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41 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Package</FONT> </TD>
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42 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
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84 Hierarchy For All Packages</H2>
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87 <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>
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93 <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>
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94 <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>
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95 <LI TYPE="circle">compbio.data.sequence.<A HREF="compbio/data/sequence/AnnotatedSequence.html" title="class in compbio.data.sequence"><B>AnnotatedSequence</B></A></UL>
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96 <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><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>)
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98 <LI TYPE="circle">compbio.metadata.<A HREF="compbio/metadata/Parameter.html" title="class in compbio.metadata"><B>Parameter</B></A><T></UL>
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99 <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>)
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101 <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>
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102 <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>
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103 <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>
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104 <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>
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106 <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>
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109 Interface Hierarchy
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112 <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>
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113 <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>)
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114 <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>)
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116 <LI TYPE="circle">compbio.data.msa.<A HREF="compbio/data/msa/JManagement.html" title="interface in compbio.data.msa"><B>JManagement</B></A><UL>
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117 <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>)
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118 <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>)
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120 <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>
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121 <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>)
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122 <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>)
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129 <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>
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130 <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>)
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132 <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>
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