/compbio/ws/server/ProbconsWS.html
+++ /dev/null
@@ -1,599 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-ProbconsWS\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="ProbconsWS";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/ProbconsWS.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/ws/server/MuscleWS.html" title="class in compbio.ws.server"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../compbio/ws/server/SimpleWSPublisher.html" title="class in compbio.ws.server"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/ws/server/ProbconsWS.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="ProbconsWS.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.ws.server</FONT>\r
-<BR>\r
-Class ProbconsWS</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.ws.server.ProbconsWS</B>\r
-</PRE>\r
-<DL>\r
-<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>&lt;<A HREF="../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>&gt;</DD>\r
-</DL>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public class <B>ProbconsWS</B><DT>extends java.lang.Object<DT>implements <A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>&lt;<A HREF="../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>&gt;</DL>\r
-</PRE>\r
-\r
-<P>\r
-<HR>\r
-\r
-<P>\r
-\r
-<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
-\r
-<A NAME="constructor_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Constructor Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/ws/server/ProbconsWS.html#ProbconsWS()">ProbconsWS</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/ws/server/ProbconsWS.html#align(java.util.List)">align</A></B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Align a list of sequences with default settings.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/ws/server/ProbconsWS.html#cancelJob(java.lang.String)">cancelJob</A></B>(java.lang.String&nbsp;jobId)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Stop running job but leave its output untouched</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/ws/server/ProbconsWS.html#customAlign(java.util.List, java.util.List)">customAlign</A></B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-            java.util.List&lt;<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>&gt;&gt;&nbsp;options)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Align a list of sequences with options.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/ws/server/ProbconsWS.html#getJobStatus(java.lang.String)">getJobStatus</A></B>(java.lang.String&nbsp;jobId)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Return the status of the job.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;<A HREF="../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/ws/server/ProbconsWS.html#getLimit(java.lang.String)">getLimit</A></B>(java.lang.String&nbsp;presetName)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Get a Limit for a preset.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;<A HREF="../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/ws/server/ProbconsWS.html#getLimits()">getLimits</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;List Limits supported by a web service.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>&lt;<A HREF="../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/ws/server/ProbconsWS.html#getPresets()">getPresets</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Get presets supported by a web service</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/ws/server/ProbconsWS.html#getResult(java.lang.String)">getResult</A></B>(java.lang.String&nbsp;jobId)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Return the result of the job.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&lt;<A HREF="../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/ws/server/ProbconsWS.html#getRunnerOptions()">getRunnerOptions</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Get options supported by a web service</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/ws/server/ProbconsWS.html#presetAlign(java.util.List, compbio.metadata.Preset)">presetAlign</A></B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-            <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>&lt;<A HREF="../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>&gt;&nbsp;preset)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Align a list of sequences with preset.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/ws/server/ProbconsWS.html#pullExecStatistics(java.lang.String, long)">pullExecStatistics</A></B>(java.lang.String&nbsp;jobId,\r
-                   long&nbsp;position)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Reads 1kb chunk from the statistics file which is specific to a given web
- service from the position.</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
-\r
-<A NAME="constructor_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Constructor Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="ProbconsWS()"><!-- --></A><H3>\r
-ProbconsWS</H3>\r
-<PRE>\r
-public <B>ProbconsWS</B>()</PRE>\r
-<DL>\r
-</DL>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
-<A NAME="method_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="align(java.util.List)"><!-- --></A><H3>\r
-align</H3>\r
-<PRE>\r
-public java.lang.String <B>align</B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences)\r
-                       throws <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></PRE>\r
-<DL>\r
-<DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/data/msa/MsaWS.html#align(java.util.List)">MsaWS</A></CODE></B></DD>\r
-<DD>Align a list of sequences with default settings.
- 
- Any dataset containing a greater number of sequences or the average
- length of the sequences are greater then defined in the default Limit
- will not be accepted for an alignment operation and
- JobSubmissionException will be thrown.\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/data/msa/MsaWS.html#align(java.util.List)">align</A></CODE> in interface <CODE><A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>&lt;<A HREF="../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>sequences</CODE> - List of FastaSequence objects. The programme does not perform
-            any sequence validity checks. Nor does it checks whether the
-            sequences names are unique. It is responsibility of the caller
-            to validate this information\r
-<DT><B>Returns:</B><DD>jobId - unique identifier for the job\r
-<DT><B>Throws:</B>\r
-<DD><CODE><A HREF="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A></CODE> - thrown if server OS does not support native executables for a
-             given web service, e.g. JWS2 is deployed on Windows and Mafft
-             service is called\r
-<DD><CODE><A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A></CODE> - is throw if the input sequences number or average length
-             exceeds what is defined by the limit\r
-<DD><CODE><A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></CODE></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="customAlign(java.util.List, java.util.List)"><!-- --></A><H3>\r
-customAlign</H3>\r
-<PRE>\r
-public java.lang.String <B>customAlign</B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-                                    java.util.List&lt;<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>&gt;&gt;&nbsp;options)\r
-                             throws <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A>,\r
-                                    <A HREF="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></PRE>\r
-<DL>\r
-<DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/data/msa/MsaWS.html#customAlign(java.util.List, java.util.List)">MsaWS</A></CODE></B></DD>\r
-<DD>Align a list of sequences with options.\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/data/msa/MsaWS.html#customAlign(java.util.List, java.util.List)">customAlign</A></CODE> in interface <CODE><A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>&lt;<A HREF="../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>sequences</CODE> - List of FastaSequence objects. The programme does not perform
-            any sequence validity checks. Nor does it checks whether the
-            sequences names are unique. It is responsibility of the caller
-            to validate this information<DD><CODE>options</CODE> - A list of Options\r
-<DT><B>Returns:</B><DD>jobId - unique identifier for the job\r
-<DT><B>Throws:</B>\r
-<DD><CODE><A HREF="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A></CODE> - thrown if server OS does not support native executables for a
-             given web service, e.g. JWS2 is deployed on Windows and Mafft
-             service is called\r
-<DD><CODE><A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A></CODE> - is throw if the input sequences number or average length
-             exceeds what is defined by the limit\r
-<DD><CODE><A HREF="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></CODE> - is throws when 1) One of the Options provided is not
-             supported, 2) The value of the option is defined outside the
-             boundaries. In both cases exception object contain the
-             information on the violating Option.\r
-<DD><CODE><A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></CODE><DT><B>See Also:</B><DD><A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata"><CODE>Default Limit is used to decide whether the calculation will be
-      permitted or denied</CODE></A></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="presetAlign(java.util.List, compbio.metadata.Preset)"><!-- --></A><H3>\r
-presetAlign</H3>\r
-<PRE>\r
-public java.lang.String <B>presetAlign</B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-                                    <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>&lt;<A HREF="../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>&gt;&nbsp;preset)\r
-                             throws <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A>,\r
-                                    <A HREF="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></PRE>\r
-<DL>\r
-<DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/data/msa/MsaWS.html#presetAlign(java.util.List, compbio.metadata.Preset)">MsaWS</A></CODE></B></DD>\r
-<DD>Align a list of sequences with preset. @see Preset
- 
- Limit for a presetName is used whether the calculation will be permitted
- or denied. If no Limit was defined for a presetName, than default limit
- is used.\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/data/msa/MsaWS.html#presetAlign(java.util.List, compbio.metadata.Preset)">presetAlign</A></CODE> in interface <CODE><A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>&lt;<A HREF="../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>sequences</CODE> - List of FastaSequence objects. The programme does not perform
-            any sequence validity checks. Nor does it checks whether the
-            sequences names are unique. It is responsibility of the caller
-            to validate this information<DD><CODE>preset</CODE> - A list of Options\r
-<DT><B>Returns:</B><DD>String - jobId - unique identifier for the job\r
-<DT><B>Throws:</B>\r
-<DD><CODE><A HREF="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A></CODE> - thrown if server OS does not support native executables for a
-             given web service, e.g. JWS2 is deployed on Windows and Mafft
-             service is called\r
-<DD><CODE><A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A></CODE> - is throw if the input sequences number or average length
-             exceeds what is defined by the limit\r
-<DD><CODE><A HREF="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></CODE> - is throws when 1) One of the Options provided is not
-             supported, 2) The value of the option is defined outside the
-             boundaries. In both cases exception object contain the
-             information on the violating Option.\r
-<DD><CODE><A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></CODE></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getResult(java.lang.String)"><!-- --></A><H3>\r
-getResult</H3>\r
-<PRE>\r
-public <A HREF="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A> <B>getResult</B>(java.lang.String&nbsp;jobId)\r
-                    throws <A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></PRE>\r
-<DL>\r
-<DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/data/msa/MsaWS.html#getResult(java.lang.String)">MsaWS</A></CODE></B></DD>\r
-<DD>Return the result of the job.\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/data/msa/MsaWS.html#getResult(java.lang.String)">getResult</A></CODE> in interface <CODE><A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>&lt;<A HREF="../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>jobId</CODE> - a unique job identifier\r
-<DT><B>Returns:</B><DD>Alignment\r
-<DT><B>Throws:</B>\r
-<DD><CODE><A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></CODE> - this exception is throw if the job execution was not
-             successful or the result of the execution could not be found.
-             (e.g. removed). Exception could also be thrown is dues to the
-             lower level problems on the server i.e. IOException,
-             FileNotFoundException problems as well as
-             UnknownFileFormatException.</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getLimit(java.lang.String)"><!-- --></A><H3>\r
-getLimit</H3>\r
-<PRE>\r
-public <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;<A HREF="../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>&gt; <B>getLimit</B>(java.lang.String&nbsp;presetName)</PRE>\r
-<DL>\r
-<DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/data/msa/MsaWS.html#getLimit(java.lang.String)">MsaWS</A></CODE></B></DD>\r
-<DD>Get a Limit for a preset.\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/data/msa/MsaWS.html#getLimit(java.lang.String)">getLimit</A></CODE> in interface <CODE><A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>&lt;<A HREF="../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>presetName</CODE> - the name of the preset. if no name is provided, then the
-            default preset is returned. If no limit for a particular
-            preset is defined then the default preset is returned\r
-<DT><B>Returns:</B><DD>Limit</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getLimits()"><!-- --></A><H3>\r
-getLimits</H3>\r
-<PRE>\r
-public <A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;<A HREF="../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>&gt; <B>getLimits</B>()</PRE>\r
-<DL>\r
-<DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/data/msa/MsaWS.html#getLimits()">MsaWS</A></CODE></B></DD>\r
-<DD>List Limits supported by a web service.\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/data/msa/MsaWS.html#getLimits()">getLimits</A></CODE> in interface <CODE><A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>&lt;<A HREF="../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>LimitManager</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="pullExecStatistics(java.lang.String, long)"><!-- --></A><H3>\r
-pullExecStatistics</H3>\r
-<PRE>\r
-public <A HREF="../../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A> <B>pullExecStatistics</B>(java.lang.String&nbsp;jobId,\r
-                                      long&nbsp;position)</PRE>\r
-<DL>\r
-<DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/data/msa/MsaWS.html#pullExecStatistics(java.lang.String, long)">MsaWS</A></CODE></B></DD>\r
-<DD>Reads 1kb chunk from the statistics file which is specific to a given web
- service from the position. If in time of a request less then 1kb data is
- available from the position to the end of the file, then it returns all
- the data available from the position to the end of the file.\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/data/msa/MsaWS.html#pullExecStatistics(java.lang.String, long)">pullExecStatistics</A></CODE> in interface <CODE><A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>&lt;<A HREF="../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>jobId</CODE> - - unique job identifier<DD><CODE>position</CODE> - - next position within the file to read\r
-<DT><B>Returns:</B><DD>ChunkHolder - @see ChunkHolder which contains a chuink of data
-         and a next position within the file from which no data has been
-         read</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="cancelJob(java.lang.String)"><!-- --></A><H3>\r
-cancelJob</H3>\r
-<PRE>\r
-public boolean <B>cancelJob</B>(java.lang.String&nbsp;jobId)</PRE>\r
-<DL>\r
-<DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/data/msa/MsaWS.html#cancelJob(java.lang.String)">MsaWS</A></CODE></B></DD>\r
-<DD>Stop running job but leave its output untouched\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/data/msa/MsaWS.html#cancelJob(java.lang.String)">cancelJob</A></CODE> in interface <CODE><A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>&lt;<A HREF="../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>true if job was cancelled successfully, false otherwise</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getJobStatus(java.lang.String)"><!-- --></A><H3>\r
-getJobStatus</H3>\r
-<PRE>\r
-public <A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A> <B>getJobStatus</B>(java.lang.String&nbsp;jobId)</PRE>\r
-<DL>\r
-<DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/data/msa/MsaWS.html#getJobStatus(java.lang.String)">MsaWS</A></CODE></B></DD>\r
-<DD>Return the status of the job. @see JobStatus\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/data/msa/MsaWS.html#getJobStatus(java.lang.String)">getJobStatus</A></CODE> in interface <CODE><A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>&lt;<A HREF="../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>jobId</CODE> - - unique job identifier\r
-<DT><B>Returns:</B><DD>JobStatus - status of the job</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getPresets()"><!-- --></A><H3>\r
-getPresets</H3>\r
-<PRE>\r
-public <A HREF="../../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>&lt;<A HREF="../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>&gt; <B>getPresets</B>()</PRE>\r
-<DL>\r
-<DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/data/msa/MsaWS.html#getPresets()">MsaWS</A></CODE></B></DD>\r
-<DD>Get presets supported by a web service\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/data/msa/MsaWS.html#getPresets()">getPresets</A></CODE> in interface <CODE><A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>&lt;<A HREF="../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>PresetManager the object contains information about presets
-         supported by a web service</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getRunnerOptions()"><!-- --></A><H3>\r
-getRunnerOptions</H3>\r
-<PRE>\r
-public <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&lt;<A HREF="../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>&gt; <B>getRunnerOptions</B>()</PRE>\r
-<DL>\r
-<DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/data/msa/MsaWS.html#getRunnerOptions()">MsaWS</A></CODE></B></DD>\r
-<DD>Get options supported by a web service\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/data/msa/MsaWS.html#getRunnerOptions()">getRunnerOptions</A></CODE> in interface <CODE><A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>&lt;<A HREF="../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>RunnerConfig the list of options and parameters supported by a
-         web service.</DL>\r
-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/ProbconsWS.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/ws/server/MuscleWS.html" title="class in compbio.ws.server"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../compbio/ws/server/SimpleWSPublisher.html" title="class in compbio.ws.server"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/ws/server/ProbconsWS.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="ProbconsWS.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/ws/server/SimpleWSPublisher.html b/website/full_javadoc/compbio/ws/server/SimpleWSPublisher.html

deleted file mode 100644 (file)

index e4fd0ac..0000000
--- a/website/full_javadoc/compbio/ws/server/SimpleWSPublisher.html
+++ /dev/null
@@ -1,263 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-SimpleWSPublisher\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="SimpleWSPublisher";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/SimpleWSPublisher.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/ws/server/ProbconsWS.html" title="class in compbio.ws.server"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../compbio/ws/server/TcoffeeWS.html" title="class in compbio.ws.server"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/ws/server/SimpleWSPublisher.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="SimpleWSPublisher.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.ws.server</FONT>\r
-<BR>\r
-Class SimpleWSPublisher</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.ws.server.SimpleWSPublisher</B>\r
-</PRE>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public class <B>SimpleWSPublisher</B><DT>extends java.lang.Object</DL>\r
-</PRE>\r
-\r
-<P>\r
-This class publish a web service. This is not a production implementation.
- Should be used only for during development and testing\r
-<P>\r
-\r
-<P>\r
-<DL>\r
-<DT><B>Author:</B></DT>\r
-  <DD>pvtroshin</DD>\r
-</DL>\r
-<HR>\r
-\r
-<P>\r
-\r
-<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
-\r
-<A NAME="constructor_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Constructor Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/ws/server/SimpleWSPublisher.html#SimpleWSPublisher(java.lang.Object, java.lang.String)">SimpleWSPublisher</A></B>(java.lang.Object&nbsp;exec,\r
-                  java.lang.String&nbsp;context)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/ws/server/SimpleWSPublisher.html#main(java.lang.String[])">main</A></B>(java.lang.String[]&nbsp;args)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
-\r
-<A NAME="constructor_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Constructor Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="SimpleWSPublisher(java.lang.Object, java.lang.String)"><!-- --></A><H3>\r
-SimpleWSPublisher</H3>\r
-<PRE>\r
-public <B>SimpleWSPublisher</B>(java.lang.Object&nbsp;exec,\r
-                         java.lang.String&nbsp;context)</PRE>\r
-<DL>\r
-</DL>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
-<A NAME="method_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="main(java.lang.String[])"><!-- --></A><H3>\r
-main</H3>\r
-<PRE>\r
-public static void <B>main</B>(java.lang.String[]&nbsp;args)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/SimpleWSPublisher.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/ws/server/ProbconsWS.html" title="class in compbio.ws.server"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../compbio/ws/server/TcoffeeWS.html" title="class in compbio.ws.server"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/ws/server/SimpleWSPublisher.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="SimpleWSPublisher.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/ws/server/TcoffeeWS.html b/website/full_javadoc/compbio/ws/server/TcoffeeWS.html

deleted file mode 100644 (file)

index bc9ed89..0000000
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-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-TcoffeeWS\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="TcoffeeWS";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/TcoffeeWS.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
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-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/ws/server/SimpleWSPublisher.html" title="class in compbio.ws.server"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../compbio/ws/server/WSUtil.html" title="class in compbio.ws.server"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/ws/server/TcoffeeWS.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="TcoffeeWS.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.ws.server</FONT>\r
-<BR>\r
-Class TcoffeeWS</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.ws.server.TcoffeeWS</B>\r
-</PRE>\r
-<DL>\r
-<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>&lt;<A HREF="../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>&gt;</DD>\r
-</DL>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public class <B>TcoffeeWS</B><DT>extends java.lang.Object<DT>implements <A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>&lt;<A HREF="../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>&gt;</DL>\r
-</PRE>\r
-\r
-<P>\r
-<HR>\r
-\r
-<P>\r
-\r
-<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
-\r
-<A NAME="constructor_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Constructor Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/ws/server/TcoffeeWS.html#TcoffeeWS()">TcoffeeWS</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/ws/server/TcoffeeWS.html#align(java.util.List)">align</A></B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Align a list of sequences with default settings.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/ws/server/TcoffeeWS.html#cancelJob(java.lang.String)">cancelJob</A></B>(java.lang.String&nbsp;jobId)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Stop running job but leave its output untouched</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/ws/server/TcoffeeWS.html#customAlign(java.util.List, java.util.List)">customAlign</A></B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-            java.util.List&lt;<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>&gt;&gt;&nbsp;options)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Align a list of sequences with options.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/ws/server/TcoffeeWS.html#getJobStatus(java.lang.String)">getJobStatus</A></B>(java.lang.String&nbsp;jobId)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Return the status of the job.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;<A HREF="../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/ws/server/TcoffeeWS.html#getLimit(java.lang.String)">getLimit</A></B>(java.lang.String&nbsp;presetName)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Get a Limit for a preset.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;<A HREF="../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/ws/server/TcoffeeWS.html#getLimits()">getLimits</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;List Limits supported by a web service.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>&lt;<A HREF="../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/ws/server/TcoffeeWS.html#getPresets()">getPresets</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Get presets supported by a web service</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/ws/server/TcoffeeWS.html#getResult(java.lang.String)">getResult</A></B>(java.lang.String&nbsp;jobId)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Return the result of the job.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&lt;<A HREF="../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/ws/server/TcoffeeWS.html#getRunnerOptions()">getRunnerOptions</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Get options supported by a web service</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/ws/server/TcoffeeWS.html#presetAlign(java.util.List, compbio.metadata.Preset)">presetAlign</A></B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-            <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>&lt;<A HREF="../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>&gt;&nbsp;preset)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Align a list of sequences with preset.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/ws/server/TcoffeeWS.html#pullExecStatistics(java.lang.String, long)">pullExecStatistics</A></B>(java.lang.String&nbsp;jobId,\r
-                   long&nbsp;position)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Reads 1kb chunk from the statistics file which is specific to a given web
- service from the position.</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
-\r
-<A NAME="constructor_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Constructor Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="TcoffeeWS()"><!-- --></A><H3>\r
-TcoffeeWS</H3>\r
-<PRE>\r
-public <B>TcoffeeWS</B>()</PRE>\r
-<DL>\r
-</DL>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
-<A NAME="method_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="align(java.util.List)"><!-- --></A><H3>\r
-align</H3>\r
-<PRE>\r
-public java.lang.String <B>align</B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences)\r
-                       throws <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></PRE>\r
-<DL>\r
-<DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/data/msa/MsaWS.html#align(java.util.List)">MsaWS</A></CODE></B></DD>\r
-<DD>Align a list of sequences with default settings.
- 
- Any dataset containing a greater number of sequences or the average
- length of the sequences are greater then defined in the default Limit
- will not be accepted for an alignment operation and
- JobSubmissionException will be thrown.\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/data/msa/MsaWS.html#align(java.util.List)">align</A></CODE> in interface <CODE><A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>&lt;<A HREF="../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>sequences</CODE> - List of FastaSequence objects. The programme does not perform
-            any sequence validity checks. Nor does it checks whether the
-            sequences names are unique. It is responsibility of the caller
-            to validate this information\r
-<DT><B>Returns:</B><DD>jobId - unique identifier for the job\r
-<DT><B>Throws:</B>\r
-<DD><CODE><A HREF="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A></CODE> - thrown if server OS does not support native executables for a
-             given web service, e.g. JWS2 is deployed on Windows and Mafft
-             service is called\r
-<DD><CODE><A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A></CODE> - is throw if the input sequences number or average length
-             exceeds what is defined by the limit\r
-<DD><CODE><A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></CODE></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="customAlign(java.util.List, java.util.List)"><!-- --></A><H3>\r
-customAlign</H3>\r
-<PRE>\r
-public java.lang.String <B>customAlign</B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-                                    java.util.List&lt;<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>&gt;&gt;&nbsp;options)\r
-                             throws <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A>,\r
-                                    <A HREF="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></PRE>\r
-<DL>\r
-<DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/data/msa/MsaWS.html#customAlign(java.util.List, java.util.List)">MsaWS</A></CODE></B></DD>\r
-<DD>Align a list of sequences with options.\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/data/msa/MsaWS.html#customAlign(java.util.List, java.util.List)">customAlign</A></CODE> in interface <CODE><A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>&lt;<A HREF="../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>sequences</CODE> - List of FastaSequence objects. The programme does not perform
-            any sequence validity checks. Nor does it checks whether the
-            sequences names are unique. It is responsibility of the caller
-            to validate this information<DD><CODE>options</CODE> - A list of Options\r
-<DT><B>Returns:</B><DD>jobId - unique identifier for the job\r
-<DT><B>Throws:</B>\r
-<DD><CODE><A HREF="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A></CODE> - thrown if server OS does not support native executables for a
-             given web service, e.g. JWS2 is deployed on Windows and Mafft
-             service is called\r
-<DD><CODE><A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A></CODE> - is throw if the input sequences number or average length
-             exceeds what is defined by the limit\r
-<DD><CODE><A HREF="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></CODE> - is throws when 1) One of the Options provided is not
-             supported, 2) The value of the option is defined outside the
-             boundaries. In both cases exception object contain the
-             information on the violating Option.\r
-<DD><CODE><A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></CODE><DT><B>See Also:</B><DD><A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata"><CODE>Default Limit is used to decide whether the calculation will be
-      permitted or denied</CODE></A></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="presetAlign(java.util.List, compbio.metadata.Preset)"><!-- --></A><H3>\r
-presetAlign</H3>\r
-<PRE>\r
-public java.lang.String <B>presetAlign</B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-                                    <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>&lt;<A HREF="../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>&gt;&nbsp;preset)\r
-                             throws <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A>,\r
-                                    <A HREF="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></PRE>\r
-<DL>\r
-<DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/data/msa/MsaWS.html#presetAlign(java.util.List, compbio.metadata.Preset)">MsaWS</A></CODE></B></DD>\r
-<DD>Align a list of sequences with preset. @see Preset
- 
- Limit for a presetName is used whether the calculation will be permitted
- or denied. If no Limit was defined for a presetName, than default limit
- is used.\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/data/msa/MsaWS.html#presetAlign(java.util.List, compbio.metadata.Preset)">presetAlign</A></CODE> in interface <CODE><A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>&lt;<A HREF="../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>sequences</CODE> - List of FastaSequence objects. The programme does not perform
-            any sequence validity checks. Nor does it checks whether the
-            sequences names are unique. It is responsibility of the caller
-            to validate this information<DD><CODE>preset</CODE> - A list of Options\r
-<DT><B>Returns:</B><DD>String - jobId - unique identifier for the job\r
-<DT><B>Throws:</B>\r
-<DD><CODE><A HREF="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A></CODE> - thrown if server OS does not support native executables for a
-             given web service, e.g. JWS2 is deployed on Windows and Mafft
-             service is called\r
-<DD><CODE><A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A></CODE> - is throw if the input sequences number or average length
-             exceeds what is defined by the limit\r
-<DD><CODE><A HREF="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></CODE> - is throws when 1) One of the Options provided is not
-             supported, 2) The value of the option is defined outside the
-             boundaries. In both cases exception object contain the
-             information on the violating Option.\r
-<DD><CODE><A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></CODE></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getResult(java.lang.String)"><!-- --></A><H3>\r
-getResult</H3>\r
-<PRE>\r
-public <A HREF="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A> <B>getResult</B>(java.lang.String&nbsp;jobId)\r
-                    throws <A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></PRE>\r
-<DL>\r
-<DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/data/msa/MsaWS.html#getResult(java.lang.String)">MsaWS</A></CODE></B></DD>\r
-<DD>Return the result of the job.\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/data/msa/MsaWS.html#getResult(java.lang.String)">getResult</A></CODE> in interface <CODE><A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>&lt;<A HREF="../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>jobId</CODE> - a unique job identifier\r
-<DT><B>Returns:</B><DD>Alignment\r
-<DT><B>Throws:</B>\r
-<DD><CODE><A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></CODE> - this exception is throw if the job execution was not
-             successful or the result of the execution could not be found.
-             (e.g. removed). Exception could also be thrown is dues to the
-             lower level problems on the server i.e. IOException,
-             FileNotFoundException problems as well as
-             UnknownFileFormatException.</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getLimit(java.lang.String)"><!-- --></A><H3>\r
-getLimit</H3>\r
-<PRE>\r
-public <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;<A HREF="../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>&gt; <B>getLimit</B>(java.lang.String&nbsp;presetName)</PRE>\r
-<DL>\r
-<DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/data/msa/MsaWS.html#getLimit(java.lang.String)">MsaWS</A></CODE></B></DD>\r
-<DD>Get a Limit for a preset.\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/data/msa/MsaWS.html#getLimit(java.lang.String)">getLimit</A></CODE> in interface <CODE><A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>&lt;<A HREF="../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>presetName</CODE> - the name of the preset. if no name is provided, then the
-            default preset is returned. If no limit for a particular
-            preset is defined then the default preset is returned\r
-<DT><B>Returns:</B><DD>Limit</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getLimits()"><!-- --></A><H3>\r
-getLimits</H3>\r
-<PRE>\r
-public <A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;<A HREF="../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>&gt; <B>getLimits</B>()</PRE>\r
-<DL>\r
-<DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/data/msa/MsaWS.html#getLimits()">MsaWS</A></CODE></B></DD>\r
-<DD>List Limits supported by a web service.\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/data/msa/MsaWS.html#getLimits()">getLimits</A></CODE> in interface <CODE><A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>&lt;<A HREF="../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>LimitManager</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="pullExecStatistics(java.lang.String, long)"><!-- --></A><H3>\r
-pullExecStatistics</H3>\r
-<PRE>\r
-public <A HREF="../../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A> <B>pullExecStatistics</B>(java.lang.String&nbsp;jobId,\r
-                                      long&nbsp;position)</PRE>\r
-<DL>\r
-<DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/data/msa/MsaWS.html#pullExecStatistics(java.lang.String, long)">MsaWS</A></CODE></B></DD>\r
-<DD>Reads 1kb chunk from the statistics file which is specific to a given web
- service from the position. If in time of a request less then 1kb data is
- available from the position to the end of the file, then it returns all
- the data available from the position to the end of the file.\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/data/msa/MsaWS.html#pullExecStatistics(java.lang.String, long)">pullExecStatistics</A></CODE> in interface <CODE><A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>&lt;<A HREF="../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>jobId</CODE> - - unique job identifier<DD><CODE>position</CODE> - - next position within the file to read\r
-<DT><B>Returns:</B><DD>ChunkHolder - @see ChunkHolder which contains a chuink of data
-         and a next position within the file from which no data has been
-         read</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="cancelJob(java.lang.String)"><!-- --></A><H3>\r
-cancelJob</H3>\r
-<PRE>\r
-public boolean <B>cancelJob</B>(java.lang.String&nbsp;jobId)</PRE>\r
-<DL>\r
-<DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/data/msa/MsaWS.html#cancelJob(java.lang.String)">MsaWS</A></CODE></B></DD>\r
-<DD>Stop running job but leave its output untouched\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/data/msa/MsaWS.html#cancelJob(java.lang.String)">cancelJob</A></CODE> in interface <CODE><A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>&lt;<A HREF="../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>true if job was cancelled successfully, false otherwise</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getJobStatus(java.lang.String)"><!-- --></A><H3>\r
-getJobStatus</H3>\r
-<PRE>\r
-public <A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A> <B>getJobStatus</B>(java.lang.String&nbsp;jobId)</PRE>\r
-<DL>\r
-<DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/data/msa/MsaWS.html#getJobStatus(java.lang.String)">MsaWS</A></CODE></B></DD>\r
-<DD>Return the status of the job. @see JobStatus\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/data/msa/MsaWS.html#getJobStatus(java.lang.String)">getJobStatus</A></CODE> in interface <CODE><A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>&lt;<A HREF="../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>jobId</CODE> - - unique job identifier\r
-<DT><B>Returns:</B><DD>JobStatus - status of the job</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getPresets()"><!-- --></A><H3>\r
-getPresets</H3>\r
-<PRE>\r
-public <A HREF="../../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>&lt;<A HREF="../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>&gt; <B>getPresets</B>()</PRE>\r
-<DL>\r
-<DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/data/msa/MsaWS.html#getPresets()">MsaWS</A></CODE></B></DD>\r
-<DD>Get presets supported by a web service\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/data/msa/MsaWS.html#getPresets()">getPresets</A></CODE> in interface <CODE><A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>&lt;<A HREF="../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>PresetManager the object contains information about presets
-         supported by a web service</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getRunnerOptions()"><!-- --></A><H3>\r
-getRunnerOptions</H3>\r
-<PRE>\r
-public <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&lt;<A HREF="../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>&gt; <B>getRunnerOptions</B>()</PRE>\r
-<DL>\r
-<DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/data/msa/MsaWS.html#getRunnerOptions()">MsaWS</A></CODE></B></DD>\r
-<DD>Get options supported by a web service\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/data/msa/MsaWS.html#getRunnerOptions()">getRunnerOptions</A></CODE> in interface <CODE><A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>&lt;<A HREF="../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>RunnerConfig the list of options and parameters supported by a
-         web service.</DL>\r
-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/TcoffeeWS.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/ws/server/SimpleWSPublisher.html" title="class in compbio.ws.server"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../compbio/ws/server/WSUtil.html" title="class in compbio.ws.server"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/ws/server/TcoffeeWS.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="TcoffeeWS.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/ws/server/WSUtil.html b/website/full_javadoc/compbio/ws/server/WSUtil.html

deleted file mode 100644 (file)

index cb07ea7..0000000
--- a/website/full_javadoc/compbio/ws/server/WSUtil.html
+++ /dev/null
@@ -1,510 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-WSUtil\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="WSUtil";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
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-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/ws/server/TcoffeeWS.html" title="class in compbio.ws.server"><B>PREV CLASS</B></A>&nbsp;\r
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-<A NAME="skip-navbar_top"></A>\r
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-\r
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-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.ws.server</FONT>\r
-<BR>\r
-Class WSUtil</H2>\r
-<PRE>\r
-java.lang.Object\r
-  <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.ws.server.WSUtil</B>\r
-</PRE>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public final class <B>WSUtil</B><DT>extends java.lang.Object</DL>\r
-</PRE>\r
-\r
-<P>\r
-<HR>\r
-\r
-<P>\r
-\r
-<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
-\r
-<A NAME="constructor_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Constructor Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/ws/server/WSUtil.html#WSUtil()">WSUtil</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
-<TR ALIGN="right" VALIGN="">\r
-<TD NOWRAP><FONT SIZE="-1">\r
-<CODE>&lt;T&gt; java.lang.String</CODE></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/ws/server/WSUtil.html#align(java.util.List, compbio.engine.client.ConfiguredExecutable, org.apache.log4j.Logger, javax.xml.ws.WebServiceContext, java.lang.String, compbio.metadata.Limit)">align</A></B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-      <A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;T&gt;&nbsp;confExec,\r
-      org.apache.log4j.Logger&nbsp;statLog,\r
-      javax.xml.ws.WebServiceContext&nbsp;wsContext,\r
-      java.lang.String&nbsp;callingMethod,\r
-      <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;T&gt;&nbsp;limit)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/ws/server/WSUtil.html#cancelJob(java.lang.String)">cancelJob</A></B>(java.lang.String&nbsp;jobId)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
-<TR ALIGN="right" VALIGN="">\r
-<TD NOWRAP><FONT SIZE="-1">\r
-<CODE>&lt;T&gt; java.util.List&lt;java.lang.String&gt;</CODE></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/ws/server/WSUtil.html#getCommands(java.util.List, java.lang.String)">getCommands</A></B>(java.util.List&lt;<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;T&gt;&gt;&nbsp;options,\r
-            java.lang.String&nbsp;keyValueSeparator)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine">AsyncExecutor</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/ws/server/WSUtil.html#getEngine(compbio.engine.client.ConfiguredExecutable)">getEngine</A></B>(<A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;confClustal)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/ws/server/WSUtil.html#getJobStatus(java.lang.String)">getJobStatus</A></B>(java.lang.String&nbsp;jobId)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;byte</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/ws/server/WSUtil.html#getProgress(java.lang.String)">getProgress</A></B>(java.lang.String&nbsp;jobId)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/ws/server/WSUtil.html#getRemoteAddress(javax.xml.ws.WebServiceContext)">getRemoteAddress</A></B>(javax.xml.ws.WebServiceContext&nbsp;wsContext)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/ws/server/WSUtil.html#log(org.apache.log4j.Logger, javax.xml.ws.WebServiceContext, java.lang.String)">log</A></B>(org.apache.log4j.Logger&nbsp;statLog,\r
-    javax.xml.ws.WebServiceContext&nbsp;wsContext,\r
-    java.lang.String&nbsp;activity)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/ws/server/WSUtil.html#log(org.apache.log4j.Logger, javax.xml.ws.WebServiceContext, java.lang.String, java.lang.String)">log</A></B>(org.apache.log4j.Logger&nbsp;statLog,\r
-    javax.xml.ws.WebServiceContext&nbsp;wsContext,\r
-    java.lang.String&nbsp;jobId,\r
-    java.lang.String&nbsp;activity)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<A HREF="../../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/ws/server/WSUtil.html#pullFile(java.lang.String, long)">pullFile</A></B>(java.lang.String&nbsp;jobId,\r
-         long&nbsp;position)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/ws/server/WSUtil.html#validateFastaInput(java.util.List)">validateFastaInput</A></B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/ws/server/WSUtil.html#validateJobId(java.lang.String)">validateJobId</A></B>(java.lang.String&nbsp;jobId)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
-\r
-<A NAME="constructor_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Constructor Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="WSUtil()"><!-- --></A><H3>\r
-WSUtil</H3>\r
-<PRE>\r
-public <B>WSUtil</B>()</PRE>\r
-<DL>\r
-</DL>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
-<A NAME="method_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="log(org.apache.log4j.Logger, javax.xml.ws.WebServiceContext, java.lang.String)"><!-- --></A><H3>\r
-log</H3>\r
-<PRE>\r
-public static void <B>log</B>(org.apache.log4j.Logger&nbsp;statLog,\r
-                       javax.xml.ws.WebServiceContext&nbsp;wsContext,\r
-                       java.lang.String&nbsp;activity)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="validateJobId(java.lang.String)"><!-- --></A><H3>\r
-validateJobId</H3>\r
-<PRE>\r
-public static final void <B>validateJobId</B>(java.lang.String&nbsp;jobId)\r
-                                throws java.security.InvalidParameterException</PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Throws:</B>\r
-<DD><CODE>java.security.InvalidParameterException</CODE></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="validateFastaInput(java.util.List)"><!-- --></A><H3>\r
-validateFastaInput</H3>\r
-<PRE>\r
-public static final void <B>validateFastaInput</B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences)\r
-                                     throws java.security.InvalidParameterException</PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Throws:</B>\r
-<DD><CODE>java.security.InvalidParameterException</CODE></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="log(org.apache.log4j.Logger, javax.xml.ws.WebServiceContext, java.lang.String, java.lang.String)"><!-- --></A><H3>\r
-log</H3>\r
-<PRE>\r
-public static void <B>log</B>(org.apache.log4j.Logger&nbsp;statLog,\r
-                       javax.xml.ws.WebServiceContext&nbsp;wsContext,\r
-                       java.lang.String&nbsp;jobId,\r
-                       java.lang.String&nbsp;activity)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getJobStatus(java.lang.String)"><!-- --></A><H3>\r
-getJobStatus</H3>\r
-<PRE>\r
-public static <A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A> <B>getJobStatus</B>(java.lang.String&nbsp;jobId)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="pullFile(java.lang.String, long)"><!-- --></A><H3>\r
-pullFile</H3>\r
-<PRE>\r
-public static <A HREF="../../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A> <B>pullFile</B>(java.lang.String&nbsp;jobId,\r
-                                   long&nbsp;position)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getProgress(java.lang.String)"><!-- --></A><H3>\r
-getProgress</H3>\r
-<PRE>\r
-public static byte <B>getProgress</B>(java.lang.String&nbsp;jobId)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getEngine(compbio.engine.client.ConfiguredExecutable)"><!-- --></A><H3>\r
-getEngine</H3>\r
-<PRE>\r
-public static <A HREF="../../../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine">AsyncExecutor</A> <B>getEngine</B>(<A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;confClustal)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="cancelJob(java.lang.String)"><!-- --></A><H3>\r
-cancelJob</H3>\r
-<PRE>\r
-public static boolean <B>cancelJob</B>(java.lang.String&nbsp;jobId)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getRemoteAddress(javax.xml.ws.WebServiceContext)"><!-- --></A><H3>\r
-getRemoteAddress</H3>\r
-<PRE>\r
-public static java.lang.String <B>getRemoteAddress</B>(javax.xml.ws.WebServiceContext&nbsp;wsContext)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="align(java.util.List, compbio.engine.client.ConfiguredExecutable, org.apache.log4j.Logger, javax.xml.ws.WebServiceContext, java.lang.String, compbio.metadata.Limit)"><!-- --></A><H3>\r
-align</H3>\r
-<PRE>\r
-public static &lt;T&gt; java.lang.String <B>align</B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-                                         <A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;T&gt;&nbsp;confExec,\r
-                                         org.apache.log4j.Logger&nbsp;statLog,\r
-                                         javax.xml.ws.WebServiceContext&nbsp;wsContext,\r
-                                         java.lang.String&nbsp;callingMethod,\r
-                                         <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;T&gt;&nbsp;limit)\r
-                              throws <A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A>,\r
-                                     <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Throws:</B>\r
-<DD><CODE><A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A></CODE>\r
-<DD><CODE><A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></CODE></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getCommands(java.util.List, java.lang.String)"><!-- --></A><H3>\r
-getCommands</H3>\r
-<PRE>\r
-public static final &lt;T&gt; java.util.List&lt;java.lang.String&gt; <B>getCommands</B>(java.util.List&lt;<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;T&gt;&gt;&nbsp;options,\r
-                                                                     java.lang.String&nbsp;keyValueSeparator)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/WSUtil.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/ws/server/TcoffeeWS.html" title="class in compbio.ws.server"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;NEXT CLASS</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/ws/server/WSUtil.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
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-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/ws/server/class-use/ClustalWS.html b/website/full_javadoc/compbio/ws/server/class-use/ClustalWS.html

deleted file mode 100644 (file)

index b33dc12..0000000
--- a/website/full_javadoc/compbio/ws/server/class-use/ClustalWS.html
+++ /dev/null
@@ -1,144 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Uses of Class compbio.ws.server.ClustalWS\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Uses of Class compbio.ws.server.ClustalWS";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../compbio/ws/server/ClustalWS.html" title="class in compbio.ws.server"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/ws/server/\class-useClustalWS.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="ClustalWS.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-<B>Uses of Class<br>compbio.ws.server.ClustalWS</B></H2>\r
-</CENTER>\r
-No usage of compbio.ws.server.ClustalWS\r
-<P>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../compbio/ws/server/ClustalWS.html" title="class in compbio.ws.server"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/ws/server/\class-useClustalWS.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="ClustalWS.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/ws/server/class-use/MafftWS.html b/website/full_javadoc/compbio/ws/server/class-use/MafftWS.html

deleted file mode 100644 (file)

index 5b7bfba..0000000
--- a/website/full_javadoc/compbio/ws/server/class-use/MafftWS.html
+++ /dev/null
@@ -1,144 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Uses of Class compbio.ws.server.MafftWS\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Uses of Class compbio.ws.server.MafftWS";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../compbio/ws/server/MafftWS.html" title="class in compbio.ws.server"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/ws/server/\class-useMafftWS.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="MafftWS.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-<B>Uses of Class<br>compbio.ws.server.MafftWS</B></H2>\r
-</CENTER>\r
-No usage of compbio.ws.server.MafftWS\r
-<P>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../compbio/ws/server/MafftWS.html" title="class in compbio.ws.server"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/ws/server/\class-useMafftWS.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="MafftWS.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/ws/server/class-use/MuscleWS.html b/website/full_javadoc/compbio/ws/server/class-use/MuscleWS.html

deleted file mode 100644 (file)

index 9628b96..0000000
--- a/website/full_javadoc/compbio/ws/server/class-use/MuscleWS.html
+++ /dev/null
@@ -1,144 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Uses of Class compbio.ws.server.MuscleWS\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Uses of Class compbio.ws.server.MuscleWS";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../compbio/ws/server/MuscleWS.html" title="class in compbio.ws.server"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/ws/server/\class-useMuscleWS.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="MuscleWS.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-<B>Uses of Class<br>compbio.ws.server.MuscleWS</B></H2>\r
-</CENTER>\r
-No usage of compbio.ws.server.MuscleWS\r
-<P>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../compbio/ws/server/MuscleWS.html" title="class in compbio.ws.server"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/ws/server/\class-useMuscleWS.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="MuscleWS.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/ws/server/class-use/ProbconsWS.html b/website/full_javadoc/compbio/ws/server/class-use/ProbconsWS.html

deleted file mode 100644 (file)

index 67df8c7..0000000
--- a/website/full_javadoc/compbio/ws/server/class-use/ProbconsWS.html
+++ /dev/null
@@ -1,144 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Uses of Class compbio.ws.server.ProbconsWS\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Uses of Class compbio.ws.server.ProbconsWS";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../compbio/ws/server/ProbconsWS.html" title="class in compbio.ws.server"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/ws/server/\class-useProbconsWS.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="ProbconsWS.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-<B>Uses of Class<br>compbio.ws.server.ProbconsWS</B></H2>\r
-</CENTER>\r
-No usage of compbio.ws.server.ProbconsWS\r
-<P>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/ws/server/\class-useProbconsWS.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="ProbconsWS.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/ws/server/class-use/SimpleWSPublisher.html b/website/full_javadoc/compbio/ws/server/class-use/SimpleWSPublisher.html

deleted file mode 100644 (file)

index 32b96ee..0000000
--- a/website/full_javadoc/compbio/ws/server/class-use/SimpleWSPublisher.html
+++ /dev/null
@@ -1,144 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Uses of Class compbio.ws.server.SimpleWSPublisher\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Uses of Class compbio.ws.server.SimpleWSPublisher";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../compbio/ws/server/SimpleWSPublisher.html" title="class in compbio.ws.server"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/ws/server/\class-useSimpleWSPublisher.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="SimpleWSPublisher.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-<B>Uses of Class<br>compbio.ws.server.SimpleWSPublisher</B></H2>\r
-</CENTER>\r
-No usage of compbio.ws.server.SimpleWSPublisher\r
-<P>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../compbio/ws/server/SimpleWSPublisher.html" title="class in compbio.ws.server"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/ws/server/\class-useSimpleWSPublisher.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="SimpleWSPublisher.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/ws/server/class-use/TcoffeeWS.html b/website/full_javadoc/compbio/ws/server/class-use/TcoffeeWS.html

deleted file mode 100644 (file)

index 76756d7..0000000
--- a/website/full_javadoc/compbio/ws/server/class-use/TcoffeeWS.html
+++ /dev/null
@@ -1,144 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Uses of Class compbio.ws.server.TcoffeeWS\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Uses of Class compbio.ws.server.TcoffeeWS";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../compbio/ws/server/TcoffeeWS.html" title="class in compbio.ws.server"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/ws/server/\class-useTcoffeeWS.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="TcoffeeWS.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-<B>Uses of Class<br>compbio.ws.server.TcoffeeWS</B></H2>\r
-</CENTER>\r
-No usage of compbio.ws.server.TcoffeeWS\r
-<P>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../compbio/ws/server/TcoffeeWS.html" title="class in compbio.ws.server"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/ws/server/\class-useTcoffeeWS.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="TcoffeeWS.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/ws/server/class-use/WSUtil.html b/website/full_javadoc/compbio/ws/server/class-use/WSUtil.html

deleted file mode 100644 (file)

index d4457fd..0000000
--- a/website/full_javadoc/compbio/ws/server/class-use/WSUtil.html
+++ /dev/null
@@ -1,144 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Uses of Class compbio.ws.server.WSUtil\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Uses of Class compbio.ws.server.WSUtil";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../compbio/ws/server/WSUtil.html" title="class in compbio.ws.server"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/ws/server/\class-useWSUtil.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="WSUtil.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-<B>Uses of Class<br>compbio.ws.server.WSUtil</B></H2>\r
-</CENTER>\r
-No usage of compbio.ws.server.WSUtil\r
-<P>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../compbio/ws/server/WSUtil.html" title="class in compbio.ws.server"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../../index.html?compbio/ws/server/\class-useWSUtil.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="WSUtil.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/ws/server/package-frame.html b/website/full_javadoc/compbio/ws/server/package-frame.html

deleted file mode 100644 (file)

index cdb7eee..0000000
--- a/website/full_javadoc/compbio/ws/server/package-frame.html
+++ /dev/null
@@ -1,44 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-compbio.ws.server\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white">\r
-<FONT size="+1" CLASS="FrameTitleFont">\r
-<A HREF="../../../compbio/ws/server/package-summary.html" target="classFrame">compbio.ws.server</A></FONT>\r
-<TABLE BORDER="0" WIDTH="100%" SUMMARY="">\r
-<TR>\r
-<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">\r
-Classes</FONT>&nbsp;\r
-<FONT CLASS="FrameItemFont">\r
-<BR>\r
-<A HREF="ClustalWS.html" title="class in compbio.ws.server" target="classFrame">ClustalWS</A>\r
-<BR>\r
-<A HREF="MafftWS.html" title="class in compbio.ws.server" target="classFrame">MafftWS</A>\r
-<BR>\r
-<A HREF="MuscleWS.html" title="class in compbio.ws.server" target="classFrame">MuscleWS</A>\r
-<BR>\r
-<A HREF="ProbconsWS.html" title="class in compbio.ws.server" target="classFrame">ProbconsWS</A>\r
-<BR>\r
-<A HREF="SimpleWSPublisher.html" title="class in compbio.ws.server" target="classFrame">SimpleWSPublisher</A>\r
-<BR>\r
-<A HREF="TcoffeeWS.html" title="class in compbio.ws.server" target="classFrame">TcoffeeWS</A>\r
-<BR>\r
-<A HREF="WSUtil.html" title="class in compbio.ws.server" target="classFrame">WSUtil</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/ws/server/package-summary.html b/website/full_javadoc/compbio/ws/server/package-summary.html

deleted file mode 100644 (file)

index 4937713..0000000
--- a/website/full_javadoc/compbio/ws/server/package-summary.html
+++ /dev/null
@@ -1,181 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-compbio.ws.server\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="compbio.ws.server";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Class</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-use.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/ws/client/package-summary.html"><B>PREV PACKAGE</B></A>&nbsp;\r
-&nbsp;NEXT PACKAGE</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/ws/server/package-summary.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="package-summary.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<H2>\r
-Package compbio.ws.server\r
-</H2>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Class Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../../compbio/ws/server/ClustalWS.html" title="class in compbio.ws.server">ClustalWS</A></B></TD>\r
-<TD>&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../../compbio/ws/server/MafftWS.html" title="class in compbio.ws.server">MafftWS</A></B></TD>\r
-<TD>&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../../compbio/ws/server/MuscleWS.html" title="class in compbio.ws.server">MuscleWS</A></B></TD>\r
-<TD>&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../../compbio/ws/server/ProbconsWS.html" title="class in compbio.ws.server">ProbconsWS</A></B></TD>\r
-<TD>&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../../compbio/ws/server/SimpleWSPublisher.html" title="class in compbio.ws.server">SimpleWSPublisher</A></B></TD>\r
-<TD>This class publish a web service.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../../compbio/ws/server/TcoffeeWS.html" title="class in compbio.ws.server">TcoffeeWS</A></B></TD>\r
-<TD>&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../../compbio/ws/server/WSUtil.html" title="class in compbio.ws.server">WSUtil</A></B></TD>\r
-<TD>&nbsp;</TD>\r
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-</TABLE>\r
-&nbsp;\r
-\r
-<P>\r
-<DL>\r
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-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
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-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
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-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
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-\r
-\r
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-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/ws/server/package-tree.html b/website/full_javadoc/compbio/ws/server/package-tree.html

deleted file mode 100644 (file)

index 709f0cf..0000000
--- a/website/full_javadoc/compbio/ws/server/package-tree.html
+++ /dev/null
@@ -1,158 +0,0 @@
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-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-compbio.ws.server Class Hierarchy\r
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-\r
-<META NAME="date" CONTENT="2010-02-17">\r
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-\r
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-{\r
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-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
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-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
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-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/ws/client/package-tree.html"><B>PREV</B></A>&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
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-  <A HREF="../../../index.html?compbio/ws/server/package-tree.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
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-\r
-\r
-</FONT></TD>\r
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-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-Hierarchy For Package compbio.ws.server\r
-</H2>\r
-</CENTER>\r
-<DL>\r
-<DT><B>Package Hierarchies:</B><DD><A HREF="../../../overview-tree.html">All Packages</A></DL>\r
-<HR>\r
-<H2>\r
-Class Hierarchy\r
-</H2>\r
-<UL>\r
-<LI TYPE="circle">java.lang.Object<UL>\r
-<LI TYPE="circle">compbio.ws.server.<A HREF="../../../compbio/ws/server/ClustalWS.html" title="class in compbio.ws.server"><B>ClustalWS</B></A> (implements compbio.data.msa.<A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>&lt;T&gt;)\r
-<LI TYPE="circle">compbio.ws.server.<A HREF="../../../compbio/ws/server/MafftWS.html" title="class in compbio.ws.server"><B>MafftWS</B></A> (implements compbio.data.msa.<A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>&lt;T&gt;)\r
-<LI TYPE="circle">compbio.ws.server.<A HREF="../../../compbio/ws/server/MuscleWS.html" title="class in compbio.ws.server"><B>MuscleWS</B></A> (implements compbio.data.msa.<A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>&lt;T&gt;)\r
-<LI TYPE="circle">compbio.ws.server.<A HREF="../../../compbio/ws/server/ProbconsWS.html" title="class in compbio.ws.server"><B>ProbconsWS</B></A> (implements compbio.data.msa.<A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>&lt;T&gt;)\r
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-<LI TYPE="circle">compbio.ws.server.<A HREF="../../../compbio/ws/server/WSUtil.html" title="class in compbio.ws.server"><B>WSUtil</B></A></UL>\r
-</UL>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
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-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
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-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
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-</TR>\r
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-  <!--\r
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-\r
-\r
-</FONT></TD>\r
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-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/compbio/ws/server/package-use.html b/website/full_javadoc/compbio/ws/server/package-use.html

deleted file mode 100644 (file)

index 9249a6d..0000000
--- a/website/full_javadoc/compbio/ws/server/package-use.html
+++ /dev/null
@@ -1,144 +0,0 @@
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-<!--NewPage-->\r
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-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
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-Uses of Package compbio.ws.server\r
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-\r
-<META NAME="date" CONTENT="2010-02-17">\r
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-\r
-<SCRIPT type="text/javascript">\r
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-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Uses of Package compbio.ws.server";\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
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-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/ws/server/package-use.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
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-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-<B>Uses of Package<br>compbio.ws.server</B></H2>\r
-</CENTER>\r
-No usage of compbio.ws.server\r
-<P>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
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-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Class</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/ws/server/package-use.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="package-use.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
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-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/constant-values.html b/website/full_javadoc/constant-values.html

deleted file mode 100644 (file)

index 85d4d02..0000000
--- a/website/full_javadoc/constant-values.html
+++ /dev/null
@@ -1,498 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Constant Field Values\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Constant Field Values";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Package</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Class</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Use</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="index.html?constant-values.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="constant-values.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H1>\r
-Constant Field Values</H1>\r
-</CENTER>\r
-<HR SIZE="4" NOSHADE>\r
-<B>Contents</B><UL>\r
-<LI><A HREF="#compbio.data">compbio.data.*</A>\r
-<LI><A HREF="#compbio.engine">compbio.engine.*</A>\r
-<LI><A HREF="#compbio.metadata">compbio.metadata.*</A>\r
-<LI><A HREF="#compbio.runner">compbio.runner.*</A>\r
-</UL>\r
-\r
-<A NAME="compbio.data"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left"><FONT SIZE="+2">\r
-compbio.data.*</FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<P>\r
-\r
-<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="3">compbio.data.sequence.<A HREF="compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence">ClustalAlignmentUtil</A></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<A NAME="compbio.data.sequence.ClustalAlignmentUtil.gapchar"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">\r
-<CODE>public&nbsp;static&nbsp;final&nbsp;char</CODE></FONT></TD>\r
-<TD ALIGN="left"><CODE><A HREF="compbio/data/sequence/ClustalAlignmentUtil.html#gapchar">gapchar</A></CODE></TD>\r
-<TD ALIGN="right"><CODE>45</CODE></TD>\r
-</TR>\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-\r
-<P>\r
-\r
-<P>\r
-<A NAME="compbio.engine"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left"><FONT SIZE="+2">\r
-compbio.engine.*</FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<P>\r
-\r
-<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="3">compbio.engine.client.<A HREF="compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>&lt;<A HREF="compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt;</TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<A NAME="compbio.engine.client.ConfExecutable.CLUSTER_TASK_ID_PREFIX"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">\r
-<CODE>public&nbsp;static&nbsp;final&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD ALIGN="left"><CODE><A HREF="compbio/engine/client/ConfExecutable.html#CLUSTER_TASK_ID_PREFIX">CLUSTER_TASK_ID_PREFIX</A></CODE></TD>\r
-<TD ALIGN="right"><CODE>"@"</CODE></TD>\r
-</TR>\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-\r
-<P>\r
-\r
-<P>\r
-\r
-<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="3">compbio.engine.client.<A HREF="compbio/engine/client/EnvVariableProcessor.html" title="class in compbio.engine.client">EnvVariableProcessor</A></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<A NAME="compbio.engine.client.EnvVariableProcessor.PATH"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">\r
-<CODE>public&nbsp;static&nbsp;final&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD ALIGN="left"><CODE><A HREF="compbio/engine/client/EnvVariableProcessor.html#PATH">PATH</A></CODE></TD>\r
-<TD ALIGN="right"><CODE>"PATH"</CODE></TD>\r
-</TR>\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-\r
-<P>\r
-\r
-<P>\r
-\r
-<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="3">compbio.engine.client.<A HREF="compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<A NAME="compbio.engine.client.RunConfiguration.rconfigFile"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">\r
-<CODE>public&nbsp;static&nbsp;final&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD ALIGN="left"><CODE><A HREF="compbio/engine/client/RunConfiguration.html#rconfigFile">rconfigFile</A></CODE></TD>\r
-<TD ALIGN="right"><CODE>"RunnerConfig.xml"</CODE></TD>\r
-</TR>\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-\r
-<P>\r
-\r
-<P>\r
-\r
-<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="3">compbio.engine.cluster.drmaa.<A HREF="compbio/engine/cluster/drmaa/ClusterSession.html" title="class in compbio.engine.cluster.drmaa">ClusterSession</A></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<A NAME="compbio.engine.cluster.drmaa.ClusterSession.JOBID"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">\r
-<CODE>public&nbsp;static&nbsp;final&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD ALIGN="left"><CODE><A HREF="compbio/engine/cluster/drmaa/ClusterSession.html#JOBID">JOBID</A></CODE></TD>\r
-<TD ALIGN="right"><CODE>"JOBID"</CODE></TD>\r
-</TR>\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-\r
-<P>\r
-\r
-<P>\r
-\r
-<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="3">compbio.engine.cluster.dundee.<A HREF="compbio/engine/cluster/dundee/_QueueConstraints.html" title="class in compbio.engine.cluster.dundee">_QueueConstraints</A></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<A NAME="compbio.engine.cluster.dundee._QueueConstraints.FIRST_MEMORY_LIMIT"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">\r
-<CODE>public&nbsp;static&nbsp;final&nbsp;int</CODE></FONT></TD>\r
-<TD ALIGN="left"><CODE><A HREF="compbio/engine/cluster/dundee/_QueueConstraints.html#FIRST_MEMORY_LIMIT">FIRST_MEMORY_LIMIT</A></CODE></TD>\r
-<TD ALIGN="right"><CODE>14000</CODE></TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<A NAME="compbio.engine.cluster.dundee._QueueConstraints.LONG_TIME_LIMIT"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">\r
-<CODE>public&nbsp;static&nbsp;final&nbsp;int</CODE></FONT></TD>\r
-<TD ALIGN="left"><CODE><A HREF="compbio/engine/cluster/dundee/_QueueConstraints.html#LONG_TIME_LIMIT">LONG_TIME_LIMIT</A></CODE></TD>\r
-<TD ALIGN="right"><CODE>24</CODE></TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<A NAME="compbio.engine.cluster.dundee._QueueConstraints.MAX_MEMORY_LIMIT"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">\r
-<CODE>public&nbsp;static&nbsp;final&nbsp;int</CODE></FONT></TD>\r
-<TD ALIGN="left"><CODE><A HREF="compbio/engine/cluster/dundee/_QueueConstraints.html#MAX_MEMORY_LIMIT">MAX_MEMORY_LIMIT</A></CODE></TD>\r
-<TD ALIGN="right"><CODE>30000</CODE></TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<A NAME="compbio.engine.cluster.dundee._QueueConstraints.SHORT_TIME_LIMIT"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">\r
-<CODE>public&nbsp;static&nbsp;final&nbsp;int</CODE></FONT></TD>\r
-<TD ALIGN="left"><CODE><A HREF="compbio/engine/cluster/dundee/_QueueConstraints.html#SHORT_TIME_LIMIT">SHORT_TIME_LIMIT</A></CODE></TD>\r
-<TD ALIGN="right"><CODE>8</CODE></TD>\r
-</TR>\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-\r
-<P>\r
-\r
-<P>\r
-\r
-<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="3">compbio.engine.conf.<A HREF="compbio/engine/conf/_Key.html" title="class in compbio.engine.conf">_Key</A></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<A NAME="compbio.engine.conf._Key.DELIM"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">\r
-<CODE>public&nbsp;static&nbsp;final&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD ALIGN="left"><CODE><A HREF="compbio/engine/conf/_Key.html#DELIM">DELIM</A></CODE></TD>\r
-<TD ALIGN="right"><CODE>"#"</CODE></TD>\r
-</TR>\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-\r
-<P>\r
-\r
-<P>\r
-\r
-<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="3">compbio.engine.conf.<A HREF="compbio/engine/conf/DirectoryManager.html" title="class in compbio.engine.conf">DirectoryManager</A></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<A NAME="compbio.engine.conf.DirectoryManager.DELIM"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">\r
-<CODE>public&nbsp;static&nbsp;final&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD ALIGN="left"><CODE><A HREF="compbio/engine/conf/DirectoryManager.html#DELIM">DELIM</A></CODE></TD>\r
-<TD ALIGN="right"><CODE>"#"</CODE></TD>\r
-</TR>\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-\r
-<P>\r
-\r
-<P>\r
-\r
-<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="3">compbio.engine.local.<A HREF="compbio/engine/local/ExecutableWrapper.html" title="class in compbio.engine.local">ExecutableWrapper</A></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<A NAME="compbio.engine.local.ExecutableWrapper.PROC_ERR_FILE"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">\r
-<CODE>public&nbsp;static&nbsp;final&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD ALIGN="left"><CODE><A HREF="compbio/engine/local/ExecutableWrapper.html#PROC_ERR_FILE">PROC_ERR_FILE</A></CODE></TD>\r
-<TD ALIGN="right"><CODE>"procError.txt"</CODE></TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<A NAME="compbio.engine.local.ExecutableWrapper.PROC_OUT_FILE"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">\r
-<CODE>public&nbsp;static&nbsp;final&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD ALIGN="left"><CODE><A HREF="compbio/engine/local/ExecutableWrapper.html#PROC_OUT_FILE">PROC_OUT_FILE</A></CODE></TD>\r
-<TD ALIGN="right"><CODE>"procOutput.txt"</CODE></TD>\r
-</TR>\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-\r
-<P>\r
-\r
-<P>\r
-<A NAME="compbio.metadata"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left"><FONT SIZE="+2">\r
-compbio.metadata.*</FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<P>\r
-\r
-<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="3">compbio.metadata.<A HREF="compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>&lt;<A HREF="compbio/metadata/PresetManager.html" title="type parameter in PresetManager">T</A>&gt;</TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<A NAME="compbio.metadata.PresetManager.LOCAL_ENGINE_LIMIT_PRESET"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">\r
-<CODE>public&nbsp;static&nbsp;final&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD ALIGN="left"><CODE><A HREF="compbio/metadata/PresetManager.html#LOCAL_ENGINE_LIMIT_PRESET">LOCAL_ENGINE_LIMIT_PRESET</A></CODE></TD>\r
-<TD ALIGN="right"><CODE>"# LocalEngineExecutionLimit #"</CODE></TD>\r
-</TR>\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-\r
-<P>\r
-\r
-<P>\r
-<A NAME="compbio.runner"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left"><FONT SIZE="+2">\r
-compbio.runner.*</FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
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deleted file mode 100644 (file)

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-\r
-<P>\r
-The <A HREF="overview-summary.html">Overview</A> page is the front page of this API document and provides a list of all packages with a summary for each.  This page can also contain an overall description of the set of packages.</BLOCKQUOTE>\r
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-<H3>\r
-Tree (Class Hierarchy)</H3>\r
-<BLOCKQUOTE>\r
-There is a <A HREF="overview-tree.html">Class Hierarchy</A> page for all packages, plus a hierarchy for each package. Each hierarchy page contains a list of classes and a list of interfaces. The classes are organized by inheritance structure starting with <code>java.lang.Object</code>. The interfaces do not inherit from <code>java.lang.Object</code>.<UL>\r
-<LI>When viewing the Overview page, clicking on "Tree" displays the hierarchy for all packages.<LI>When viewing a particular package, class or interface page, clicking "Tree" displays the hierarchy for only that package.</UL>\r
-</BLOCKQUOTE>\r
-<H3>\r
-Deprecated API</H3>\r
-<BLOCKQUOTE>\r
-The <A HREF="deprecated-list.html">Deprecated API</A> page lists all of the API that have been deprecated. A deprecated API is not recommended for use, generally due to improvements, and a replacement API is usually given. Deprecated APIs may be removed in future implementations.</BLOCKQUOTE>\r
-<H3>\r
-Index</H3>\r
-<BLOCKQUOTE>\r
-The <A HREF="index-files/index-1.html">Index</A> contains an alphabetic list of all classes, interfaces, constructors, methods, and fields.</BLOCKQUOTE>\r
-<H3>\r
-Prev/Next</H3>\r
-These links take you to the next or previous class, interface, package, or related page.<H3>\r
-Frames/No Frames</H3>\r
-These links show and hide the HTML frames.  All pages are available with or without frames.\r
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-<H3>\r
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-Each serializable or externalizable class has a description of its serialization fields and methods. This information is of interest to re-implementors, not to developers using the API. While there is no link in the navigation bar, you can get to this information by going to any serialized class and clicking "Serialized Form" in the "See also" section of the class description.\r
-<P>\r
-<H3>\r
-Constant Field Values</H3>\r
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-<P>\r
-<FONT SIZE="-1">\r
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-\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Use</FONT>&nbsp;</TD>\r
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diff --git a/website/full_javadoc/index-files/index-1.html b/website/full_javadoc/index-files/index-1.html

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index 03324d7..0000000
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Use</FONT>&nbsp;</TD>\r
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-<B>A</B></H2>\r
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-<DD>Valid Amino acids\r
-<DT><A HREF="../compbio/metadata/RunnerConfig.html#addOption(compbio.metadata.Option)"><B>addOption(Option&lt;T&gt;)</B></A> - \r
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-<DD>&nbsp;\r
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-<DD>&nbsp;\r
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-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/_SkeletalCommandBuilder.html#addParameter(java.lang.String)"><B>addParameter(String)</B></A> - \r
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-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/ConfExecutable.html#addParameters(java.util.List)"><B>addParameters(List&lt;String&gt;)</B></A> - \r
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-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/Executable.html#addParameters(java.util.List)"><B>addParameters(List&lt;String&gt;)</B></A> - \r
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-<DD>Adds parameter to the list of parameters for a native executable\r
-<DT><A HREF="../compbio/engine/client/SkeletalExecutable.html#addParameters(java.util.List)"><B>addParameters(List&lt;String&gt;)</B></A> - \r
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-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/_impl/NetNglyc.html#addParameters(java.util.List)"><B>addParameters(List&lt;String&gt;)</B></A> - \r
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-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/_SkeletalCommandBuilder.html#addParameters(java.lang.String[])"><B>addParameters(String[])</B></A> - \r
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-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/_SkeletalCommandBuilder.html#addParameters(java.util.List)"><B>addParameters(List&lt;String&gt;)</B></A> - \r
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-<DD>Mafft input must always be the last parameter!\r
-<DT><A HREF="../compbio/engine/client/CommandBuilder.html#addParams(java.util.List)"><B>addParams(List&lt;String&gt;)</B></A> - \r
-Method in class compbio.engine.client.<A HREF="../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/Parameter.html#addPossibleValues(java.lang.String...)"><B>addPossibleValues(String...)</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/SubmissionManager.html#addTask(compbio.engine.client.ConfiguredExecutable, java.util.concurrent.Future)"><B>addTask(ConfiguredExecutable&lt;?&gt;, Future&lt;ConfiguredExecutable&lt;?&gt;&gt;)</B></A> - \r
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-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/jaxws/Align.html" title="class in compbio.data.msa.jaxws"><B>Align</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/Align.html#Align()"><B>Align()</B></A> - \r
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-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/MsaWS.html#align(java.util.List)"><B>align(List&lt;FastaSequence&gt;)</B></A> - \r
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-<DD>Align a list of sequences with default settings.\r
-<DT><A HREF="../compbio/ws/server/ClustalWS.html#align(java.util.List)"><B>align(List&lt;FastaSequence&gt;)</B></A> - \r
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-<DD>&nbsp;\r
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-<DD>&nbsp;\r
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-<DD>&nbsp;\r
-<DT><A HREF="../compbio/ws/server/TcoffeeWS.html#align(java.util.List)"><B>align(List&lt;FastaSequence&gt;)</B></A> - \r
-Method in class compbio.ws.server.<A HREF="../compbio/ws/server/TcoffeeWS.html" title="class in compbio.ws.server">TcoffeeWS</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/ws/server/WSUtil.html#align(java.util.List, compbio.engine.client.ConfiguredExecutable, org.apache.log4j.Logger, javax.xml.ws.WebServiceContext, java.lang.String, compbio.metadata.Limit)"><B>align(List&lt;FastaSequence&gt;, ConfiguredExecutable&lt;T&gt;, Logger, WebServiceContext, String, Limit&lt;T&gt;)</B></A> - \r
-Static method in class compbio.ws.server.<A HREF="../compbio/ws/server/WSUtil.html" title="class in compbio.ws.server">WSUtil</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence"><B>Alignment</B></A> - Class in <A HREF="../compbio/data/sequence/package-summary.html">compbio.data.sequence</A><DD>Multiple sequence alignment.<DT><A HREF="../compbio/data/sequence/Alignment.html#Alignment(java.util.List, compbio.data.sequence.Program, char)"><B>Alignment(List&lt;FastaSequence&gt;, Program, char)</B></A> - \r
-Constructor for class compbio.data.sequence.<A HREF="../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/sequence/Alignment.html#Alignment(java.util.List, compbio.data.sequence.AlignmentMetadata)"><B>Alignment(List&lt;FastaSequence&gt;, AlignmentMetadata)</B></A> - \r
-Constructor for class compbio.data.sequence.<A HREF="../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence"><B>AlignmentMetadata</B></A> - Class in <A HREF="../compbio/data/sequence/package-summary.html">compbio.data.sequence</A><DD>Alignment metadata e.g.<DT><A HREF="../compbio/data/sequence/AlignmentMetadata.html#AlignmentMetadata(compbio.data.sequence.Program, char)"><B>AlignmentMetadata(Program, char)</B></A> - \r
-Constructor for class compbio.data.sequence.<A HREF="../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence">AlignmentMetadata</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/jaxws/AlignResponse.html" title="class in compbio.data.msa.jaxws"><B>AlignResponse</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/AlignResponse.html#AlignResponse()"><B>AlignResponse()</B></A> - \r
-Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/AlignResponse.html" title="class in compbio.data.msa.jaxws">AlignResponse</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/sequence/SequenceUtil.html#AMBIGUOUS_AA"><B>AMBIGUOUS_AA</B></A> - \r
-Static variable in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
-<DD>Same as AA pattern but with two additional letters - XU\r
-<DT><A HREF="../compbio/data/sequence/SequenceUtil.html#AMBIGUOUS_NUCLEOTIDE"><B>AMBIGUOUS_NUCLEOTIDE</B></A> - \r
-Static variable in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
-<DD>Ambiguous nucleotide\r
-<DT><A HREF="../compbio/metadata/Argument.html" title="interface in compbio.metadata"><B>Argument</B></A>&lt;<A HREF="../compbio/metadata/Argument.html" title="type parameter in Argument">T</A>&gt; - Interface in <A HREF="../compbio/metadata/package-summary.html">compbio.metadata</A><DD>An unmodifiable view for the options and parameters, with one exception - it
- allows to set a value<DT><A HREF="../compbio/runner/OptionCombinator.html#argumentsToCommandString(java.util.List)"><B>argumentsToCommandString(List&lt;? extends Option&lt;?&gt;&gt;)</B></A> - \r
-Method in class compbio.runner.<A HREF="../compbio/runner/OptionCombinator.html" title="class in compbio.runner">OptionCombinator</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/OptionCombinator.html#argumentsToCommandString(java.util.List, compbio.metadata.RunnerConfig)"><B>argumentsToCommandString(List&lt;? extends Option&lt;?&gt;&gt;, RunnerConfig&lt;? extends Executable&lt;?&gt;&gt;)</B></A> - \r
-Static method in class compbio.runner.<A HREF="../compbio/runner/OptionCombinator.html" title="class in compbio.runner">OptionCombinator</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine"><B>AsyncExecutor</B></A> - Interface in <A HREF="../compbio/engine/package-summary.html">compbio.engine</A><DD>An asynchronous executor engine, capable of running, cancelling, 
- obtaining results calculated by a native executable wrapper in Executable interface.<DT><A HREF="../compbio/engine/cluster/drmaa/AsyncJobRunner.html" title="class in compbio.engine.cluster.drmaa"><B>AsyncJobRunner</B></A> - Class in <A HREF="../compbio/engine/cluster/drmaa/package-summary.html">compbio.engine.cluster.drmaa</A><DD>Single cluster job runner class<DT><A HREF="../compbio/engine/cluster/drmaa/AsyncJobRunner.html#AsyncJobRunner()"><B>AsyncJobRunner()</B></A> - \r
-Constructor for class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/AsyncJobRunner.html" title="class in compbio.engine.cluster.drmaa">AsyncJobRunner</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/local/AsyncLocalRunner.html" title="class in compbio.engine.local"><B>AsyncLocalRunner</B></A> - Class in <A HREF="../compbio/engine/local/package-summary.html">compbio.engine.local</A><DD>&nbsp;<DT><A HREF="../compbio/engine/local/AsyncLocalRunner.html#AsyncLocalRunner()"><B>AsyncLocalRunner()</B></A> - \r
-Constructor for class compbio.engine.local.<A HREF="../compbio/engine/local/AsyncLocalRunner.html" title="class in compbio.engine.local">AsyncLocalRunner</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/local/_TrackingExecutor.html#awaitTermination(long, java.util.concurrent.TimeUnit)"><B>awaitTermination(long, TimeUnit)</B></A> - \r
-Method in class compbio.engine.local.<A HREF="../compbio/engine/local/_TrackingExecutor.html" title="class in compbio.engine.local">_TrackingExecutor</A>\r
-<DD>&nbsp;\r
-</DL>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
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diff --git a/website/full_javadoc/index-files/index-10.html b/website/full_javadoc/index-files/index-10.html

deleted file mode 100644 (file)

index a54536b..0000000
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Class</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Use</FONT>&nbsp;</TD>\r
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-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/JobExecutionException.html" title="class in compbio.metadata"><B>JobExecutionException</B></A> - Exception in <A HREF="../compbio/metadata/package-summary.html">compbio.metadata</A><DD>JobExecutionException is thrown wherever the results of the calculation
- cannot be obtained.<DT><A HREF="../compbio/metadata/JobExecutionException.html#JobExecutionException(java.lang.String)"><B>JobExecutionException(String)</B></A> - \r
-Constructor for exception compbio.metadata.<A HREF="../compbio/metadata/JobExecutionException.html" title="class in compbio.metadata">JobExecutionException</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/JobExecutionException.html#JobExecutionException(java.lang.Throwable)"><B>JobExecutionException(Throwable)</B></A> - \r
-Constructor for exception compbio.metadata.<A HREF="../compbio/metadata/JobExecutionException.html" title="class in compbio.metadata">JobExecutionException</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/JobExecutionException.html#JobExecutionException(java.lang.String, java.lang.Throwable)"><B>JobExecutionException(String, Throwable)</B></A> - \r
-Constructor for exception compbio.metadata.<A HREF="../compbio/metadata/JobExecutionException.html" title="class in compbio.metadata">JobExecutionException</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/jaxws/JobExecutionExceptionBean.html" title="class in compbio.data.msa.jaxws"><B>JobExecutionExceptionBean</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>This class was generated by the JAX-WS RI.<DT><A HREF="../compbio/data/msa/jaxws/JobExecutionExceptionBean.html#JobExecutionExceptionBean()"><B>JobExecutionExceptionBean()</B></A> - \r
-Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/JobExecutionExceptionBean.html" title="class in compbio.data.msa.jaxws">JobExecutionExceptionBean</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/cluster/drmaa/ClusterSession.html#JOBID"><B>JOBID</B></A> - \r
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-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/cluster/drmaa/JobRunner.html" title="class in compbio.engine.cluster.drmaa"><B>JobRunner</B></A> - Class in <A HREF="../compbio/engine/cluster/drmaa/package-summary.html">compbio.engine.cluster.drmaa</A><DD>Single cluster job runner class<DT><A HREF="../compbio/engine/cluster/drmaa/JobRunner.html#JobRunner(compbio.engine.client.ConfiguredExecutable)"><B>JobRunner(ConfiguredExecutable&lt;?&gt;)</B></A> - \r
-Constructor for class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/JobRunner.html" title="class in compbio.engine.cluster.drmaa">JobRunner</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/JobStatus.html" title="enum in compbio.metadata"><B>JobStatus</B></A> - Enum in <A HREF="../compbio/metadata/package-summary.html">compbio.metadata</A><DD>The status of the job.<DT><A HREF="../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata"><B>JobSubmissionException</B></A> - Exception in <A HREF="../compbio/metadata/package-summary.html">compbio.metadata</A><DD>Exception for generic problems with JobSubmission it is often thrown as a
- wrapper for the lower level exceptions like IOException or DrmaaException.<DT><A HREF="../compbio/metadata/JobSubmissionException.html#JobSubmissionException(java.lang.String)"><B>JobSubmissionException(String)</B></A> - \r
-Constructor for exception compbio.metadata.<A HREF="../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/JobSubmissionException.html#JobSubmissionException(java.lang.Throwable)"><B>JobSubmissionException(Throwable)</B></A> - \r
-Constructor for exception compbio.metadata.<A HREF="../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/JobSubmissionException.html#JobSubmissionException(java.lang.String, java.lang.Throwable)"><B>JobSubmissionException(String, Throwable)</B></A> - \r
-Constructor for exception compbio.metadata.<A HREF="../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/jaxws/JobSubmissionExceptionBean.html" title="class in compbio.data.msa.jaxws"><B>JobSubmissionExceptionBean</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>This class was generated by the JAX-WS RI.<DT><A HREF="../compbio/data/msa/jaxws/JobSubmissionExceptionBean.html#JobSubmissionExceptionBean()"><B>JobSubmissionExceptionBean()</B></A> - \r
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- <database>] [--pred-nohits] [--logLevel=(ERROR|INFO|DEBUG)] [--help]
- 
- jpred4 --sequence <fasta file> The path to the sequence (in FASTA format) you
- want to predict OR
- 
- [--alignment <clustalW alignment>] The alignment which to use for prediction
- 
- [--profile=<path to HMM profile>]
- 
- [--db <database>] Database to use for PSI-BLAST querying.<DT><A HREF="../compbio/pipeline/_jpred/Jpred4.html#Jpred4()"><B>Jpred4()</B></A> - \r
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-<DD>&nbsp;\r
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- 
- jnetpred:-,H,H,H,H,H,H,H,H,H,H,H,-,-,-,-,-,-,-,-,E,E,E,-,-,-,-,-,-,-,-,-,-,-,
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- ,0.1591,0.7399,0.1456,0.2488,0.5824,0.1017,
- JNETPROPE:0.0107,0.6245,0.3614,0.0120
- ,0.8702,0.1238,0.0120,0.9335,0.0656,0.0102
- ,0.9586,0.0465,0.0094,0.9662,0.0433,
- ,0.1525,0.7103,0.1088,0.1181,0.7425,0.1784,<DT><A HREF="../compbio/data/_structure/JpredResult.html#JpredResult()"><B>JpredResult()</B></A> - \r
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diff --git a/website/full_javadoc/index-files/index-12.html b/website/full_javadoc/index-files/index-12.html

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@@ -1,207 +0,0 @@
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-<!--NewPage-->\r
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-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Package</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Class</FONT>&nbsp;</TD>\r
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-<A HREF="index-1.html">A</A> <A HREF="index-2.html">B</A> <A HREF="index-3.html">C</A> <A HREF="index-4.html">D</A> <A HREF="index-5.html">E</A> <A HREF="index-6.html">F</A> <A HREF="index-7.html">G</A> <A HREF="index-8.html">H</A> <A HREF="index-9.html">I</A> <A HREF="index-10.html">J</A> <A HREF="index-11.html">K</A> <A HREF="index-12.html">L</A> <A HREF="index-13.html">M</A> <A HREF="index-14.html">N</A> <A HREF="index-15.html">O</A> <A HREF="index-16.html">P</A> <A HREF="index-17.html">R</A> <A HREF="index-18.html">S</A> <A HREF="index-19.html">T</A> <A HREF="index-20.html">U</A> <A HREF="index-21.html">V</A> <A HREF="index-22.html">W</A> <A HREF="index-23.html">_</A> <HR>\r
-<A NAME="_L_"><!-- --></A><H2>\r
-<B>L</B></H2>\r
-<DL>\r
-<DT><A HREF="../compbio/metadata/Limit.html" title="class in compbio.metadata"><B>Limit</B></A>&lt;<A HREF="../compbio/metadata/Limit.html" title="type parameter in Limit">T</A>&gt; - Class in <A HREF="../compbio/metadata/package-summary.html">compbio.metadata</A><DD>A value object containing a maximum number of sequences and a maximum average
- sequence length for a preset.<DT><A HREF="../compbio/metadata/Limit.html#Limit(int, int, java.lang.String)"><B>Limit(int, int, String)</B></A> - \r
-Constructor for class compbio.metadata.<A HREF="../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/Limit.html#Limit(int, int, java.lang.String, boolean)"><B>Limit(int, int, String, boolean)</B></A> - \r
-Constructor for class compbio.metadata.<A HREF="../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata"><B>LimitExceededException</B></A> - Exception in <A HREF="../compbio/metadata/package-summary.html">compbio.metadata</A><DD>Thrown if the task larger in size that the limit that applies to the
- calculation.<DT><A HREF="../compbio/metadata/LimitExceededException.html#LimitExceededException(java.lang.String)"><B>LimitExceededException(String)</B></A> - \r
-Constructor for exception compbio.metadata.<A HREF="../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html" title="class in compbio.data.msa.jaxws"><B>LimitExceededExceptionBean</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>This class was generated by the JAX-WS RI.<DT><A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html#LimitExceededExceptionBean()"><B>LimitExceededExceptionBean()</B></A> - \r
-Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html" title="class in compbio.data.msa.jaxws">LimitExceededExceptionBean</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/LimitsManager.html" title="class in compbio.metadata"><B>LimitsManager</B></A>&lt;<A HREF="../compbio/metadata/LimitsManager.html" title="type parameter in LimitsManager">T</A>&gt; - Class in <A HREF="../compbio/metadata/package-summary.html">compbio.metadata</A><DD>A collection of Limits<DT><A HREF="../compbio/metadata/LimitsManager.html#LimitsManager()"><B>LimitsManager()</B></A> - \r
-Constructor for class compbio.metadata.<A HREF="../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/RunConfiguration.html#load(java.io.InputStream)"><B>load(InputStream)</B></A> - \r
-Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/LoadBalancer.html" title="class in compbio.engine"><B>LoadBalancer</B></A> - Class in <A HREF="../compbio/engine/package-summary.html">compbio.engine</A><DD>&nbsp;<DT><A HREF="../compbio/engine/client/Util.html#loadExecutable(java.lang.String)"><B>loadExecutable(String)</B></A> - \r
-Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/Util.html" title="class in compbio.engine.client">Util</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/ConfExecutable.html#loadRunConfiguration(compbio.engine.client.RunConfiguration)"><B>loadRunConfiguration(RunConfiguration)</B></A> - \r
-Method in class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/ConfExecutable.html#loadRunConfiguration(java.io.InputStream)"><B>loadRunConfiguration(InputStream)</B></A> - \r
-Method in class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/ConfiguredExecutable.html#loadRunConfiguration(java.io.InputStream)"><B>loadRunConfiguration(InputStream)</B></A> - \r
-Method in interface compbio.engine.client.<A HREF="../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/Executable.html#loadRunConfiguration(compbio.engine.client.RunConfiguration)"><B>loadRunConfiguration(RunConfiguration)</B></A> - \r
-Method in interface compbio.engine.client.<A HREF="../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/SkeletalExecutable.html#loadRunConfiguration(compbio.engine.client.RunConfiguration)"><B>loadRunConfiguration(RunConfiguration)</B></A> - \r
-Method in class compbio.engine.client.<A HREF="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/_impl/NetNglyc.html#loadRunConfiguration(compbio.engine.client.RunConfiguration)"><B>loadRunConfiguration(RunConfiguration)</B></A> - \r
-Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/_SkeletalCommandBuilder.html#loadRunConfiguration(compbio.engine.client.RunConfiguration)"><B>loadRunConfiguration(RunConfiguration)</B></A> - \r
-Method in class compbio.runner.<A HREF="../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/PresetManager.html#LOCAL_ENGINE_LIMIT_PRESET"><B>LOCAL_ENGINE_LIMIT_PRESET</B></A> - \r
-Static variable in class compbio.metadata.<A HREF="../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/Configurator.html#LOCAL_WORK_DIRECTORY"><B>LOCAL_WORK_DIRECTORY</B></A> - \r
-Static variable in class compbio.engine.<A HREF="../compbio/engine/Configurator.html" title="class in compbio.engine">Configurator</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/local/LocalEngineUtil.html" title="class in compbio.engine.local"><B>LocalEngineUtil</B></A> - Class in <A HREF="../compbio/engine/local/package-summary.html">compbio.engine.local</A><DD>&nbsp;<DT><A HREF="../compbio/engine/local/LocalEngineUtil.html#LocalEngineUtil()"><B>LocalEngineUtil()</B></A> - \r
-Constructor for class compbio.engine.local.<A HREF="../compbio/engine/local/LocalEngineUtil.html" title="class in compbio.engine.local">LocalEngineUtil</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/local/LocalExecutorService.html" title="class in compbio.engine.local"><B>LocalExecutorService</B></A> - Class in <A HREF="../compbio/engine/local/package-summary.html">compbio.engine.local</A><DD>&nbsp;<DT><A HREF="../compbio/engine/local/LocalRunner.html" title="class in compbio.engine.local"><B>LocalRunner</B></A> - Class in <A HREF="../compbio/engine/local/package-summary.html">compbio.engine.local</A><DD>&nbsp;<DT><A HREF="../compbio/engine/local/LocalRunner.html#LocalRunner(compbio.engine.client.ConfiguredExecutable)"><B>LocalRunner(ConfiguredExecutable&lt;?&gt;)</B></A> - \r
-Constructor for class compbio.engine.local.<A HREF="../compbio/engine/local/LocalRunner.html" title="class in compbio.engine.local">LocalRunner</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/ws/server/WSUtil.html#log(org.apache.log4j.Logger, javax.xml.ws.WebServiceContext, java.lang.String)"><B>log(Logger, WebServiceContext, String)</B></A> - \r
-Static method in class compbio.ws.server.<A HREF="../compbio/ws/server/WSUtil.html" title="class in compbio.ws.server">WSUtil</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/ws/server/WSUtil.html#log(org.apache.log4j.Logger, javax.xml.ws.WebServiceContext, java.lang.String, java.lang.String)"><B>log(Logger, WebServiceContext, String, String)</B></A> - \r
-Static method in class compbio.ws.server.<A HREF="../compbio/ws/server/WSUtil.html" title="class in compbio.ws.server">WSUtil</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/cluster/dundee/_QueueConstraints.html#LONG_TIME_LIMIT"><B>LONG_TIME_LIMIT</B></A> - \r
-Static variable in class compbio.engine.cluster.dundee.<A HREF="../compbio/engine/cluster/dundee/_QueueConstraints.html" title="class in compbio.engine.cluster.dundee">_QueueConstraints</A>\r
-<DD>&nbsp;\r
-</DL>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
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-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
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diff --git a/website/full_javadoc/index-files/index-13.html b/website/full_javadoc/index-files/index-13.html

deleted file mode 100644 (file)

index 7668e9d..0000000
--- a/website/full_javadoc/index-files/index-13.html
+++ /dev/null
@@ -1,189 +0,0 @@
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-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-M-Index\r
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-\r
-<META NAME="date" CONTENT="2010-02-17">\r
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-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="M-Index";\r
-    }\r
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-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
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-\r
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-<!-- ========= START OF TOP NAVBAR ======= -->\r
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-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
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-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Use</FONT>&nbsp;</TD>\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Index</B></FONT>&nbsp;</TD>\r
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-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
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-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="index-12.html"><B>PREV LETTER</B></A>&nbsp;\r
-&nbsp;<A HREF="index-14.html"><B>NEXT LETTER</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../index.html?index-filesindex-13.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="index-13.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
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-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<A HREF="index-1.html">A</A> <A HREF="index-2.html">B</A> <A HREF="index-3.html">C</A> <A HREF="index-4.html">D</A> <A HREF="index-5.html">E</A> <A HREF="index-6.html">F</A> <A HREF="index-7.html">G</A> <A HREF="index-8.html">H</A> <A HREF="index-9.html">I</A> <A HREF="index-10.html">J</A> <A HREF="index-11.html">K</A> <A HREF="index-12.html">L</A> <A HREF="index-13.html">M</A> <A HREF="index-14.html">N</A> <A HREF="index-15.html">O</A> <A HREF="index-16.html">P</A> <A HREF="index-17.html">R</A> <A HREF="index-18.html">S</A> <A HREF="index-19.html">T</A> <A HREF="index-20.html">U</A> <A HREF="index-21.html">V</A> <A HREF="index-22.html">W</A> <A HREF="index-23.html">_</A> <HR>\r
-<A NAME="_M_"><!-- --></A><H2>\r
-<B>M</B></H2>\r
-<DL>\r
-<DT><A HREF="../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa"><B>Mafft</B></A> - Class in <A HREF="../compbio/runner/msa/package-summary.html">compbio.runner.msa</A><DD>&nbsp;<DT><A HREF="../compbio/runner/msa/Mafft.html#Mafft()"><B>Mafft()</B></A> - \r
-Constructor for class compbio.runner.msa.<A HREF="../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/ws/server/MafftWS.html" title="class in compbio.ws.server"><B>MafftWS</B></A> - Class in <A HREF="../compbio/ws/server/package-summary.html">compbio.ws.server</A><DD>&nbsp;<DT><A HREF="../compbio/ws/server/MafftWS.html#MafftWS()"><B>MafftWS()</B></A> - \r
-Constructor for class compbio.ws.server.<A HREF="../compbio/ws/server/MafftWS.html" title="class in compbio.ws.server">MafftWS</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/cluster/drmaa/_DrmaaExample.html#main(java.lang.String[])"><B>main(String[])</B></A> - \r
-Static method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/_DrmaaExample.html" title="class in compbio.engine.cluster.drmaa">_DrmaaExample</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/cluster/drmaa/_JobStatus.html#main(java.lang.String[])"><B>main(String[])</B></A> - \r
-Static method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/_JobStatus.html" title="class in compbio.engine.cluster.drmaa">_JobStatus</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/pipeline/_jpred/BlastParser.html#main(java.lang.String[])"><B>main(String[])</B></A> - \r
-Static method in class compbio.pipeline._jpred.<A HREF="../compbio/pipeline/_jpred/BlastParser.html" title="class in compbio.pipeline._jpred">BlastParser</A>\r
-<DD>args[0] is assumed to be the name of a Blast output file\r
-<DT><A HREF="../compbio/pipeline/_jpred/Pairwise.html#main(java.lang.String[])"><B>main(String[])</B></A> - \r
-Static method in class compbio.pipeline._jpred.<A HREF="../compbio/pipeline/_jpred/Pairwise.html" title="class in compbio.pipeline._jpred">Pairwise</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/_impl/OB.html#main(java.lang.String[])"><B>main(String[])</B></A> - \r
-Static method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/OB.html" title="class in compbio.runner._impl">OB</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/ws/client/Jws2Client.html#main(java.lang.String[])"><B>main(String[])</B></A> - \r
-Static method in class compbio.ws.client.<A HREF="../compbio/ws/client/Jws2Client.html" title="class in compbio.ws.client">Jws2Client</A>\r
-<DD>Starts command line client, if no parameter are supported print help.\r
-<DT><A HREF="../compbio/ws/client/WSTester.html#main(java.lang.String[])"><B>main(String[])</B></A> - \r
-Static method in class compbio.ws.client.<A HREF="../compbio/ws/client/WSTester.html" title="class in compbio.ws.client">WSTester</A>\r
-<DD>Test JWS2 web services\r
-<DT><A HREF="../compbio/ws/server/SimpleWSPublisher.html#main(java.lang.String[])"><B>main(String[])</B></A> - \r
-Static method in class compbio.ws.server.<A HREF="../compbio/ws/server/SimpleWSPublisher.html" title="class in compbio.ws.server">SimpleWSPublisher</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/cluster/dundee/_QueueConstraints.html#MAX_MEMORY_LIMIT"><B>MAX_MEMORY_LIMIT</B></A> - \r
-Static variable in class compbio.engine.cluster.dundee.<A HREF="../compbio/engine/cluster/dundee/_QueueConstraints.html" title="class in compbio.engine.cluster.dundee">_QueueConstraints</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/_impl/Mcl.html" title="class in compbio.runner._impl"><B>Mcl</B></A> - Class in <A HREF="../compbio/runner/_impl/package-summary.html">compbio.runner._impl</A><DD>&nbsp;<DT><A HREF="../compbio/runner/_impl/Mcl.html#Mcl(java.lang.String)"><B>Mcl(String)</B></A> - \r
-Constructor for class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Mcl.html" title="class in compbio.runner._impl">Mcl</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/Util.html#mergeEnvVariables(java.util.Map, java.util.Map)"><B>mergeEnvVariables(Map&lt;String, String&gt;, Map&lt;String, String&gt;)</B></A> - \r
-Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/Util.html" title="class in compbio.engine.client">Util</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa"><B>MsaWS</B></A>&lt;<A HREF="../compbio/data/msa/MsaWS.html" title="type parameter in MsaWS">T</A>&gt; - Interface in <A HREF="../compbio/data/msa/package-summary.html">compbio.data.msa</A><DD>Multiple Sequence Alignment (MSA) Web Services Interface<DT><A HREF="../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa"><B>Muscle</B></A> - Class in <A HREF="../compbio/runner/msa/package-summary.html">compbio.runner.msa</A><DD>&nbsp;<DT><A HREF="../compbio/runner/msa/Muscle.html#Muscle()"><B>Muscle()</B></A> - \r
-Constructor for class compbio.runner.msa.<A HREF="../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>\r
-<DD>Default options are
- 
- -clwstrict - write output in clustal format\r
-<DT><A HREF="../compbio/ws/server/MuscleWS.html" title="class in compbio.ws.server"><B>MuscleWS</B></A> - Class in <A HREF="../compbio/ws/server/package-summary.html">compbio.ws.server</A><DD>&nbsp;<DT><A HREF="../compbio/ws/server/MuscleWS.html#MuscleWS()"><B>MuscleWS()</B></A> - \r
-Constructor for class compbio.ws.server.<A HREF="../compbio/ws/server/MuscleWS.html" title="class in compbio.ws.server">MuscleWS</A>\r
-<DD>&nbsp;\r
-</DL>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Package</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Class</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Use</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Index</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="index-12.html"><B>PREV LETTER</B></A>&nbsp;\r
-&nbsp;<A HREF="index-14.html"><B>NEXT LETTER</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../index.html?index-filesindex-13.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="index-13.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<A HREF="index-1.html">A</A> <A HREF="index-2.html">B</A> <A HREF="index-3.html">C</A> <A HREF="index-4.html">D</A> <A HREF="index-5.html">E</A> <A HREF="index-6.html">F</A> <A HREF="index-7.html">G</A> <A HREF="index-8.html">H</A> <A HREF="index-9.html">I</A> <A HREF="index-10.html">J</A> <A HREF="index-11.html">K</A> <A HREF="index-12.html">L</A> <A HREF="index-13.html">M</A> <A HREF="index-14.html">N</A> <A HREF="index-15.html">O</A> <A HREF="index-16.html">P</A> <A HREF="index-17.html">R</A> <A HREF="index-18.html">S</A> <A HREF="index-19.html">T</A> <A HREF="index-20.html">U</A> <A HREF="index-21.html">V</A> <A HREF="index-22.html">W</A> <A HREF="index-23.html">_</A> <HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/index-files/index-14.html b/website/full_javadoc/index-files/index-14.html

deleted file mode 100644 (file)

index 7db8e89..0000000
--- a/website/full_javadoc/index-files/index-14.html
+++ /dev/null
@@ -1,173 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-N-Index\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="N-Index";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Package</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Class</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Use</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Index</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="index-13.html"><B>PREV LETTER</B></A>&nbsp;\r
-&nbsp;<A HREF="index-15.html"><B>NEXT LETTER</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../index.html?index-filesindex-14.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="index-14.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<A HREF="index-1.html">A</A> <A HREF="index-2.html">B</A> <A HREF="index-3.html">C</A> <A HREF="index-4.html">D</A> <A HREF="index-5.html">E</A> <A HREF="index-6.html">F</A> <A HREF="index-7.html">G</A> <A HREF="index-8.html">H</A> <A HREF="index-9.html">I</A> <A HREF="index-10.html">J</A> <A HREF="index-11.html">K</A> <A HREF="index-12.html">L</A> <A HREF="index-13.html">M</A> <A HREF="index-14.html">N</A> <A HREF="index-15.html">O</A> <A HREF="index-16.html">P</A> <A HREF="index-17.html">R</A> <A HREF="index-18.html">S</A> <A HREF="index-19.html">T</A> <A HREF="index-20.html">U</A> <A HREF="index-21.html">V</A> <A HREF="index-22.html">W</A> <A HREF="index-23.html">_</A> <HR>\r
-<A NAME="_N_"><!-- --></A><H2>\r
-<B>N</B></H2>\r
-<DL>\r
-<DT><A HREF="../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl"><B>NetNglyc</B></A> - Class in <A HREF="../compbio/runner/_impl/package-summary.html">compbio.runner._impl</A><DD>&nbsp;<DT><A HREF="../compbio/runner/_impl/NetNglyc.html#NetNglyc()"><B>NetNglyc()</B></A> - \r
-Constructor for class compbio.runner._impl.<A HREF="../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/CommandBuilder.html#newCommandBuilder(java.util.List, java.lang.String)"><B>newCommandBuilder(List&lt;? extends Option&lt;T&gt;&gt;, String)</B></A> - \r
-Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>\r
-<DD>This produces the same result as getCommands method.\r
-<DT><A HREF="../compbio/engine/client/ConfExecutable.html#newConfExecutable(compbio.engine.client.RunConfiguration)"><B>newConfExecutable(RunConfiguration)</B></A> - \r
-Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/FilePuller.html#newFilePuller(java.lang.String, int)"><B>newFilePuller(String, int)</B></A> - \r
-Static method in class compbio.engine.<A HREF="../compbio/engine/FilePuller.html" title="class in compbio.engine">FilePuller</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/LimitExceededException.html#newLimitExceeded(compbio.metadata.Limit, java.util.List)"><B>newLimitExceeded(Limit&lt;?&gt;, List&lt;FastaSequence&gt;)</B></A> - \r
-Static method in exception compbio.metadata.<A HREF="../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/FilePuller.html#newProgressPuller(java.lang.String)"><B>newProgressPuller(String)</B></A> - \r
-Static method in class compbio.engine.<A HREF="../compbio/engine/FilePuller.html" title="class in compbio.engine">FilePuller</A>\r
-<DD>Progress Puller is designed to read 3 characters from the beginning of
- the file, nothing more.\r
-<DT><A HREF="../compbio/data/sequence/SequenceUtil.html#NON_AA"><B>NON_AA</B></A> - \r
-Static variable in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
-<DD>inversion of AA pattern\r
-<DT><A HREF="../compbio/data/sequence/SequenceUtil.html#NON_NUCLEOTIDE"><B>NON_NUCLEOTIDE</B></A> - \r
-Static variable in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
-<DD>Non nucleotide\r
-<DT><A HREF="../compbio/data/sequence/SequenceUtil.html#NONWORD"><B>NONWORD</B></A> - \r
-Static variable in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
-<DD>Non word\r
-<DT><A HREF="../compbio/data/sequence/SequenceUtil.html#NUCLEOTIDE"><B>NUCLEOTIDE</B></A> - \r
-Static variable in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
-<DD>Nucleotides a, t, g, c, u\r
-</DL>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
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-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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diff --git a/website/full_javadoc/index-files/index-15.html b/website/full_javadoc/index-files/index-15.html

deleted file mode 100644 (file)

index 20d4d09..0000000
--- a/website/full_javadoc/index-files/index-15.html
+++ /dev/null
@@ -1,157 +0,0 @@
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-<!--NewPage-->\r
-<HTML>\r
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-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
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-O-Index\r
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-<META NAME="date" CONTENT="2010-02-17">\r
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-{\r
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-\r
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-  if(window==top) {\r
-    document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
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-</SCRIPT>\r
-<NOSCRIPT>\r
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-\r
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-</TR>\r
-</TABLE>\r
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-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<A HREF="index-1.html">A</A> <A HREF="index-2.html">B</A> <A HREF="index-3.html">C</A> <A HREF="index-4.html">D</A> <A HREF="index-5.html">E</A> <A HREF="index-6.html">F</A> <A HREF="index-7.html">G</A> <A HREF="index-8.html">H</A> <A HREF="index-9.html">I</A> <A HREF="index-10.html">J</A> <A HREF="index-11.html">K</A> <A HREF="index-12.html">L</A> <A HREF="index-13.html">M</A> <A HREF="index-14.html">N</A> <A HREF="index-15.html">O</A> <A HREF="index-16.html">P</A> <A HREF="index-17.html">R</A> <A HREF="index-18.html">S</A> <A HREF="index-19.html">T</A> <A HREF="index-20.html">U</A> <A HREF="index-21.html">V</A> <A HREF="index-22.html">W</A> <A HREF="index-23.html">_</A> <HR>\r
-<A NAME="_O_"><!-- --></A><H2>\r
-<B>O</B></H2>\r
-<DL>\r
-<DT><A HREF="../compbio/runner/_impl/OB.html" title="class in compbio.runner._impl"><B>OB</B></A> - Class in <A HREF="../compbio/runner/_impl/package-summary.html">compbio.runner._impl</A><DD>TODO this needs fixing! Executable does not work<DT><A HREF="../compbio/runner/_impl/OB.html#OB()"><B>OB()</B></A> - \r
-Constructor for class compbio.runner._impl.<A HREF="../compbio/runner/_impl/OB.html" title="class in compbio.runner._impl">OB</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/_impl/OB.html#OB(java.lang.String)"><B>OB(String)</B></A> - \r
-Constructor for class compbio.runner._impl.<A HREF="../compbio/runner/_impl/OB.html" title="class in compbio.runner._impl">OB</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata"><B>Option</B></A>&lt;<A HREF="../compbio/metadata/Option.html" title="type parameter in Option">T</A>&gt; - Class in <A HREF="../compbio/metadata/package-summary.html">compbio.metadata</A><DD>Command line option/flag or multiple exclusive options with no value.<DT><A HREF="../compbio/metadata/Option.html#Option(java.lang.String, java.lang.String)"><B>Option(String, String)</B></A> - \r
-Constructor for class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/OptionCombinator.html" title="class in compbio.runner"><B>OptionCombinator</B></A> - Class in <A HREF="../compbio/runner/package-summary.html">compbio.runner</A><DD>This class solve the following problems.<DT><A HREF="../compbio/runner/OptionCombinator.html#OptionCombinator(compbio.metadata.RunnerConfig)"><B>OptionCombinator(RunnerConfig&lt;? extends Executable&lt;?&gt;&gt;)</B></A> - \r
-Constructor for class compbio.runner.<A HREF="../compbio/runner/OptionCombinator.html" title="class in compbio.runner">OptionCombinator</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/OptionCombinator.html#optionsToCommandString(java.util.List)"><B>optionsToCommandString(List&lt;Option&lt;?&gt;&gt;)</B></A> - \r
-Method in class compbio.runner.<A HREF="../compbio/runner/OptionCombinator.html" title="class in compbio.runner">OptionCombinator</A>\r
-<DD>&nbsp;\r
-</DL>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
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-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Index</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
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-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="index-14.html"><B>PREV LETTER</B></A>&nbsp;\r
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-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
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diff --git a/website/full_javadoc/index-files/index-16.html b/website/full_javadoc/index-files/index-16.html

deleted file mode 100644 (file)

index 5c24c63..0000000
--- a/website/full_javadoc/index-files/index-16.html
+++ /dev/null
@@ -1,265 +0,0 @@
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-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-P-Index\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
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-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="P-Index";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
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-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
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-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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-<A HREF="index-1.html">A</A> <A HREF="index-2.html">B</A> <A HREF="index-3.html">C</A> <A HREF="index-4.html">D</A> <A HREF="index-5.html">E</A> <A HREF="index-6.html">F</A> <A HREF="index-7.html">G</A> <A HREF="index-8.html">H</A> <A HREF="index-9.html">I</A> <A HREF="index-10.html">J</A> <A HREF="index-11.html">K</A> <A HREF="index-12.html">L</A> <A HREF="index-13.html">M</A> <A HREF="index-14.html">N</A> <A HREF="index-15.html">O</A> <A HREF="index-16.html">P</A> <A HREF="index-17.html">R</A> <A HREF="index-18.html">S</A> <A HREF="index-19.html">T</A> <A HREF="index-20.html">U</A> <A HREF="index-21.html">V</A> <A HREF="index-22.html">W</A> <A HREF="index-23.html">_</A> <HR>\r
-<A NAME="_P_"><!-- --></A><H2>\r
-<B>P</B></H2>\r
-<DL>\r
-<DT><A HREF="../compbio/pipeline/_jpred/Pairwise.html" title="class in compbio.pipeline._jpred"><B>Pairwise</B></A> - Class in <A HREF="../compbio/pipeline/_jpred/package-summary.html">compbio.pipeline._jpred</A><DD>&nbsp;<DT><A HREF="../compbio/pipeline/_jpred/Pairwise.html#Pairwise(java.util.List)"><B>Pairwise(List&lt;FastaSequence&gt;)</B></A> - \r
-Constructor for class compbio.pipeline._jpred.<A HREF="../compbio/pipeline/_jpred/Pairwise.html" title="class in compbio.pipeline._jpred">Pairwise</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata"><B>Parameter</B></A>&lt;<A HREF="../compbio/metadata/Parameter.html" title="type parameter in Parameter">T</A>&gt; - Class in <A HREF="../compbio/metadata/package-summary.html">compbio.metadata</A><DD>A single value containing option supported by the web service e.g.<DT><A HREF="../compbio/metadata/Parameter.html#Parameter(java.lang.String, java.lang.String)"><B>Parameter(String, String)</B></A> - \r
-Constructor for class compbio.metadata.<A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/OptionCombinator.html#parametersToCommandString(java.util.List, java.util.Map)"><B>parametersToCommandString(List&lt;Parameter&lt;?&gt;&gt;, Map&lt;Parameter&lt;?&gt;, String&gt;)</B></A> - \r
-Method in class compbio.runner.<A HREF="../compbio/runner/OptionCombinator.html" title="class in compbio.runner">OptionCombinator</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/conf/_Key.html#parse(java.lang.String)"><B>parse(String)</B></A> - \r
-Static method in class compbio.engine.conf.<A HREF="../compbio/engine/conf/_Key.html" title="class in compbio.engine.conf">_Key</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/EnvVariableProcessor.html#PATH"><B>PATH</B></A> - \r
-Static variable in class compbio.engine.client.<A HREF="../compbio/engine/client/EnvVariableProcessor.html" title="class in compbio.engine.client">EnvVariableProcessor</A>\r
-<DD>Special variable keys Absolute path(s) will be merged with the content of
- the system PATH variable\r
-<DT><A HREF="../compbio/engine/client/PathValidator.html" title="class in compbio.engine.client"><B>PathValidator</B></A> - Class in <A HREF="../compbio/engine/client/package-summary.html">compbio.engine.client</A><DD>&nbsp;<DT><A HREF="../compbio/engine/client/PathValidator.html#PathValidator()"><B>PathValidator()</B></A> - \r
-Constructor for class compbio.engine.client.<A HREF="../compbio/engine/client/PathValidator.html" title="class in compbio.engine.client">PathValidator</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/PipedExecutable.html" title="interface in compbio.engine.client"><B>PipedExecutable</B></A>&lt;<A HREF="../compbio/engine/client/PipedExecutable.html" title="type parameter in PipedExecutable">T</A>&gt; - Interface in <A HREF="../compbio/engine/client/package-summary.html">compbio.engine.client</A><DD>This is a marker interface to indicate that the output of the process must be
- captured.<DT><A HREF="../compbio/metadata/Preset.html" title="class in compbio.metadata"><B>Preset</B></A>&lt;<A HREF="../compbio/metadata/Preset.html" title="type parameter in Preset">T</A>&gt; - Class in <A HREF="../compbio/metadata/package-summary.html">compbio.metadata</A><DD>Collection of Options and Parameters with their values<DT><A HREF="../compbio/metadata/Preset.html#Preset()"><B>Preset()</B></A> - \r
-Constructor for class compbio.metadata.<A HREF="../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/jaxws/PresetAlign.html" title="class in compbio.data.msa.jaxws"><B>PresetAlign</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/PresetAlign.html#PresetAlign()"><B>PresetAlign()</B></A> - \r
-Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/PresetAlign.html" title="class in compbio.data.msa.jaxws">PresetAlign</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/MsaWS.html#presetAlign(java.util.List, compbio.metadata.Preset)"><B>presetAlign(List&lt;FastaSequence&gt;, Preset&lt;T&gt;)</B></A> - \r
-Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>\r
-<DD>Align a list of sequences with preset.\r
-<DT><A HREF="../compbio/ws/server/ClustalWS.html#presetAlign(java.util.List, compbio.metadata.Preset)"><B>presetAlign(List&lt;FastaSequence&gt;, Preset&lt;ClustalW&gt;)</B></A> - \r
-Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ClustalWS.html" title="class in compbio.ws.server">ClustalWS</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/ws/server/MafftWS.html#presetAlign(java.util.List, compbio.metadata.Preset)"><B>presetAlign(List&lt;FastaSequence&gt;, Preset&lt;Mafft&gt;)</B></A> - \r
-Method in class compbio.ws.server.<A HREF="../compbio/ws/server/MafftWS.html" title="class in compbio.ws.server">MafftWS</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/ws/server/MuscleWS.html#presetAlign(java.util.List, compbio.metadata.Preset)"><B>presetAlign(List&lt;FastaSequence&gt;, Preset&lt;Muscle&gt;)</B></A> - \r
-Method in class compbio.ws.server.<A HREF="../compbio/ws/server/MuscleWS.html" title="class in compbio.ws.server">MuscleWS</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/ws/server/ProbconsWS.html#presetAlign(java.util.List, compbio.metadata.Preset)"><B>presetAlign(List&lt;FastaSequence&gt;, Preset&lt;Probcons&gt;)</B></A> - \r
-Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ProbconsWS.html" title="class in compbio.ws.server">ProbconsWS</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/ws/server/TcoffeeWS.html#presetAlign(java.util.List, compbio.metadata.Preset)"><B>presetAlign(List&lt;FastaSequence&gt;, Preset&lt;Tcoffee&gt;)</B></A> - \r
-Method in class compbio.ws.server.<A HREF="../compbio/ws/server/TcoffeeWS.html" title="class in compbio.ws.server">TcoffeeWS</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/jaxws/PresetAlignResponse.html" title="class in compbio.data.msa.jaxws"><B>PresetAlignResponse</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/PresetAlignResponse.html#PresetAlignResponse()"><B>PresetAlignResponse()</B></A> - \r
-Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/PresetAlignResponse.html" title="class in compbio.data.msa.jaxws">PresetAlignResponse</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/PresetManager.html" title="class in compbio.metadata"><B>PresetManager</B></A>&lt;<A HREF="../compbio/metadata/PresetManager.html" title="type parameter in PresetManager">T</A>&gt; - Class in <A HREF="../compbio/metadata/package-summary.html">compbio.metadata</A><DD>Collection of presets and methods to manipulate them @see <A HREF="../compbio/metadata/Preset.html" title="class in compbio.metadata"><CODE>Preset</CODE></A><DT><A HREF="../compbio/metadata/PresetManager.html#PresetManager()"><B>PresetManager()</B></A> - \r
-Constructor for class compbio.metadata.<A HREF="../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa"><B>Probcons</B></A> - Class in <A HREF="../compbio/runner/msa/package-summary.html">compbio.runner.msa</A><DD>&nbsp;<DT><A HREF="../compbio/runner/msa/Probcons.html#Probcons()"><B>Probcons()</B></A> - \r
-Constructor for class compbio.runner.msa.<A HREF="../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/ws/server/ProbconsWS.html" title="class in compbio.ws.server"><B>ProbconsWS</B></A> - Class in <A HREF="../compbio/ws/server/package-summary.html">compbio.ws.server</A><DD>&nbsp;<DT><A HREF="../compbio/ws/server/ProbconsWS.html#ProbconsWS()"><B>ProbconsWS()</B></A> - \r
-Constructor for class compbio.ws.server.<A HREF="../compbio/ws/server/ProbconsWS.html" title="class in compbio.ws.server">ProbconsWS</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/local/ExecutableWrapper.html#PROC_ERR_FILE"><B>PROC_ERR_FILE</B></A> - \r
-Static variable in class compbio.engine.local.<A HREF="../compbio/engine/local/ExecutableWrapper.html" title="class in compbio.engine.local">ExecutableWrapper</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/local/ExecutableWrapper.html#PROC_OUT_FILE"><B>PROC_OUT_FILE</B></A> - \r
-Static variable in class compbio.engine.local.<A HREF="../compbio/engine/local/ExecutableWrapper.html" title="class in compbio.engine.local">ExecutableWrapper</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence"><B>Program</B></A> - Enum in <A HREF="../compbio/data/sequence/package-summary.html">compbio.data.sequence</A><DD>Programmes that can produce alignments<DT><A HREF="../compbio/engine/ProgressGetter.html" title="class in compbio.engine"><B>ProgressGetter</B></A> - Class in <A HREF="../compbio/engine/package-summary.html">compbio.engine</A><DD>&nbsp;<DT><A HREF="../compbio/engine/ProgressGetter.html#ProgressGetter()"><B>ProgressGetter()</B></A> - \r
-Constructor for class compbio.engine.<A HREF="../compbio/engine/ProgressGetter.html" title="class in compbio.engine">ProgressGetter</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/conf/PropertyHelperManager.html" title="class in compbio.engine.conf"><B>PropertyHelperManager</B></A> - Class in <A HREF="../compbio/engine/conf/package-summary.html">compbio.engine.conf</A><DD>&nbsp;<DT><A HREF="../compbio/engine/conf/PropertyHelperManager.html#PropertyHelperManager()"><B>PropertyHelperManager()</B></A> - \r
-Constructor for class compbio.engine.conf.<A HREF="../compbio/engine/conf/PropertyHelperManager.html" title="class in compbio.engine.conf">PropertyHelperManager</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/pipeline/_jpred/PScore.html" title="class in compbio.pipeline._jpred"><B>PScore</B></A> - Class in <A HREF="../compbio/pipeline/_jpred/package-summary.html">compbio.pipeline._jpred</A><DD>&nbsp;<DT><A HREF="../compbio/pipeline/_jpred/PScore.html#PScore()"><B>PScore()</B></A> - \r
-Constructor for class compbio.pipeline._jpred.<A HREF="../compbio/pipeline/_jpred/PScore.html" title="class in compbio.pipeline._jpred">PScore</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/_impl/PSIBlast.html" title="class in compbio.runner._impl"><B>PSIBlast</B></A> - Class in <A HREF="../compbio/runner/_impl/package-summary.html">compbio.runner._impl</A><DD>&nbsp;<DT><A HREF="../compbio/runner/_impl/PSIBlast.html#PSIBlast(java.lang.String)"><B>PSIBlast(String)</B></A> - \r
-Constructor for class compbio.runner._impl.<A HREF="../compbio/runner/_impl/PSIBlast.html" title="class in compbio.runner._impl">PSIBlast</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/psiblast/PsiBlast.html" title="class in compbio.runner.psiblast"><B>PsiBlast</B></A> - Class in <A HREF="../compbio/runner/psiblast/package-summary.html">compbio.runner.psiblast</A><DD>&nbsp;<DT><A HREF="../compbio/runner/psiblast/PsiBlast.html#PsiBlast()"><B>PsiBlast()</B></A> - \r
-Constructor for class compbio.runner.psiblast.<A HREF="../compbio/runner/psiblast/PsiBlast.html" title="class in compbio.runner.psiblast">PsiBlast</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/FilePuller.html#pull(long)"><B>pull(long)</B></A> - \r
-Method in class compbio.engine.<A HREF="../compbio/engine/FilePuller.html" title="class in compbio.engine">FilePuller</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/ProgressGetter.html#pull(java.lang.String, long)"><B>pull(String, long)</B></A> - \r
-Static method in class compbio.engine.<A HREF="../compbio/engine/ProgressGetter.html" title="class in compbio.engine">ProgressGetter</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/PulledFileCache.html" title="class in compbio.engine"><B>PulledFileCache</B></A> - Class in <A HREF="../compbio/engine/package-summary.html">compbio.engine</A><DD>&nbsp;<DT><A HREF="../compbio/engine/PulledFileCache.html#PulledFileCache()"><B>PulledFileCache()</B></A> - \r
-Constructor for class compbio.engine.<A HREF="../compbio/engine/PulledFileCache.html" title="class in compbio.engine">PulledFileCache</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/jaxws/PullExecStatistics.html" title="class in compbio.data.msa.jaxws"><B>PullExecStatistics</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/PullExecStatistics.html#PullExecStatistics()"><B>PullExecStatistics()</B></A> - \r
-Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/PullExecStatistics.html" title="class in compbio.data.msa.jaxws">PullExecStatistics</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/MsaWS.html#pullExecStatistics(java.lang.String, long)"><B>pullExecStatistics(String, long)</B></A> - \r
-Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>\r
-<DD>Reads 1kb chunk from the statistics file which is specific to a given web
- service from the position.\r
-<DT><A HREF="../compbio/ws/server/ClustalWS.html#pullExecStatistics(java.lang.String, long)"><B>pullExecStatistics(String, long)</B></A> - \r
-Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ClustalWS.html" title="class in compbio.ws.server">ClustalWS</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/ws/server/MafftWS.html#pullExecStatistics(java.lang.String, long)"><B>pullExecStatistics(String, long)</B></A> - \r
-Method in class compbio.ws.server.<A HREF="../compbio/ws/server/MafftWS.html" title="class in compbio.ws.server">MafftWS</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/ws/server/MuscleWS.html#pullExecStatistics(java.lang.String, long)"><B>pullExecStatistics(String, long)</B></A> - \r
-Method in class compbio.ws.server.<A HREF="../compbio/ws/server/MuscleWS.html" title="class in compbio.ws.server">MuscleWS</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/ws/server/ProbconsWS.html#pullExecStatistics(java.lang.String, long)"><B>pullExecStatistics(String, long)</B></A> - \r
-Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ProbconsWS.html" title="class in compbio.ws.server">ProbconsWS</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/ws/server/TcoffeeWS.html#pullExecStatistics(java.lang.String, long)"><B>pullExecStatistics(String, long)</B></A> - \r
-Method in class compbio.ws.server.<A HREF="../compbio/ws/server/TcoffeeWS.html" title="class in compbio.ws.server">TcoffeeWS</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/jaxws/PullExecStatisticsResponse.html" title="class in compbio.data.msa.jaxws"><B>PullExecStatisticsResponse</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/PullExecStatisticsResponse.html#PullExecStatisticsResponse()"><B>PullExecStatisticsResponse()</B></A> - \r
-Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/PullExecStatisticsResponse.html" title="class in compbio.data.msa.jaxws">PullExecStatisticsResponse</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/jaxws/PullFile.html" title="class in compbio.data.msa.jaxws"><B>PullFile</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/PullFile.html#PullFile()"><B>PullFile()</B></A> - \r
-Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/PullFile.html" title="class in compbio.data.msa.jaxws">PullFile</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/ws/server/WSUtil.html#pullFile(java.lang.String, long)"><B>pullFile(String, long)</B></A> - \r
-Static method in class compbio.ws.server.<A HREF="../compbio/ws/server/WSUtil.html" title="class in compbio.ws.server">WSUtil</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/jaxws/PullFileResponse.html" title="class in compbio.data.msa.jaxws"><B>PullFileResponse</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/PullFileResponse.html#PullFileResponse()"><B>PullFileResponse()</B></A> - \r
-Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/PullFileResponse.html" title="class in compbio.data.msa.jaxws">PullFileResponse</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/PulledFileCache.html#put(compbio.engine.FilePuller)"><B>put(FilePuller)</B></A> - \r
-Static method in class compbio.engine.<A HREF="../compbio/engine/PulledFileCache.html" title="class in compbio.engine">PulledFileCache</A>\r
-<DD>This method allows duplicates to be added.\r
-</DL>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Package</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Class</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Use</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Index</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
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-&nbsp;<A HREF="index-15.html"><B>PREV LETTER</B></A>&nbsp;\r
-&nbsp;<A HREF="index-17.html"><B>NEXT LETTER</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../index.html?index-filesindex-16.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="index-16.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
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-</SCRIPT>\r
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-  <A HREF="../allclasses-noframe.html"><B>All Classes</B></A>\r
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-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/index-files/index-17.html b/website/full_javadoc/index-files/index-17.html

deleted file mode 100644 (file)

index 8fddf82..0000000
--- a/website/full_javadoc/index-files/index-17.html
+++ /dev/null
@@ -1,231 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-R-Index\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="R-Index";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Package</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Class</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Use</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Index</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
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-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="index-16.html"><B>PREV LETTER</B></A>&nbsp;\r
-&nbsp;<A HREF="index-18.html"><B>NEXT LETTER</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../index.html?index-filesindex-17.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="index-17.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<A HREF="index-1.html">A</A> <A HREF="index-2.html">B</A> <A HREF="index-3.html">C</A> <A HREF="index-4.html">D</A> <A HREF="index-5.html">E</A> <A HREF="index-6.html">F</A> <A HREF="index-7.html">G</A> <A HREF="index-8.html">H</A> <A HREF="index-9.html">I</A> <A HREF="index-10.html">J</A> <A HREF="index-11.html">K</A> <A HREF="index-12.html">L</A> <A HREF="index-13.html">M</A> <A HREF="index-14.html">N</A> <A HREF="index-15.html">O</A> <A HREF="index-16.html">P</A> <A HREF="index-17.html">R</A> <A HREF="index-18.html">S</A> <A HREF="index-19.html">T</A> <A HREF="index-20.html">U</A> <A HREF="index-21.html">V</A> <A HREF="index-22.html">W</A> <A HREF="index-23.html">_</A> <HR>\r
-<A NAME="_R_"><!-- --></A><H2>\r
-<B>R</B></H2>\r
-<DL>\r
-<DT><A HREF="../compbio/engine/client/RunConfiguration.html#rconfigFile"><B>rconfigFile</B></A> - \r
-Static variable in class compbio.engine.client.<A HREF="../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/conf/RunnerConfigMarshaller.html#read(java.io.InputStream, java.lang.Class)"><B>read(InputStream, Class&lt;V&gt;)</B></A> - \r
-Method in class compbio.engine.conf.<A HREF="../compbio/engine/conf/RunnerConfigMarshaller.html" title="class in compbio.engine.conf">RunnerConfigMarshaller</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/conf/RunnerConfigMarshaller.html#read(java.io.InputStream, java.lang.Class, java.lang.Class...)"><B>read(InputStream, Class&lt;V&gt;, Class&lt;?&gt;...)</B></A> - \r
-Method in class compbio.engine.conf.<A HREF="../compbio/engine/conf/RunnerConfigMarshaller.html" title="class in compbio.engine.conf">RunnerConfigMarshaller</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/conf/RunnerConfigMarshaller.html#readAndValidate(java.io.InputStream, java.lang.Class)"><B>readAndValidate(InputStream, Class&lt;V&gt;)</B></A> - \r
-Method in class compbio.engine.conf.<A HREF="../compbio/engine/conf/RunnerConfigMarshaller.html" title="class in compbio.engine.conf">RunnerConfigMarshaller</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html#readClustalFile(java.io.InputStream)"><B>readClustalFile(InputStream)</B></A> - \r
-Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence">ClustalAlignmentUtil</A>\r
-<DD>Read Clustal formatted alignment.\r
-<DT><A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html#readClustalFile(java.io.File)"><B>readClustalFile(File)</B></A> - \r
-Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence">ClustalAlignmentUtil</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/Util.html#readClustalFile(java.lang.String, java.lang.String)"><B>readClustalFile(String, String)</B></A> - \r
-Static method in class compbio.runner.<A HREF="../compbio/runner/Util.html" title="class in compbio.runner">Util</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/sequence/SequenceUtil.html#readFasta(java.io.InputStream)"><B>readFasta(InputStream)</B></A> - \r
-Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
-<DD>Reads fasta sequences from inStream into the list of FastaSequence
- objects\r
-<DT><A HREF="../compbio/metadata/RunnerConfig.html#removeArgument(java.lang.String)"><B>removeArgument(String)</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
-<DD>Removes the argument <A HREF="../compbio/metadata/Argument.html" title="interface in compbio.metadata"><CODE>Argument</CODE></A> if found.\r
-<DT><A HREF="../compbio/metadata/RunnerConfig.html#removeArgumentByOptionName(java.lang.String)"><B>removeArgumentByOptionName(String)</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
-<DD>Removes the argument\r
-<DT><A HREF="../compbio/engine/cluster/drmaa/ClusterSession.html#removeJob(java.lang.String)"><B>removeJob(String)</B></A> - \r
-Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/ClusterSession.html" title="class in compbio.engine.cluster.drmaa">ClusterSession</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/_impl/BlastAll.html#removeOutput(java.lang.String)"><B>removeOutput(String)</B></A> - \r
-Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/BlastAll.html" title="class in compbio.runner._impl">BlastAll</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/_impl/PSIBlast.html#removeOutput(java.lang.String)"><B>removeOutput(String)</B></A> - \r
-Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/PSIBlast.html" title="class in compbio.runner._impl">PSIBlast</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/CommandBuilder.html#removeParam(java.lang.String)"><B>removeParam(String)</B></A> - \r
-Method in class compbio.engine.client.<A HREF="../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/SubmissionManager.html#removeTask(compbio.engine.client.ConfiguredExecutable)"><B>removeTask(ConfiguredExecutable&lt;?&gt;)</B></A> - \r
-Static method in class compbio.engine.<A HREF="../compbio/engine/SubmissionManager.html" title="class in compbio.engine">SubmissionManager</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/SubmissionManager.html#removeTask(java.lang.String)"><B>removeTask(String)</B></A> - \r
-Static method in class compbio.engine.<A HREF="../compbio/engine/SubmissionManager.html" title="class in compbio.engine">SubmissionManager</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata"><B>ResultNotAvailableException</B></A> - Exception in <A HREF="../compbio/metadata/package-summary.html">compbio.metadata</A><DD>ResultNotAvailableException is thrown wherever the results of the calculation
- cannot be obtained.<DT><A HREF="../compbio/metadata/ResultNotAvailableException.html#ResultNotAvailableException(java.lang.String)"><B>ResultNotAvailableException(String)</B></A> - \r
-Constructor for exception compbio.metadata.<A HREF="../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/ResultNotAvailableException.html#ResultNotAvailableException(java.lang.Throwable)"><B>ResultNotAvailableException(Throwable)</B></A> - \r
-Constructor for exception compbio.metadata.<A HREF="../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/ResultNotAvailableException.html#ResultNotAvailableException(java.lang.String, java.lang.Throwable)"><B>ResultNotAvailableException(String, Throwable)</B></A> - \r
-Constructor for exception compbio.metadata.<A HREF="../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/jaxws/ResultNotAvailableExceptionBean.html" title="class in compbio.data.msa.jaxws"><B>ResultNotAvailableExceptionBean</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>This class was generated by the JAX-WS RI.<DT><A HREF="../compbio/data/msa/jaxws/ResultNotAvailableExceptionBean.html#ResultNotAvailableExceptionBean()"><B>ResultNotAvailableExceptionBean()</B></A> - \r
-Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/ResultNotAvailableExceptionBean.html" title="class in compbio.data.msa.jaxws">ResultNotAvailableExceptionBean</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/_impl/Ronn.html" title="class in compbio.runner._impl"><B>Ronn</B></A> - Class in <A HREF="../compbio/runner/_impl/package-summary.html">compbio.runner._impl</A><DD>&nbsp;<DT><A HREF="../compbio/runner/_impl/Ronn.html#Ronn(java.lang.String)"><B>Ronn(String)</B></A> - \r
-Constructor for class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Ronn.html" title="class in compbio.runner._impl">Ronn</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/_impl/RPSBlast.html" title="class in compbio.runner._impl"><B>RPSBlast</B></A> - Class in <A HREF="../compbio/runner/_impl/package-summary.html">compbio.runner._impl</A><DD>&nbsp;<DT><A HREF="../compbio/runner/_impl/RPSBlast.html#RPSBlast(java.lang.String)"><B>RPSBlast(String)</B></A> - \r
-Constructor for class compbio.runner._impl.<A HREF="../compbio/runner/_impl/RPSBlast.html" title="class in compbio.runner._impl">RPSBlast</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/local/StreamGobbler.html#run()"><B>run()</B></A> - \r
-Method in class compbio.engine.local.<A HREF="../compbio/engine/local/StreamGobbler.html" title="class in compbio.engine.local">StreamGobbler</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client"><B>RunConfiguration</B></A> - Class in <A HREF="../compbio/engine/client/package-summary.html">compbio.engine.client</A><DD>Value class for persisting ConfExecutable instances<DT><A HREF="../compbio/engine/client/RunConfiguration.html#RunConfiguration()"><B>RunConfiguration()</B></A> - \r
-Constructor for class compbio.engine.client.<A HREF="../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/RunConfiguration.html#RunConfiguration(compbio.engine.client.ConfExecutable)"><B>RunConfiguration(ConfExecutable&lt;?&gt;)</B></A> - \r
-Constructor for class compbio.engine.client.<A HREF="../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata"><B>RunnerConfig</B></A>&lt;<A HREF="../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>&gt; - Class in <A HREF="../compbio/metadata/package-summary.html">compbio.metadata</A><DD>The list of <A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata"><CODE>Parameter</CODE></A>s and <A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata"><CODE>Option</CODE></A>s supported by executable.<DT><A HREF="../compbio/metadata/RunnerConfig.html#RunnerConfig()"><B>RunnerConfig()</B></A> - \r
-Constructor for class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/conf/RunnerConfigMarshaller.html" title="class in compbio.engine.conf"><B>RunnerConfigMarshaller</B></A>&lt;<A HREF="../compbio/engine/conf/RunnerConfigMarshaller.html" title="type parameter in RunnerConfigMarshaller">T</A>&gt; - Class in <A HREF="../compbio/engine/conf/package-summary.html">compbio.engine.conf</A><DD>&nbsp;<DT><A HREF="../compbio/engine/conf/RunnerConfigMarshaller.html#RunnerConfigMarshaller(java.lang.Class)"><B>RunnerConfigMarshaller(Class&lt;?&gt;)</B></A> - \r
-Constructor for class compbio.engine.conf.<A HREF="../compbio/engine/conf/RunnerConfigMarshaller.html" title="class in compbio.engine.conf">RunnerConfigMarshaller</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/conf/RunnerConfigMarshaller.html#RunnerConfigMarshaller(java.lang.Class, java.lang.Class...)"><B>RunnerConfigMarshaller(Class&lt;?&gt;, Class&lt;?&gt;...)</B></A> - \r
-Constructor for class compbio.engine.conf.<A HREF="../compbio/engine/conf/RunnerConfigMarshaller.html" title="class in compbio.engine.conf">RunnerConfigMarshaller</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/_impl/Runners.html" title="class in compbio.runner._impl"><B>Runners</B></A> - Class in <A HREF="../compbio/runner/_impl/package-summary.html">compbio.runner._impl</A><DD>&nbsp;<DT><A HREF="../compbio/pipeline/_jpred/Jpred4.html#runPsiBlast()"><B>runPsiBlast()</B></A> - \r
-Method in class compbio.pipeline._jpred.<A HREF="../compbio/pipeline/_jpred/Jpred4.html" title="class in compbio.pipeline._jpred">Jpred4</A>\r
-<DD>&nbsp;\r
-</DL>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Package</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Class</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Use</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Index</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
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-    document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');\r
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diff --git a/website/full_javadoc/index-files/index-18.html b/website/full_javadoc/index-files/index-18.html

deleted file mode 100644 (file)

index 7b39aed..0000000
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-\r
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-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
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-\r
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-\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Class</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Use</FONT>&nbsp;</TD>\r
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-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
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-<DT><A HREF="../compbio/engine/client/ConfiguredExecutable.html#saveRunConfiguration()"><B>saveRunConfiguration()</B></A> - \r
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-<DD>Sets one of the values defined in optionList as default.\r
-<DT><A HREF="../compbio/metadata/Parameter.html#setDefaultValue(java.lang.String)"><B>setDefaultValue(String)</B></A> - \r
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-<DD>&nbsp;\r
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-<DD>&nbsp;\r
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-<DD>&nbsp;\r
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-<DT><A HREF="../compbio/data/msa/jaxws/GetJobStatus.html#setJobId(java.lang.String)"><B>setJobId(String)</B></A> - \r
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-<DD>&nbsp;\r
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-<DT><A HREF="../compbio/engine/client/CommandBuilder.html#setLast(java.lang.String)"><B>setLast(String)</B></A> - \r
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-<DT><A HREF="../compbio/data/msa/jaxws/ResultNotAvailableExceptionBean.html#setMessage(java.lang.String)"><B>setMessage(String)</B></A> - \r
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-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/jaxws/UnsupportedRuntimeExceptionBean.html#setMessage(java.lang.String)"><B>setMessage(String)</B></A> - \r
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-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/jaxws/WrongParameterExceptionBean.html#setMessage(java.lang.String)"><B>setMessage(String)</B></A> - \r
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-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/ValueConstrain.html#setMin(java.lang.String)"><B>setMin(String)</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/Option.html#setName(java.lang.String)"><B>setName(String)</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/Preset.html#setName(java.lang.String)"><B>setName(String)</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/_SkeletalCommandBuilder.html#setName(java.lang.String)"><B>setName(String)</B></A> - \r
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-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/msa/Tcoffee.html#setNCore(int)"><B>setNCore(int)</B></A> - \r
-Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html#setNumberOfSequencesAllowed(int)"><B>setNumberOfSequencesAllowed(int)</B></A> - \r
-Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html" title="class in compbio.data.msa.jaxws">LimitExceededExceptionBean</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/Parameter.html#setOptionName(java.lang.String)"><B>setOptionName(String)</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/Option.html#setOptionNames(java.util.Set)"><B>setOptionNames(Set&lt;String&gt;)</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/Parameter.html#setOptionNames(java.util.Set)"><B>setOptionNames(Set&lt;String&gt;)</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/jaxws/CustomAlign.html#setOptions(java.util.List)"><B>setOptions(List&lt;Option&gt;)</B></A> - \r
-Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/CustomAlign.html" title="class in compbio.data.msa.jaxws">CustomAlign</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/Preset.html#setOptions(java.util.List)"><B>setOptions(List&lt;String&gt;)</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/RunnerConfig.html#setOptions(java.util.List)"><B>setOptions(List&lt;Option&lt;T&gt;&gt;)</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/RunConfiguration.html#setOutput(java.lang.String)"><B>setOutput(String)</B></A> - \r
-Method in class compbio.engine.client.<A HREF="../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/SkeletalExecutable.html#setOutput(java.lang.String)"><B>setOutput(String)</B></A> - \r
-Method in class compbio.engine.client.<A HREF="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/msa/ClustalW.html#setOutput(java.lang.String)"><B>setOutput(String)</B></A> - \r
-Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/msa/Muscle.html#setOutput(java.lang.String)"><B>setOutput(String)</B></A> - \r
-Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/CommandBuilder.html#setParam(java.lang.String)"><B>setParam(String)</B></A> - \r
-Method in class compbio.engine.client.<A HREF="../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/CommandBuilder.html#setParam(java.lang.String, java.lang.String)"><B>setParam(String, String)</B></A> - \r
-Method in class compbio.engine.client.<A HREF="../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/SkeletalExecutable.html#setParameter(java.lang.String)"><B>setParameter(String)</B></A> - \r
-Method in class compbio.engine.client.<A HREF="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/RunConfiguration.html#setParameters(compbio.engine.client.CommandBuilder)"><B>setParameters(CommandBuilder&lt;?&gt;)</B></A> - \r
-Method in class compbio.engine.client.<A HREF="../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/RunnerConfig.html#setParameters(java.util.List)"><B>setParameters(List&lt;Parameter&lt;T&gt;&gt;)</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/CommandBuilder.html#setParams(java.util.List)"><B>setParams(List&lt;String&gt;)</B></A> - \r
-Method in class compbio.engine.client.<A HREF="../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/jaxws/PullExecStatistics.html#setPosition(long)"><B>setPosition(long)</B></A> - \r
-Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/PullExecStatistics.html" title="class in compbio.data.msa.jaxws">PullExecStatistics</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/jaxws/PullFile.html#setPosition(long)"><B>setPosition(long)</B></A> - \r
-Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/PullFile.html" title="class in compbio.data.msa.jaxws">PullFile</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/Parameter.html#setPossibleValues(java.util.Set)"><B>setPossibleValues(Set&lt;String&gt;)</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/jaxws/PresetAlign.html#setPreset(compbio.metadata.Preset)"><B>setPreset(Preset)</B></A> - \r
-Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/PresetAlign.html" title="class in compbio.data.msa.jaxws">PresetAlign</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/jaxws/GetLimit.html#setPresetName(java.lang.String)"><B>setPresetName(String)</B></A> - \r
-Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetLimit.html" title="class in compbio.data.msa.jaxws">GetLimit</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/PresetManager.html#setPresets(java.util.List)"><B>setPresets(List&lt;Preset&lt;T&gt;&gt;)</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/RunnerConfig.html#setPrmSeparator(java.lang.String)"><B>setPrmSeparator(String)</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/_NativeSpecHelper.html#setQueue(java.lang.String)"><B>setQueue(String)</B></A> - \r
-Method in class compbio.runner.<A HREF="../compbio/runner/_NativeSpecHelper.html" title="class in compbio.runner">_NativeSpecHelper</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/Option.html#setRequired(boolean)"><B>setRequired(boolean)</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/_NativeSpecHelper.html#setRequiredMemory(int)"><B>setRequiredMemory(int)</B></A> - \r
-Method in class compbio.runner.<A HREF="../compbio/runner/_NativeSpecHelper.html" title="class in compbio.runner">_NativeSpecHelper</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/jaxws/AlignResponse.html#setReturn(java.lang.String)"><B>setReturn(String)</B></A> - \r
-Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/AlignResponse.html" title="class in compbio.data.msa.jaxws">AlignResponse</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/jaxws/CancelJobResponse.html#setReturn(boolean)"><B>setReturn(boolean)</B></A> - \r
-Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/CancelJobResponse.html" title="class in compbio.data.msa.jaxws">CancelJobResponse</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/jaxws/CustomAlignResponse.html#setReturn(java.lang.String)"><B>setReturn(String)</B></A> - \r
-Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/CustomAlignResponse.html" title="class in compbio.data.msa.jaxws">CustomAlignResponse</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/jaxws/GetJobStatusResponse.html#setReturn(compbio.metadata.JobStatus)"><B>setReturn(JobStatus)</B></A> - \r
-Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetJobStatusResponse.html" title="class in compbio.data.msa.jaxws">GetJobStatusResponse</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/jaxws/GetLimitResponse.html#setReturn(compbio.metadata.Limit)"><B>setReturn(Limit)</B></A> - \r
-Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetLimitResponse.html" title="class in compbio.data.msa.jaxws">GetLimitResponse</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/jaxws/GetLimitsResponse.html#setReturn(compbio.metadata.LimitsManager)"><B>setReturn(LimitsManager)</B></A> - \r
-Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetLimitsResponse.html" title="class in compbio.data.msa.jaxws">GetLimitsResponse</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/jaxws/GetPresetsResponse.html#setReturn(compbio.metadata.PresetManager)"><B>setReturn(PresetManager)</B></A> - \r
-Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetPresetsResponse.html" title="class in compbio.data.msa.jaxws">GetPresetsResponse</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/jaxws/GetProgressResponse.html#setReturn(byte)"><B>setReturn(byte)</B></A> - \r
-Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetProgressResponse.html" title="class in compbio.data.msa.jaxws">GetProgressResponse</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/jaxws/GetResultResponse.html#setReturn(compbio.data.sequence.Alignment)"><B>setReturn(Alignment)</B></A> - \r
-Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetResultResponse.html" title="class in compbio.data.msa.jaxws">GetResultResponse</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/jaxws/GetRunnerOptionsResponse.html#setReturn(compbio.metadata.RunnerConfig)"><B>setReturn(RunnerConfig)</B></A> - \r
-Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetRunnerOptionsResponse.html" title="class in compbio.data.msa.jaxws">GetRunnerOptionsResponse</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/jaxws/PresetAlignResponse.html#setReturn(java.lang.String)"><B>setReturn(String)</B></A> - \r
-Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/PresetAlignResponse.html" title="class in compbio.data.msa.jaxws">PresetAlignResponse</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/jaxws/PullExecStatisticsResponse.html#setReturn(compbio.metadata.ChunkHolder)"><B>setReturn(ChunkHolder)</B></A> - \r
-Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/PullExecStatisticsResponse.html" title="class in compbio.data.msa.jaxws">PullExecStatisticsResponse</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/jaxws/PullFileResponse.html#setReturn(compbio.metadata.ChunkHolder)"><B>setReturn(ChunkHolder)</B></A> - \r
-Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/PullFileResponse.html" title="class in compbio.data.msa.jaxws">PullFileResponse</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/PresetManager.html#setRunnerClassName(java.lang.String)"><B>setRunnerClassName(String)</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/RunnerConfig.html#setRunnerClassName(java.lang.String)"><B>setRunnerClassName(String)</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html#setSequenceLenghtActual(int)"><B>setSequenceLenghtActual(int)</B></A> - \r
-Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html" title="class in compbio.data.msa.jaxws">LimitExceededExceptionBean</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html#setSequenceLenghtAllowed(int)"><B>setSequenceLenghtAllowed(int)</B></A> - \r
-Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html" title="class in compbio.data.msa.jaxws">LimitExceededExceptionBean</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/ValueConstrain.html#setType(compbio.metadata.ValueConstrain.Type)"><B>setType(ValueConstrain.Type)</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/Parameter.html#setValidValue(compbio.metadata.ValueConstrain)"><B>setValidValue(ValueConstrain)</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/Argument.html#setValue(java.lang.String)"><B>setValue(String)</B></A> - \r
-Method in interface compbio.metadata.<A HREF="../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</A>\r
-<DD>Set default values for the parameter or an option\r
-<DT><A HREF="../compbio/metadata/Option.html#setValue(java.lang.String)"><B>setValue(String)</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/ConfExecutable.html#setWorkDirectory(java.lang.String)"><B>setWorkDirectory(String)</B></A> - \r
-Method in class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/ConfiguredExecutable.html#setWorkDirectory(java.lang.String)"><B>setWorkDirectory(String)</B></A> - \r
-Method in interface compbio.engine.client.<A HREF="../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/cluster/dundee/_QueueConstraints.html#SHORT_TIME_LIMIT"><B>SHORT_TIME_LIMIT</B></A> - \r
-Static variable in class compbio.engine.cluster.dundee.<A HREF="../compbio/engine/cluster/dundee/_QueueConstraints.html" title="class in compbio.engine.cluster.dundee">_QueueConstraints</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/local/_TrackingExecutor.html#shutdown()"><B>shutdown()</B></A> - \r
-Method in class compbio.engine.local.<A HREF="../compbio/engine/local/_TrackingExecutor.html" title="class in compbio.engine.local">_TrackingExecutor</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/local/LocalExecutorService.html#shutDown()"><B>shutDown()</B></A> - \r
-Static method in class compbio.engine.local.<A HREF="../compbio/engine/local/LocalExecutorService.html" title="class in compbio.engine.local">LocalExecutorService</A>\r
-<DD>This stops all executing processes via interruption.\r
-<DT><A HREF="../compbio/engine/local/_TrackingExecutor.html#shutdownNow()"><B>shutdownNow()</B></A> - \r
-Method in class compbio.engine.local.<A HREF="../compbio/engine/local/_TrackingExecutor.html" title="class in compbio.engine.local">_TrackingExecutor</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/ws/server/SimpleWSPublisher.html" title="class in compbio.ws.server"><B>SimpleWSPublisher</B></A> - Class in <A HREF="../compbio/ws/server/package-summary.html">compbio.ws.server</A><DD>This class publish a web service.<DT><A HREF="../compbio/ws/server/SimpleWSPublisher.html#SimpleWSPublisher(java.lang.Object, java.lang.String)"><B>SimpleWSPublisher(Object, String)</B></A> - \r
-Constructor for class compbio.ws.server.<A HREF="../compbio/ws/server/SimpleWSPublisher.html" title="class in compbio.ws.server">SimpleWSPublisher</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/CommandBuilder.html#size()"><B>size()</B></A> - \r
-Method in class compbio.engine.client.<A HREF="../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client"><B>SkeletalExecutable</B></A>&lt;<A HREF="../compbio/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>&gt; - Class in <A HREF="../compbio/engine/client/package-summary.html">compbio.engine.client</A><DD>&nbsp;<DT><A HREF="../compbio/engine/client/SkeletalExecutable.html#SkeletalExecutable()"><B>SkeletalExecutable()</B></A> - \r
-Constructor for class compbio.engine.client.<A HREF="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/SkeletalExecutable.html#SkeletalExecutable(java.lang.String)"><B>SkeletalExecutable(String)</B></A> - \r
-Constructor for class compbio.engine.client.<A HREF="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/Util.html#SPACE"><B>SPACE</B></A> - \r
-Static variable in class compbio.runner.<A HREF="../compbio/runner/Util.html" title="class in compbio.runner">Util</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa"><B>StatisticManager</B></A> - Class in <A HREF="../compbio/engine/cluster/drmaa/package-summary.html">compbio.engine.cluster.drmaa</A><DD>&nbsp;<DT><A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html#StatisticManager(org.ggf.drmaa.JobInfo)"><B>StatisticManager(JobInfo)</B></A> - \r
-Constructor for class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/local/StreamGobbler.html" title="class in compbio.engine.local"><B>StreamGobbler</B></A> - Class in <A HREF="../compbio/engine/local/package-summary.html">compbio.engine.local</A><DD>&nbsp;<DT><A HREF="../compbio/engine/SubmissionManager.html" title="class in compbio.engine"><B>SubmissionManager</B></A> - Class in <A HREF="../compbio/engine/package-summary.html">compbio.engine</A><DD>Submit jobs for execution<DT><A HREF="../compbio/engine/local/_TrackingExecutor.html#submit(java.util.concurrent.Callable)"><B>submit(Callable&lt;T&gt;)</B></A> - \r
-Method in class compbio.engine.local.<A HREF="../compbio/engine/local/_TrackingExecutor.html" title="class in compbio.engine.local">_TrackingExecutor</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/AsyncExecutor.html#submitJob(compbio.engine.client.ConfiguredExecutable)"><B>submitJob(ConfiguredExecutable&lt;?&gt;)</B></A> - \r
-Method in interface compbio.engine.<A HREF="../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine">AsyncExecutor</A>\r
-<DD>Submits job for the execution
- Immediate execution is not guaranteed, this method puts the job in the queue.\r
-<DT><A HREF="../compbio/engine/cluster/drmaa/AsyncJobRunner.html#submitJob(compbio.engine.client.ConfiguredExecutable)"><B>submitJob(ConfiguredExecutable&lt;?&gt;)</B></A> - \r
-Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/AsyncJobRunner.html" title="class in compbio.engine.cluster.drmaa">AsyncJobRunner</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/local/AsyncLocalRunner.html#submitJob(compbio.engine.client.ConfiguredExecutable)"><B>submitJob(ConfiguredExecutable&lt;?&gt;)</B></A> - \r
-Method in class compbio.engine.local.<A HREF="../compbio/engine/local/AsyncLocalRunner.html" title="class in compbio.engine.local">AsyncLocalRunner</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/SyncExecutor.html" title="interface in compbio.engine"><B>SyncExecutor</B></A> - Interface in <A HREF="../compbio/engine/package-summary.html">compbio.engine</A><DD>Synchronous executor, is an engine to run the Executable synchronously.</DL>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Use</FONT>&nbsp;</TD>\r
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-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');\r
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diff --git a/website/full_javadoc/index-files/index-19.html b/website/full_javadoc/index-files/index-19.html

deleted file mode 100644 (file)

index 134ddda..0000000
--- a/website/full_javadoc/index-files/index-19.html
+++ /dev/null
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-<!--NewPage-->\r
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-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
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-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
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-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Package</FONT>&nbsp;</TD>\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Use</FONT>&nbsp;</TD>\r
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-  <!--\r
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-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<A HREF="index-1.html">A</A> <A HREF="index-2.html">B</A> <A HREF="index-3.html">C</A> <A HREF="index-4.html">D</A> <A HREF="index-5.html">E</A> <A HREF="index-6.html">F</A> <A HREF="index-7.html">G</A> <A HREF="index-8.html">H</A> <A HREF="index-9.html">I</A> <A HREF="index-10.html">J</A> <A HREF="index-11.html">K</A> <A HREF="index-12.html">L</A> <A HREF="index-13.html">M</A> <A HREF="index-14.html">N</A> <A HREF="index-15.html">O</A> <A HREF="index-16.html">P</A> <A HREF="index-17.html">R</A> <A HREF="index-18.html">S</A> <A HREF="index-19.html">T</A> <A HREF="index-20.html">U</A> <A HREF="index-21.html">V</A> <A HREF="index-22.html">W</A> <A HREF="index-23.html">_</A> <HR>\r
-<A NAME="_T_"><!-- --></A><H2>\r
-<B>T</B></H2>\r
-<DL>\r
-<DT><A HREF="../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa"><B>Tcoffee</B></A> - Class in <A HREF="../compbio/runner/msa/package-summary.html">compbio.runner.msa</A><DD>&nbsp;<DT><A HREF="../compbio/runner/msa/Tcoffee.html#Tcoffee()"><B>Tcoffee()</B></A> - \r
-Constructor for class compbio.runner.msa.<A HREF="../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/ws/server/TcoffeeWS.html" title="class in compbio.ws.server"><B>TcoffeeWS</B></A> - Class in <A HREF="../compbio/ws/server/package-summary.html">compbio.ws.server</A><DD>&nbsp;<DT><A HREF="../compbio/ws/server/TcoffeeWS.html#TcoffeeWS()"><B>TcoffeeWS()</B></A> - \r
-Constructor for class compbio.ws.server.<A HREF="../compbio/ws/server/TcoffeeWS.html" title="class in compbio.ws.server">TcoffeeWS</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html#termSignal()"><B>termSignal()</B></A> - \r
-Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/Option.html#toCommand(java.lang.String)"><B>toCommand(String)</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
-<DD>Convert the option to the command string.\r
-<DT><A HREF="../compbio/metadata/Parameter.html#toCommand(java.lang.String)"><B>toCommand(String)</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/sequence/Alignment.html#toString()"><B>toString()</B></A> - \r
-Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/sequence/FastaSequence.html#toString()"><B>toString()</B></A> - \r
-Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>\r
-<DD>Same as oneLineFasta\r
-<DT><A HREF="../compbio/engine/client/CommandBuilder.html#toString()"><B>toString()</B></A> - \r
-Method in class compbio.engine.client.<A HREF="../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/ConfExecutable.html#toString()"><B>toString()</B></A> - \r
-Method in class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/RunConfiguration.html#toString()"><B>toString()</B></A> - \r
-Method in class compbio.engine.client.<A HREF="../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/SkeletalExecutable.html#toString()"><B>toString()</B></A> - \r
-Method in class compbio.engine.client.<A HREF="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html#toString()"><B>toString()</B></A> - \r
-Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/cluster/dundee/_Queue.html#toString()"><B>toString()</B></A> - \r
-Method in enum compbio.engine.cluster.dundee.<A HREF="../compbio/engine/cluster/dundee/_Queue.html" title="enum in compbio.engine.cluster.dundee">_Queue</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/conf/_Key.html#toString()"><B>toString()</B></A> - \r
-Method in class compbio.engine.conf.<A HREF="../compbio/engine/conf/_Key.html" title="class in compbio.engine.conf">_Key</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/FilePuller.html#toString()"><B>toString()</B></A> - \r
-Method in class compbio.engine.<A HREF="../compbio/engine/FilePuller.html" title="class in compbio.engine">FilePuller</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/Job.html#toString()"><B>toString()</B></A> - \r
-Method in class compbio.engine.<A HREF="../compbio/engine/Job.html" title="class in compbio.engine">Job</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/ChunkHolder.html#toString()"><B>toString()</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/Limit.html#toString()"><B>toString()</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/LimitsManager.html#toString()"><B>toString()</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/Option.html#toString()"><B>toString()</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/Parameter.html#toString()"><B>toString()</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/Preset.html#toString()"><B>toString()</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/PresetManager.html#toString()"><B>toString()</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/RunnerConfig.html#toString()"><B>toString()</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/ValueConstrain.html#toString()"><B>toString()</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/pipeline/_jpred/PScore.html#toString()"><B>toString()</B></A> - \r
-Method in class compbio.pipeline._jpred.<A HREF="../compbio/pipeline/_jpred/PScore.html" title="class in compbio.pipeline._jpred">PScore</A>\r
-<DD>&nbsp;\r
-</DL>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Package</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Class</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Use</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Index</B></FONT>&nbsp;</TD>\r
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-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
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-</TR>\r
-\r
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-  <!--\r
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-    document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');\r
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diff --git a/website/full_javadoc/index-files/index-2.html b/website/full_javadoc/index-files/index-2.html

deleted file mode 100644 (file)

index a82cdfb..0000000
--- a/website/full_javadoc/index-files/index-2.html
+++ /dev/null
@@ -1,148 +0,0 @@
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-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
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-B-Index\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
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-\r
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-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Use</FONT>&nbsp;</TD>\r
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-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
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-</TD>\r
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-  <!--\r
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-<A NAME="skip-navbar_top"></A>\r
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-<A HREF="index-1.html">A</A> <A HREF="index-2.html">B</A> <A HREF="index-3.html">C</A> <A HREF="index-4.html">D</A> <A HREF="index-5.html">E</A> <A HREF="index-6.html">F</A> <A HREF="index-7.html">G</A> <A HREF="index-8.html">H</A> <A HREF="index-9.html">I</A> <A HREF="index-10.html">J</A> <A HREF="index-11.html">K</A> <A HREF="index-12.html">L</A> <A HREF="index-13.html">M</A> <A HREF="index-14.html">N</A> <A HREF="index-15.html">O</A> <A HREF="index-16.html">P</A> <A HREF="index-17.html">R</A> <A HREF="index-18.html">S</A> <A HREF="index-19.html">T</A> <A HREF="index-20.html">U</A> <A HREF="index-21.html">V</A> <A HREF="index-22.html">W</A> <A HREF="index-23.html">_</A> <HR>\r
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-<DD>&nbsp;\r
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-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
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-  <!--\r
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diff --git a/website/full_javadoc/index-files/index-20.html b/website/full_javadoc/index-files/index-20.html

deleted file mode 100644 (file)

index 4e45df6..0000000
--- a/website/full_javadoc/index-files/index-20.html
+++ /dev/null
@@ -1,172 +0,0 @@
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-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
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-\r
-<META NAME="date" CONTENT="2010-02-17">\r
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-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
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-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Package</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Class</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Use</FONT>&nbsp;</TD>\r
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-  </TR>\r
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-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
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-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/sequence/UnknownFileFormatException.html#UnknownFileFormatException(java.lang.Throwable)"><B>UnknownFileFormatException(Throwable)</B></A> - \r
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-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata"><B>UnsupportedRuntimeException</B></A> - Exception in <A HREF="../compbio/metadata/package-summary.html">compbio.metadata</A><DD>Indicates that the server could not execute native executables.<DT><A HREF="../compbio/metadata/UnsupportedRuntimeException.html#UnsupportedRuntimeException(java.lang.String)"><B>UnsupportedRuntimeException(String)</B></A> - \r
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-Constructor for class compbio.engine.client.<A HREF="../compbio/engine/client/Util.html" title="class in compbio.engine.client">Util</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/Util.html" title="class in compbio.runner"><B>Util</B></A> - Class in <A HREF="../compbio/runner/package-summary.html">compbio.runner</A><DD>&nbsp;<DT><A HREF="../compbio/runner/Util.html#Util()"><B>Util()</B></A> - \r
-Constructor for class compbio.runner.<A HREF="../compbio/runner/Util.html" title="class in compbio.runner">Util</A>\r
-<DD>&nbsp;\r
-</DL>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Package</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Class</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Use</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Index</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="index-19.html"><B>PREV LETTER</B></A>&nbsp;\r
-&nbsp;<A HREF="index-21.html"><B>NEXT LETTER</B></A></FONT></TD>\r
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-  <A HREF="../index.html?index-filesindex-20.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="index-20.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
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-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
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-<A HREF="index-1.html">A</A> <A HREF="index-2.html">B</A> <A HREF="index-3.html">C</A> <A HREF="index-4.html">D</A> <A HREF="index-5.html">E</A> <A HREF="index-6.html">F</A> <A HREF="index-7.html">G</A> <A HREF="index-8.html">H</A> <A HREF="index-9.html">I</A> <A HREF="index-10.html">J</A> <A HREF="index-11.html">K</A> <A HREF="index-12.html">L</A> <A HREF="index-13.html">M</A> <A HREF="index-14.html">N</A> <A HREF="index-15.html">O</A> <A HREF="index-16.html">P</A> <A HREF="index-17.html">R</A> <A HREF="index-18.html">S</A> <A HREF="index-19.html">T</A> <A HREF="index-20.html">U</A> <A HREF="index-21.html">V</A> <A HREF="index-22.html">W</A> <A HREF="index-23.html">_</A> <HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/index-files/index-21.html b/website/full_javadoc/index-files/index-21.html

deleted file mode 100644 (file)

index 058a209..0000000
--- a/website/full_javadoc/index-files/index-21.html
+++ /dev/null
@@ -1,232 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-V-Index\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="V-Index";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Package</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Class</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Use</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Index</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="index-20.html"><B>PREV LETTER</B></A>&nbsp;\r
-&nbsp;<A HREF="index-22.html"><B>NEXT LETTER</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../index.html?index-filesindex-21.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="index-21.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<A HREF="index-1.html">A</A> <A HREF="index-2.html">B</A> <A HREF="index-3.html">C</A> <A HREF="index-4.html">D</A> <A HREF="index-5.html">E</A> <A HREF="index-6.html">F</A> <A HREF="index-7.html">G</A> <A HREF="index-8.html">H</A> <A HREF="index-9.html">I</A> <A HREF="index-10.html">J</A> <A HREF="index-11.html">K</A> <A HREF="index-12.html">L</A> <A HREF="index-13.html">M</A> <A HREF="index-14.html">N</A> <A HREF="index-15.html">O</A> <A HREF="index-16.html">P</A> <A HREF="index-17.html">R</A> <A HREF="index-18.html">S</A> <A HREF="index-19.html">T</A> <A HREF="index-20.html">U</A> <A HREF="index-21.html">V</A> <A HREF="index-22.html">W</A> <A HREF="index-23.html">_</A> <HR>\r
-<A NAME="_V_"><!-- --></A><H2>\r
-<B>V</B></H2>\r
-<DL>\r
-<DT><A HREF="../compbio/engine/conf/RunnerConfigMarshaller.html#validate(javax.xml.validation.Validator, java.lang.String)"><B>validate(Validator, String)</B></A> - \r
-Static method in class compbio.engine.conf.<A HREF="../compbio/engine/conf/RunnerConfigMarshaller.html" title="class in compbio.engine.conf">RunnerConfigMarshaller</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/LimitsManager.html#validate(compbio.metadata.PresetManager)"><B>validate(PresetManager&lt;T&gt;)</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>\r
-<DD>Validate Limits\r
-<DT><A HREF="../compbio/metadata/PresetManager.html#validate(compbio.metadata.RunnerConfig)"><B>validate(RunnerConfig&lt;T&gt;)</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>\r
-<DD>Checks whether preset option and parameter are defined in RunnerConfig
- object.\r
-<DT><A HREF="../compbio/metadata/RunnerConfig.html#validate()"><B>validate()</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
-<DD>Validate the arguments\r
-<DT><A HREF="../compbio/engine/client/PathValidator.html#validateDirectory(java.lang.String)"><B>validateDirectory(String)</B></A> - \r
-Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/PathValidator.html" title="class in compbio.engine.client">PathValidator</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/PathValidator.html#validateExecutable(java.lang.String)"><B>validateExecutable(String)</B></A> - \r
-Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/PathValidator.html" title="class in compbio.engine.client">PathValidator</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/ws/server/WSUtil.html#validateFastaInput(java.util.List)"><B>validateFastaInput(List&lt;FastaSequence&gt;)</B></A> - \r
-Static method in class compbio.ws.server.<A HREF="../compbio/ws/server/WSUtil.html" title="class in compbio.ws.server">WSUtil</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/ws/server/WSUtil.html#validateJobId(java.lang.String)"><B>validateJobId(String)</B></A> - \r
-Static method in class compbio.ws.server.<A HREF="../compbio/ws/server/WSUtil.html" title="class in compbio.ws.server">WSUtil</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/PathValidator.html#validatePathNames(java.util.List, java.lang.String)"><B>validatePathNames(List&lt;String&gt;, String)</B></A> - \r
-Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/PathValidator.html" title="class in compbio.engine.client">PathValidator</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/ws/client/Jws2Client.html#validURL(java.lang.String)"><B>validURL(String)</B></A> - \r
-Static method in class compbio.ws.client.<A HREF="../compbio/ws/client/Jws2Client.html" title="class in compbio.ws.client">Jws2Client</A>\r
-<DD>Attempt to construct the URL object from the string\r
-<DT><A HREF="../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata"><B>ValueConstrain</B></A> - Class in <A HREF="../compbio/metadata/package-summary.html">compbio.metadata</A><DD>The type and the lower and upper boundaries for numerical value.<DT><A HREF="../compbio/metadata/ValueConstrain.html#ValueConstrain()"><B>ValueConstrain()</B></A> - \r
-Constructor for class compbio.metadata.<A HREF="../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/ValueConstrain.Type.html" title="enum in compbio.metadata"><B>ValueConstrain.Type</B></A> - Enum in <A HREF="../compbio/metadata/package-summary.html">compbio.metadata</A><DD>&nbsp;<DT><A HREF="../compbio/data/_structure/JnetAnnotation.html#valueOf(java.lang.String)"><B>valueOf(String)</B></A> - \r
-Static method in enum compbio.data._structure.<A HREF="../compbio/data/_structure/JnetAnnotation.html" title="enum in compbio.data._structure">JnetAnnotation</A>\r
-<DD>Returns the enum constant of this type with the specified name.\r
-<DT><A HREF="../compbio/data/_structure/JpredAnnotation.html#valueOf(java.lang.String)"><B>valueOf(String)</B></A> - \r
-Static method in enum compbio.data._structure.<A HREF="../compbio/data/_structure/JpredAnnotation.html" title="enum in compbio.data._structure">JpredAnnotation</A>\r
-<DD>Returns the enum constant of this type with the specified name.\r
-<DT><A HREF="../compbio/data/sequence/Program.html#valueOf(java.lang.String)"><B>valueOf(String)</B></A> - \r
-Static method in enum compbio.data.sequence.<A HREF="../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A>\r
-<DD>Returns the enum constant of this type with the specified name.\r
-<DT><A HREF="../compbio/engine/client/Executable.ExecProvider.html#valueOf(java.lang.String)"><B>valueOf(String)</B></A> - \r
-Static method in enum compbio.engine.client.<A HREF="../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>\r
-<DD>Returns the enum constant of this type with the specified name.\r
-<DT><A HREF="../compbio/engine/cluster/dundee/_Queue.html#valueOf(java.lang.String)"><B>valueOf(String)</B></A> - \r
-Static method in enum compbio.engine.cluster.dundee.<A HREF="../compbio/engine/cluster/dundee/_Queue.html" title="enum in compbio.engine.cluster.dundee">_Queue</A>\r
-<DD>Returns the enum constant of this type with the specified name.\r
-<DT><A HREF="../compbio/metadata/JobStatus.html#valueOf(java.lang.String)"><B>valueOf(String)</B></A> - \r
-Static method in enum compbio.metadata.<A HREF="../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A>\r
-<DD>Returns the enum constant of this type with the specified name.\r
-<DT><A HREF="../compbio/metadata/ValueConstrain.Type.html#valueOf(java.lang.String)"><B>valueOf(String)</B></A> - \r
-Static method in enum compbio.metadata.<A HREF="../compbio/metadata/ValueConstrain.Type.html" title="enum in compbio.metadata">ValueConstrain.Type</A>\r
-<DD>Returns the enum constant of this type with the specified name.\r
-<DT><A HREF="../compbio/ws/client/Jws2Client.Services.html#valueOf(java.lang.String)"><B>valueOf(String)</B></A> - \r
-Static method in enum compbio.ws.client.<A HREF="../compbio/ws/client/Jws2Client.Services.html" title="enum in compbio.ws.client">Jws2Client.Services</A>\r
-<DD>Returns the enum constant of this type with the specified name.\r
-<DT><A HREF="../compbio/data/_structure/JnetAnnotation.html#values()"><B>values()</B></A> - \r
-Static method in enum compbio.data._structure.<A HREF="../compbio/data/_structure/JnetAnnotation.html" title="enum in compbio.data._structure">JnetAnnotation</A>\r
-<DD>Returns an array containing the constants of this enum type, in
-the order they are declared.\r
-<DT><A HREF="../compbio/data/_structure/JpredAnnotation.html#values()"><B>values()</B></A> - \r
-Static method in enum compbio.data._structure.<A HREF="../compbio/data/_structure/JpredAnnotation.html" title="enum in compbio.data._structure">JpredAnnotation</A>\r
-<DD>Returns an array containing the constants of this enum type, in
-the order they are declared.\r
-<DT><A HREF="../compbio/data/sequence/Program.html#values()"><B>values()</B></A> - \r
-Static method in enum compbio.data.sequence.<A HREF="../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A>\r
-<DD>Returns an array containing the constants of this enum type, in
-the order they are declared.\r
-<DT><A HREF="../compbio/engine/client/Executable.ExecProvider.html#values()"><B>values()</B></A> - \r
-Static method in enum compbio.engine.client.<A HREF="../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>\r
-<DD>Returns an array containing the constants of this enum type, in
-the order they are declared.\r
-<DT><A HREF="../compbio/engine/cluster/dundee/_Queue.html#values()"><B>values()</B></A> - \r
-Static method in enum compbio.engine.cluster.dundee.<A HREF="../compbio/engine/cluster/dundee/_Queue.html" title="enum in compbio.engine.cluster.dundee">_Queue</A>\r
-<DD>Returns an array containing the constants of this enum type, in
-the order they are declared.\r
-<DT><A HREF="../compbio/metadata/JobStatus.html#values()"><B>values()</B></A> - \r
-Static method in enum compbio.metadata.<A HREF="../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A>\r
-<DD>Returns an array containing the constants of this enum type, in
-the order they are declared.\r
-<DT><A HREF="../compbio/metadata/ValueConstrain.Type.html#values()"><B>values()</B></A> - \r
-Static method in enum compbio.metadata.<A HREF="../compbio/metadata/ValueConstrain.Type.html" title="enum in compbio.metadata">ValueConstrain.Type</A>\r
-<DD>Returns an array containing the constants of this enum type, in
-the order they are declared.\r
-<DT><A HREF="../compbio/ws/client/Jws2Client.Services.html#values()"><B>values()</B></A> - \r
-Static method in enum compbio.ws.client.<A HREF="../compbio/ws/client/Jws2Client.Services.html" title="enum in compbio.ws.client">Jws2Client.Services</A>\r
-<DD>Returns an array containing the constants of this enum type, in
-the order they are declared.\r
-</DL>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Package</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Class</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Use</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Index</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="index-20.html"><B>PREV LETTER</B></A>&nbsp;\r
-&nbsp;<A HREF="index-22.html"><B>NEXT LETTER</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../index.html?index-filesindex-21.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="index-21.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
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-<A HREF="index-1.html">A</A> <A HREF="index-2.html">B</A> <A HREF="index-3.html">C</A> <A HREF="index-4.html">D</A> <A HREF="index-5.html">E</A> <A HREF="index-6.html">F</A> <A HREF="index-7.html">G</A> <A HREF="index-8.html">H</A> <A HREF="index-9.html">I</A> <A HREF="index-10.html">J</A> <A HREF="index-11.html">K</A> <A HREF="index-12.html">L</A> <A HREF="index-13.html">M</A> <A HREF="index-14.html">N</A> <A HREF="index-15.html">O</A> <A HREF="index-16.html">P</A> <A HREF="index-17.html">R</A> <A HREF="index-18.html">S</A> <A HREF="index-19.html">T</A> <A HREF="index-20.html">U</A> <A HREF="index-21.html">V</A> <A HREF="index-22.html">W</A> <A HREF="index-23.html">_</A> <HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/index-files/index-22.html b/website/full_javadoc/index-files/index-22.html

deleted file mode 100644 (file)

index 8537653..0000000
--- a/website/full_javadoc/index-files/index-22.html
+++ /dev/null
@@ -1,224 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:51 GMT 2010 -->\r
-<TITLE>\r
-W-Index\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="W-Index";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Package</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Class</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Use</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Index</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="index-21.html"><B>PREV LETTER</B></A>&nbsp;\r
-&nbsp;<A HREF="index-23.html"><B>NEXT LETTER</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../index.html?index-filesindex-22.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="index-22.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<A HREF="index-1.html">A</A> <A HREF="index-2.html">B</A> <A HREF="index-3.html">C</A> <A HREF="index-4.html">D</A> <A HREF="index-5.html">E</A> <A HREF="index-6.html">F</A> <A HREF="index-7.html">G</A> <A HREF="index-8.html">H</A> <A HREF="index-9.html">I</A> <A HREF="index-10.html">J</A> <A HREF="index-11.html">K</A> <A HREF="index-12.html">L</A> <A HREF="index-13.html">M</A> <A HREF="index-14.html">N</A> <A HREF="index-15.html">O</A> <A HREF="index-16.html">P</A> <A HREF="index-17.html">R</A> <A HREF="index-18.html">S</A> <A HREF="index-19.html">T</A> <A HREF="index-20.html">U</A> <A HREF="index-21.html">V</A> <A HREF="index-22.html">W</A> <A HREF="index-23.html">_</A> <HR>\r
-<A NAME="_W_"><!-- --></A><H2>\r
-<B>W</B></H2>\r
-<DL>\r
-<DT><A HREF="../compbio/engine/FilePuller.html#waitForFile(long)"><B>waitForFile(long)</B></A> - \r
-Method in class compbio.engine.<A HREF="../compbio/engine/FilePuller.html" title="class in compbio.engine">FilePuller</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/cluster/drmaa/ClusterSession.html#waitForJob(java.lang.String)"><B>waitForJob(String)</B></A> - \r
-Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/ClusterSession.html" title="class in compbio.engine.cluster.drmaa">ClusterSession</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/cluster/drmaa/ClusterSession.html#waitForJob(java.lang.String, long)"><B>waitForJob(String, long)</B></A> - \r
-Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/ClusterSession.html" title="class in compbio.engine.cluster.drmaa">ClusterSession</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/cluster/drmaa/ClusterUtil.html#waitForResult(compbio.engine.cluster.drmaa.ClusterSession, java.lang.String)"><B>waitForResult(ClusterSession, String)</B></A> - \r
-Static method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/ClusterUtil.html" title="class in compbio.engine.cluster.drmaa">ClusterUtil</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/cluster/drmaa/JobRunner.html#waitForResult()"><B>waitForResult()</B></A> - \r
-Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/JobRunner.html" title="class in compbio.engine.cluster.drmaa">JobRunner</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/local/LocalRunner.html#waitForResult()"><B>waitForResult()</B></A> - \r
-Method in class compbio.engine.local.<A HREF="../compbio/engine/local/LocalRunner.html" title="class in compbio.engine.local">LocalRunner</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/SyncExecutor.html#waitForResult()"><B>waitForResult()</B></A> - \r
-Method in interface compbio.engine.<A HREF="../compbio/engine/SyncExecutor.html" title="interface in compbio.engine">SyncExecutor</A>\r
-<DD>Call to this method block for as long as it is required for an executable to finish its job.\r
-<DT><A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html#wasAborted()"><B>wasAborted()</B></A> - \r
-Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/sequence/SequenceUtil.html#WHITE_SPACE"><B>WHITE_SPACE</B></A> - \r
-Static variable in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
-<DD>A whitespace character: [\t\n\x0B\f\r]\r
-<DT><A HREF="../compbio/engine/client/RunConfiguration.html#write(compbio.engine.client.RunConfiguration)"><B>write(RunConfiguration)</B></A> - \r
-Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/conf/RunnerConfigMarshaller.html#write(java.lang.Object, java.io.OutputStream)"><B>write(Object, OutputStream)</B></A> - \r
-Method in class compbio.engine.conf.<A HREF="../compbio/engine/conf/RunnerConfigMarshaller.html" title="class in compbio.engine.conf">RunnerConfigMarshaller</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/conf/RunnerConfigMarshaller.html#writeAndValidate(java.lang.Object, java.lang.String, java.io.OutputStream)"><B>writeAndValidate(Object, String, OutputStream)</B></A> - \r
-Method in class compbio.engine.conf.<A HREF="../compbio/engine/conf/RunnerConfigMarshaller.html" title="class in compbio.engine.conf">RunnerConfigMarshaller</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html#writeClustalAlignment(java.io.OutputStream, compbio.data.sequence.Alignment)"><B>writeClustalAlignment(OutputStream, Alignment)</B></A> - \r
-Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence">ClustalAlignmentUtil</A>\r
-<DD>Write Clustal formatted alignment Limitations: does not record the
- consensus.\r
-<DT><A HREF="../compbio/data/sequence/SequenceUtil.html#writeFasta(java.io.OutputStream, java.util.List, int)"><B>writeFasta(OutputStream, List&lt;FastaSequence&gt;, int)</B></A> - \r
-Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
-<DD>Writes list of FastaSequeces into the outstream formatting the sequence
- so that it contains width chars on each line\r
-<DT><A HREF="../compbio/data/sequence/SequenceUtil.html#writeFasta(java.io.OutputStream, java.util.List)"><B>writeFasta(OutputStream, List&lt;FastaSequence&gt;)</B></A> - \r
-Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
-<DD>Writes FastaSequence in the file, each sequence will take one line only\r
-<DT><A HREF="../compbio/engine/client/Util.html#writeFile(java.lang.String, java.lang.String, java.lang.String, boolean)"><B>writeFile(String, String, String, boolean)</B></A> - \r
-Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/Util.html" title="class in compbio.engine.client">Util</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/Util.html#writeInput(java.util.List, compbio.engine.client.ConfiguredExecutable)"><B>writeInput(List&lt;FastaSequence&gt;, ConfiguredExecutable&lt;?&gt;)</B></A> - \r
-Static method in class compbio.runner.<A HREF="../compbio/runner/Util.html" title="class in compbio.runner">Util</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/Util.html#writeMarker(java.lang.String, compbio.metadata.JobStatus)"><B>writeMarker(String, JobStatus)</B></A> - \r
-Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/Util.html" title="class in compbio.engine.client">Util</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/Util.html#writeStatFile(java.lang.String, java.lang.String)"><B>writeStatFile(String, String)</B></A> - \r
-Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/Util.html" title="class in compbio.engine.client">Util</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata"><B>WrongParameterException</B></A> - Exception in <A HREF="../compbio/metadata/package-summary.html">compbio.metadata</A><DD>WrongParameterException is thrown wherever the <A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata"><CODE>RunnerConfig</CODE></A> object
- does not match the actual runnable or then attempting to set the value of
- <A HREF="../compbio/metadata/Argument.html" title="interface in compbio.metadata"><CODE>Argument</CODE></A> to invalid value.<DT><A HREF="../compbio/metadata/WrongParameterException.html#WrongParameterException(compbio.metadata.Option)"><B>WrongParameterException(Option&lt;?&gt;)</B></A> - \r
-Constructor for exception compbio.metadata.<A HREF="../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/WrongParameterException.html#WrongParameterException(java.lang.String)"><B>WrongParameterException(String)</B></A> - \r
-Constructor for exception compbio.metadata.<A HREF="../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/WrongParameterException.html#WrongParameterException(java.lang.Throwable)"><B>WrongParameterException(Throwable)</B></A> - \r
-Constructor for exception compbio.metadata.<A HREF="../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/WrongParameterException.html#WrongParameterException(java.lang.String, java.lang.Throwable)"><B>WrongParameterException(String, Throwable)</B></A> - \r
-Constructor for exception compbio.metadata.<A HREF="../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/jaxws/WrongParameterExceptionBean.html" title="class in compbio.data.msa.jaxws"><B>WrongParameterExceptionBean</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>This class was generated by the JAX-WS RI.<DT><A HREF="../compbio/data/msa/jaxws/WrongParameterExceptionBean.html#WrongParameterExceptionBean()"><B>WrongParameterExceptionBean()</B></A> - \r
-Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/WrongParameterExceptionBean.html" title="class in compbio.data.msa.jaxws">WrongParameterExceptionBean</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/ws/client/WSTester.html" title="class in compbio.ws.client"><B>WSTester</B></A> - Class in <A HREF="../compbio/ws/client/package-summary.html">compbio.ws.client</A><DD>Class for testing web services<DT><A HREF="../compbio/ws/client/WSTester.html#WSTester()"><B>WSTester()</B></A> - \r
-Constructor for class compbio.ws.client.<A HREF="../compbio/ws/client/WSTester.html" title="class in compbio.ws.client">WSTester</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/ws/server/WSUtil.html" title="class in compbio.ws.server"><B>WSUtil</B></A> - Class in <A HREF="../compbio/ws/server/package-summary.html">compbio.ws.server</A><DD>&nbsp;<DT><A HREF="../compbio/ws/server/WSUtil.html#WSUtil()"><B>WSUtil()</B></A> - \r
-Constructor for class compbio.ws.server.<A HREF="../compbio/ws/server/WSUtil.html" title="class in compbio.ws.server">WSUtil</A>\r
-<DD>&nbsp;\r
-</DL>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Package</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Class</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Use</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Index</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
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-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="index-21.html"><B>PREV LETTER</B></A>&nbsp;\r
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-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../index.html?index-filesindex-22.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="index-22.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
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-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<A HREF="index-1.html">A</A> <A HREF="index-2.html">B</A> <A HREF="index-3.html">C</A> <A HREF="index-4.html">D</A> <A HREF="index-5.html">E</A> <A HREF="index-6.html">F</A> <A HREF="index-7.html">G</A> <A HREF="index-8.html">H</A> <A HREF="index-9.html">I</A> <A HREF="index-10.html">J</A> <A HREF="index-11.html">K</A> <A HREF="index-12.html">L</A> <A HREF="index-13.html">M</A> <A HREF="index-14.html">N</A> <A HREF="index-15.html">O</A> <A HREF="index-16.html">P</A> <A HREF="index-17.html">R</A> <A HREF="index-18.html">S</A> <A HREF="index-19.html">T</A> <A HREF="index-20.html">U</A> <A HREF="index-21.html">V</A> <A HREF="index-22.html">W</A> <A HREF="index-23.html">_</A> <HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/index-files/index-23.html b/website/full_javadoc/index-files/index-23.html

deleted file mode 100644 (file)

index 88e7b27..0000000
--- a/website/full_javadoc/index-files/index-23.html
+++ /dev/null
@@ -1,168 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:51 GMT 2010 -->\r
-<TITLE>\r
-_-Index\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
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-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="_-Index";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Package</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Class</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Use</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
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-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="index-22.html"><B>PREV LETTER</B></A>&nbsp;\r
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-  <A HREF="../index.html?index-filesindex-23.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="index-23.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<A HREF="index-1.html">A</A> <A HREF="index-2.html">B</A> <A HREF="index-3.html">C</A> <A HREF="index-4.html">D</A> <A HREF="index-5.html">E</A> <A HREF="index-6.html">F</A> <A HREF="index-7.html">G</A> <A HREF="index-8.html">H</A> <A HREF="index-9.html">I</A> <A HREF="index-10.html">J</A> <A HREF="index-11.html">K</A> <A HREF="index-12.html">L</A> <A HREF="index-13.html">M</A> <A HREF="index-14.html">N</A> <A HREF="index-15.html">O</A> <A HREF="index-16.html">P</A> <A HREF="index-17.html">R</A> <A HREF="index-18.html">S</A> <A HREF="index-19.html">T</A> <A HREF="index-20.html">U</A> <A HREF="index-21.html">V</A> <A HREF="index-22.html">W</A> <A HREF="index-23.html">_</A> <HR>\r
-<A NAME="___"><!-- --></A><H2>\r
-<B>_</B></H2>\r
-<DL>\r
-<DT><A HREF="../compbio/engine/cluster/drmaa/_DrmaaExample.html" title="class in compbio.engine.cluster.drmaa"><B>_DrmaaExample</B></A> - Class in <A HREF="../compbio/engine/cluster/drmaa/package-summary.html">compbio.engine.cluster.drmaa</A><DD>&nbsp;<DT><A HREF="../compbio/engine/cluster/drmaa/_DrmaaExample.html#_DrmaaExample()"><B>_DrmaaExample()</B></A> - \r
-Constructor for class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/_DrmaaExample.html" title="class in compbio.engine.cluster.drmaa">_DrmaaExample</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/cluster/drmaa/_JobStatus.html" title="class in compbio.engine.cluster.drmaa"><B>_JobStatus</B></A> - Class in <A HREF="../compbio/engine/cluster/drmaa/package-summary.html">compbio.engine.cluster.drmaa</A><DD>&nbsp;<DT><A HREF="../compbio/engine/cluster/drmaa/_JobStatus.html#_JobStatus()"><B>_JobStatus()</B></A> - \r
-Constructor for class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/_JobStatus.html" title="class in compbio.engine.cluster.drmaa">_JobStatus</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/_jpred/_Jpred.html" title="class in compbio.runner._jpred"><B>_Jpred</B></A> - Class in <A HREF="../compbio/runner/_jpred/package-summary.html">compbio.runner._jpred</A><DD>&nbsp;<DT><A HREF="../compbio/runner/_jpred/_Jpred.html#_Jpred()"><B>_Jpred()</B></A> - \r
-Constructor for class compbio.runner._jpred.<A HREF="../compbio/runner/_jpred/_Jpred.html" title="class in compbio.runner._jpred">_Jpred</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/conf/_Key.html" title="class in compbio.engine.conf"><B>_Key</B></A> - Class in <A HREF="../compbio/engine/conf/package-summary.html">compbio.engine.conf</A><DD>&nbsp;<DT><A HREF="../compbio/engine/conf/_Key.html#_Key(java.lang.Class)"><B>_Key(Class&lt;?&gt;)</B></A> - \r
-Constructor for class compbio.engine.conf.<A HREF="../compbio/engine/conf/_Key.html" title="class in compbio.engine.conf">_Key</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/_NativeSpecHelper.html" title="class in compbio.runner"><B>_NativeSpecHelper</B></A> - Class in <A HREF="../compbio/runner/package-summary.html">compbio.runner</A><DD>&nbsp;<DT><A HREF="../compbio/runner/_NativeSpecHelper.html#_NativeSpecHelper(int)"><B>_NativeSpecHelper(int)</B></A> - \r
-Constructor for class compbio.runner.<A HREF="../compbio/runner/_NativeSpecHelper.html" title="class in compbio.runner">_NativeSpecHelper</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/_NativeSpecHelper.html#_NativeSpecHelper(int, int)"><B>_NativeSpecHelper(int, int)</B></A> - \r
-Constructor for class compbio.runner.<A HREF="../compbio/runner/_NativeSpecHelper.html" title="class in compbio.runner">_NativeSpecHelper</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/cluster/dundee/_Queue.html" title="enum in compbio.engine.cluster.dundee"><B>_Queue</B></A> - Enum in <A HREF="../compbio/engine/cluster/dundee/package-summary.html">compbio.engine.cluster.dundee</A><DD>&nbsp;<DT><A HREF="../compbio/engine/cluster/dundee/_QueueConstraints.html" title="class in compbio.engine.cluster.dundee"><B>_QueueConstraints</B></A> - Class in <A HREF="../compbio/engine/cluster/dundee/package-summary.html">compbio.engine.cluster.dundee</A><DD>&nbsp;<DT><A HREF="../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner"><B>_SkeletalCommandBuilder</B></A> - Class in <A HREF="../compbio/runner/package-summary.html">compbio.runner</A><DD>&nbsp;<DT><A HREF="../compbio/runner/_SkeletalCommandBuilder.html#_SkeletalCommandBuilder()"><B>_SkeletalCommandBuilder()</B></A> - \r
-Constructor for class compbio.runner.<A HREF="../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/local/_TrackingExecutor.html" title="class in compbio.engine.local"><B>_TrackingExecutor</B></A> - Class in <A HREF="../compbio/engine/local/package-summary.html">compbio.engine.local</A><DD>This executor extends standard Java ExecutorService by adding the method to
- obtain all Runnables which were running and did not complete upon executor
- termination.<DT><A HREF="../compbio/engine/local/_TrackingExecutor.html#_TrackingExecutor(java.util.concurrent.ExecutorService)"><B>_TrackingExecutor(ExecutorService)</B></A> - \r
-Constructor for class compbio.engine.local.<A HREF="../compbio/engine/local/_TrackingExecutor.html" title="class in compbio.engine.local">_TrackingExecutor</A>\r
-<DD>&nbsp;\r
-</DL>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Package</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Class</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Use</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Index</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
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-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="index-22.html"><B>PREV LETTER</B></A>&nbsp;\r
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-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../index.html?index-filesindex-23.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="index-23.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<A HREF="index-1.html">A</A> <A HREF="index-2.html">B</A> <A HREF="index-3.html">C</A> <A HREF="index-4.html">D</A> <A HREF="index-5.html">E</A> <A HREF="index-6.html">F</A> <A HREF="index-7.html">G</A> <A HREF="index-8.html">H</A> <A HREF="index-9.html">I</A> <A HREF="index-10.html">J</A> <A HREF="index-11.html">K</A> <A HREF="index-12.html">L</A> <A HREF="index-13.html">M</A> <A HREF="index-14.html">N</A> <A HREF="index-15.html">O</A> <A HREF="index-16.html">P</A> <A HREF="index-17.html">R</A> <A HREF="index-18.html">S</A> <A HREF="index-19.html">T</A> <A HREF="index-20.html">U</A> <A HREF="index-21.html">V</A> <A HREF="index-22.html">W</A> <A HREF="index-23.html">_</A> <HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/index-files/index-3.html b/website/full_javadoc/index-files/index-3.html

deleted file mode 100644 (file)

index 02682d7..0000000
--- a/website/full_javadoc/index-files/index-3.html
+++ /dev/null
@@ -1,318 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-C-Index\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="C-Index";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Package</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Class</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Use</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Index</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="index-2.html"><B>PREV LETTER</B></A>&nbsp;\r
-&nbsp;<A HREF="index-4.html"><B>NEXT LETTER</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../index.html?index-filesindex-3.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="index-3.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<A HREF="index-1.html">A</A> <A HREF="index-2.html">B</A> <A HREF="index-3.html">C</A> <A HREF="index-4.html">D</A> <A HREF="index-5.html">E</A> <A HREF="index-6.html">F</A> <A HREF="index-7.html">G</A> <A HREF="index-8.html">H</A> <A HREF="index-9.html">I</A> <A HREF="index-10.html">J</A> <A HREF="index-11.html">K</A> <A HREF="index-12.html">L</A> <A HREF="index-13.html">M</A> <A HREF="index-14.html">N</A> <A HREF="index-15.html">O</A> <A HREF="index-16.html">P</A> <A HREF="index-17.html">R</A> <A HREF="index-18.html">S</A> <A HREF="index-19.html">T</A> <A HREF="index-20.html">U</A> <A HREF="index-21.html">V</A> <A HREF="index-22.html">W</A> <A HREF="index-23.html">_</A> <HR>\r
-<A NAME="_C_"><!-- --></A><H2>\r
-<B>C</B></H2>\r
-<DL>\r
-<DT><A HREF="../compbio/engine/local/ExecutableWrapper.html#call()"><B>call()</B></A> - \r
-Method in class compbio.engine.local.<A HREF="../compbio/engine/local/ExecutableWrapper.html" title="class in compbio.engine.local">ExecutableWrapper</A>\r
-<DD>It is vital that output and error streams are captured immediately for
- this call() to succeed.\r
-<DT><A HREF="../compbio/engine/local/LocalExecutorService.html#canAcceptMoreWork()"><B>canAcceptMoreWork()</B></A> - \r
-Method in class compbio.engine.local.<A HREF="../compbio/engine/local/LocalExecutorService.html" title="class in compbio.engine.local">LocalExecutorService</A>\r
-<DD>If the Executor queue is empty\r
-<DT><A HREF="../compbio/data/msa/jaxws/CancelJob.html" title="class in compbio.data.msa.jaxws"><B>CancelJob</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/CancelJob.html#CancelJob()"><B>CancelJob()</B></A> - \r
-Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/CancelJob.html" title="class in compbio.data.msa.jaxws">CancelJob</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/MsaWS.html#cancelJob(java.lang.String)"><B>cancelJob(String)</B></A> - \r
-Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>\r
-<DD>Stop running job but leave its output untouched\r
-<DT><A HREF="../compbio/engine/AsyncExecutor.html#cancelJob(java.lang.String)"><B>cancelJob(String)</B></A> - \r
-Method in interface compbio.engine.<A HREF="../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine">AsyncExecutor</A>\r
-<DD>Stop running job.\r
-<DT><A HREF="../compbio/engine/cluster/drmaa/AsyncJobRunner.html#cancelJob(java.lang.String)"><B>cancelJob(String)</B></A> - \r
-Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/AsyncJobRunner.html" title="class in compbio.engine.cluster.drmaa">AsyncJobRunner</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/cluster/drmaa/ClusterUtil.html#cancelJob(java.lang.String, compbio.engine.cluster.drmaa.ClusterSession)"><B>cancelJob(String, ClusterSession)</B></A> - \r
-Static method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/ClusterUtil.html" title="class in compbio.engine.cluster.drmaa">ClusterUtil</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/cluster/drmaa/JobRunner.html#cancelJob()"><B>cancelJob()</B></A> - \r
-Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/JobRunner.html" title="class in compbio.engine.cluster.drmaa">JobRunner</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/local/AsyncLocalRunner.html#cancelJob(java.lang.String)"><B>cancelJob(String)</B></A> - \r
-Method in class compbio.engine.local.<A HREF="../compbio/engine/local/AsyncLocalRunner.html" title="class in compbio.engine.local">AsyncLocalRunner</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/local/LocalEngineUtil.html#cancelJob(java.util.concurrent.Future, java.lang.String)"><B>cancelJob(Future&lt;ConfiguredExecutable&lt;?&gt;&gt;, String)</B></A> - \r
-Static method in class compbio.engine.local.<A HREF="../compbio/engine/local/LocalEngineUtil.html" title="class in compbio.engine.local">LocalEngineUtil</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/local/LocalRunner.html#cancelJob()"><B>cancelJob()</B></A> - \r
-Method in class compbio.engine.local.<A HREF="../compbio/engine/local/LocalRunner.html" title="class in compbio.engine.local">LocalRunner</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/SyncExecutor.html#cancelJob()"><B>cancelJob()</B></A> - \r
-Method in interface compbio.engine.<A HREF="../compbio/engine/SyncExecutor.html" title="interface in compbio.engine">SyncExecutor</A>\r
-<DD>Stops running job.\r
-<DT><A HREF="../compbio/ws/server/ClustalWS.html#cancelJob(java.lang.String)"><B>cancelJob(String)</B></A> - \r
-Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ClustalWS.html" title="class in compbio.ws.server">ClustalWS</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/ws/server/MafftWS.html#cancelJob(java.lang.String)"><B>cancelJob(String)</B></A> - \r
-Method in class compbio.ws.server.<A HREF="../compbio/ws/server/MafftWS.html" title="class in compbio.ws.server">MafftWS</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/ws/server/MuscleWS.html#cancelJob(java.lang.String)"><B>cancelJob(String)</B></A> - \r
-Method in class compbio.ws.server.<A HREF="../compbio/ws/server/MuscleWS.html" title="class in compbio.ws.server">MuscleWS</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/ws/server/ProbconsWS.html#cancelJob(java.lang.String)"><B>cancelJob(String)</B></A> - \r
-Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ProbconsWS.html" title="class in compbio.ws.server">ProbconsWS</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/ws/server/TcoffeeWS.html#cancelJob(java.lang.String)"><B>cancelJob(String)</B></A> - \r
-Method in class compbio.ws.server.<A HREF="../compbio/ws/server/TcoffeeWS.html" title="class in compbio.ws.server">TcoffeeWS</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/ws/server/WSUtil.html#cancelJob(java.lang.String)"><B>cancelJob(String)</B></A> - \r
-Static method in class compbio.ws.server.<A HREF="../compbio/ws/server/WSUtil.html" title="class in compbio.ws.server">WSUtil</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/jaxws/CancelJobResponse.html" title="class in compbio.data.msa.jaxws"><B>CancelJobResponse</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/CancelJobResponse.html#CancelJobResponse()"><B>CancelJobResponse()</B></A> - \r
-Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/CancelJobResponse.html" title="class in compbio.data.msa.jaxws">CancelJobResponse</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata"><B>ChunkHolder</B></A> - Class in <A HREF="../compbio/metadata/package-summary.html">compbio.metadata</A><DD>Represents a chunk of string data together with the position in a file from
- where corresponding to of the data.<DT><A HREF="../compbio/metadata/ChunkHolder.html#ChunkHolder(java.lang.String, long)"><B>ChunkHolder(String, long)</B></A> - \r
-Constructor for class compbio.metadata.<A HREF="../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/Cleaner.html" title="class in compbio.engine"><B>Cleaner</B></A> - Class in <A HREF="../compbio/engine/package-summary.html">compbio.engine</A><DD>&nbsp;<DT><A HREF="../compbio/engine/Cleaner.html#Cleaner()"><B>Cleaner()</B></A> - \r
-Constructor for class compbio.engine.<A HREF="../compbio/engine/Cleaner.html" title="class in compbio.engine">Cleaner</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/sequence/SequenceUtil.html#cleanSequence(java.lang.String)"><B>cleanSequence(String)</B></A> - \r
-Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
-<DD>Removes all whitespace chars in the sequence string\r
-<DT><A HREF="../compbio/engine/AsyncExecutor.html#cleanup(java.lang.String)"><B>cleanup(String)</B></A> - \r
-Method in interface compbio.engine.<A HREF="../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine">AsyncExecutor</A>\r
-<DD>Remove all files and a job directory for a jobid.\r
-<DT><A HREF="../compbio/engine/cluster/drmaa/AsyncJobRunner.html#cleanup(java.lang.String)"><B>cleanup(String)</B></A> - \r
-Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/AsyncJobRunner.html" title="class in compbio.engine.cluster.drmaa">AsyncJobRunner</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/cluster/drmaa/JobRunner.html#cleanup()"><B>cleanup()</B></A> - \r
-Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/JobRunner.html" title="class in compbio.engine.cluster.drmaa">JobRunner</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/local/AsyncLocalRunner.html#cleanup(java.lang.String)"><B>cleanup(String)</B></A> - \r
-Method in class compbio.engine.local.<A HREF="../compbio/engine/local/AsyncLocalRunner.html" title="class in compbio.engine.local">AsyncLocalRunner</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/local/LocalEngineUtil.html#cleanup(compbio.engine.client.ConfiguredExecutable)"><B>cleanup(ConfiguredExecutable&lt;?&gt;)</B></A> - \r
-Static method in class compbio.engine.local.<A HREF="../compbio/engine/local/LocalEngineUtil.html" title="class in compbio.engine.local">LocalEngineUtil</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/local/LocalRunner.html#cleanup()"><B>cleanup()</B></A> - \r
-Method in class compbio.engine.local.<A HREF="../compbio/engine/local/LocalRunner.html" title="class in compbio.engine.local">LocalRunner</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/SyncExecutor.html#cleanup()"><B>cleanup()</B></A> - \r
-Method in interface compbio.engine.<A HREF="../compbio/engine/SyncExecutor.html" title="interface in compbio.engine">SyncExecutor</A>\r
-<DD>Clean up after the job\r
-<DT><A HREF="../compbio/engine/cluster/drmaa/ClusterSession.html#close()"><B>close()</B></A> - \r
-Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/ClusterSession.html" title="class in compbio.engine.cluster.drmaa">ClusterSession</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence"><B>ClustalAlignmentUtil</B></A> - Class in <A HREF="../compbio/data/sequence/package-summary.html">compbio.data.sequence</A><DD>Tools to read and write clustal formated files<DT><A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html#ClustalAlignmentUtil()"><B>ClustalAlignmentUtil()</B></A> - \r
-Constructor for class compbio.data.sequence.<A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence">ClustalAlignmentUtil</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa"><B>ClustalW</B></A> - Class in <A HREF="../compbio/runner/msa/package-summary.html">compbio.runner.msa</A><DD>&nbsp;<DT><A HREF="../compbio/runner/msa/ClustalW.html#ClustalW()"><B>ClustalW()</B></A> - \r
-Constructor for class compbio.runner.msa.<A HREF="../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/ws/server/ClustalWS.html" title="class in compbio.ws.server"><B>ClustalWS</B></A> - Class in <A HREF="../compbio/ws/server/package-summary.html">compbio.ws.server</A><DD>&nbsp;<DT><A HREF="../compbio/ws/server/ClustalWS.html#ClustalWS()"><B>ClustalWS()</B></A> - \r
-Constructor for class compbio.ws.server.<A HREF="../compbio/ws/server/ClustalWS.html" title="class in compbio.ws.server">ClustalWS</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/cluster/drmaa/ClusterUtil.html#CLUSTER_STAT_IN_SEC"><B>CLUSTER_STAT_IN_SEC</B></A> - \r
-Static variable in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/ClusterUtil.html" title="class in compbio.engine.cluster.drmaa">ClusterUtil</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/ConfExecutable.html#CLUSTER_TASK_ID_PREFIX"><B>CLUSTER_TASK_ID_PREFIX</B></A> - \r
-Static variable in class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/Configurator.html#CLUSTER_WORK_DIRECTORY"><B>CLUSTER_WORK_DIRECTORY</B></A> - \r
-Static variable in class compbio.engine.<A HREF="../compbio/engine/Configurator.html" title="class in compbio.engine">Configurator</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/ClusterJobId.html" title="class in compbio.engine"><B>ClusterJobId</B></A> - Class in <A HREF="../compbio/engine/package-summary.html">compbio.engine</A><DD>&nbsp;<DT><A HREF="../compbio/engine/ClusterJobId.html#ClusterJobId(java.lang.String)"><B>ClusterJobId(String)</B></A> - \r
-Constructor for class compbio.engine.<A HREF="../compbio/engine/ClusterJobId.html" title="class in compbio.engine">ClusterJobId</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/ClusterNativeSpecExecutable.html" title="interface in compbio.engine.client"><B>ClusterNativeSpecExecutable</B></A>&lt;<A HREF="../compbio/engine/client/ClusterNativeSpecExecutable.html" title="type parameter in ClusterNativeSpecExecutable">T</A>&gt; - Interface in <A HREF="../compbio/engine/client/package-summary.html">compbio.engine.client</A><DD>&nbsp;<DT><A HREF="../compbio/engine/cluster/drmaa/ClusterSession.html" title="class in compbio.engine.cluster.drmaa"><B>ClusterSession</B></A> - Class in <A HREF="../compbio/engine/cluster/drmaa/package-summary.html">compbio.engine.cluster.drmaa</A><DD>&nbsp;<DT><A HREF="../compbio/engine/cluster/drmaa/ClusterUtil.html" title="class in compbio.engine.cluster.drmaa"><B>ClusterUtil</B></A> - Class in <A HREF="../compbio/engine/cluster/drmaa/package-summary.html">compbio.engine.cluster.drmaa</A><DD>&nbsp;<DT><A HREF="../compbio/engine/cluster/drmaa/ClusterUtil.html#ClusterUtil()"><B>ClusterUtil()</B></A> - \r
-Constructor for class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/ClusterUtil.html" title="class in compbio.engine.cluster.drmaa">ClusterUtil</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client"><B>CommandBuilder</B></A>&lt;<A HREF="../compbio/engine/client/CommandBuilder.html" title="type parameter in CommandBuilder">T</A>&gt; - Class in <A HREF="../compbio/engine/client/package-summary.html">compbio.engine.client</A><DD>&nbsp;<DT><A HREF="../compbio/engine/client/CommandBuilder.html#CommandBuilder(java.lang.String)"><B>CommandBuilder(String)</B></A> - \r
-Constructor for class compbio.engine.client.<A HREF="../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/FilePuller.html#compareTo(java.util.concurrent.Delayed)"><B>compareTo(Delayed)</B></A> - \r
-Method in class compbio.engine.<A HREF="../compbio/engine/FilePuller.html" title="class in compbio.engine">FilePuller</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/_structure/package-summary.html"><B>compbio.data._structure</B></A> - package compbio.data._structure<DD>&nbsp;<DT><A HREF="../compbio/data/msa/package-summary.html"><B>compbio.data.msa</B></A> - package compbio.data.msa<DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/package-summary.html"><B>compbio.data.msa.jaxws</B></A> - package compbio.data.msa.jaxws<DD>&nbsp;<DT><A HREF="../compbio/pipeline/_jpred/package-summary.html"><B>compbio.pipeline._jpred</B></A> - package compbio.pipeline._jpred<DD>&nbsp;<DT><A HREF="../compbio/runner/_jpred/package-summary.html"><B>compbio.runner._jpred</B></A> - package compbio.runner._jpred<DD>&nbsp;<DT><A HREF="../compbio/runner/psiblast/package-summary.html"><B>compbio.runner.psiblast</B></A> - package compbio.runner.psiblast<DD>&nbsp;<DT><A HREF="../compbio/ws/client/package-summary.html"><B>compbio.ws.client</B></A> - package compbio.ws.client<DD>&nbsp;<DT><A HREF="../compbio/ws/server/package-summary.html"><B>compbio.ws.server</B></A> - package compbio.ws.server<DD>&nbsp;<DT><A HREF="../compbio/engine/conf/PropertyHelperManager.html#confDir"><B>confDir</B></A> - \r
-Static variable in class compbio.engine.conf.<A HREF="../compbio/engine/conf/PropertyHelperManager.html" title="class in compbio.engine.conf">PropertyHelperManager</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client"><B>ConfExecutable</B></A>&lt;<A HREF="../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt; - Class in <A HREF="../compbio/engine/client/package-summary.html">compbio.engine.client</A><DD>&nbsp;<DT><A HREF="../compbio/engine/client/ConfExecutable.html#ConfExecutable(compbio.engine.client.Executable, java.lang.String)"><B>ConfExecutable(Executable&lt;T&gt;, String)</B></A> - \r
-Constructor for class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/Configurator.html" title="class in compbio.engine"><B>Configurator</B></A> - Class in <A HREF="../compbio/engine/package-summary.html">compbio.engine</A><DD>&nbsp;<DT><A HREF="../compbio/engine/Configurator.html#Configurator()"><B>Configurator()</B></A> - \r
-Constructor for class compbio.engine.<A HREF="../compbio/engine/Configurator.html" title="class in compbio.engine">Configurator</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client"><B>ConfiguredExecutable</B></A>&lt;<A HREF="../compbio/engine/client/ConfiguredExecutable.html" title="type parameter in ConfiguredExecutable">T</A>&gt; - Interface in <A HREF="../compbio/engine/client/package-summary.html">compbio.engine.client</A><DD>&nbsp;<DT><A HREF="../compbio/engine/Configurator.html#configureExecutable(compbio.engine.client.Executable)"><B>configureExecutable(Executable&lt;T&gt;)</B></A> - \r
-Static method in class compbio.engine.<A HREF="../compbio/engine/Configurator.html" title="class in compbio.engine">Configurator</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/Configurator.html#configureExecutable(compbio.engine.client.Executable, java.util.List)"><B>configureExecutable(Executable&lt;T&gt;, List&lt;FastaSequence&gt;)</B></A> - \r
-Static method in class compbio.engine.<A HREF="../compbio/engine/Configurator.html" title="class in compbio.engine">Configurator</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/Configurator.html#configureExecutable(compbio.engine.client.Executable, compbio.engine.client.Executable.ExecProvider)"><B>configureExecutable(Executable&lt;T&gt;, Executable.ExecProvider)</B></A> - \r
-Static method in class compbio.engine.<A HREF="../compbio/engine/Configurator.html" title="class in compbio.engine">Configurator</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/ws/client/Jws2Client.html#connect(java.lang.String, compbio.ws.client.Jws2Client.Services)"><B>connect(String, Jws2Client.Services)</B></A> - \r
-Static method in class compbio.ws.client.<A HREF="../compbio/ws/client/Jws2Client.html" title="class in compbio.ws.client">Jws2Client</A>\r
-<DD>Connects to a web service by the host and the service name\r
-<DT><A HREF="../compbio/engine/client/Util.html#convertToAbsolute(java.lang.String)"><B>convertToAbsolute(String)</B></A> - \r
-Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/Util.html" title="class in compbio.engine.client">Util</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/RunnerConfig.html#copyAndValidateRConfig(compbio.metadata.RunnerConfig)"><B>copyAndValidateRConfig(RunnerConfig&lt;?&gt;)</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/sequence/FastaSequence.html#countMatchesInSequence(java.lang.String, java.lang.String)"><B>countMatchesInSequence(String, String)</B></A> - \r
-Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/jaxws/CustomAlign.html" title="class in compbio.data.msa.jaxws"><B>CustomAlign</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/CustomAlign.html#CustomAlign()"><B>CustomAlign()</B></A> - \r
-Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/CustomAlign.html" title="class in compbio.data.msa.jaxws">CustomAlign</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/MsaWS.html#customAlign(java.util.List, java.util.List)"><B>customAlign(List&lt;FastaSequence&gt;, List&lt;Option&lt;T&gt;&gt;)</B></A> - \r
-Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>\r
-<DD>Align a list of sequences with options.\r
-<DT><A HREF="../compbio/ws/server/ClustalWS.html#customAlign(java.util.List, java.util.List)"><B>customAlign(List&lt;FastaSequence&gt;, List&lt;Option&lt;ClustalW&gt;&gt;)</B></A> - \r
-Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ClustalWS.html" title="class in compbio.ws.server">ClustalWS</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/ws/server/MafftWS.html#customAlign(java.util.List, java.util.List)"><B>customAlign(List&lt;FastaSequence&gt;, List&lt;Option&lt;Mafft&gt;&gt;)</B></A> - \r
-Method in class compbio.ws.server.<A HREF="../compbio/ws/server/MafftWS.html" title="class in compbio.ws.server">MafftWS</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/ws/server/MuscleWS.html#customAlign(java.util.List, java.util.List)"><B>customAlign(List&lt;FastaSequence&gt;, List&lt;Option&lt;Muscle&gt;&gt;)</B></A> - \r
-Method in class compbio.ws.server.<A HREF="../compbio/ws/server/MuscleWS.html" title="class in compbio.ws.server">MuscleWS</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/ws/server/ProbconsWS.html#customAlign(java.util.List, java.util.List)"><B>customAlign(List&lt;FastaSequence&gt;, List&lt;Option&lt;Probcons&gt;&gt;)</B></A> - \r
-Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ProbconsWS.html" title="class in compbio.ws.server">ProbconsWS</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/ws/server/TcoffeeWS.html#customAlign(java.util.List, java.util.List)"><B>customAlign(List&lt;FastaSequence&gt;, List&lt;Option&lt;Tcoffee&gt;&gt;)</B></A> - \r
-Method in class compbio.ws.server.<A HREF="../compbio/ws/server/TcoffeeWS.html" title="class in compbio.ws.server">TcoffeeWS</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/jaxws/CustomAlignResponse.html" title="class in compbio.data.msa.jaxws"><B>CustomAlignResponse</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/CustomAlignResponse.html#CustomAlignResponse()"><B>CustomAlignResponse()</B></A> - \r
-Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/CustomAlignResponse.html" title="class in compbio.data.msa.jaxws">CustomAlignResponse</A>\r
-<DD>&nbsp;\r
-</DL>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Package</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Class</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Use</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Index</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="index-2.html"><B>PREV LETTER</B></A>&nbsp;\r
-&nbsp;<A HREF="index-4.html"><B>NEXT LETTER</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../index.html?index-filesindex-3.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="index-3.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<A HREF="index-1.html">A</A> <A HREF="index-2.html">B</A> <A HREF="index-3.html">C</A> <A HREF="index-4.html">D</A> <A HREF="index-5.html">E</A> <A HREF="index-6.html">F</A> <A HREF="index-7.html">G</A> <A HREF="index-8.html">H</A> <A HREF="index-9.html">I</A> <A HREF="index-10.html">J</A> <A HREF="index-11.html">K</A> <A HREF="index-12.html">L</A> <A HREF="index-13.html">M</A> <A HREF="index-14.html">N</A> <A HREF="index-15.html">O</A> <A HREF="index-16.html">P</A> <A HREF="index-17.html">R</A> <A HREF="index-18.html">S</A> <A HREF="index-19.html">T</A> <A HREF="index-20.html">U</A> <A HREF="index-21.html">V</A> <A HREF="index-22.html">W</A> <A HREF="index-23.html">_</A> <HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/index-files/index-4.html b/website/full_javadoc/index-files/index-4.html

deleted file mode 100644 (file)

index 0c13bf1..0000000
--- a/website/full_javadoc/index-files/index-4.html
+++ /dev/null
@@ -1,175 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-D-Index\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="D-Index";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Package</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Class</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Use</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Index</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="index-3.html"><B>PREV LETTER</B></A>&nbsp;\r
-&nbsp;<A HREF="index-5.html"><B>NEXT LETTER</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../index.html?index-filesindex-4.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="index-4.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<A HREF="index-1.html">A</A> <A HREF="index-2.html">B</A> <A HREF="index-3.html">C</A> <A HREF="index-4.html">D</A> <A HREF="index-5.html">E</A> <A HREF="index-6.html">F</A> <A HREF="index-7.html">G</A> <A HREF="index-8.html">H</A> <A HREF="index-9.html">I</A> <A HREF="index-10.html">J</A> <A HREF="index-11.html">K</A> <A HREF="index-12.html">L</A> <A HREF="index-13.html">M</A> <A HREF="index-14.html">N</A> <A HREF="index-15.html">O</A> <A HREF="index-16.html">P</A> <A HREF="index-17.html">R</A> <A HREF="index-18.html">S</A> <A HREF="index-19.html">T</A> <A HREF="index-20.html">U</A> <A HREF="index-21.html">V</A> <A HREF="index-22.html">W</A> <A HREF="index-23.html">_</A> <HR>\r
-<A NAME="_D_"><!-- --></A><H2>\r
-<B>D</B></H2>\r
-<DL>\r
-<DT><A HREF="../compbio/engine/cluster/drmaa/JobRunner.html#deepClean()"><B>deepClean()</B></A> - \r
-Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/JobRunner.html" title="class in compbio.engine.cluster.drmaa">JobRunner</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/sequence/SequenceUtil.html#deepCleanSequence(java.lang.String)"><B>deepCleanSequence(String)</B></A> - \r
-Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
-<DD>Removes all special characters and digits as well as whitespace chars
- from the sequence\r
-<DT><A HREF="../compbio/engine/Cleaner.html#deleteAllFiles(java.lang.String)"><B>deleteAllFiles(String)</B></A> - \r
-Static method in class compbio.engine.<A HREF="../compbio/engine/Cleaner.html" title="class in compbio.engine">Cleaner</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/Cleaner.html#deleteFiles(compbio.engine.client.ConfiguredExecutable)"><B>deleteFiles(ConfiguredExecutable&lt;?&gt;)</B></A> - \r
-Static method in class compbio.engine.<A HREF="../compbio/engine/Cleaner.html" title="class in compbio.engine">Cleaner</A>\r
-<DD>This method returns true if all files specified by List files were
- successfully removed or there was no files to remove (files list was
- empty)\r
-<DT><A HREF="../compbio/engine/conf/_Key.html#DELIM"><B>DELIM</B></A> - \r
-Static variable in class compbio.engine.conf.<A HREF="../compbio/engine/conf/_Key.html" title="class in compbio.engine.conf">_Key</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/conf/DirectoryManager.html#DELIM"><B>DELIM</B></A> - \r
-Static variable in class compbio.engine.conf.<A HREF="../compbio/engine/conf/DirectoryManager.html" title="class in compbio.engine.conf">DirectoryManager</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/sequence/SequenceUtil.html#DIGIT"><B>DIGIT</B></A> - \r
-Static variable in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
-<DD>A digit\r
-<DT><A HREF="../compbio/engine/conf/DirectoryManager.html" title="class in compbio.engine.conf"><B>DirectoryManager</B></A> - Class in <A HREF="../compbio/engine/conf/package-summary.html">compbio.engine.conf</A><DD>&nbsp;<DT><A HREF="../compbio/engine/conf/DirectoryManager.html#DirectoryManager()"><B>DirectoryManager()</B></A> - \r
-Constructor for class compbio.engine.conf.<A HREF="../compbio/engine/conf/DirectoryManager.html" title="class in compbio.engine.conf">DirectoryManager</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/FilePuller.html#disconnect()"><B>disconnect()</B></A> - \r
-Method in class compbio.engine.<A HREF="../compbio/engine/FilePuller.html" title="class in compbio.engine">FilePuller</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/_impl/Disembl.html" title="class in compbio.runner._impl"><B>Disembl</B></A> - Class in <A HREF="../compbio/runner/_impl/package-summary.html">compbio.runner._impl</A><DD>&nbsp;<DT><A HREF="../compbio/runner/_impl/Disembl.html#Disembl(java.lang.String)"><B>Disembl(String)</B></A> - \r
-Constructor for class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Disembl.html" title="class in compbio.runner._impl">Disembl</A>\r
-<DD>&nbsp;\r
-</DL>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Package</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Class</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Use</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Index</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="index-3.html"><B>PREV LETTER</B></A>&nbsp;\r
-&nbsp;<A HREF="index-5.html"><B>NEXT LETTER</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../index.html?index-filesindex-4.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="index-4.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<A HREF="index-1.html">A</A> <A HREF="index-2.html">B</A> <A HREF="index-3.html">C</A> <A HREF="index-4.html">D</A> <A HREF="index-5.html">E</A> <A HREF="index-6.html">F</A> <A HREF="index-7.html">G</A> <A HREF="index-8.html">H</A> <A HREF="index-9.html">I</A> <A HREF="index-10.html">J</A> <A HREF="index-11.html">K</A> <A HREF="index-12.html">L</A> <A HREF="index-13.html">M</A> <A HREF="index-14.html">N</A> <A HREF="index-15.html">O</A> <A HREF="index-16.html">P</A> <A HREF="index-17.html">R</A> <A HREF="index-18.html">S</A> <A HREF="index-19.html">T</A> <A HREF="index-20.html">U</A> <A HREF="index-21.html">V</A> <A HREF="index-22.html">W</A> <A HREF="index-23.html">_</A> <HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/index-files/index-5.html b/website/full_javadoc/index-files/index-5.html

deleted file mode 100644 (file)

index 46a4b47..0000000
--- a/website/full_javadoc/index-files/index-5.html
+++ /dev/null
@@ -1,215 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-E-Index\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="E-Index";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
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-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
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-</TD>\r
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-  <!--\r
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-    document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');\r
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-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<A HREF="index-1.html">A</A> <A HREF="index-2.html">B</A> <A HREF="index-3.html">C</A> <A HREF="index-4.html">D</A> <A HREF="index-5.html">E</A> <A HREF="index-6.html">F</A> <A HREF="index-7.html">G</A> <A HREF="index-8.html">H</A> <A HREF="index-9.html">I</A> <A HREF="index-10.html">J</A> <A HREF="index-11.html">K</A> <A HREF="index-12.html">L</A> <A HREF="index-13.html">M</A> <A HREF="index-14.html">N</A> <A HREF="index-15.html">O</A> <A HREF="index-16.html">P</A> <A HREF="index-17.html">R</A> <A HREF="index-18.html">S</A> <A HREF="index-19.html">T</A> <A HREF="index-20.html">U</A> <A HREF="index-21.html">V</A> <A HREF="index-22.html">W</A> <A HREF="index-23.html">_</A> <HR>\r
-<A NAME="_E_"><!-- --></A><H2>\r
-<B>E</B></H2>\r
-<DL>\r
-<DT><A HREF="../compbio/runner/_impl/Environment.html" title="class in compbio.runner._impl"><B>Environment</B></A> - Class in <A HREF="../compbio/runner/_impl/package-summary.html">compbio.runner._impl</A><DD>This is utility class to encapsulate environmental variables like directory paths<DT><A HREF="../compbio/engine/client/EnvVariableProcessor.html" title="class in compbio.engine.client"><B>EnvVariableProcessor</B></A> - Class in <A HREF="../compbio/engine/client/package-summary.html">compbio.engine.client</A><DD>&nbsp;<DT><A HREF="../compbio/engine/client/EnvVariableProcessor.html#EnvVariableProcessor()"><B>EnvVariableProcessor()</B></A> - \r
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-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/sequence/Alignment.html#equals(java.lang.Object)"><B>equals(Object)</B></A> - \r
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-<DD>Please note that this implementation does not take the order of sequences
- into account!\r
-<DT><A HREF="../compbio/data/sequence/AlignmentMetadata.html#equals(java.lang.Object)"><B>equals(Object)</B></A> - \r
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-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/sequence/FastaSequence.html#equals(java.lang.Object)"><B>equals(Object)</B></A> - \r
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-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/CommandBuilder.html#equals(java.lang.Object)"><B>equals(Object)</B></A> - \r
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-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/RunConfiguration.html#equals(java.lang.Object)"><B>equals(Object)</B></A> - \r
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-<DD>&nbsp;\r
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-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/ClusterJobId.html#equals(java.lang.Object)"><B>equals(Object)</B></A> - \r
-Method in class compbio.engine.<A HREF="../compbio/engine/ClusterJobId.html" title="class in compbio.engine">ClusterJobId</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/conf/_Key.html#equals(java.lang.Object)"><B>equals(Object)</B></A> - \r
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-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/FilePuller.html#equals(java.lang.Object)"><B>equals(Object)</B></A> - \r
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-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/Job.html#equals(java.lang.Object)"><B>equals(Object)</B></A> - \r
-Method in class compbio.engine.<A HREF="../compbio/engine/Job.html" title="class in compbio.engine">Job</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/ChunkHolder.html#equals(java.lang.Object)"><B>equals(Object)</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/Limit.html#equals(java.lang.Object)"><B>equals(Object)</B></A> - \r
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-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/Option.html#equals(java.lang.Object)"><B>equals(Object)</B></A> - \r
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-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/Parameter.html#equals(java.lang.Object)"><B>equals(Object)</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/Preset.html#equals(java.lang.Object)"><B>equals(Object)</B></A> - \r
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-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/RunnerConfig.html#equals(java.lang.Object)"><B>equals(Object)</B></A> - \r
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-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/ValueConstrain.html#equals(java.lang.Object)"><B>equals(Object)</B></A> - \r
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-<DD>&nbsp;\r
-<DT><A HREF="../compbio/pipeline/_jpred/PScore.html#equals(java.lang.Object)"><B>equals(Object)</B></A> - \r
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-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/Executable.html" title="interface in compbio.engine.client"><B>Executable</B></A>&lt;<A HREF="../compbio/engine/client/Executable.html" title="type parameter in Executable">T</A>&gt; - Interface in <A HREF="../compbio/engine/client/package-summary.html">compbio.engine.client</A><DD>Interface to a native executable.<DT><A HREF="../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client"><B>Executable.ExecProvider</B></A> - Enum in <A HREF="../compbio/engine/client/package-summary.html">compbio.engine.client</A><DD>&nbsp;<DT><A HREF="../compbio/engine/local/ExecutableWrapper.html" title="class in compbio.engine.local"><B>ExecutableWrapper</B></A> - Class in <A HREF="../compbio/engine/local/package-summary.html">compbio.engine.local</A><DD>&nbsp;<DT><A HREF="../compbio/engine/local/ExecutableWrapper.html#ExecutableWrapper(compbio.engine.client.ConfiguredExecutable, java.lang.String)"><B>ExecutableWrapper(ConfiguredExecutable&lt;?&gt;, String)</B></A> - \r
-Constructor for class compbio.engine.local.<A HREF="../compbio/engine/local/ExecutableWrapper.html" title="class in compbio.engine.local">ExecutableWrapper</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/local/_TrackingExecutor.html#execute(java.lang.Runnable)"><B>execute(Runnable)</B></A> - \r
-Method in class compbio.engine.local.<A HREF="../compbio/engine/local/_TrackingExecutor.html" title="class in compbio.engine.local">_TrackingExecutor</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/cluster/drmaa/JobRunner.html#executeJob()"><B>executeJob()</B></A> - \r
-Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/JobRunner.html" title="class in compbio.engine.cluster.drmaa">JobRunner</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/local/LocalRunner.html#executeJob()"><B>executeJob()</B></A> - \r
-Method in class compbio.engine.local.<A HREF="../compbio/engine/local/LocalRunner.html" title="class in compbio.engine.local">LocalRunner</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/SyncExecutor.html#executeJob()"><B>executeJob()</B></A> - \r
-Method in interface compbio.engine.<A HREF="../compbio/engine/SyncExecutor.html" title="interface in compbio.engine">SyncExecutor</A>\r
-<DD>Execute the job\r
-</DL>\r
-<HR>\r
-\r
-\r
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diff --git a/website/full_javadoc/index-files/index-6.html b/website/full_javadoc/index-files/index-6.html

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-<A HREF="index-1.html">A</A> <A HREF="index-2.html">B</A> <A HREF="index-3.html">C</A> <A HREF="index-4.html">D</A> <A HREF="index-5.html">E</A> <A HREF="index-6.html">F</A> <A HREF="index-7.html">G</A> <A HREF="index-8.html">H</A> <A HREF="index-9.html">I</A> <A HREF="index-10.html">J</A> <A HREF="index-11.html">K</A> <A HREF="index-12.html">L</A> <A HREF="index-13.html">M</A> <A HREF="index-14.html">N</A> <A HREF="index-15.html">O</A> <A HREF="index-16.html">P</A> <A HREF="index-17.html">R</A> <A HREF="index-18.html">S</A> <A HREF="index-19.html">T</A> <A HREF="index-20.html">U</A> <A HREF="index-21.html">V</A> <A HREF="index-22.html">W</A> <A HREF="index-23.html">_</A> <HR>\r
-<A NAME="_F_"><!-- --></A><H2>\r
-<B>F</B></H2>\r
-<DL>\r
-<DT><A HREF="../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence"><B>FastaSequence</B></A> - Class in <A HREF="../compbio/data/sequence/package-summary.html">compbio.data.sequence</A><DD>A FASTA formatted sequence.<DT><A HREF="../compbio/data/sequence/FastaSequence.html#FastaSequence(java.lang.String, java.lang.String)"><B>FastaSequence(String, String)</B></A> - \r
-Constructor for class compbio.data.sequence.<A HREF="../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>\r
-<DD>Upon construction the any whitespace characters are removed from the
- sequence\r
-<DT><A HREF="../compbio/engine/FilePuller.html" title="class in compbio.engine"><B>FilePuller</B></A> - Class in <A HREF="../compbio/engine/package-summary.html">compbio.engine</A><DD>&nbsp;<DT><A HREF="../compbio/engine/cluster/dundee/_QueueConstraints.html#FIRST_MEMORY_LIMIT"><B>FIRST_MEMORY_LIMIT</B></A> - \r
-Static variable in class compbio.engine.cluster.dundee.<A HREF="../compbio/engine/cluster/dundee/_QueueConstraints.html" title="class in compbio.engine.cluster.dundee">_QueueConstraints</A>\r
-<DD>&nbsp;\r
-</DL>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
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-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Package</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Class</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Use</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Index</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="index-5.html"><B>PREV LETTER</B></A>&nbsp;\r
-&nbsp;<A HREF="index-7.html"><B>NEXT LETTER</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../index.html?index-filesindex-6.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="index-6.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
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-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../allclasses-noframe.html"><B>All Classes</B></A>\r
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-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
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-<A HREF="index-1.html">A</A> <A HREF="index-2.html">B</A> <A HREF="index-3.html">C</A> <A HREF="index-4.html">D</A> <A HREF="index-5.html">E</A> <A HREF="index-6.html">F</A> <A HREF="index-7.html">G</A> <A HREF="index-8.html">H</A> <A HREF="index-9.html">I</A> <A HREF="index-10.html">J</A> <A HREF="index-11.html">K</A> <A HREF="index-12.html">L</A> <A HREF="index-13.html">M</A> <A HREF="index-14.html">N</A> <A HREF="index-15.html">O</A> <A HREF="index-16.html">P</A> <A HREF="index-17.html">R</A> <A HREF="index-18.html">S</A> <A HREF="index-19.html">T</A> <A HREF="index-20.html">U</A> <A HREF="index-21.html">V</A> <A HREF="index-22.html">W</A> <A HREF="index-23.html">_</A> <HR>\r
-\r
-</BODY>\r
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diff --git a/website/full_javadoc/index-files/index-7.html b/website/full_javadoc/index-files/index-7.html

deleted file mode 100644 (file)

index f2382f2..0000000
--- a/website/full_javadoc/index-files/index-7.html
+++ /dev/null
@@ -1,1344 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-G-Index\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="G-Index";\r
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-</HEAD>\r
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-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
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-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Package</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Class</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Use</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Index</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="index-6.html"><B>PREV LETTER</B></A>&nbsp;\r
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-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
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-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
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-  <A HREF="../allclasses-noframe.html"><B>All Classes</B></A>\r
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-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<A HREF="index-1.html">A</A> <A HREF="index-2.html">B</A> <A HREF="index-3.html">C</A> <A HREF="index-4.html">D</A> <A HREF="index-5.html">E</A> <A HREF="index-6.html">F</A> <A HREF="index-7.html">G</A> <A HREF="index-8.html">H</A> <A HREF="index-9.html">I</A> <A HREF="index-10.html">J</A> <A HREF="index-11.html">K</A> <A HREF="index-12.html">L</A> <A HREF="index-13.html">M</A> <A HREF="index-14.html">N</A> <A HREF="index-15.html">O</A> <A HREF="index-16.html">P</A> <A HREF="index-17.html">R</A> <A HREF="index-18.html">S</A> <A HREF="index-19.html">T</A> <A HREF="index-20.html">U</A> <A HREF="index-21.html">V</A> <A HREF="index-22.html">W</A> <A HREF="index-23.html">_</A> <HR>\r
-<A NAME="_G_"><!-- --></A><H2>\r
-<B>G</B></H2>\r
-<DL>\r
-<DT><A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html#gapchar"><B>gapchar</B></A> - \r
-Static variable in class compbio.data.sequence.<A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence">ClustalAlignmentUtil</A>\r
-<DD>Dash char to be used as gap char in the alignments\r
-<DT><A HREF="../compbio/engine/PulledFileCache.html#get(java.lang.String)"><B>get(String)</B></A> - \r
-Static method in class compbio.engine.<A HREF="../compbio/engine/PulledFileCache.html" title="class in compbio.engine">PulledFileCache</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html#getActualNumberofSequences()"><B>getActualNumberofSequences()</B></A> - \r
-Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html" title="class in compbio.data.msa.jaxws">LimitExceededExceptionBean</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/LimitExceededException.html#getActualNumberofSequences()"><B>getActualNumberofSequences()</B></A> - \r
-Method in exception compbio.metadata.<A HREF="../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/OptionCombinator.html#getAllConstrainedParametersWithBorderValues(boolean)"><B>getAllConstrainedParametersWithBorderValues(boolean)</B></A> - \r
-Method in class compbio.runner.<A HREF="../compbio/runner/OptionCombinator.html" title="class in compbio.runner">OptionCombinator</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/OptionCombinator.html#getAllConstrainedParametersWithRandomValues()"><B>getAllConstrainedParametersWithRandomValues()</B></A> - \r
-Method in class compbio.runner.<A HREF="../compbio/runner/OptionCombinator.html" title="class in compbio.runner">OptionCombinator</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/OptionCombinator.html#getAllOptions()"><B>getAllOptions()</B></A> - \r
-Method in class compbio.runner.<A HREF="../compbio/runner/OptionCombinator.html" title="class in compbio.runner">OptionCombinator</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/OptionCombinator.html#getAllParameters()"><B>getAllParameters()</B></A> - \r
-Method in class compbio.runner.<A HREF="../compbio/runner/OptionCombinator.html" title="class in compbio.runner">OptionCombinator</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html#getAllStats()"><B>getAllStats()</B></A> - \r
-Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/_NativeSpecHelper.html#getApproprieteQueue()"><B>getApproprieteQueue()</B></A> - \r
-Method in class compbio.runner.<A HREF="../compbio/runner/_NativeSpecHelper.html" title="class in compbio.runner">_NativeSpecHelper</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/RunnerConfig.html#getArgument(java.lang.String)"><B>getArgument(String)</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
-<DD>Returns the argument by its name if found, NULL otherwise\r
-<DT><A HREF="../compbio/metadata/RunnerConfig.html#getArgumentByOptionName(java.lang.String)"><B>getArgumentByOptionName(String)</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
-<DD>Returns the argument by option name, NULL if the argument is not found\r
-<DT><A HREF="../compbio/metadata/Preset.html#getArguments(compbio.metadata.RunnerConfig)"><B>getArguments(RunnerConfig&lt;T&gt;)</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>\r
-<DD>Converts list of options as String to type Option\r
-<DT><A HREF="../compbio/metadata/RunnerConfig.html#getArguments()"><B>getArguments()</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/Configurator.html#getAsyncEngine(compbio.engine.client.ConfiguredExecutable, compbio.engine.client.Executable.ExecProvider)"><B>getAsyncEngine(ConfiguredExecutable&lt;?&gt;, Executable.ExecProvider)</B></A> - \r
-Static method in class compbio.engine.<A HREF="../compbio/engine/Configurator.html" title="class in compbio.engine">Configurator</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/Configurator.html#getAsyncEngine(compbio.engine.client.ConfiguredExecutable)"><B>getAsyncEngine(ConfiguredExecutable&lt;?&gt;)</B></A> - \r
-Static method in class compbio.engine.<A HREF="../compbio/engine/Configurator.html" title="class in compbio.engine">Configurator</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/Configurator.html#getAsyncEngine(java.lang.String)"><B>getAsyncEngine(String)</B></A> - \r
-Static method in class compbio.engine.<A HREF="../compbio/engine/Configurator.html" title="class in compbio.engine">Configurator</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/Limit.html#getAvgSeqLength()"><B>getAvgSeqLength()</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/Limit.html#getAvgSequenceLength(java.util.List)"><B>getAvgSequenceLength(List&lt;FastaSequence&gt;)</B></A> - \r
-Static method in class compbio.metadata.<A HREF="../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>\r
-<DD>Calculates an average sequence length of the dataset\r
-<DT><A HREF="../compbio/runner/_impl/Runners.html#getBlastAllRunnable(java.lang.String)"><B>getBlastAllRunnable(String)</B></A> - \r
-Static method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Runners.html" title="class in compbio.runner._impl">Runners</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/_impl/Environment.html#getBlastBinDir()"><B>getBlastBinDir()</B></A> - \r
-Static method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Environment.html" title="class in compbio.runner._impl">Environment</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/_impl/Environment.html#getBlastDatabasesDir()"><B>getBlastDatabasesDir()</B></A> - \r
-Static method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Environment.html" title="class in compbio.runner._impl">Environment</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/Job.html#getByJobId(java.lang.String, java.util.List)"><B>getByJobId(String, List&lt;Job&gt;)</B></A> - \r
-Static method in class compbio.engine.<A HREF="../compbio/engine/Job.html" title="class in compbio.engine">Job</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/Job.html#getByTaskId(java.lang.String, java.util.List)"><B>getByTaskId(String, List&lt;Job&gt;)</B></A> - \r
-Static method in class compbio.engine.<A HREF="../compbio/engine/Job.html" title="class in compbio.engine">Job</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html#getCalculationTime()"><B>getCalculationTime()</B></A> - \r
-Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/local/_TrackingExecutor.html#getCancelledTasks()"><B>getCancelledTasks()</B></A> - \r
-Method in class compbio.engine.local.<A HREF="../compbio/engine/local/_TrackingExecutor.html" title="class in compbio.engine.local">_TrackingExecutor</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/ChunkHolder.html#getChunk()"><B>getChunk()</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/conf/DirectoryManager.html#getClass(java.lang.String)"><B>getClass(String)</B></A> - \r
-Static method in class compbio.engine.conf.<A HREF="../compbio/engine/conf/DirectoryManager.html" title="class in compbio.engine.conf">DirectoryManager</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/msa/Tcoffee.html#getClusterCpuNum()"><B>getClusterCpuNum()</B></A> - \r
-Static method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/cluster/drmaa/ClusterSession.html#getClusterJobId(java.lang.String)"><B>getClusterJobId(String)</B></A> - \r
-Static method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/ClusterSession.html" title="class in compbio.engine.cluster.drmaa">ClusterSession</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/SkeletalExecutable.html#getClusterSettings()"><B>getClusterSettings()</B></A> - \r
-Method in class compbio.engine.client.<A HREF="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/ConfExecutable.html#getCommand(compbio.engine.client.Executable.ExecProvider)"><B>getCommand(Executable.ExecProvider)</B></A> - \r
-Method in class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/ConfiguredExecutable.html#getCommand(compbio.engine.client.Executable.ExecProvider)"><B>getCommand(Executable.ExecProvider)</B></A> - \r
-Method in interface compbio.engine.client.<A HREF="../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/Util.html#getCommand(compbio.engine.client.Executable.ExecProvider, java.lang.Class)"><B>getCommand(Executable.ExecProvider, Class&lt;?&gt;)</B></A> - \r
-Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/Util.html" title="class in compbio.engine.client">Util</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/_impl/BlastAll.html#getCommand(compbio.engine.client.Executable.ExecProvider)"><B>getCommand(Executable.ExecProvider)</B></A> - \r
-Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/BlastAll.html" title="class in compbio.runner._impl">BlastAll</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/_impl/Disembl.html#getCommand(compbio.engine.client.Executable.ExecProvider)"><B>getCommand(Executable.ExecProvider)</B></A> - \r
-Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Disembl.html" title="class in compbio.runner._impl">Disembl</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/_impl/Mcl.html#getCommand(compbio.engine.client.Executable.ExecProvider)"><B>getCommand(Executable.ExecProvider)</B></A> - \r
-Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Mcl.html" title="class in compbio.runner._impl">Mcl</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/_impl/PSIBlast.html#getCommand(compbio.engine.client.Executable.ExecProvider)"><B>getCommand(Executable.ExecProvider)</B></A> - \r
-Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/PSIBlast.html" title="class in compbio.runner._impl">PSIBlast</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/_impl/Ronn.html#getCommand(compbio.engine.client.Executable.ExecProvider)"><B>getCommand(Executable.ExecProvider)</B></A> - \r
-Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Ronn.html" title="class in compbio.runner._impl">Ronn</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/_impl/RPSBlast.html#getCommand(compbio.engine.client.Executable.ExecProvider)"><B>getCommand(Executable.ExecProvider)</B></A> - \r
-Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/RPSBlast.html" title="class in compbio.runner._impl">RPSBlast</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/_impl/BlastAll.html#getCommandName()"><B>getCommandName()</B></A> - \r
-Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/BlastAll.html" title="class in compbio.runner._impl">BlastAll</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/_impl/Disembl.html#getCommandName()"><B>getCommandName()</B></A> - \r
-Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Disembl.html" title="class in compbio.runner._impl">Disembl</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/_impl/Mcl.html#getCommandName()"><B>getCommandName()</B></A> - \r
-Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Mcl.html" title="class in compbio.runner._impl">Mcl</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/_impl/NetNglyc.html#getCommandName()"><B>getCommandName()</B></A> - \r
-Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/_impl/PSIBlast.html#getCommandName()"><B>getCommandName()</B></A> - \r
-Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/PSIBlast.html" title="class in compbio.runner._impl">PSIBlast</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/_impl/Ronn.html#getCommandName()"><B>getCommandName()</B></A> - \r
-Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Ronn.html" title="class in compbio.runner._impl">Ronn</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/_impl/RPSBlast.html#getCommandName()"><B>getCommandName()</B></A> - \r
-Static method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/RPSBlast.html" title="class in compbio.runner._impl">RPSBlast</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/CommandBuilder.html#getCommands()"><B>getCommands()</B></A> - \r
-Method in class compbio.engine.client.<A HREF="../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/ws/server/WSUtil.html#getCommands(java.util.List, java.lang.String)"><B>getCommands(List&lt;Option&lt;T&gt;&gt;, String)</B></A> - \r
-Static method in class compbio.ws.server.<A HREF="../compbio/ws/server/WSUtil.html" title="class in compbio.ws.server">WSUtil</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/CommandBuilder.html#getCommandString()"><B>getCommandString()</B></A> - \r
-Method in class compbio.engine.client.<A HREF="../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/Job.html#getConfExecutable()"><B>getConfExecutable()</B></A> - \r
-Method in class compbio.engine.<A HREF="../compbio/engine/Job.html" title="class in compbio.engine">Job</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html#getCPUTimeStat()"><B>getCPUTimeStat()</B></A> - \r
-Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html#getCPUUsageTime()"><B>getCPUUsageTime()</B></A> - \r
-Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/ConfExecutable.html#getCreatedFiles()"><B>getCreatedFiles()</B></A> - \r
-Method in class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/Executable.html#getCreatedFiles()"><B>getCreatedFiles()</B></A> - \r
-Method in interface compbio.engine.client.<A HREF="../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/SkeletalExecutable.html#getCreatedFiles()"><B>getCreatedFiles()</B></A> - \r
-Method in class compbio.engine.client.<A HREF="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>\r
-<DD>This method cannot really tell whether the files has actually been
- created or not.\r
-<DT><A HREF="../compbio/runner/_impl/BlastAll.html#getCreatedFiles()"><B>getCreatedFiles()</B></A> - \r
-Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/BlastAll.html" title="class in compbio.runner._impl">BlastAll</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/_impl/Disembl.html#getCreatedFiles()"><B>getCreatedFiles()</B></A> - \r
-Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Disembl.html" title="class in compbio.runner._impl">Disembl</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/_impl/Mcl.html#getCreatedFiles()"><B>getCreatedFiles()</B></A> - \r
-Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Mcl.html" title="class in compbio.runner._impl">Mcl</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/_impl/NetNglyc.html#getCreatedFiles()"><B>getCreatedFiles()</B></A> - \r
-Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/_impl/OB.html#getCreatedFiles()"><B>getCreatedFiles()</B></A> - \r
-Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/OB.html" title="class in compbio.runner._impl">OB</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/_impl/PSIBlast.html#getCreatedFiles()"><B>getCreatedFiles()</B></A> - \r
-Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/PSIBlast.html" title="class in compbio.runner._impl">PSIBlast</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/_impl/Ronn.html#getCreatedFiles()"><B>getCreatedFiles()</B></A> - \r
-Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Ronn.html" title="class in compbio.runner._impl">Ronn</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/_impl/RPSBlast.html#getCreatedFiles()"><B>getCreatedFiles()</B></A> - \r
-Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/RPSBlast.html" title="class in compbio.runner._impl">RPSBlast</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/msa/ClustalW.html#getCreatedFiles()"><B>getCreatedFiles()</B></A> - \r
-Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/msa/Muscle.html#getCreatedFiles()"><B>getCreatedFiles()</B></A> - \r
-Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/msa/Probcons.html#getCreatedFiles()"><B>getCreatedFiles()</B></A> - \r
-Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/msa/Tcoffee.html#getCreatedFiles()"><B>getCreatedFiles()</B></A> - \r
-Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html#getDataTransfered()"><B>getDataTransfered()</B></A> - \r
-Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/LimitsManager.html#getDefaultLimit()"><B>getDefaultLimit()</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/Argument.html#getDefaultValue()"><B>getDefaultValue()</B></A> - \r
-Method in interface compbio.metadata.<A HREF="../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/Option.html#getDefaultValue()"><B>getDefaultValue()</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
-<DD>A default value of the option.\r
-<DT><A HREF="../compbio/engine/FilePuller.html#getDelay(java.util.concurrent.TimeUnit)"><B>getDelay(TimeUnit)</B></A> - \r
-Method in class compbio.engine.<A HREF="../compbio/engine/FilePuller.html" title="class in compbio.engine">FilePuller</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/Argument.html#getDescription()"><B>getDescription()</B></A> - \r
-Method in interface compbio.metadata.<A HREF="../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/Option.html#getDescription()"><B>getDescription()</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
-<DD>A long description of the Option\r
-<DT><A HREF="../compbio/metadata/Preset.html#getDescription()"><B>getDescription()</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/_impl/Runners.html#getDisemblRunnable(java.lang.String)"><B>getDisemblRunnable(String)</B></A> - \r
-Static method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Runners.html" title="class in compbio.runner._impl">Runners</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/_SkeletalCommandBuilder.html#getEmail()"><B>getEmail()</B></A> - \r
-Method in class compbio.runner.<A HREF="../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html#getEndTime()"><B>getEndTime()</B></A> - \r
-Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/LoadBalancer.html#getEngine(compbio.engine.client.Executable)"><B>getEngine(Executable&lt;?&gt;)</B></A> - \r
-Static method in class compbio.engine.<A HREF="../compbio/engine/LoadBalancer.html" title="class in compbio.engine">LoadBalancer</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/LoadBalancer.html#getEngine(compbio.engine.client.Executable, java.util.List)"><B>getEngine(Executable&lt;V&gt;, List&lt;FastaSequence&gt;)</B></A> - \r
-Static method in class compbio.engine.<A HREF="../compbio/engine/LoadBalancer.html" title="class in compbio.engine">LoadBalancer</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/ws/server/WSUtil.html#getEngine(compbio.engine.client.ConfiguredExecutable)"><B>getEngine(ConfiguredExecutable&lt;?&gt;)</B></A> - \r
-Static method in class compbio.ws.server.<A HREF="../compbio/ws/server/WSUtil.html" title="class in compbio.ws.server">WSUtil</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/ConfExecutable.html#getEnvironment()"><B>getEnvironment()</B></A> - \r
-Method in class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/ConfiguredExecutable.html#getEnvironment()"><B>getEnvironment()</B></A> - \r
-Method in interface compbio.engine.client.<A HREF="../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/EnvVariableProcessor.html#getEnvVariables(java.lang.String, java.lang.Class)"><B>getEnvVariables(String, Class&lt;?&gt;)</B></A> - \r
-Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/EnvVariableProcessor.html" title="class in compbio.engine.client">EnvVariableProcessor</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/ConfExecutable.html#getError()"><B>getError()</B></A> - \r
-Method in class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/Executable.html#getError()"><B>getError()</B></A> - \r
-Method in interface compbio.engine.client.<A HREF="../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/RunConfiguration.html#getError()"><B>getError()</B></A> - \r
-Method in class compbio.engine.client.<A HREF="../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/SkeletalExecutable.html#getError()"><B>getError()</B></A> - \r
-Method in class compbio.engine.client.<A HREF="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/_impl/NetNglyc.html#getError()"><B>getError()</B></A> - \r
-Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/_SkeletalCommandBuilder.html#getError()"><B>getError()</B></A> - \r
-Method in class compbio.runner.<A HREF="../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/Util.html#getExecProperty(java.lang.String, compbio.engine.client.Executable)"><B>getExecProperty(String, Executable&lt;?&gt;)</B></A> - \r
-Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/Util.html" title="class in compbio.engine.client">Util</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/Util.html#getExecProperty(java.lang.String, java.lang.Class)"><B>getExecProperty(String, Class&lt;?&gt;)</B></A> - \r
-Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/Util.html" title="class in compbio.engine.client">Util</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/ConfExecutable.html#getExecProvider()"><B>getExecProvider()</B></A> - \r
-Method in class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/ConfiguredExecutable.html#getExecProvider()"><B>getExecProvider()</B></A> - \r
-Method in interface compbio.engine.client.<A HREF="../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/ConfExecutable.html#getExecutable()"><B>getExecutable()</B></A> - \r
-Method in class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/ConfiguredExecutable.html#getExecutable()"><B>getExecutable()</B></A> - \r
-Method in interface compbio.engine.client.<A HREF="../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html#getExecutionStat()"><B>getExecutionStat()</B></A> - \r
-Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/local/LocalExecutorService.html#getExecutor()"><B>getExecutor()</B></A> - \r
-Static method in class compbio.engine.local.<A HREF="../compbio/engine/local/LocalExecutorService.html" title="class in compbio.engine.local">LocalExecutorService</A>\r
-<DD>This method returns the single instance of CachedThreadPoolExecutor which
- it cashes internally\r
-<DT><A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html#getExitStatus()"><B>getExitStatus()</B></A> - \r
-Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/jaxws/Align.html#getFastaSequences()"><B>getFastaSequences()</B></A> - \r
-Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/Align.html" title="class in compbio.data.msa.jaxws">Align</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/jaxws/CustomAlign.html#getFastaSequences()"><B>getFastaSequences()</B></A> - \r
-Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/CustomAlign.html" title="class in compbio.data.msa.jaxws">CustomAlign</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/jaxws/PresetAlign.html#getFastaSequences()"><B>getFastaSequences()</B></A> - \r
-Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/PresetAlign.html" title="class in compbio.data.msa.jaxws">PresetAlign</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/FilePuller.html#getFile()"><B>getFile()</B></A> - \r
-Method in class compbio.engine.<A HREF="../compbio/engine/FilePuller.html" title="class in compbio.engine">FilePuller</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/sequence/FastaSequence.html#getFormatedSequence(int)"><B>getFormatedSequence(int)</B></A> - \r
-Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>\r
-<DD>Format sequence per width letter in one string.\r
-<DT><A HREF="../compbio/data/sequence/FastaSequence.html#getFormattedFasta()"><B>getFormattedFasta()</B></A> - \r
-Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/Util.html#getFullPath(java.lang.String, java.lang.String)"><B>getFullPath(String, String)</B></A> - \r
-Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/Util.html" title="class in compbio.engine.client">Util</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/Argument.html#getFurtherDetails()"><B>getFurtherDetails()</B></A> - \r
-Method in interface compbio.metadata.<A HREF="../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/Option.html#getFurtherDetails()"><B>getFurtherDetails()</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
-<DD>The URL where further details about the option can be found\r
-<DT><A HREF="../compbio/data/sequence/AlignmentMetadata.html#getGapchar()"><B>getGapchar()</B></A> - \r
-Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence">AlignmentMetadata</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/ws/client/Jws2Client.html#getHost(java.lang.String[])"><B>getHost(String[])</B></A> - \r
-Static method in class compbio.ws.client.<A HREF="../compbio/ws/client/Jws2Client.html" title="class in compbio.ws.client">Jws2Client</A>\r
-<DD>Extracts host name from the command line\r
-<DT><A HREF="../compbio/data/sequence/FastaSequence.html#getId()"><B>getId()</B></A> - \r
-Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>\r
-<DD>Gets the value of id\r
-<DT><A HREF="../compbio/engine/client/ConfExecutable.html#getInput()"><B>getInput()</B></A> - \r
-Method in class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>\r
-<DD>Not all input paths are relative! Input path could be absolute!\r
-<DT><A HREF="../compbio/engine/client/Executable.html#getInput()"><B>getInput()</B></A> - \r
-Method in interface compbio.engine.client.<A HREF="../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/RunConfiguration.html#getInput()"><B>getInput()</B></A> - \r
-Method in class compbio.engine.client.<A HREF="../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/SkeletalExecutable.html#getInput()"><B>getInput()</B></A> - \r
-Method in class compbio.engine.client.<A HREF="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/_impl/BlastAll.html#getInput()"><B>getInput()</B></A> - \r
-Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/BlastAll.html" title="class in compbio.runner._impl">BlastAll</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/_impl/Disembl.html#getInput()"><B>getInput()</B></A> - \r
-Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Disembl.html" title="class in compbio.runner._impl">Disembl</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/_impl/Mcl.html#getInput()"><B>getInput()</B></A> - \r
-Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Mcl.html" title="class in compbio.runner._impl">Mcl</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/_impl/NetNglyc.html#getInput()"><B>getInput()</B></A> - \r
-Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/_impl/OB.html#getInput()"><B>getInput()</B></A> - \r
-Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/OB.html" title="class in compbio.runner._impl">OB</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/_impl/PSIBlast.html#getInput()"><B>getInput()</B></A> - \r
-Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/PSIBlast.html" title="class in compbio.runner._impl">PSIBlast</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/_impl/Ronn.html#getInput()"><B>getInput()</B></A> - \r
-Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Ronn.html" title="class in compbio.runner._impl">Ronn</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/_impl/RPSBlast.html#getInput()"><B>getInput()</B></A> - \r
-Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/RPSBlast.html" title="class in compbio.runner._impl">RPSBlast</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/cluster/drmaa/JobRunner.html#getInstance(compbio.engine.client.ConfiguredExecutable)"><B>getInstance(ConfiguredExecutable&lt;?&gt;)</B></A> - \r
-Static method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/JobRunner.html" title="class in compbio.engine.cluster.drmaa">JobRunner</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html#getIOWait()"><B>getIOWait()</B></A> - \r
-Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/jaxws/CancelJob.html#getJobId()"><B>getJobId()</B></A> - \r
-Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/CancelJob.html" title="class in compbio.data.msa.jaxws">CancelJob</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/jaxws/GetJobStatus.html#getJobId()"><B>getJobId()</B></A> - \r
-Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetJobStatus.html" title="class in compbio.data.msa.jaxws">GetJobStatus</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/jaxws/GetProgress.html#getJobId()"><B>getJobId()</B></A> - \r
-Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetProgress.html" title="class in compbio.data.msa.jaxws">GetProgress</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/jaxws/GetResult.html#getJobId()"><B>getJobId()</B></A> - \r
-Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetResult.html" title="class in compbio.data.msa.jaxws">GetResult</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/jaxws/PullExecStatistics.html#getJobId()"><B>getJobId()</B></A> - \r
-Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/PullExecStatistics.html" title="class in compbio.data.msa.jaxws">PullExecStatistics</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/jaxws/PullFile.html#getJobId()"><B>getJobId()</B></A> - \r
-Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/PullFile.html" title="class in compbio.data.msa.jaxws">PullFile</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html#getJobId()"><B>getJobId()</B></A> - \r
-Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/ClusterJobId.html#getJobId()"><B>getJobId()</B></A> - \r
-Method in class compbio.engine.<A HREF="../compbio/engine/ClusterJobId.html" title="class in compbio.engine">ClusterJobId</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/Job.html#getJobId()"><B>getJobId()</B></A> - \r
-Method in class compbio.engine.<A HREF="../compbio/engine/Job.html" title="class in compbio.engine">Job</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/cluster/drmaa/JobRunner.html#getJobInfo()"><B>getJobInfo()</B></A> - \r
-Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/JobRunner.html" title="class in compbio.engine.cluster.drmaa">JobRunner</A>\r
-<DD>This method will block before the calculation has completed and then
- return the object containing a job execution statistics\r
-<DT><A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html#getJobPriority()"><B>getJobPriority()</B></A> - \r
-Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/jaxws/GetJobStatus.html" title="class in compbio.data.msa.jaxws"><B>GetJobStatus</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/GetJobStatus.html#GetJobStatus()"><B>GetJobStatus()</B></A> - \r
-Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetJobStatus.html" title="class in compbio.data.msa.jaxws">GetJobStatus</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/MsaWS.html#getJobStatus(java.lang.String)"><B>getJobStatus(String)</B></A> - \r
-Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>\r
-<DD>Return the status of the job.\r
-<DT><A HREF="../compbio/engine/AsyncExecutor.html#getJobStatus(java.lang.String)"><B>getJobStatus(String)</B></A> - \r
-Method in interface compbio.engine.<A HREF="../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine">AsyncExecutor</A>\r
-<DD>Query the status of the job\r
-<DT><A HREF="../compbio/engine/cluster/drmaa/AsyncJobRunner.html#getJobStatus(java.lang.String)"><B>getJobStatus(String)</B></A> - \r
-Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/AsyncJobRunner.html" title="class in compbio.engine.cluster.drmaa">AsyncJobRunner</A>\r
-<DD>This will never return clust.engine.JobStatus.CANCELLED as for sun grid
- engine cancelled job is the same as failed.\r
-<DT><A HREF="../compbio/engine/cluster/drmaa/ClusterSession.html#getJobStatus(compbio.engine.ClusterJobId)"><B>getJobStatus(ClusterJobId)</B></A> - \r
-Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/ClusterSession.html" title="class in compbio.engine.cluster.drmaa">ClusterSession</A>\r
-<DD>Apparently completed jobs cannot be found! If this happened most likely
- that the job is not running any more and Most likely it has been
- cancelled, finished or failed.\r
-<DT><A HREF="../compbio/engine/cluster/drmaa/ClusterSession.html#getJobStatus(int)"><B>getJobStatus(int)</B></A> - \r
-Static method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/ClusterSession.html" title="class in compbio.engine.cluster.drmaa">ClusterSession</A>\r
-<DD><B>Deprecated.</B>&nbsp;\r
-<DT><A HREF="../compbio/engine/cluster/drmaa/JobRunner.html#getJobStatus()"><B>getJobStatus()</B></A> - \r
-Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/JobRunner.html" title="class in compbio.engine.cluster.drmaa">JobRunner</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/local/AsyncLocalRunner.html#getJobStatus(java.lang.String)"><B>getJobStatus(String)</B></A> - \r
-Method in class compbio.engine.local.<A HREF="../compbio/engine/local/AsyncLocalRunner.html" title="class in compbio.engine.local">AsyncLocalRunner</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/local/LocalEngineUtil.html#getJobStatus(java.util.concurrent.Future)"><B>getJobStatus(Future&lt;ConfiguredExecutable&lt;?&gt;&gt;)</B></A> - \r
-Static method in class compbio.engine.local.<A HREF="../compbio/engine/local/LocalEngineUtil.html" title="class in compbio.engine.local">LocalEngineUtil</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/local/LocalRunner.html#getJobStatus()"><B>getJobStatus()</B></A> - \r
-Method in class compbio.engine.local.<A HREF="../compbio/engine/local/LocalRunner.html" title="class in compbio.engine.local">LocalRunner</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/SyncExecutor.html#getJobStatus()"><B>getJobStatus()</B></A> - \r
-Method in interface compbio.engine.<A HREF="../compbio/engine/SyncExecutor.html" title="interface in compbio.engine">SyncExecutor</A>\r
-<DD>Query the status of the job by its id.\r
-<DT><A HREF="../compbio/ws/server/ClustalWS.html#getJobStatus(java.lang.String)"><B>getJobStatus(String)</B></A> - \r
-Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ClustalWS.html" title="class in compbio.ws.server">ClustalWS</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/ws/server/MafftWS.html#getJobStatus(java.lang.String)"><B>getJobStatus(String)</B></A> - \r
-Method in class compbio.ws.server.<A HREF="../compbio/ws/server/MafftWS.html" title="class in compbio.ws.server">MafftWS</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/ws/server/MuscleWS.html#getJobStatus(java.lang.String)"><B>getJobStatus(String)</B></A> - \r
-Method in class compbio.ws.server.<A HREF="../compbio/ws/server/MuscleWS.html" title="class in compbio.ws.server">MuscleWS</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/ws/server/ProbconsWS.html#getJobStatus(java.lang.String)"><B>getJobStatus(String)</B></A> - \r
-Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ProbconsWS.html" title="class in compbio.ws.server">ProbconsWS</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/ws/server/TcoffeeWS.html#getJobStatus(java.lang.String)"><B>getJobStatus(String)</B></A> - \r
-Method in class compbio.ws.server.<A HREF="../compbio/ws/server/TcoffeeWS.html" title="class in compbio.ws.server">TcoffeeWS</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/ws/server/WSUtil.html#getJobStatus(java.lang.String)"><B>getJobStatus(String)</B></A> - \r
-Static method in class compbio.ws.server.<A HREF="../compbio/ws/server/WSUtil.html" title="class in compbio.ws.server">WSUtil</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/jaxws/GetJobStatusResponse.html" title="class in compbio.data.msa.jaxws"><B>GetJobStatusResponse</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/GetJobStatusResponse.html#GetJobStatusResponse()"><B>GetJobStatusResponse()</B></A> - \r
-Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetJobStatusResponse.html" title="class in compbio.data.msa.jaxws">GetJobStatusResponse</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/sequence/FastaSequence.html#getLength()"><B>getLength()</B></A> - \r
-Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/jaxws/GetLimit.html" title="class in compbio.data.msa.jaxws"><B>GetLimit</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/GetLimit.html#GetLimit()"><B>GetLimit()</B></A> - \r
-Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetLimit.html" title="class in compbio.data.msa.jaxws">GetLimit</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/MsaWS.html#getLimit(java.lang.String)"><B>getLimit(String)</B></A> - \r
-Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>\r
-<DD>Get a Limit for a preset.\r
-<DT><A HREF="../compbio/engine/client/ConfExecutable.html#getLimit(java.lang.String)"><B>getLimit(String)</B></A> - \r
-Method in class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/Executable.html#getLimit(java.lang.String)"><B>getLimit(String)</B></A> - \r
-Method in interface compbio.engine.client.<A HREF="../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/_impl/NetNglyc.html#getLimit(java.lang.String)"><B>getLimit(String)</B></A> - \r
-Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/_SkeletalCommandBuilder.html#getLimit(java.lang.String)"><B>getLimit(String)</B></A> - \r
-Method in class compbio.runner.<A HREF="../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/msa/ClustalW.html#getLimit(java.lang.String)"><B>getLimit(String)</B></A> - \r
-Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/msa/Mafft.html#getLimit(java.lang.String)"><B>getLimit(String)</B></A> - \r
-Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/msa/Muscle.html#getLimit(java.lang.String)"><B>getLimit(String)</B></A> - \r
-Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/msa/Probcons.html#getLimit(java.lang.String)"><B>getLimit(String)</B></A> - \r
-Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/msa/Tcoffee.html#getLimit(java.lang.String)"><B>getLimit(String)</B></A> - \r
-Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/psiblast/PsiBlast.html#getLimit(java.lang.String)"><B>getLimit(String)</B></A> - \r
-Method in class compbio.runner.psiblast.<A HREF="../compbio/runner/psiblast/PsiBlast.html" title="class in compbio.runner.psiblast">PsiBlast</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/ws/server/ClustalWS.html#getLimit(java.lang.String)"><B>getLimit(String)</B></A> - \r
-Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ClustalWS.html" title="class in compbio.ws.server">ClustalWS</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/ws/server/MafftWS.html#getLimit(java.lang.String)"><B>getLimit(String)</B></A> - \r
-Method in class compbio.ws.server.<A HREF="../compbio/ws/server/MafftWS.html" title="class in compbio.ws.server">MafftWS</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/ws/server/MuscleWS.html#getLimit(java.lang.String)"><B>getLimit(String)</B></A> - \r
-Method in class compbio.ws.server.<A HREF="../compbio/ws/server/MuscleWS.html" title="class in compbio.ws.server">MuscleWS</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/ws/server/ProbconsWS.html#getLimit(java.lang.String)"><B>getLimit(String)</B></A> - \r
-Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ProbconsWS.html" title="class in compbio.ws.server">ProbconsWS</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/ws/server/TcoffeeWS.html#getLimit(java.lang.String)"><B>getLimit(String)</B></A> - \r
-Method in class compbio.ws.server.<A HREF="../compbio/ws/server/TcoffeeWS.html" title="class in compbio.ws.server">TcoffeeWS</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/LimitsManager.html#getLimitByName(java.lang.String)"><B>getLimitByName(String)</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/jaxws/GetLimitResponse.html" title="class in compbio.data.msa.jaxws"><B>GetLimitResponse</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/GetLimitResponse.html#GetLimitResponse()"><B>GetLimitResponse()</B></A> - \r
-Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetLimitResponse.html" title="class in compbio.data.msa.jaxws">GetLimitResponse</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/jaxws/GetLimits.html" title="class in compbio.data.msa.jaxws"><B>GetLimits</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/GetLimits.html#GetLimits()"><B>GetLimits()</B></A> - \r
-Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetLimits.html" title="class in compbio.data.msa.jaxws">GetLimits</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/MsaWS.html#getLimits()"><B>getLimits()</B></A> - \r
-Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>\r
-<DD>List Limits supported by a web service.\r
-<DT><A HREF="../compbio/engine/client/ConfExecutable.html#getLimits()"><B>getLimits()</B></A> - \r
-Method in class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/Executable.html#getLimits()"><B>getLimits()</B></A> - \r
-Method in interface compbio.engine.client.<A HREF="../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/LimitsManager.html#getLimits()"><B>getLimits()</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/_impl/NetNglyc.html#getLimits()"><B>getLimits()</B></A> - \r
-Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/_SkeletalCommandBuilder.html#getLimits()"><B>getLimits()</B></A> - \r
-Method in class compbio.runner.<A HREF="../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/msa/ClustalW.html#getLimits()"><B>getLimits()</B></A> - \r
-Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/msa/Mafft.html#getLimits()"><B>getLimits()</B></A> - \r
-Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/msa/Muscle.html#getLimits()"><B>getLimits()</B></A> - \r
-Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/msa/Probcons.html#getLimits()"><B>getLimits()</B></A> - \r
-Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/msa/Tcoffee.html#getLimits()"><B>getLimits()</B></A> - \r
-Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/psiblast/PsiBlast.html#getLimits()"><B>getLimits()</B></A> - \r
-Method in class compbio.runner.psiblast.<A HREF="../compbio/runner/psiblast/PsiBlast.html" title="class in compbio.runner.psiblast">PsiBlast</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/Util.html#getLimits(java.lang.Class)"><B>getLimits(Class&lt;? extends Executable&lt;T&gt;&gt;)</B></A> - \r
-Static method in class compbio.runner.<A HREF="../compbio/runner/Util.html" title="class in compbio.runner">Util</A>\r
-<DD>For now just assume that all parameters which came in needs setting it
- will be a client responsibility to prepare RunnerConfig object then\r
-<DT><A HREF="../compbio/ws/server/ClustalWS.html#getLimits()"><B>getLimits()</B></A> - \r
-Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ClustalWS.html" title="class in compbio.ws.server">ClustalWS</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/ws/server/MafftWS.html#getLimits()"><B>getLimits()</B></A> - \r
-Method in class compbio.ws.server.<A HREF="../compbio/ws/server/MafftWS.html" title="class in compbio.ws.server">MafftWS</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/ws/server/MuscleWS.html#getLimits()"><B>getLimits()</B></A> - \r
-Method in class compbio.ws.server.<A HREF="../compbio/ws/server/MuscleWS.html" title="class in compbio.ws.server">MuscleWS</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/ws/server/ProbconsWS.html#getLimits()"><B>getLimits()</B></A> - \r
-Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ProbconsWS.html" title="class in compbio.ws.server">ProbconsWS</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/ws/server/TcoffeeWS.html#getLimits()"><B>getLimits()</B></A> - \r
-Method in class compbio.ws.server.<A HREF="../compbio/ws/server/TcoffeeWS.html" title="class in compbio.ws.server">TcoffeeWS</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/jaxws/GetLimitsResponse.html" title="class in compbio.data.msa.jaxws"><B>GetLimitsResponse</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/GetLimitsResponse.html#GetLimitsResponse()"><B>GetLimitsResponse()</B></A> - \r
-Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetLimitsResponse.html" title="class in compbio.data.msa.jaxws">GetLimitsResponse</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/conf/PropertyHelperManager.html#getLocalPath()"><B>getLocalPath()</B></A> - \r
-Static method in class compbio.engine.conf.<A HREF="../compbio/engine/conf/PropertyHelperManager.html" title="class in compbio.engine.conf">PropertyHelperManager</A>\r
-<DD>Method return the absolute path to the project root directory.\r
-<DT><A HREF="../compbio/metadata/ValueConstrain.html#getMax()"><B>getMax()</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html#getMaxVMem()"><B>getMaxVMem()</B></A> - \r
-Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/_impl/Runners.html#getMclRunnable(java.lang.String)"><B>getMclRunnable(String)</B></A> - \r
-Static method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Runners.html" title="class in compbio.runner._impl">Runners</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/cluster/dundee/_Queue.html#getMemoryLimit()"><B>getMemoryLimit()</B></A> - \r
-Method in enum compbio.engine.cluster.dundee.<A HREF="../compbio/engine/cluster/dundee/_Queue.html" title="enum in compbio.engine.cluster.dundee">_Queue</A>\r
-<DD>return max memory limit in Mb\r
-<DT><A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html#getMemoryStat()"><B>getMemoryStat()</B></A> - \r
-Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/jaxws/JobExecutionExceptionBean.html#getMessage()"><B>getMessage()</B></A> - \r
-Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/JobExecutionExceptionBean.html" title="class in compbio.data.msa.jaxws">JobExecutionExceptionBean</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/jaxws/JobSubmissionExceptionBean.html#getMessage()"><B>getMessage()</B></A> - \r
-Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/JobSubmissionExceptionBean.html" title="class in compbio.data.msa.jaxws">JobSubmissionExceptionBean</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html#getMessage()"><B>getMessage()</B></A> - \r
-Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html" title="class in compbio.data.msa.jaxws">LimitExceededExceptionBean</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/jaxws/ResultNotAvailableExceptionBean.html#getMessage()"><B>getMessage()</B></A> - \r
-Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/ResultNotAvailableExceptionBean.html" title="class in compbio.data.msa.jaxws">ResultNotAvailableExceptionBean</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/jaxws/UnsupportedRuntimeExceptionBean.html#getMessage()"><B>getMessage()</B></A> - \r
-Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/UnsupportedRuntimeExceptionBean.html" title="class in compbio.data.msa.jaxws">UnsupportedRuntimeExceptionBean</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/jaxws/WrongParameterExceptionBean.html#getMessage()"><B>getMessage()</B></A> - \r
-Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/WrongParameterExceptionBean.html" title="class in compbio.data.msa.jaxws">WrongParameterExceptionBean</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/sequence/Alignment.html#getMetadata()"><B>getMetadata()</B></A> - \r
-Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/ValueConstrain.html#getMin()"><B>getMin()</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/Argument.html#getName()"><B>getName()</B></A> - \r
-Method in interface compbio.metadata.<A HREF="../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/Option.html#getName()"><B>getName()</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
-<DD>Human readable name of the option\r
-<DT><A HREF="../compbio/metadata/Preset.html#getName()"><B>getName()</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/_SkeletalCommandBuilder.html#getName()"><B>getName()</B></A> - \r
-Method in class compbio.runner.<A HREF="../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/_NativeSpecHelper.html#getNativeSpec()"><B>getNativeSpec()</B></A> - \r
-Method in class compbio.runner.<A HREF="../compbio/runner/_NativeSpecHelper.html" title="class in compbio.runner">_NativeSpecHelper</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/ClusterNativeSpecExecutable.html#getNativeSpecs()"><B>getNativeSpecs()</B></A> - \r
-Method in interface compbio.engine.client.<A HREF="../compbio/engine/client/ClusterNativeSpecExecutable.html" title="interface in compbio.engine.client">ClusterNativeSpecExecutable</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/msa/Tcoffee.html#getNativeSpecs()"><B>getNativeSpecs()</B></A> - \r
-Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/_impl/Runners.html#getNetNglycRunnable(java.lang.String)"><B>getNetNglycRunnable(String)</B></A> - \r
-Static method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Runners.html" title="class in compbio.runner._impl">Runners</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/ChunkHolder.html#getNextPosition()"><B>getNextPosition()</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html#getNumberOfSequencesAllowed()"><B>getNumberOfSequencesAllowed()</B></A> - \r
-Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html" title="class in compbio.data.msa.jaxws">LimitExceededExceptionBean</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/LimitExceededException.html#getNumberOfSequencesAllowed()"><B>getNumberOfSequencesAllowed()</B></A> - \r
-Method in exception compbio.metadata.<A HREF="../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/_impl/Runners.html#getOBRunnable(java.lang.String)"><B>getOBRunnable(String)</B></A> - \r
-Static method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Runners.html" title="class in compbio.runner._impl">Runners</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/sequence/FastaSequence.html#getOnelineFasta()"><B>getOnelineFasta()</B></A> - \r
-Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/Parameter.html#getOptionName()"><B>getOptionName()</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/Option.html#getOptionNames()"><B>getOptionNames()</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/jaxws/CustomAlign.html#getOptions()"><B>getOptions()</B></A> - \r
-Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/CustomAlign.html" title="class in compbio.data.msa.jaxws">CustomAlign</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/Preset.html#getOptions()"><B>getOptions()</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/RunnerConfig.html#getOptions()"><B>getOptions()</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/OptionCombinator.html#getOptionsAtRandom()"><B>getOptionsAtRandom()</B></A> - \r
-Method in class compbio.runner.<A HREF="../compbio/runner/OptionCombinator.html" title="class in compbio.runner">OptionCombinator</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/ConfExecutable.html#getOutput()"><B>getOutput()</B></A> - \r
-Method in class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/Executable.html#getOutput()"><B>getOutput()</B></A> - \r
-Method in interface compbio.engine.client.<A HREF="../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/RunConfiguration.html#getOutput()"><B>getOutput()</B></A> - \r
-Method in class compbio.engine.client.<A HREF="../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/SkeletalExecutable.html#getOutput()"><B>getOutput()</B></A> - \r
-Method in class compbio.engine.client.<A HREF="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/_impl/NetNglyc.html#getOutput()"><B>getOutput()</B></A> - \r
-Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/_SkeletalCommandBuilder.html#getOutput()"><B>getOutput()</B></A> - \r
-Method in class compbio.runner.<A HREF="../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/ConfExecutable.html#getParameters()"><B>getParameters()</B></A> - \r
-Method in class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/ConfExecutable.html#getParameters(compbio.engine.client.Executable.ExecProvider)"><B>getParameters(Executable.ExecProvider)</B></A> - \r
-Method in class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/ConfiguredExecutable.html#getParameters()"><B>getParameters()</B></A> - \r
-Method in interface compbio.engine.client.<A HREF="../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/Executable.html#getParameters(compbio.engine.client.Executable.ExecProvider)"><B>getParameters(Executable.ExecProvider)</B></A> - \r
-Method in interface compbio.engine.client.<A HREF="../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/RunConfiguration.html#getParameters()"><B>getParameters()</B></A> - \r
-Method in class compbio.engine.client.<A HREF="../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/SkeletalExecutable.html#getParameters(compbio.engine.client.Executable.ExecProvider)"><B>getParameters(Executable.ExecProvider)</B></A> - \r
-Method in class compbio.engine.client.<A HREF="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/RunnerConfig.html#getParameters()"><B>getParameters()</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/_impl/NetNglyc.html#getParameters(compbio.engine.client.Executable.ExecProvider)"><B>getParameters(Executable.ExecProvider)</B></A> - \r
-Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/_SkeletalCommandBuilder.html#getParameters(compbio.engine.client.Executable.ExecProvider)"><B>getParameters(Executable.ExecProvider)</B></A> - \r
-Method in class compbio.runner.<A HREF="../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/msa/Tcoffee.html#getParameters(compbio.engine.client.Executable.ExecProvider)"><B>getParameters(Executable.ExecProvider)</B></A> - \r
-Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/CommandBuilder.html#getParamValue(java.lang.String)"><B>getParamValue(String)</B></A> - \r
-Method in class compbio.engine.client.<A HREF="../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/jaxws/PullExecStatistics.html#getPosition()"><B>getPosition()</B></A> - \r
-Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/PullExecStatistics.html" title="class in compbio.data.msa.jaxws">PullExecStatistics</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/jaxws/PullFile.html#getPosition()"><B>getPosition()</B></A> - \r
-Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/PullFile.html" title="class in compbio.data.msa.jaxws">PullFile</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/Argument.html#getPossibleValues()"><B>getPossibleValues()</B></A> - \r
-Method in interface compbio.metadata.<A HREF="../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/Option.html#getPossibleValues()"><B>getPossibleValues()</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
-<DD>List of possible optionNames\r
-<DT><A HREF="../compbio/metadata/Parameter.html#getPossibleValues()"><B>getPossibleValues()</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>\r
-<DD>List is more convenient to work with\r
-<DT><A HREF="../compbio/data/msa/jaxws/PresetAlign.html#getPreset()"><B>getPreset()</B></A> - \r
-Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/PresetAlign.html" title="class in compbio.data.msa.jaxws">PresetAlign</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/Limit.html#getPreset()"><B>getPreset()</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/PresetManager.html#getPresetByName(java.lang.String)"><B>getPresetByName(String)</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/jaxws/GetLimit.html#getPresetName()"><B>getPresetName()</B></A> - \r
-Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetLimit.html" title="class in compbio.data.msa.jaxws">GetLimit</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/jaxws/GetPresets.html" title="class in compbio.data.msa.jaxws"><B>GetPresets</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/GetPresets.html#GetPresets()"><B>GetPresets()</B></A> - \r
-Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetPresets.html" title="class in compbio.data.msa.jaxws">GetPresets</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/MsaWS.html#getPresets()"><B>getPresets()</B></A> - \r
-Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>\r
-<DD>Get presets supported by a web service\r
-<DT><A HREF="../compbio/metadata/PresetManager.html#getPresets()"><B>getPresets()</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/Util.html#getPresets(java.lang.Class)"><B>getPresets(Class&lt;? extends Executable&lt;T&gt;&gt;)</B></A> - \r
-Static method in class compbio.runner.<A HREF="../compbio/runner/Util.html" title="class in compbio.runner">Util</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/ws/server/ClustalWS.html#getPresets()"><B>getPresets()</B></A> - \r
-Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ClustalWS.html" title="class in compbio.ws.server">ClustalWS</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/ws/server/MafftWS.html#getPresets()"><B>getPresets()</B></A> - \r
-Method in class compbio.ws.server.<A HREF="../compbio/ws/server/MafftWS.html" title="class in compbio.ws.server">MafftWS</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/ws/server/MuscleWS.html#getPresets()"><B>getPresets()</B></A> - \r
-Method in class compbio.ws.server.<A HREF="../compbio/ws/server/MuscleWS.html" title="class in compbio.ws.server">MuscleWS</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/ws/server/ProbconsWS.html#getPresets()"><B>getPresets()</B></A> - \r
-Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ProbconsWS.html" title="class in compbio.ws.server">ProbconsWS</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/ws/server/TcoffeeWS.html#getPresets()"><B>getPresets()</B></A> - \r
-Method in class compbio.ws.server.<A HREF="../compbio/ws/server/TcoffeeWS.html" title="class in compbio.ws.server">TcoffeeWS</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/jaxws/GetPresetsResponse.html" title="class in compbio.data.msa.jaxws"><B>GetPresetsResponse</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/GetPresetsResponse.html#GetPresetsResponse()"><B>GetPresetsResponse()</B></A> - \r
-Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetPresetsResponse.html" title="class in compbio.data.msa.jaxws">GetPresetsResponse</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/RunnerConfig.html#getPrmSeparator()"><B>getPrmSeparator()</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/sequence/AlignmentMetadata.html#getProgram()"><B>getProgram()</B></A> - \r
-Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence">AlignmentMetadata</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/jaxws/GetProgress.html" title="class in compbio.data.msa.jaxws"><B>GetProgress</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/GetProgress.html#GetProgress()"><B>GetProgress()</B></A> - \r
-Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetProgress.html" title="class in compbio.data.msa.jaxws">GetProgress</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/FilePuller.html#getProgress()"><B>getProgress()</B></A> - \r
-Method in class compbio.engine.<A HREF="../compbio/engine/FilePuller.html" title="class in compbio.engine">FilePuller</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/ProgressGetter.html#getProgress(java.lang.String)"><B>getProgress(String)</B></A> - \r
-Static method in class compbio.engine.<A HREF="../compbio/engine/ProgressGetter.html" title="class in compbio.engine">ProgressGetter</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/ws/server/WSUtil.html#getProgress(java.lang.String)"><B>getProgress(String)</B></A> - \r
-Static method in class compbio.ws.server.<A HREF="../compbio/ws/server/WSUtil.html" title="class in compbio.ws.server">WSUtil</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/jaxws/GetProgressResponse.html" title="class in compbio.data.msa.jaxws"><B>GetProgressResponse</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/GetProgressResponse.html#GetProgressResponse()"><B>GetProgressResponse()</B></A> - \r
-Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetProgressResponse.html" title="class in compbio.data.msa.jaxws">GetProgressResponse</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/conf/PropertyHelperManager.html#getPropertyHelper()"><B>getPropertyHelper()</B></A> - \r
-Static method in class compbio.engine.conf.<A HREF="../compbio/engine/conf/PropertyHelperManager.html" title="class in compbio.engine.conf">PropertyHelperManager</A>\r
-<DD>Ways to fix path problem: 1) find a path to WEB-INF directory based on
- the path to a known class.\r
-<DT><A HREF="../compbio/runner/_impl/Runners.html#getPSIBlastRunnable(java.lang.String)"><B>getPSIBlastRunnable(String)</B></A> - \r
-Static method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Runners.html" title="class in compbio.runner._impl">Runners</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/cluster/dundee/_Queue.html#getQueue(int, int)"><B>getQueue(int, int)</B></A> - \r
-Static method in enum compbio.engine.cluster.dundee.<A HREF="../compbio/engine/cluster/dundee/_Queue.html" title="enum in compbio.engine.cluster.dundee">_Queue</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/cluster/dundee/_Queue.html#getQueue(java.lang.String)"><B>getQueue(String)</B></A> - \r
-Method in enum compbio.engine.cluster.dundee.<A HREF="../compbio/engine/cluster/dundee/_Queue.html" title="enum in compbio.engine.cluster.dundee">_Queue</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/_NativeSpecHelper.html#getQueue()"><B>getQueue()</B></A> - \r
-Method in class compbio.runner.<A HREF="../compbio/runner/_NativeSpecHelper.html" title="class in compbio.runner">_NativeSpecHelper</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/cluster/dundee/_Queue.html#getQueueByMemoryRequirements(int)"><B>getQueueByMemoryRequirements(int)</B></A> - \r
-Static method in enum compbio.engine.cluster.dundee.<A HREF="../compbio/engine/cluster/dundee/_Queue.html" title="enum in compbio.engine.cluster.dundee">_Queue</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html#getRawUsage()"><B>getRawUsage()</B></A> - \r
-Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/local/LocalEngineUtil.html#getRecordedJobStatus(java.lang.String)"><B>getRecordedJobStatus(String)</B></A> - \r
-Static method in class compbio.engine.local.<A HREF="../compbio/engine/local/LocalEngineUtil.html" title="class in compbio.engine.local">LocalEngineUtil</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/ws/server/WSUtil.html#getRemoteAddress(javax.xml.ws.WebServiceContext)"><B>getRemoteAddress(WebServiceContext)</B></A> - \r
-Static method in class compbio.ws.server.<A HREF="../compbio/ws/server/WSUtil.html" title="class in compbio.ws.server">WSUtil</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/jaxws/GetResult.html" title="class in compbio.data.msa.jaxws"><B>GetResult</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/GetResult.html#GetResult()"><B>GetResult()</B></A> - \r
-Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetResult.html" title="class in compbio.data.msa.jaxws">GetResult</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/MsaWS.html#getResult(java.lang.String)"><B>getResult(String)</B></A> - \r
-Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>\r
-<DD>Return the result of the job.\r
-<DT><A HREF="../compbio/ws/server/ClustalWS.html#getResult(java.lang.String)"><B>getResult(String)</B></A> - \r
-Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ClustalWS.html" title="class in compbio.ws.server">ClustalWS</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/ws/server/MafftWS.html#getResult(java.lang.String)"><B>getResult(String)</B></A> - \r
-Method in class compbio.ws.server.<A HREF="../compbio/ws/server/MafftWS.html" title="class in compbio.ws.server">MafftWS</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/ws/server/MuscleWS.html#getResult(java.lang.String)"><B>getResult(String)</B></A> - \r
-Method in class compbio.ws.server.<A HREF="../compbio/ws/server/MuscleWS.html" title="class in compbio.ws.server">MuscleWS</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/ws/server/ProbconsWS.html#getResult(java.lang.String)"><B>getResult(String)</B></A> - \r
-Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ProbconsWS.html" title="class in compbio.ws.server">ProbconsWS</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/ws/server/TcoffeeWS.html#getResult(java.lang.String)"><B>getResult(String)</B></A> - \r
-Method in class compbio.ws.server.<A HREF="../compbio/ws/server/TcoffeeWS.html" title="class in compbio.ws.server">TcoffeeWS</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/jaxws/GetResultResponse.html" title="class in compbio.data.msa.jaxws"><B>GetResultResponse</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/GetResultResponse.html#GetResultResponse()"><B>GetResultResponse()</B></A> - \r
-Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetResultResponse.html" title="class in compbio.data.msa.jaxws">GetResultResponse</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/AsyncExecutor.html#getResults(java.lang.String)"><B>getResults(String)</B></A> - \r
-Method in interface compbio.engine.<A HREF="../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine">AsyncExecutor</A>\r
-<DD>Retrieve the results of the job.\r
-<DT><A HREF="../compbio/engine/client/ConfExecutable.html#getResults()"><B>getResults()</B></A> - \r
-Method in class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/ConfExecutable.html#getResults(java.lang.String)"><B>getResults(String)</B></A> - \r
-Method in class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/ConfiguredExecutable.html#getResults()"><B>getResults()</B></A> - \r
-Method in interface compbio.engine.client.<A HREF="../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/Executable.html#getResults(java.lang.String)"><B>getResults(String)</B></A> - \r
-Method in interface compbio.engine.client.<A HREF="../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/cluster/drmaa/AsyncJobRunner.html#getResults(java.lang.String)"><B>getResults(String)</B></A> - \r
-Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/AsyncJobRunner.html" title="class in compbio.engine.cluster.drmaa">AsyncJobRunner</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/cluster/drmaa/ClusterSession.html#getResults(java.lang.String)"><B>getResults(String)</B></A> - \r
-Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/ClusterSession.html" title="class in compbio.engine.cluster.drmaa">ClusterSession</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/local/AsyncLocalRunner.html#getResults(java.lang.String)"><B>getResults(String)</B></A> - \r
-Method in class compbio.engine.local.<A HREF="../compbio/engine/local/AsyncLocalRunner.html" title="class in compbio.engine.local">AsyncLocalRunner</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/local/LocalEngineUtil.html#getResults(java.util.concurrent.Future, java.lang.String)"><B>getResults(Future&lt;ConfiguredExecutable&lt;?&gt;&gt;, String)</B></A> - \r
-Static method in class compbio.engine.local.<A HREF="../compbio/engine/local/LocalEngineUtil.html" title="class in compbio.engine.local">LocalEngineUtil</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/_impl/NetNglyc.html#getResults(java.lang.String)"><B>getResults(String)</B></A> - \r
-Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/_SkeletalCommandBuilder.html#getResults(java.lang.String)"><B>getResults(String)</B></A> - \r
-Method in class compbio.runner.<A HREF="../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/msa/ClustalW.html#getResults(java.lang.String)"><B>getResults(String)</B></A> - \r
-Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/msa/Mafft.html#getResults(java.lang.String)"><B>getResults(String)</B></A> - \r
-Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/msa/Muscle.html#getResults(java.lang.String)"><B>getResults(String)</B></A> - \r
-Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/msa/Probcons.html#getResults(java.lang.String)"><B>getResults(String)</B></A> - \r
-Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/msa/Tcoffee.html#getResults(java.lang.String)"><B>getResults(String)</B></A> - \r
-Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/psiblast/PsiBlast.html#getResults(java.lang.String)"><B>getResults(String)</B></A> - \r
-Method in class compbio.runner.psiblast.<A HREF="../compbio/runner/psiblast/PsiBlast.html" title="class in compbio.runner.psiblast">PsiBlast</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/jaxws/AlignResponse.html#getReturn()"><B>getReturn()</B></A> - \r
-Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/AlignResponse.html" title="class in compbio.data.msa.jaxws">AlignResponse</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/jaxws/CustomAlignResponse.html#getReturn()"><B>getReturn()</B></A> - \r
-Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/CustomAlignResponse.html" title="class in compbio.data.msa.jaxws">CustomAlignResponse</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/jaxws/GetJobStatusResponse.html#getReturn()"><B>getReturn()</B></A> - \r
-Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetJobStatusResponse.html" title="class in compbio.data.msa.jaxws">GetJobStatusResponse</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/jaxws/GetLimitResponse.html#getReturn()"><B>getReturn()</B></A> - \r
-Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetLimitResponse.html" title="class in compbio.data.msa.jaxws">GetLimitResponse</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/jaxws/GetLimitsResponse.html#getReturn()"><B>getReturn()</B></A> - \r
-Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetLimitsResponse.html" title="class in compbio.data.msa.jaxws">GetLimitsResponse</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/jaxws/GetPresetsResponse.html#getReturn()"><B>getReturn()</B></A> - \r
-Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetPresetsResponse.html" title="class in compbio.data.msa.jaxws">GetPresetsResponse</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/jaxws/GetProgressResponse.html#getReturn()"><B>getReturn()</B></A> - \r
-Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetProgressResponse.html" title="class in compbio.data.msa.jaxws">GetProgressResponse</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/jaxws/GetResultResponse.html#getReturn()"><B>getReturn()</B></A> - \r
-Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetResultResponse.html" title="class in compbio.data.msa.jaxws">GetResultResponse</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/jaxws/GetRunnerOptionsResponse.html#getReturn()"><B>getReturn()</B></A> - \r
-Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetRunnerOptionsResponse.html" title="class in compbio.data.msa.jaxws">GetRunnerOptionsResponse</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/jaxws/PresetAlignResponse.html#getReturn()"><B>getReturn()</B></A> - \r
-Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/PresetAlignResponse.html" title="class in compbio.data.msa.jaxws">PresetAlignResponse</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/jaxws/PullExecStatisticsResponse.html#getReturn()"><B>getReturn()</B></A> - \r
-Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/PullExecStatisticsResponse.html" title="class in compbio.data.msa.jaxws">PullExecStatisticsResponse</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/jaxws/PullFileResponse.html#getReturn()"><B>getReturn()</B></A> - \r
-Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/PullFileResponse.html" title="class in compbio.data.msa.jaxws">PullFileResponse</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/_impl/Runners.html#getRonnRunnable(java.lang.String)"><B>getRonnRunnable(String)</B></A> - \r
-Static method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Runners.html" title="class in compbio.runner._impl">Runners</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/_impl/Environment.html#getRPSBlastDatabasesDir()"><B>getRPSBlastDatabasesDir()</B></A> - \r
-Static method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Environment.html" title="class in compbio.runner._impl">Environment</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/_impl/Runners.html#getRPSBlastRunnable(java.lang.String)"><B>getRPSBlastRunnable(String)</B></A> - \r
-Static method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Runners.html" title="class in compbio.runner._impl">Runners</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/ConfExecutable.html#getRunConfiguration()"><B>getRunConfiguration()</B></A> - \r
-Method in class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/RunConfiguration.html#getRunnerClassName()"><B>getRunnerClassName()</B></A> - \r
-Method in class compbio.engine.client.<A HREF="../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/PresetManager.html#getRunnerClassName()"><B>getRunnerClassName()</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/RunnerConfig.html#getRunnerClassName()"><B>getRunnerClassName()</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/ConfExecutable.html#getRunnerLimits(java.lang.Class)"><B>getRunnerLimits(Class&lt;? extends Executable&lt;V&gt;&gt;)</B></A> - \r
-Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>\r
-<DD>This method should be executed once and result of its execution reused.\r
-<DT><A HREF="../compbio/data/msa/jaxws/GetRunnerOptions.html" title="class in compbio.data.msa.jaxws"><B>GetRunnerOptions</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/GetRunnerOptions.html#GetRunnerOptions()"><B>GetRunnerOptions()</B></A> - \r
-Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetRunnerOptions.html" title="class in compbio.data.msa.jaxws">GetRunnerOptions</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/MsaWS.html#getRunnerOptions()"><B>getRunnerOptions()</B></A> - \r
-Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>\r
-<DD>Get options supported by a web service\r
-<DT><A HREF="../compbio/engine/client/ConfExecutable.html#getRunnerOptions(java.lang.Class)"><B>getRunnerOptions(Class&lt;? extends Executable&lt;V&gt;&gt;)</B></A> - \r
-Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/ws/server/ClustalWS.html#getRunnerOptions()"><B>getRunnerOptions()</B></A> - \r
-Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ClustalWS.html" title="class in compbio.ws.server">ClustalWS</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/ws/server/MafftWS.html#getRunnerOptions()"><B>getRunnerOptions()</B></A> - \r
-Method in class compbio.ws.server.<A HREF="../compbio/ws/server/MafftWS.html" title="class in compbio.ws.server">MafftWS</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/ws/server/MuscleWS.html#getRunnerOptions()"><B>getRunnerOptions()</B></A> - \r
-Method in class compbio.ws.server.<A HREF="../compbio/ws/server/MuscleWS.html" title="class in compbio.ws.server">MuscleWS</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/ws/server/ProbconsWS.html#getRunnerOptions()"><B>getRunnerOptions()</B></A> - \r
-Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ProbconsWS.html" title="class in compbio.ws.server">ProbconsWS</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/ws/server/TcoffeeWS.html#getRunnerOptions()"><B>getRunnerOptions()</B></A> - \r
-Method in class compbio.ws.server.<A HREF="../compbio/ws/server/TcoffeeWS.html" title="class in compbio.ws.server">TcoffeeWS</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/jaxws/GetRunnerOptionsResponse.html" title="class in compbio.data.msa.jaxws"><B>GetRunnerOptionsResponse</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/GetRunnerOptionsResponse.html#GetRunnerOptionsResponse()"><B>GetRunnerOptionsResponse()</B></A> - \r
-Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetRunnerOptionsResponse.html" title="class in compbio.data.msa.jaxws">GetRunnerOptionsResponse</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/ConfExecutable.html#getRunnerPresets(java.lang.Class)"><B>getRunnerPresets(Class&lt;? extends Executable&lt;V&gt;&gt;)</B></A> - \r
-Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/conf/RunnerConfigMarshaller.html#getSchema(java.lang.String)"><B>getSchema(String)</B></A> - \r
-Static method in class compbio.engine.conf.<A HREF="../compbio/engine/conf/RunnerConfigMarshaller.html" title="class in compbio.engine.conf">RunnerConfigMarshaller</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/Limit.html#getSeqNumber()"><B>getSeqNumber()</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/sequence/FastaSequence.html#getSequence()"><B>getSequence()</B></A> - \r
-Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>\r
-<DD>Gets the value of sequence\r
-<DT><A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html#getSequenceLenghtActual()"><B>getSequenceLenghtActual()</B></A> - \r
-Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html" title="class in compbio.data.msa.jaxws">LimitExceededExceptionBean</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/LimitExceededException.html#getSequenceLenghtActual()"><B>getSequenceLenghtActual()</B></A> - \r
-Method in exception compbio.metadata.<A HREF="../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html#getSequenceLenghtAllowed()"><B>getSequenceLenghtAllowed()</B></A> - \r
-Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html" title="class in compbio.data.msa.jaxws">LimitExceededExceptionBean</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/LimitExceededException.html#getSequenceLenghtAllowed()"><B>getSequenceLenghtAllowed()</B></A> - \r
-Method in exception compbio.metadata.<A HREF="../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/sequence/Alignment.html#getSequences()"><B>getSequences()</B></A> - \r
-Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/ws/client/Jws2Client.html#getServiceName(java.lang.String[])"><B>getServiceName(String[])</B></A> - \r
-Static method in class compbio.ws.client.<A HREF="../compbio/ws/client/Jws2Client.html" title="class in compbio.ws.client">Jws2Client</A>\r
-<DD>Extracts service name from the command line\r
-<DT><A HREF="../compbio/engine/cluster/drmaa/ClusterSession.html#getSession()"><B>getSession()</B></A> - \r
-Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/ClusterSession.html" title="class in compbio.engine.cluster.drmaa">ClusterSession</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/sequence/Alignment.html#getSize()"><B>getSize()</B></A> - \r
-Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html#getStartTime()"><B>getStartTime()</B></A> - \r
-Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/msa/ClustalW.html#getStatFile()"><B>getStatFile()</B></A> - \r
-Static method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/msa/Muscle.html#getStatFile()"><B>getStatFile()</B></A> - \r
-Static method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/cluster/drmaa/ClusterSession.html#getStatistics(org.ggf.drmaa.JobInfo)"><B>getStatistics(JobInfo)</B></A> - \r
-Static method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/ClusterSession.html" title="class in compbio.engine.cluster.drmaa">ClusterSession</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html#getSubmissionTime()"><B>getSubmissionTime()</B></A> - \r
-Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/Util.html#getSupportedOptions(java.lang.Class)"><B>getSupportedOptions(Class&lt;? extends Executable&lt;T&gt;&gt;)</B></A> - \r
-Static method in class compbio.runner.<A HREF="../compbio/runner/Util.html" title="class in compbio.runner">Util</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/ConfExecutable.html#getSupportedRuntimes()"><B>getSupportedRuntimes()</B></A> - \r
-Method in class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/ConfiguredExecutable.html#getSupportedRuntimes()"><B>getSupportedRuntimes()</B></A> - \r
-Method in interface compbio.engine.client.<A HREF="../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/Util.html#getSupportedRuntimes(java.lang.Class)"><B>getSupportedRuntimes(Class&lt;?&gt;)</B></A> - \r
-Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/Util.html" title="class in compbio.engine.client">Util</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/Configurator.html#getSyncEngine(compbio.engine.client.ConfiguredExecutable, compbio.engine.client.Executable.ExecProvider)"><B>getSyncEngine(ConfiguredExecutable&lt;?&gt;, Executable.ExecProvider)</B></A> - \r
-Static method in class compbio.engine.<A HREF="../compbio/engine/Configurator.html" title="class in compbio.engine">Configurator</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/Configurator.html#getSyncEngine(compbio.engine.client.ConfiguredExecutable)"><B>getSyncEngine(ConfiguredExecutable&lt;?&gt;)</B></A> - \r
-Static method in class compbio.engine.<A HREF="../compbio/engine/Configurator.html" title="class in compbio.engine">Configurator</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/SubmissionManager.html#getTask(java.lang.String)"><B>getTask(String)</B></A> - \r
-Static method in class compbio.engine.<A HREF="../compbio/engine/SubmissionManager.html" title="class in compbio.engine">SubmissionManager</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/conf/DirectoryManager.html#getTaskDirectory(java.lang.Class)"><B>getTaskDirectory(Class&lt;?&gt;)</B></A> - \r
-Static method in class compbio.engine.conf.<A HREF="../compbio/engine/conf/DirectoryManager.html" title="class in compbio.engine.conf">DirectoryManager</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/ConfExecutable.html#getTaskId()"><B>getTaskId()</B></A> - \r
-Method in class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/ConfiguredExecutable.html#getTaskId()"><B>getTaskId()</B></A> - \r
-Method in interface compbio.engine.client.<A HREF="../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/Job.html#getTaskId()"><B>getTaskId()</B></A> - \r
-Method in class compbio.engine.<A HREF="../compbio/engine/Job.html" title="class in compbio.engine">Job</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/_impl/Disembl.html#getTestArgs()"><B>getTestArgs()</B></A> - \r
-Static method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Disembl.html" title="class in compbio.runner._impl">Disembl</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/_impl/NetNglyc.html#getTestArgs()"><B>getTestArgs()</B></A> - \r
-Static method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/_impl/OB.html#getTestArgs()"><B>getTestArgs()</B></A> - \r
-Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/OB.html" title="class in compbio.runner._impl">OB</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/_impl/Disembl.html#getTestCommand()"><B>getTestCommand()</B></A> - \r
-Static method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Disembl.html" title="class in compbio.runner._impl">Disembl</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/_impl/Mcl.html#getTestCommand()"><B>getTestCommand()</B></A> - \r
-Static method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Mcl.html" title="class in compbio.runner._impl">Mcl</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/_impl/NetNglyc.html#getTestCommand()"><B>getTestCommand()</B></A> - \r
-Static method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/_impl/OB.html#getTestCommand()"><B>getTestCommand()</B></A> - \r
-Static method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/OB.html" title="class in compbio.runner._impl">OB</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/_impl/Ronn.html#getTestCommand()"><B>getTestCommand()</B></A> - \r
-Static method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Ronn.html" title="class in compbio.runner._impl">Ronn</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/_impl/RPSBlast.html#getTestCommand()"><B>getTestCommand()</B></A> - \r
-Static method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/RPSBlast.html" title="class in compbio.runner._impl">RPSBlast</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/_impl/Mcl.html#getTestParams()"><B>getTestParams()</B></A> - \r
-Static method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Mcl.html" title="class in compbio.runner._impl">Mcl</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/cluster/dundee/_Queue.html#getTimeLimit()"><B>getTimeLimit()</B></A> - \r
-Method in enum compbio.engine.cluster.dundee.<A HREF="../compbio/engine/cluster/dundee/_Queue.html" title="enum in compbio.engine.cluster.dundee">_Queue</A>\r
-<DD>0 - unlimited\r
-<DT><A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html#getTimeStat()"><B>getTimeStat()</B></A> - \r
-Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/_impl/Runners.html#getTmhmm2Runnable(java.lang.String)"><B>getTmhmm2Runnable(String)</B></A> - \r
-Static method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Runners.html" title="class in compbio.runner._impl">Runners</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/SkeletalExecutable.html#getType()"><B>getType()</B></A> - \r
-Method in class compbio.engine.client.<A HREF="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/ValueConstrain.html#getType()"><B>getType()</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/msa/ClustalW.html#getType()"><B>getType()</B></A> - \r
-Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/msa/Mafft.html#getType()"><B>getType()</B></A> - \r
-Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/msa/Muscle.html#getType()"><B>getType()</B></A> - \r
-Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/msa/Probcons.html#getType()"><B>getType()</B></A> - \r
-Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/msa/Tcoffee.html#getType()"><B>getType()</B></A> - \r
-Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/psiblast/PsiBlast.html#getType()"><B>getType()</B></A> - \r
-Method in class compbio.runner.psiblast.<A HREF="../compbio/runner/psiblast/PsiBlast.html" title="class in compbio.runner.psiblast">PsiBlast</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html#getUsedSysTime()"><B>getUsedSysTime()</B></A> - \r
-Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html#getUsedUserTime()"><B>getUsedUserTime()</B></A> - \r
-Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/conf/RunnerConfigMarshaller.html#getValidator(java.lang.String)"><B>getValidator(String)</B></A> - \r
-Static method in class compbio.engine.conf.<A HREF="../compbio/engine/conf/RunnerConfigMarshaller.html" title="class in compbio.engine.conf">RunnerConfigMarshaller</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/conf/RunnerConfigMarshaller.html#getValidator(javax.xml.validation.Schema)"><B>getValidator(Schema)</B></A> - \r
-Static method in class compbio.engine.conf.<A HREF="../compbio/engine/conf/RunnerConfigMarshaller.html" title="class in compbio.engine.conf">RunnerConfigMarshaller</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/Parameter.html#getValidValue()"><B>getValidValue()</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html#getVMem()"><B>getVMem()</B></A> - \r
-Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/AsyncExecutor.html#getWorkDirectory(java.lang.String)"><B>getWorkDirectory(String)</B></A> - \r
-Method in interface compbio.engine.<A HREF="../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine">AsyncExecutor</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/ConfExecutable.html#getWorkDirectory()"><B>getWorkDirectory()</B></A> - \r
-Method in class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/ConfiguredExecutable.html#getWorkDirectory()"><B>getWorkDirectory()</B></A> - \r
-Method in interface compbio.engine.client.<A HREF="../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/cluster/drmaa/AsyncJobRunner.html#getWorkDirectory(java.lang.String)"><B>getWorkDirectory(String)</B></A> - \r
-Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/AsyncJobRunner.html" title="class in compbio.engine.cluster.drmaa">AsyncJobRunner</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/cluster/drmaa/JobRunner.html#getWorkDirectory()"><B>getWorkDirectory()</B></A> - \r
-Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/JobRunner.html" title="class in compbio.engine.cluster.drmaa">JobRunner</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/Configurator.html#getWorkDirectory(java.lang.String)"><B>getWorkDirectory(String)</B></A> - \r
-Static method in class compbio.engine.<A HREF="../compbio/engine/Configurator.html" title="class in compbio.engine">Configurator</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/local/AsyncLocalRunner.html#getWorkDirectory(java.lang.String)"><B>getWorkDirectory(String)</B></A> - \r
-Method in class compbio.engine.local.<A HREF="../compbio/engine/local/AsyncLocalRunner.html" title="class in compbio.engine.local">AsyncLocalRunner</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/local/LocalRunner.html#getWorkDirectory()"><B>getWorkDirectory()</B></A> - \r
-Method in class compbio.engine.local.<A HREF="../compbio/engine/local/LocalRunner.html" title="class in compbio.engine.local">LocalRunner</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/SyncExecutor.html#getWorkDirectory()"><B>getWorkDirectory()</B></A> - \r
-Method in interface compbio.engine.<A HREF="../compbio/engine/SyncExecutor.html" title="interface in compbio.engine">SyncExecutor</A>\r
-<DD>&nbsp;\r
-</DL>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
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-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');\r
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diff --git a/website/full_javadoc/index-files/index-8.html b/website/full_javadoc/index-files/index-8.html

deleted file mode 100644 (file)

index 9772173..0000000
--- a/website/full_javadoc/index-files/index-8.html
+++ /dev/null
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-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
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-    if (location.href.indexOf('is-external=true') == -1) {\r
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-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Package</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Class</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Use</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Index</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
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-    document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');\r
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-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<A HREF="index-1.html">A</A> <A HREF="index-2.html">B</A> <A HREF="index-3.html">C</A> <A HREF="index-4.html">D</A> <A HREF="index-5.html">E</A> <A HREF="index-6.html">F</A> <A HREF="index-7.html">G</A> <A HREF="index-8.html">H</A> <A HREF="index-9.html">I</A> <A HREF="index-10.html">J</A> <A HREF="index-11.html">K</A> <A HREF="index-12.html">L</A> <A HREF="index-13.html">M</A> <A HREF="index-14.html">N</A> <A HREF="index-15.html">O</A> <A HREF="index-16.html">P</A> <A HREF="index-17.html">R</A> <A HREF="index-18.html">S</A> <A HREF="index-19.html">T</A> <A HREF="index-20.html">U</A> <A HREF="index-21.html">V</A> <A HREF="index-22.html">W</A> <A HREF="index-23.html">_</A> <HR>\r
-<A NAME="_H_"><!-- --></A><H2>\r
-<B>H</B></H2>\r
-<DL>\r
-<DT><A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html#hasDump()"><B>hasDump()</B></A> - \r
-Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html#hasExited()"><B>hasExited()</B></A> - \r
-Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/sequence/AlignmentMetadata.html#hashCode()"><B>hashCode()</B></A> - \r
-Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence">AlignmentMetadata</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/CommandBuilder.html#hashCode()"><B>hashCode()</B></A> - \r
-Method in class compbio.engine.client.<A HREF="../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/RunConfiguration.html#hashCode()"><B>hashCode()</B></A> - \r
-Method in class compbio.engine.client.<A HREF="../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/SkeletalExecutable.html#hashCode()"><B>hashCode()</B></A> - \r
-Method in class compbio.engine.client.<A HREF="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/ClusterJobId.html#hashCode()"><B>hashCode()</B></A> - \r
-Method in class compbio.engine.<A HREF="../compbio/engine/ClusterJobId.html" title="class in compbio.engine">ClusterJobId</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/conf/_Key.html#hashCode()"><B>hashCode()</B></A> - \r
-Method in class compbio.engine.conf.<A HREF="../compbio/engine/conf/_Key.html" title="class in compbio.engine.conf">_Key</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/FilePuller.html#hashCode()"><B>hashCode()</B></A> - \r
-Method in class compbio.engine.<A HREF="../compbio/engine/FilePuller.html" title="class in compbio.engine">FilePuller</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/Job.html#hashCode()"><B>hashCode()</B></A> - \r
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-<DD>&nbsp;\r
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-<DD>&nbsp;\r
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-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/Option.html#hashCode()"><B>hashCode()</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/Parameter.html#hashCode()"><B>hashCode()</B></A> - \r
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-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/Preset.html#hashCode()"><B>hashCode()</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/ValueConstrain.html#hashCode()"><B>hashCode()</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/pipeline/_jpred/PScore.html#hashCode()"><B>hashCode()</B></A> - \r
-Method in class compbio.pipeline._jpred.<A HREF="../compbio/pipeline/_jpred/PScore.html" title="class in compbio.pipeline._jpred">PScore</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/FilePuller.html#hasMoreData()"><B>hasMoreData()</B></A> - \r
-Method in class compbio.engine.<A HREF="../compbio/engine/FilePuller.html" title="class in compbio.engine">FilePuller</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/CommandBuilder.html#hasParam(java.lang.String)"><B>hasParam(String)</B></A> - \r
-Method in class compbio.engine.client.<A HREF="../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html#hasSignaled()"><B>hasSignaled()</B></A> - \r
-Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/cluster/dundee/_Queue.html#hasTimeLimit()"><B>hasTimeLimit()</B></A> - \r
-Method in enum compbio.engine.cluster.dundee.<A HREF="../compbio/engine/cluster/dundee/_Queue.html" title="enum in compbio.engine.cluster.dundee">_Queue</A>\r
-<DD>&nbsp;\r
-</DL>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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diff --git a/website/full_javadoc/index-files/index-9.html b/website/full_javadoc/index-files/index-9.html

deleted file mode 100644 (file)

index 43d75c9..0000000
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Package</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Class</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Use</FONT>&nbsp;</TD>\r
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-\r
-<A HREF="index-1.html">A</A> <A HREF="index-2.html">B</A> <A HREF="index-3.html">C</A> <A HREF="index-4.html">D</A> <A HREF="index-5.html">E</A> <A HREF="index-6.html">F</A> <A HREF="index-7.html">G</A> <A HREF="index-8.html">H</A> <A HREF="index-9.html">I</A> <A HREF="index-10.html">J</A> <A HREF="index-11.html">K</A> <A HREF="index-12.html">L</A> <A HREF="index-13.html">M</A> <A HREF="index-14.html">N</A> <A HREF="index-15.html">O</A> <A HREF="index-16.html">P</A> <A HREF="index-17.html">R</A> <A HREF="index-18.html">S</A> <A HREF="index-19.html">T</A> <A HREF="index-20.html">U</A> <A HREF="index-21.html">V</A> <A HREF="index-22.html">W</A> <A HREF="index-23.html">_</A> <HR>\r
-<A NAME="_I_"><!-- --></A><H2>\r
-<B>I</B></H2>\r
-<DL>\r
-<DT><A HREF="../compbio/engine/FilePuller.html#initPull()"><B>initPull()</B></A> - \r
-Method in class compbio.engine.<A HREF="../compbio/engine/FilePuller.html" title="class in compbio.engine">FilePuller</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/Configurator.html#IS_CLUSTER_ENGINE_ENABLED"><B>IS_CLUSTER_ENGINE_ENABLED</B></A> - \r
-Static variable in class compbio.engine.<A HREF="../compbio/engine/Configurator.html" title="class in compbio.engine">Configurator</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/Configurator.html#IS_LOCAL_ENGINE_ENABLED"><B>IS_LOCAL_ENGINE_ENABLED</B></A> - \r
-Static variable in class compbio.engine.<A HREF="../compbio/engine/Configurator.html" title="class in compbio.engine">Configurator</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/PathValidator.html#isAbsolutePath(java.lang.String)"><B>isAbsolutePath(String)</B></A> - \r
-Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/PathValidator.html" title="class in compbio.engine.client">PathValidator</A>\r
-<DD>Whether a certain path is absolute or not is operation system dependent!\r
-<DT><A HREF="../compbio/data/sequence/SequenceUtil.html#isAmbiguosProtein(java.lang.String)"><B>isAmbiguosProtein(String)</B></A> - \r
-Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
-<DD>Check whether the sequence confirms to amboguous protein sequence\r
-<DT><A HREF="../compbio/metadata/Limit.html#isDefault()"><B>isDefault()</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/Limit.html#isExceeded(java.util.List)"><B>isExceeded(List&lt;FastaSequence&gt;)</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>\r
-<DD>Checks if the number of sequences or their average length in the dataset
- exceeds limits the values defined by this Limit\r
-<DT><A HREF="../compbio/engine/FilePuller.html#isFileCreated()"><B>isFileCreated()</B></A> - \r
-Method in class compbio.engine.<A HREF="../compbio/engine/FilePuller.html" title="class in compbio.engine">FilePuller</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/Util.html#isMarked(java.lang.String, compbio.metadata.JobStatus)"><B>isMarked(String, JobStatus)</B></A> - \r
-Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/Util.html" title="class in compbio.engine.client">Util</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/sequence/SequenceUtil.html#isNonAmbNucleotideSequence(java.lang.String)"><B>isNonAmbNucleotideSequence(String)</B></A> - \r
-Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
-<DD>Ambiguous DNA chars : AGTCRYMKSWHBVDN // differs from protein in only one
- (!) - B char\r
-<DT><A HREF="../compbio/data/sequence/SequenceUtil.html#isNucleotideSequence(compbio.data.sequence.FastaSequence)"><B>isNucleotideSequence(FastaSequence)</B></A> - \r
-Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/sequence/SequenceUtil.html#isProteinSequence(java.lang.String)"><B>isProteinSequence(String)</B></A> - \r
-Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/Option.html#isRequired()"><B>isRequired()</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
-<DD>Flag that indicated that this option must be specified in the command
- line for an executable to run\r
-<DT><A HREF="../compbio/data/msa/jaxws/CancelJobResponse.html#isReturn()"><B>isReturn()</B></A> - \r
-Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/CancelJobResponse.html" title="class in compbio.data.msa.jaxws">CancelJobResponse</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/local/_TrackingExecutor.html#isShutdown()"><B>isShutdown()</B></A> - \r
-Method in class compbio.engine.local.<A HREF="../compbio/engine/local/_TrackingExecutor.html" title="class in compbio.engine.local">_TrackingExecutor</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/local/_TrackingExecutor.html#isTerminated()"><B>isTerminated()</B></A> - \r
-Method in class compbio.engine.local.<A HREF="../compbio/engine/local/_TrackingExecutor.html" title="class in compbio.engine.local">_TrackingExecutor</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html#isValidClustalFile(java.io.InputStream)"><B>isValidClustalFile(InputStream)</B></A> - \r
-Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence">ClustalAlignmentUtil</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/PathValidator.html#isValidDirectory(java.lang.String)"><B>isValidDirectory(String)</B></A> - \r
-Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/PathValidator.html" title="class in compbio.engine.client">PathValidator</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/PathValidator.html#isValidExecutable(java.lang.String)"><B>isValidExecutable(String)</B></A> - \r
-Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/PathValidator.html" title="class in compbio.engine.client">PathValidator</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/Util.html#isValidJobId(java.lang.String)"><B>isValidJobId(String)</B></A> - \r
-Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/Util.html" title="class in compbio.engine.client">Util</A>\r
-<DD>&nbsp;\r
-</DL>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Package</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Class</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Use</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Index</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="index-8.html"><B>PREV LETTER</B></A>&nbsp;\r
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diff --git a/website/full_javadoc/index.html b/website/full_javadoc/index.html

deleted file mode 100644 (file)

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deleted file mode 100644 (file)

index 2bacf31..0000000
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diff --git a/website/full_javadoc/overview-summary.html b/website/full_javadoc/overview-summary.html

deleted file mode 100644 (file)

index 6c2e8e4..0000000
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-<TD WIDTH="20%"><B><A HREF="compbio/data/sequence/package-summary.html">compbio.data.sequence</A></B></TD>\r
-<TD>A data model for multiple sequence alignment web services 
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-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
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-<TD>An local engine classes responsible for execution of Executables on the local computer 
- (the same machine as JVM running these classes).</TD>\r
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-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="20%"><B><A HREF="compbio/metadata/package-summary.html">compbio.metadata</A></B></TD>\r
-<TD>A meta-data model for multiple sequence alignment web services 
- Classes in this package have no dependencies to other sources in the project.</TD>\r
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-<TR BGCOLOR="white" CLASS="TableRowColor">\r
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-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="20%"><B><A HREF="compbio/runner/package-summary.html">compbio.runner</A></B></TD>\r
-<TD>Utilities commonly used by all runners.</TD>\r
-</TR>\r
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-<TD WIDTH="20%"><B><A HREF="compbio/runner/_impl/package-summary.html">compbio.runner._impl</A></B></TD>\r
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-</TR>\r
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-<TD WIDTH="20%"><B><A HREF="compbio/runner/msa/package-summary.html">compbio.runner.msa</A></B></TD>\r
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-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="20%"><B><A HREF="compbio/runner/psiblast/package-summary.html">compbio.runner.psiblast</A></B></TD>\r
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diff --git a/website/full_javadoc/overview-tree.html b/website/full_javadoc/overview-tree.html

deleted file mode 100644 (file)

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-\r
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-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Package</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Class</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Use</FONT>&nbsp;</TD>\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
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-  <A HREF="index.html?overview-tree.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="overview-tree.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="allclasses-noframe.html"><B>All Classes</B></A>\r
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-\r
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-\r
-<HR>\r
-\r
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-</HTML>\r
diff --git a/website/full_javadoc/package-list b/website/full_javadoc/package-list

deleted file mode 100644 (file)

index 88de085..0000000
--- a/website/full_javadoc/package-list
+++ /dev/null
@@ -1,19 +0,0 @@
-compbio.data._structure\r
-compbio.data.msa\r
-compbio.data.msa.jaxws\r
-compbio.data.sequence\r
-compbio.engine\r
-compbio.engine.client\r
-compbio.engine.cluster.drmaa\r
-compbio.engine.cluster.dundee\r
-compbio.engine.conf\r
-compbio.engine.local\r
-compbio.metadata\r
-compbio.pipeline._jpred\r
-compbio.runner\r
-compbio.runner._impl\r
-compbio.runner._jpred\r
-compbio.runner.msa\r
-compbio.runner.psiblast\r
-compbio.ws.client\r
-compbio.ws.server\r
diff --git a/website/full_javadoc/resources/inherit.gif b/website/full_javadoc/resources/inherit.gif

deleted file mode 100644 (file)

index c814867..0000000

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diff --git a/website/full_javadoc/serialized-form.html b/website/full_javadoc/serialized-form.html

deleted file mode 100644 (file)

index a133980..0000000
--- a/website/full_javadoc/serialized-form.html
+++ /dev/null
@@ -1,317 +0,0 @@
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-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-Serialized Form\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-02-17">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="Serialized Form";\r
-    }\r
-}\r
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-<NOSCRIPT>\r
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-\r
-</HEAD>\r
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-<BODY BGCOLOR="white" onload="windowTitle();">\r
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-<!-- ========= START OF TOP NAVBAR ======= -->\r
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-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Class</FONT>&nbsp;</TD>\r
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-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
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-</TABLE>\r
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-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
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-  <A HREF="index.html?serialized-form.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
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-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
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-\r
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-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
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-\r
-<HR>\r
-<CENTER>\r
-<H1>\r
-Serialized Form</H1>\r
-</CENTER>\r
-<HR SIZE="4" NOSHADE>\r
-\r
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-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="center"><FONT SIZE="+2">\r
-<B>Package</B> <B>compbio.data.sequence</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<P>\r
-<A NAME="compbio.data.sequence.UnknownFileFormatException"><!-- --></A>\r
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-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Class <A HREF="compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">compbio.data.sequence.UnknownFileFormatException</A> extends java.lang.Exception implements Serializable</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<P>\r
-<B>serialVersionUID:&nbsp;</B>196629543695636854L\r
-\r
-<P>\r
-<A NAME="serializedForm"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Serialized Fields</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<H3>\r
-file</H3>\r
-<PRE>\r
-java.io.File <B>file</B></PRE>\r
-<DL>\r
-<DL>\r
-</DL>\r
-</DL>\r
-<HR SIZE="4" NOSHADE>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="center"><FONT SIZE="+2">\r
-<B>Package</B> <B>compbio.metadata</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<P>\r
-<A NAME="compbio.metadata.JobExecutionException"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Class <A HREF="compbio/metadata/JobExecutionException.html" title="class in compbio.metadata">compbio.metadata.JobExecutionException</A> extends java.lang.Exception implements Serializable</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<P>\r
-<B>serialVersionUID:&nbsp;</B>-5477751361755778769L\r
-\r
-<P>\r
-\r
-<P>\r
-<A NAME="compbio.metadata.JobSubmissionException"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Class <A HREF="compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">compbio.metadata.JobSubmissionException</A> extends java.lang.Exception implements Serializable</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<P>\r
-<B>serialVersionUID:&nbsp;</B>607986894357895572L\r
-\r
-<P>\r
-\r
-<P>\r
-<A NAME="compbio.metadata.LimitExceededException"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Class <A HREF="compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">compbio.metadata.LimitExceededException</A> extends <A HREF="compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A> implements Serializable</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<P>\r
-<B>serialVersionUID:&nbsp;</B>15066952180013505L\r
-\r
-<P>\r
-<A NAME="serializedForm"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Serialized Fields</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<H3>\r
-numberOfSequencesAllowed</H3>\r
-<PRE>\r
-int <B>numberOfSequencesAllowed</B></PRE>\r
-<DL>\r
-<DL>\r
-</DL>\r
-</DL>\r
-<HR>\r
-<H3>\r
-actualNumberofSequences</H3>\r
-<PRE>\r
-int <B>actualNumberofSequences</B></PRE>\r
-<DL>\r
-<DL>\r
-</DL>\r
-</DL>\r
-<HR>\r
-<H3>\r
-aSequenceLenghtAllowed</H3>\r
-<PRE>\r
-int <B>aSequenceLenghtAllowed</B></PRE>\r
-<DL>\r
-<DL>\r
-</DL>\r
-</DL>\r
-<HR>\r
-<H3>\r
-aSequenceLenghtActual</H3>\r
-<PRE>\r
-int <B>aSequenceLenghtActual</B></PRE>\r
-<DL>\r
-<DL>\r
-</DL>\r
-</DL>\r
-\r
-<P>\r
-<A NAME="compbio.metadata.ResultNotAvailableException"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Class <A HREF="compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">compbio.metadata.ResultNotAvailableException</A> extends java.lang.Exception implements Serializable</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<P>\r
-<B>serialVersionUID:&nbsp;</B>-5475613614578761L\r
-\r
-<P>\r
-\r
-<P>\r
-<A NAME="compbio.metadata.UnsupportedRuntimeException"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Class <A HREF="compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">compbio.metadata.UnsupportedRuntimeException</A> extends <A HREF="compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A> implements Serializable</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<P>\r
-<B>serialVersionUID:&nbsp;</B>-86624836785110293L\r
-\r
-<P>\r
-\r
-<P>\r
-<A NAME="compbio.metadata.WrongParameterException"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Class <A HREF="compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">compbio.metadata.WrongParameterException</A> extends java.lang.Exception implements Serializable</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<P>\r
-<B>serialVersionUID:&nbsp;</B>-547775417557345769L\r
-\r
-<P>\r
-\r
-<P>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Package</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Class</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Use</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;PREV&nbsp;\r
-&nbsp;NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="index.html?serialized-form.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="serialized-form.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
diff --git a/website/full_javadoc/stylesheet.css b/website/full_javadoc/stylesheet.css

deleted file mode 100644 (file)

index cbd3428..0000000
--- a/website/full_javadoc/stylesheet.css
+++ /dev/null
@@ -1,29 +0,0 @@
-/* Javadoc style sheet */\r
-\r
-/* Define colors, fonts and other style attributes here to override the defaults */\r
-\r
-/* Page background color */\r
-body { background-color: #FFFFFF; color:#000000 }\r
-\r
-/* Headings */\r
-h1 { font-size: 145% }\r
-\r
-/* Table colors */\r
-.TableHeadingColor     { background: #CCCCFF; color:#000000 } /* Dark mauve */\r
-.TableSubHeadingColor  { background: #EEEEFF; color:#000000 } /* Light mauve */\r
-.TableRowColor         { background: #FFFFFF; color:#000000 } /* White */\r
-\r
-/* Font used in left-hand frame lists */\r
-.FrameTitleFont   { font-size: 100%; font-family: Helvetica, Arial, sans-serif; color:#000000 }\r
-.FrameHeadingFont { font-size:  90%; font-family: Helvetica, Arial, sans-serif; color:#000000 }\r
-.FrameItemFont    { font-size:  90%; font-family: Helvetica, Arial, sans-serif; color:#000000 }\r
-\r
-/* Navigation bar fonts and colors */\r
-.NavBarCell1    { background-color:#EEEEFF; color:#000000} /* Light mauve */\r
-.NavBarCell1Rev { background-color:#00008B; color:#FFFFFF} /* Dark Blue */\r
-.NavBarFont1    { font-family: Arial, Helvetica, sans-serif; color:#000000;color:#000000;}\r
-.NavBarFont1Rev { font-family: Arial, Helvetica, sans-serif; color:#FFFFFF;color:#FFFFFF;}\r
-\r
-.NavBarCell2    { font-family: Arial, Helvetica, sans-serif; background-color:#FFFFFF; color:#000000}\r
-.NavBarCell3    { font-family: Arial, Helvetica, sans-serif; background-color:#FFFFFF; color:#000000}\r
-\r
author	pvtroshin <pvtroshin@e3abac25-378b-4346-85de-24260fe3988d>
	Fri, 12 Aug 2011 13:02:22 +0000 (13:02 +0000)
committer	pvtroshin <pvtroshin@e3abac25-378b-4346-85de-24260fe3988d>
	Fri, 12 Aug 2011 13:02:22 +0000 (13:02 +0000)