--- /dev/null
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+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:29 GMT 2010 -->\r
+<TITLE>\r
+Class Hierarchy\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
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+<LINK REL ="stylesheet" TYPE="text/css" HREF="stylesheet.css" TITLE="Style">\r
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+</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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+<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> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Package</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Use</FONT> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
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+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
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+ <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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+<NOSCRIPT>\r
+ <A HREF="allclasses-noframe.html"><B>All Classes</B></A>\r
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+<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/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.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang"><B>Object</B></A><UL>\r
+<LI TYPE="circle">compbio.data.sequence.<A HREF="compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence"><B>Alignment</B></A><LI TYPE="circle">compbio.data.sequence.<A HREF="compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence"><B>AlignmentMetadata</B></A><LI TYPE="circle">compbio.metadata.<A HREF="compbio/metadata/ChunkHolder.html" title="class in compbio.metadata"><B>ChunkHolder</B></A><LI TYPE="circle">compbio.data.sequence.<A HREF="compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence"><B>ClustalAlignmentUtil</B></A><LI TYPE="circle">compbio.data.sequence.<A HREF="compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence"><B>FastaSequence</B></A><UL>\r
+<LI TYPE="circle">compbio.data.sequence.<A HREF="compbio/data/sequence/AnnotatedSequence.html" title="class in compbio.data.sequence"><B>AnnotatedSequence</B></A></UL>\r
+<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.sequence.<A HREF="compbio/data/sequence/JalviewAnnotation.html" title="class in compbio.data.sequence"><B>JalviewAnnotation</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><T><LI TYPE="circle">compbio.metadata.<A HREF="compbio/metadata/LimitsManager.html" title="class in compbio.metadata"><B>LimitsManager</B></A><T><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.data.sequence.<A HREF="compbio/data/sequence/MultiAnnotatedSequence.html" title="class in compbio.data.sequence"><B>MultiAnnotatedSequence</B></A><T><LI TYPE="circle">compbio.metadata.<A HREF="compbio/metadata/Option.html" title="class in compbio.metadata"><B>Option</B></A><T> (implements compbio.metadata.<A HREF="compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</A><T>)\r
+<UL>\r
+<LI TYPE="circle">compbio.metadata.<A HREF="compbio/metadata/Parameter.html" title="class in compbio.metadata"><B>Parameter</B></A><T></UL>\r
+<LI TYPE="circle">compbio.metadata.<A HREF="compbio/metadata/Preset.html" title="class in compbio.metadata"><B>Preset</B></A><T><LI TYPE="circle">compbio.metadata.<A HREF="compbio/metadata/PresetManager.html" title="class in compbio.metadata"><B>PresetManager</B></A><T><LI TYPE="circle">compbio.metadata.<A HREF="compbio/metadata/RunnerConfig.html" title="class in compbio.metadata"><B>RunnerConfig</B></A><T><LI TYPE="circle">compbio.data.sequence.<A HREF="compbio/data/sequence/Score.html" title="class in compbio.data.sequence"><B>Score</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">java.lang.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true" title="class or interface in java.lang"><B>Throwable</B></A> (implements java.io.<A HREF="http://java.sun.com/javase/6/docs/api/java/io/Serializable.html?is-external=true" title="class or interface in java.io">Serializable</A>)\r
+<UL>\r
+<LI TYPE="circle">java.lang.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Exception.html?is-external=true" title="class or interface in java.lang"><B>Exception</B></A><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
+<LI TYPE="circle">compbio.metadata.<A HREF="compbio/metadata/LimitExceededException.html" title="class in compbio.metadata"><B>LimitExceededException</B></A><LI TYPE="circle">compbio.metadata.<A HREF="compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata"><B>UnsupportedRuntimeException</B></A></UL>\r
+<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
+</UL>\r
+<LI TYPE="circle">compbio.metadata.<A HREF="compbio/metadata/ValueConstrain.html" title="class in compbio.metadata"><B>ValueConstrain</B></A><LI TYPE="circle">compbio.ws.client.<A HREF="compbio/ws/client/WSTester.html" title="class in compbio.ws.client"><B>WSTester</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><T><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
+<LI TYPE="circle">compbio.data.msa.<A HREF="compbio/data/msa/Annotation.html" title="interface in compbio.data.msa"><B>Annotation</B></A><T> (also extends compbio.data.msa.<A HREF="compbio/data/msa/JManagement.html" title="interface in compbio.data.msa">JManagement</A>, compbio.data.msa.<A HREF="compbio/data/msa/Metadata.html" title="interface in compbio.data.msa">Metadata</A><T>)\r
+<LI TYPE="circle">compbio.data.msa.<A HREF="compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa"><B>MsaWS</B></A><T> (also extends compbio.data.msa.<A HREF="compbio/data/msa/JManagement.html" title="interface in compbio.data.msa">JManagement</A>, compbio.data.msa.<A HREF="compbio/data/msa/Metadata.html" title="interface in compbio.data.msa">Metadata</A><T>)\r
+</UL>\r
+<LI TYPE="circle">compbio.data.msa.<A HREF="compbio/data/msa/JManagement.html" title="interface in compbio.data.msa"><B>JManagement</B></A><UL>\r
+<LI TYPE="circle">compbio.data.msa.<A HREF="compbio/data/msa/Annotation.html" title="interface in compbio.data.msa"><B>Annotation</B></A><T> (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><T>)\r
+<LI TYPE="circle">compbio.data.msa.<A HREF="compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa"><B>MsaWS</B></A><T> (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><T>)\r
+</UL>\r
+<LI TYPE="circle">compbio.data.msa.<A HREF="compbio/data/msa/Metadata.html" title="interface in compbio.data.msa"><B>Metadata</B></A><T><UL>\r
+<LI TYPE="circle">compbio.data.msa.<A HREF="compbio/data/msa/Annotation.html" title="interface in compbio.data.msa"><B>Annotation</B></A><T> (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
+<LI TYPE="circle">compbio.data.msa.<A HREF="compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa"><B>MsaWS</B></A><T> (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.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang"><B>Object</B></A><UL>\r
+<LI TYPE="circle">java.lang.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true" title="class or interface in java.lang"><B>Enum</B></A><E> (implements java.lang.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Comparable.html?is-external=true" title="class or interface in java.lang">Comparable</A><T>, java.io.<A HREF="http://java.sun.com/javase/6/docs/api/java/io/Serializable.html?is-external=true" title="class or interface in java.io">Serializable</A>)\r
+<UL>\r
+<LI TYPE="circle">compbio.metadata.<A HREF="compbio/metadata/JobStatus.html" title="enum in compbio.metadata"><B>JobStatus</B></A><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/Program.html" title="enum in compbio.data.sequence"><B>Program</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.data.sequence.<A HREF="compbio/data/sequence/Method.html" title="enum in compbio.data.sequence"><B>Method</B></A><LI TYPE="circle">compbio.data.sequence.<A HREF="compbio/data/sequence/DisemblResultAnnot.html" title="enum in compbio.data.sequence"><B>DisemblResultAnnot</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
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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
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Package</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Use</FONT> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </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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+ <A HREF="overview-tree.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="allclasses-noframe.html"><B>All 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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+<A NAME="skip-navbar_bottom"></A>\r
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+\r
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+</HTML>\r
git://source.jalview.org / jabaws.git / blobdiff