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updated javadoc for the system as well as new redirect address for download app
[jabaws.git] / website / dm_javadoc / overview-tree.html
diff --git a/website/dm_javadoc/overview-tree.html b/website/dm_javadoc/overview-tree.html
new file mode 100644 (file)
index 0000000..31958b1
--- /dev/null
+++ b/website/dm_javadoc/overview-tree.html
@@ -0,0 +1,192 @@
+<!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 12:08:25 GMT 2011 -->\r
+<TITLE>\r
+Class Hierarchy\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="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
+  <TR ALIGN="center" VALIGN="top">\r
+  <TD BGCOLOR="#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="#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;PREV&nbsp;\r
+&nbsp;NEXT</FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+  <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
+</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 All Packages</H2>\r
+</CENTER>\r
+<DL>\r
+<DT><B>Package Hierarchies:</B><DD><A HREF="compbio/data/msa/package-tree.html">compbio.data.msa</A>, <A HREF="compbio/data/msa/jaxws/package-tree.html">compbio.data.msa.jaxws</A>, <A HREF="compbio/data/sequence/package-tree.html">compbio.data.sequence</A>, <A HREF="compbio/metadata/package-tree.html">compbio.metadata</A>, <A HREF="compbio/ws/client/package-tree.html">compbio.ws.client</A></DL>\r
+<HR>\r
+<H2>\r
+Class Hierarchy\r
+</H2>\r
+<UL>\r
+<LI TYPE="circle">java.lang.Object<UL>\r
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+<LI TYPE="circle">compbio.data.sequence.<A HREF="compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence"><B>FastaSequence</B></A><LI TYPE="circle">compbio.data.msa.jaxws.<A HREF="compbio/data/msa/jaxws/GetAnnotation.html" title="class in compbio.data.msa.jaxws"><B>GetAnnotation</B></A><LI TYPE="circle">compbio.data.msa.jaxws.<A HREF="compbio/data/msa/jaxws/GetAnnotationResponse.html" title="class in compbio.data.msa.jaxws"><B>GetAnnotationResponse</B></A><LI TYPE="circle">compbio.data.msa.jaxws.<A HREF="compbio/data/msa/jaxws/GetJobStatus.html" title="class in compbio.data.msa.jaxws"><B>GetJobStatus</B></A><LI TYPE="circle">compbio.data.msa.jaxws.<A HREF="compbio/data/msa/jaxws/GetJobStatusResponse.html" title="class in compbio.data.msa.jaxws"><B>GetJobStatusResponse</B></A><LI TYPE="circle">compbio.data.msa.jaxws.<A HREF="compbio/data/msa/jaxws/GetLastTested.html" title="class in compbio.data.msa.jaxws"><B>GetLastTested</B></A><LI TYPE="circle">compbio.data.msa.jaxws.<A HREF="compbio/data/msa/jaxws/GetLastTestedOn.html" title="class in compbio.data.msa.jaxws"><B>GetLastTestedOn</B></A><LI TYPE="circle">compbio.data.msa.jaxws.<A HREF="compbio/data/msa/jaxws/GetLastTestedOnResponse.html" title="class in compbio.data.msa.jaxws"><B>GetLastTestedOnResponse</B></A><LI TYPE="circle">compbio.data.msa.jaxws.<A HREF="compbio/data/msa/jaxws/GetLastTestedResponse.html" title="class in compbio.data.msa.jaxws"><B>GetLastTestedResponse</B></A><LI TYPE="circle">compbio.data.msa.jaxws.<A HREF="compbio/data/msa/jaxws/GetLimit.html" title="class in compbio.data.msa.jaxws"><B>GetLimit</B></A><LI TYPE="circle">compbio.data.msa.jaxws.<A HREF="compbio/data/msa/jaxws/GetLimitResponse.html" title="class in compbio.data.msa.jaxws"><B>GetLimitResponse</B></A><LI TYPE="circle">compbio.data.msa.jaxws.<A HREF="compbio/data/msa/jaxws/GetLimits.html" title="class in compbio.data.msa.jaxws"><B>GetLimits</B></A><LI TYPE="circle">compbio.data.msa.jaxws.<A HREF="compbio/data/msa/jaxws/GetLimitsResponse.html" title="class in compbio.data.msa.jaxws"><B>GetLimitsResponse</B></A><LI TYPE="circle">compbio.data.msa.jaxws.<A HREF="compbio/data/msa/jaxws/GetPresets.html" title="class in compbio.data.msa.jaxws"><B>GetPresets</B></A><LI TYPE="circle">compbio.data.msa.jaxws.<A HREF="compbio/data/msa/jaxws/GetPresetsResponse.html" title="class in compbio.data.msa.jaxws"><B>GetPresetsResponse</B></A><LI TYPE="circle">compbio.data.msa.jaxws.<A HREF="compbio/data/msa/jaxws/GetResult.html" title="class in compbio.data.msa.jaxws"><B>GetResult</B></A><LI TYPE="circle">compbio.data.msa.jaxws.<A HREF="compbio/data/msa/jaxws/GetResultResponse.html" title="class in compbio.data.msa.jaxws"><B>GetResultResponse</B></A><LI TYPE="circle">compbio.data.msa.jaxws.<A HREF="compbio/data/msa/jaxws/GetRunnerOptions.html" title="class in compbio.data.msa.jaxws"><B>GetRunnerOptions</B></A><LI TYPE="circle">compbio.data.msa.jaxws.<A HREF="compbio/data/msa/jaxws/GetRunnerOptionsResponse.html" title="class in compbio.data.msa.jaxws"><B>GetRunnerOptionsResponse</B></A><LI TYPE="circle">compbio.data.msa.jaxws.<A HREF="compbio/data/msa/jaxws/GetServiceCategories.html" title="class in compbio.data.msa.jaxws"><B>GetServiceCategories</B></A><LI TYPE="circle">compbio.data.msa.jaxws.<A HREF="compbio/data/msa/jaxws/GetServiceCategoriesResponse.html" title="class in compbio.data.msa.jaxws"><B>GetServiceCategoriesResponse</B></A><LI TYPE="circle">compbio.data.msa.jaxws.<A HREF="compbio/data/msa/jaxws/GetServiceDescription.html" title="class in compbio.data.msa.jaxws"><B>GetServiceDescription</B></A><LI TYPE="circle">compbio.data.msa.jaxws.<A HREF="compbio/data/msa/jaxws/GetServiceDescriptionResponse.html" title="class in compbio.data.msa.jaxws"><B>GetServiceDescriptionResponse</B></A><LI TYPE="circle">compbio.data.msa.jaxws.<A HREF="compbio/data/msa/jaxws/GetSupportedServices.html" title="class in compbio.data.msa.jaxws"><B>GetSupportedServices</B></A><LI TYPE="circle">compbio.data.msa.jaxws.<A HREF="compbio/data/msa/jaxws/GetSupportedServicesResponse.html" title="class in compbio.data.msa.jaxws"><B>GetSupportedServicesResponse</B></A><LI TYPE="circle">compbio.ws.client.<A HREF="compbio/ws/client/IOHelper.html" title="class in compbio.ws.client"><B>IOHelper</B></A><LI TYPE="circle">compbio.data.msa.jaxws.<A HREF="compbio/data/msa/jaxws/IsOperating.html" title="class in compbio.data.msa.jaxws"><B>IsOperating</B></A><LI TYPE="circle">compbio.data.msa.jaxws.<A HREF="compbio/data/msa/jaxws/IsOperatingResponse.html" title="class in compbio.data.msa.jaxws"><B>IsOperatingResponse</B></A><LI TYPE="circle">compbio.data.msa.jaxws.<A HREF="compbio/data/msa/jaxws/JobSubmissionExceptionBean.html" title="class in compbio.data.msa.jaxws"><B>JobSubmissionExceptionBean</B></A><LI TYPE="circle">compbio.ws.client.<A HREF="compbio/ws/client/Jws2Client.html" title="class in compbio.ws.client"><B>Jws2Client</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.data.msa.jaxws.<A HREF="compbio/data/msa/jaxws/LimitExceededExceptionBean.html" title="class in compbio.data.msa.jaxws"><B>LimitExceededExceptionBean</B></A><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.ws.client.<A HREF="compbio/ws/client/MetadataHelper.html" title="class in compbio.ws.client"><B>MetadataHelper</B></A><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
+<LI TYPE="circle">compbio.metadata.<A HREF="compbio/metadata/Preset.html" title="class in compbio.metadata"><B>Preset</B></A>&lt;T&gt;<LI TYPE="circle">compbio.data.msa.jaxws.<A HREF="compbio/data/msa/jaxws/PresetAlign.html" title="class in compbio.data.msa.jaxws"><B>PresetAlign</B></A><LI TYPE="circle">compbio.data.msa.jaxws.<A HREF="compbio/data/msa/jaxws/PresetAlignResponse.html" title="class in compbio.data.msa.jaxws"><B>PresetAlignResponse</B></A><LI TYPE="circle">compbio.data.msa.jaxws.<A HREF="compbio/data/msa/jaxws/PresetAnalize.html" title="class in compbio.data.msa.jaxws"><B>PresetAnalize</B></A><LI TYPE="circle">compbio.data.msa.jaxws.<A HREF="compbio/data/msa/jaxws/PresetAnalizeResponse.html" title="class in compbio.data.msa.jaxws"><B>PresetAnalizeResponse</B></A><LI TYPE="circle">compbio.metadata.<A HREF="compbio/metadata/PresetManager.html" title="class in compbio.metadata"><B>PresetManager</B></A>&lt;T&gt;<LI TYPE="circle">compbio.data.msa.jaxws.<A HREF="compbio/data/msa/jaxws/PullExecStatistics.html" title="class in compbio.data.msa.jaxws"><B>PullExecStatistics</B></A><LI TYPE="circle">compbio.data.msa.jaxws.<A HREF="compbio/data/msa/jaxws/PullExecStatisticsResponse.html" title="class in compbio.data.msa.jaxws"><B>PullExecStatisticsResponse</B></A><LI TYPE="circle">compbio.data.sequence.<A HREF="compbio/data/sequence/Range.html" title="class in compbio.data.sequence"><B>Range</B></A> (implements java.lang.Comparable&lt;T&gt;)\r
+<LI TYPE="circle">compbio.data.msa.jaxws.<A HREF="compbio/data/msa/jaxws/ResultNotAvailableExceptionBean.html" title="class in compbio.data.msa.jaxws"><B>ResultNotAvailableExceptionBean</B></A><LI TYPE="circle">compbio.metadata.<A HREF="compbio/metadata/RunnerConfig.html" title="class in compbio.metadata"><B>RunnerConfig</B></A>&lt;T&gt;<LI TYPE="circle">compbio.data.sequence.<A HREF="compbio/data/sequence/Score.html" title="class in compbio.data.sequence"><B>Score</B></A> (implements java.lang.Comparable&lt;T&gt;)\r
+<LI TYPE="circle">compbio.data.sequence.<A HREF="compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence"><B>ScoreManager</B></A><LI TYPE="circle">compbio.data.sequence.<A HREF="compbio/data/sequence/ScoreManager.ScoreHolder.html" title="class in compbio.data.sequence"><B>ScoreManager.ScoreHolder</B></A><LI TYPE="circle">compbio.data.sequence.<A HREF="compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence"><B>SequenceUtil</B></A><LI TYPE="circle">compbio.ws.client.<A HREF="compbio/ws/client/ServicesUtil.html" title="class in compbio.ws.client"><B>ServicesUtil</B></A><LI TYPE="circle">compbio.data.msa.jaxws.<A HREF="compbio/data/msa/jaxws/TestAllServices.html" title="class in compbio.data.msa.jaxws"><B>TestAllServices</B></A><LI TYPE="circle">compbio.data.msa.jaxws.<A HREF="compbio/data/msa/jaxws/TestAllServicesResponse.html" title="class in compbio.data.msa.jaxws"><B>TestAllServicesResponse</B></A><LI TYPE="circle">compbio.data.msa.jaxws.<A HREF="compbio/data/msa/jaxws/TestService.html" title="class in compbio.data.msa.jaxws"><B>TestService</B></A><LI TYPE="circle">compbio.data.msa.jaxws.<A HREF="compbio/data/msa/jaxws/TestServiceResponse.html" title="class in compbio.data.msa.jaxws"><B>TestServiceResponse</B></A><LI TYPE="circle">java.lang.Throwable (implements java.io.Serializable)\r
+<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.data.sequence.<A HREF="compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence"><B>UnknownFileFormatException</B></A><LI TYPE="circle">compbio.metadata.<A HREF="compbio/metadata/WrongParameterException.html" title="class in compbio.metadata"><B>WrongParameterException</B></A></UL>\r
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+</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;<LI TYPE="circle">compbio.data.msa.<A HREF="compbio/data/msa/JABAService.html" title="interface in compbio.data.msa"><B>JABAService</B></A><UL>\r
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+</UL>\r
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+<LI TYPE="circle">compbio.data.msa.<A HREF="compbio/data/msa/SequenceAnnotation.html" title="interface in compbio.data.msa"><B>SequenceAnnotation</B></A>&lt;T&gt; (also extends compbio.data.msa.<A HREF="compbio/data/msa/JABAService.html" title="interface in compbio.data.msa">JABAService</A>, compbio.data.msa.<A HREF="compbio/data/msa/Metadata.html" title="interface in compbio.data.msa">Metadata</A>&lt;T&gt;)\r
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+<LI TYPE="circle">compbio.data.msa.<A HREF="compbio/data/msa/Metadata.html" title="interface in compbio.data.msa"><B>Metadata</B></A>&lt;T&gt;<UL>\r
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+<LI TYPE="circle">compbio.data.msa.<A HREF="compbio/data/msa/SequenceAnnotation.html" title="interface in compbio.data.msa"><B>SequenceAnnotation</B></A>&lt;T&gt; (also extends compbio.data.msa.<A HREF="compbio/data/msa/JABAService.html" title="interface in compbio.data.msa">JABAService</A>, compbio.data.msa.<A HREF="compbio/data/msa/JManagement.html" title="interface in compbio.data.msa">JManagement</A>)\r
+</UL>\r
+</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.ws.client.<A HREF="compbio/ws/client/Services.html" title="enum in compbio.ws.client"><B>Services</B></A><LI TYPE="circle">compbio.data.sequence.<A HREF="compbio/data/sequence/SMERFSConstraints.html" title="enum in compbio.data.sequence"><B>SMERFSConstraints</B></A><LI TYPE="circle">compbio.data.sequence.<A HREF="compbio/data/sequence/DisorderMethod.html" title="enum in compbio.data.sequence"><B>DisorderMethod</B></A><LI TYPE="circle">compbio.data.sequence.<A HREF="compbio/data/sequence/Program.html" title="enum in compbio.data.sequence"><B>Program</B></A><LI TYPE="circle">compbio.data.sequence.<A HREF="compbio/data/sequence/ConservationMethod.html" title="enum in compbio.data.sequence"><B>ConservationMethod</B></A><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
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+</UL>\r
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