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updated javadoc for the system as well as new redirect address for download app
[jabaws.git] / website / full_javadoc / overview-summary.html
diff --git a/website/full_javadoc/overview-summary.html b/website/full_javadoc/overview-summary.html
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@@ -0,0 +1,247 @@
+<!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_24) on Wed Dec 07 12:30:43 GMT 2011 -->\r
+<TITLE>\r
+Overview\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2011-12-07">\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="Overview";\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="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Overview</B></FONT>&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?overview-summary.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
+&nbsp;<A HREF="overview-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
+<CENTER>\r
+<H1>\r
+JABAWS 2 javadoc\r
+</H1>\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
+<B>Packages</B></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD WIDTH="20%"><B><A HREF="compbio/data/_structure/package-summary.html">compbio.data._structure</A></B></TD>\r
+<TD>&nbsp;</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD WIDTH="20%"><B><A HREF="compbio/data/msa/package-summary.html">compbio.data.msa</A></B></TD>\r
+<TD>Web Service interfaces for JAva Bioinformatics Analysis Web Services.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD WIDTH="20%"><B><A HREF="compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A></B></TD>\r
+<TD>&nbsp;</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<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 and utility methods
+ that work on the objects of this model.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD WIDTH="20%"><B><A HREF="compbio/engine/package-summary.html">compbio.engine</A></B></TD>\r
+<TD>&nbsp;</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD WIDTH="20%"><B><A HREF="compbio/engine/client/package-summary.html">compbio.engine.client</A></B></TD>\r
+<TD>&nbsp;</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD WIDTH="20%"><B><A HREF="compbio/engine/cluster/drmaa/package-summary.html">compbio.engine.cluster.drmaa</A></B></TD>\r
+<TD>&nbsp;</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD WIDTH="20%"><B><A HREF="compbio/engine/cluster/dundee/package-summary.html">compbio.engine.cluster.dundee</A></B></TD>\r
+<TD>&nbsp;</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD WIDTH="20%"><B><A HREF="compbio/engine/conf/package-summary.html">compbio.engine.conf</A></B></TD>\r
+<TD>&nbsp;</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD WIDTH="20%"><B><A HREF="compbio/engine/local/package-summary.html">compbio.engine.local</A></B></TD>\r
+<TD>&nbsp;</TD>\r
+</TR>\r
+<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
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD WIDTH="20%"><B><A HREF="compbio/pipeline/_jpred/package-summary.html">compbio.pipeline._jpred</A></B></TD>\r
+<TD>&nbsp;</TD>\r
+</TR>\r
+<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
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD WIDTH="20%"><B><A HREF="compbio/runner/_impl/package-summary.html">compbio.runner._impl</A></B></TD>\r
+<TD>&nbsp;</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD WIDTH="20%"><B><A HREF="compbio/runner/_jpred/package-summary.html">compbio.runner._jpred</A></B></TD>\r
+<TD>&nbsp;</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD WIDTH="20%"><B><A HREF="compbio/runner/conservation/package-summary.html">compbio.runner.conservation</A></B></TD>\r
+<TD>&nbsp;</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD WIDTH="20%"><B><A HREF="compbio/runner/disorder/package-summary.html">compbio.runner.disorder</A></B></TD>\r
+<TD>&nbsp;</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD WIDTH="20%"><B><A HREF="compbio/runner/msa/package-summary.html">compbio.runner.msa</A></B></TD>\r
+<TD>Wrappers for native executables for multiple sequence alignment (msa)</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD WIDTH="20%"><B><A HREF="compbio/stat/collector/package-summary.html">compbio.stat.collector</A></B></TD>\r
+<TD>&nbsp;</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD WIDTH="20%"><B><A HREF="compbio/stat/servlet/package-summary.html">compbio.stat.servlet</A></B></TD>\r
+<TD>&nbsp;</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD WIDTH="20%"><B><A HREF="compbio/stat/servlet/util/package-summary.html">compbio.stat.servlet.util</A></B></TD>\r
+<TD>&nbsp;</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD WIDTH="20%"><B><A HREF="compbio/ws/client/package-summary.html">compbio.ws.client</A></B></TD>\r
+<TD>A command line client and web services testing client for    
+ JAva Bioinformatics Analysis Web Services.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD WIDTH="20%"><B><A HREF="compbio/ws/server/package-summary.html">compbio.ws.server</A></B></TD>\r
+<TD>&nbsp;</TD>\r
+</TR>\r
+</TABLE>\r
+\r
+<P>\r
+&nbsp;<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="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Overview</B></FONT>&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?overview-summary.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
+&nbsp;<A HREF="overview-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