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Make muscle executable compilation not static to fix problem on Macs
[jabaws.git] / website / dm_javadoc / overview-tree.html
diff --git a/website/dm_javadoc/overview-tree.html b/website/dm_javadoc/overview-tree.html
index 5d9832b..b77b722 100644 (file)
--- a/website/dm_javadoc/overview-tree.html
+++ b/website/dm_javadoc/overview-tree.html
@@ -2,12 +2,12 @@
 <!--NewPage-->\r
 <HTML>\r
 <HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_21) on Thu Nov 18 15:38:37 GMT 2010 -->\r
+<!-- Generated by javadoc (build 1.6.0_21) on Tue Dec 21 18:32:59 GMT 2010 -->\r
 <TITLE>\r
 Class Hierarchy\r
 </TITLE>\r
 \r
-<META NAME="date" CONTENT="2010-11-18">\r
+<META NAME="date" CONTENT="2010-12-21">\r
 \r
 <LINK REL ="stylesheet" TYPE="text/css" HREF="stylesheet.css" TITLE="Style">\r
 \r
@@ -90,13 +90,15 @@ Hierarchy For All Packages</H2>
 Class Hierarchy\r
 </H2>\r
 <UL>\r
-<LI TYPE="circle">java.lang.Object<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><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.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
+<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.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.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.data.sequence.<A HREF="compbio/data/sequence/MultiAnnotatedSequence.html" title="class in compbio.data.sequence"><B>MultiAnnotatedSequence</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
-<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.metadata.<A HREF="compbio/metadata/PresetManager.html" title="class in compbio.metadata"><B>PresetManager</B></A>&lt;T&gt;<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/SequenceUtil.html" title="class in compbio.data.sequence"><B>SequenceUtil</B></A><LI TYPE="circle">java.lang.Throwable (implements java.io.Serializable)\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.metadata.<A HREF="compbio/metadata/PresetManager.html" title="class in compbio.metadata"><B>PresetManager</B></A>&lt;T&gt;<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><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.Exception<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
@@ -107,15 +109,27 @@ Class Hierarchy
 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/MsaWS.html" title="interface in compbio.data.msa"><B>MsaWS</B></A>&lt;T&gt;</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
+<LI TYPE="circle">compbio.data.msa.<A HREF="compbio/data/msa/Annotation.html" title="interface in compbio.data.msa"><B>Annotation</B></A>&lt;T&gt; (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>&lt;T&gt;)\r
+<LI TYPE="circle">compbio.data.msa.<A HREF="compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa"><B>MsaWS</B></A>&lt;T&gt; (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>&lt;T&gt;)\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>&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
+<LI TYPE="circle">compbio.data.msa.<A HREF="compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa"><B>MsaWS</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
+</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>&lt;T&gt;<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>&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
+<LI TYPE="circle">compbio.data.msa.<A HREF="compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa"><B>MsaWS</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
+<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>&lt;E&gt; (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>&lt;T&gt;, 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.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/Program.html" title="enum in compbio.data.sequence"><B>Program</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></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.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/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.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