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remove old datamodel javadoc
[jabaws.git] / website / full_javadoc / compbio / engine / client / class-use / CommandBuilder.html
diff --git a/website/full_javadoc/compbio/engine/client/class-use/CommandBuilder.html b/website/full_javadoc/compbio/engine/client/class-use/CommandBuilder.html
index 663f217..cd5993b 100644 (file)
--- a/website/full_javadoc/compbio/engine/client/class-use/CommandBuilder.html
+++ b/website/full_javadoc/compbio/engine/client/class-use/CommandBuilder.html
@@ -2,12 +2,12 @@
 <!--NewPage-->\r
 <HTML>\r
 <HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
+<!-- Generated by javadoc (build 1.6.0_24) on Fri Aug 12 14:32:36 BST 2011 -->\r
 <TITLE>\r
 Uses of Class compbio.engine.client.CommandBuilder\r
 </TITLE>\r
 \r
-<META NAME="date" CONTENT="2010-02-17">\r
+<META NAME="date" CONTENT="2011-08-12">\r
 \r
 <LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
 \r
@@ -91,7 +91,7 @@ Packages that use <A HREF="../../../../compbio/engine/client/CommandBuilder.html
 </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
+<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
@@ -102,6 +102,14 @@ Packages that use <A HREF="../../../../compbio/engine/client/CommandBuilder.html
 <TD>&nbsp;&nbsp;</TD>\r
 </TR>\r
 <TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><A HREF="#compbio.runner.conservation"><B>compbio.runner.conservation</B></A></TD>\r
+<TD>&nbsp;&nbsp;</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><A HREF="#compbio.runner.disorder"><B>compbio.runner.disorder</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
@@ -124,40 +132,40 @@ Uses of <A HREF="../../../../compbio/engine/client/CommandBuilder.html" title="c
 </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
+<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/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
+<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;?&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>RunConfiguration.</B><B><A HREF="../../../../compbio/engine/client/RunConfiguration.html#getParameters()">getParameters</A></B>()</CODE>\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;<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
+<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/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
+<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
@@ -180,8 +188,8 @@ Uses of <A HREF="../../../../compbio/engine/client/CommandBuilder.html" title="c
 </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
+<TD><CODE><B>CommandBuilder.</B><B><A HREF="../../../../compbio/engine/client/CommandBuilder.html#newCommandBuilder(java.util.List, java.lang.String)">newCommandBuilder</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A>&lt;? extends <A HREF="../../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;T&gt;&gt;&nbsp;arguments,\r
+                  <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&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
@@ -225,7 +233,7 @@ Uses of <A HREF="../../../../compbio/engine/client/CommandBuilder.html" title="c
 <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
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<B>Deprecated.</B>&nbsp;&nbsp;</TD>\r
 </TR>\r
 </TABLE>\r
 &nbsp;\r
@@ -255,6 +263,56 @@ Uses of <A HREF="../../../../compbio/engine/client/CommandBuilder.html" title="c
 </TABLE>\r
 &nbsp;\r
 <P>\r
+<A NAME="compbio.runner.conservation"><!-- --></A>\r
+<TABLE BORDER="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/conservation/package-summary.html">compbio.runner.conservation</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/conservation/package-summary.html">compbio.runner.conservation</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/conservation/AACon.html" title="class in compbio.runner.conservation">AACon</A>&gt;</CODE></FONT></TD>\r
+<TD><CODE><B>AACon.</B><B><A HREF="../../../../compbio/runner/conservation/AACon.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.disorder"><!-- --></A>\r
+<TABLE BORDER="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/disorder/package-summary.html">compbio.runner.disorder</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/disorder/package-summary.html">compbio.runner.disorder</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/disorder/Jronn.html" title="class in compbio.runner.disorder">Jronn</A>&gt;</CODE></FONT></TD>\r
+<TD><CODE><B>Jronn.</B><B><A HREF="../../../../compbio/runner/disorder/Jronn.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
@@ -277,6 +335,14 @@ Uses of <A HREF="../../../../compbio/engine/client/CommandBuilder.html" title="c
 <BR>\r
 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&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/ClustalO.html" title="class in compbio.runner.msa">ClustalO</A>&gt;</CODE></FONT></TD>\r
+<TD><CODE><B>ClustalO.</B><B><A HREF="../../../../compbio/runner/msa/ClustalO.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