Fix core WST file
[jabaws.git] / website / full_javadoc / overview-tree.html
index 8fc9c1c..7b5b612 100644 (file)
@@ -2,12 +2,12 @@
 <!--NewPage-->\r
 <HTML>\r
 <HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_24) on Fri Aug 12 14:32:36 BST 2011 -->\r
+<!-- Generated by javadoc (build 1.6.0_24) on Wed Dec 07 12:30:43 GMT 2011 -->\r
 <TITLE>\r
 Class Hierarchy\r
 </TITLE>\r
 \r
-<META NAME="date" CONTENT="2011-08-12">\r
+<META NAME="date" CONTENT="2011-12-07">\r
 \r
 <LINK REL ="stylesheet" TYPE="text/css" HREF="stylesheet.css" TITLE="Style">\r
 \r
@@ -101,14 +101,14 @@ Class Hierarchy
 </UL>\r
 <LI TYPE="circle">compbio.data.msa.jaxws.<A HREF="compbio/data/msa/jaxws/Align.html" title="class in compbio.data.msa.jaxws"><B>Align</B></A><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.data.msa.jaxws.<A HREF="compbio/data/msa/jaxws/AlignResponse.html" title="class in compbio.data.msa.jaxws"><B>AlignResponse</B></A><LI TYPE="circle">compbio.data.msa.jaxws.<A HREF="compbio/data/msa/jaxws/Analize.html" title="class in compbio.data.msa.jaxws"><B>Analize</B></A><LI TYPE="circle">compbio.data.msa.jaxws.<A HREF="compbio/data/msa/jaxws/AnalizeResponse.html" title="class in compbio.data.msa.jaxws"><B>AnalizeResponse</B></A><LI TYPE="circle">compbio.engine.cluster.drmaa.<A HREF="compbio/engine/cluster/drmaa/AsyncJobRunner.html" title="class in compbio.engine.cluster.drmaa"><B>AsyncJobRunner</B></A> (implements compbio.engine.<A HREF="compbio/engine/AsyncExecutor.html" title="interface in compbio.engine">AsyncExecutor</A>)\r
 <LI TYPE="circle">compbio.engine.local.<A HREF="compbio/engine/local/AsyncLocalRunner.html" title="class in compbio.engine.local"><B>AsyncLocalRunner</B></A> (implements compbio.engine.<A HREF="compbio/engine/AsyncExecutor.html" title="interface in compbio.engine">AsyncExecutor</A>)\r
-<LI TYPE="circle">compbio.pipeline._jpred.<A HREF="compbio/pipeline/_jpred/BlastBlastComparator.html" title="class in compbio.pipeline._jpred"><B>BlastBlastComparator</B></A><LI TYPE="circle">compbio.pipeline._jpred.<A HREF="compbio/pipeline/_jpred/BlastHmmerComparator.html" title="class in compbio.pipeline._jpred"><B>BlastHmmerComparator</B></A><LI TYPE="circle">compbio.runner._impl.<A HREF="compbio/runner/_impl/BlastParameters.html" title="class in compbio.runner._impl"><B>BlastParameters</B></A><LI TYPE="circle">compbio.pipeline._jpred.<A HREF="compbio/pipeline/_jpred/BlastParser.html" title="class in compbio.pipeline._jpred"><B>BlastParser</B></A><LI TYPE="circle">compbio.data.msa.jaxws.<A HREF="compbio/data/msa/jaxws/CancelJob.html" title="class in compbio.data.msa.jaxws"><B>CancelJob</B></A><LI TYPE="circle">compbio.data.msa.jaxws.<A HREF="compbio/data/msa/jaxws/CancelJobResponse.html" title="class in compbio.data.msa.jaxws"><B>CancelJobResponse</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.engine.<A HREF="compbio/engine/Cleaner.html" title="class in compbio.engine"><B>Cleaner</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.ws.server.<A HREF="compbio/ws/server/ClustalOWS.html" title="class in compbio.ws.server"><B>ClustalOWS</B></A> (implements compbio.data.msa.<A HREF="compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>&lt;T&gt;)\r
+<LI TYPE="circle">compbio.pipeline._jpred.<A HREF="compbio/pipeline/_jpred/BlastBlastComparator.html" title="class in compbio.pipeline._jpred"><B>BlastBlastComparator</B></A><LI TYPE="circle">compbio.pipeline._jpred.<A HREF="compbio/pipeline/_jpred/BlastHmmerComparator.html" title="class in compbio.pipeline._jpred"><B>BlastHmmerComparator</B></A><LI TYPE="circle">compbio.runner._impl.<A HREF="compbio/runner/_impl/BlastParameters.html" title="class in compbio.runner._impl"><B>BlastParameters</B></A><LI TYPE="circle">compbio.pipeline._jpred.<A HREF="compbio/pipeline/_jpred/BlastParser.html" title="class in compbio.pipeline._jpred"><B>BlastParser</B></A><LI TYPE="circle">compbio.data.msa.jaxws.<A HREF="compbio/data/msa/jaxws/CancelJob.html" title="class in compbio.data.msa.jaxws"><B>CancelJob</B></A><LI TYPE="circle">compbio.data.msa.jaxws.<A HREF="compbio/data/msa/jaxws/CancelJobResponse.html" title="class in compbio.data.msa.jaxws"><B>CancelJobResponse</B></A><LI TYPE="circle">compbio.data.msa.<A HREF="compbio/data/msa/Category.html" title="class in compbio.data.msa"><B>Category</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.engine.<A HREF="compbio/engine/Cleaner.html" title="class in compbio.engine"><B>Cleaner</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.ws.server.<A HREF="compbio/ws/server/ClustalOWS.html" title="class in compbio.ws.server"><B>ClustalOWS</B></A> (implements compbio.data.msa.<A HREF="compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>&lt;T&gt;)\r
 <LI TYPE="circle">compbio.ws.server.<A HREF="compbio/ws/server/ClustalWS.html" title="class in compbio.ws.server"><B>ClustalWS</B></A> (implements compbio.data.msa.<A HREF="compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>&lt;T&gt;)\r
 <LI TYPE="circle">compbio.engine.<A HREF="compbio/engine/ClusterJobId.html" title="class in compbio.engine"><B>ClusterJobId</B></A><LI TYPE="circle">compbio.engine.cluster.drmaa.<A HREF="compbio/engine/cluster/drmaa/ClusterSession.html" title="class in compbio.engine.cluster.drmaa"><B>ClusterSession</B></A><LI TYPE="circle">compbio.engine.cluster.drmaa.<A HREF="compbio/engine/cluster/drmaa/ClusterUtil.html" title="class in compbio.engine.cluster.drmaa"><B>ClusterUtil</B></A><LI TYPE="circle">compbio.engine.client.<A HREF="compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client"><B>CommandBuilder</B></A>&lt;T&gt;<LI TYPE="circle">compbio.engine.client.<A HREF="compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client"><B>ConfExecutable</B></A>&lt;T&gt; (implements compbio.engine.client.<A HREF="compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;T&gt;)\r
 <LI TYPE="circle">compbio.engine.<A HREF="compbio/engine/Configurator.html" title="class in compbio.engine"><B>Configurator</B></A><LI TYPE="circle">compbio.data.msa.jaxws.<A HREF="compbio/data/msa/jaxws/CustomAlign.html" title="class in compbio.data.msa.jaxws"><B>CustomAlign</B></A><LI TYPE="circle">compbio.data.msa.jaxws.<A HREF="compbio/data/msa/jaxws/CustomAlignResponse.html" title="class in compbio.data.msa.jaxws"><B>CustomAlignResponse</B></A><LI TYPE="circle">compbio.data.msa.jaxws.<A HREF="compbio/data/msa/jaxws/CustomAnalize.html" title="class in compbio.data.msa.jaxws"><B>CustomAnalize</B></A><LI TYPE="circle">compbio.data.msa.jaxws.<A HREF="compbio/data/msa/jaxws/CustomAnalizeResponse.html" title="class in compbio.data.msa.jaxws"><B>CustomAnalizeResponse</B></A><LI TYPE="circle">compbio.engine.conf.<A HREF="compbio/engine/conf/DirectoryManager.html" title="class in compbio.engine.conf"><B>DirectoryManager</B></A><LI TYPE="circle">compbio.runner._impl.<A HREF="compbio/runner/_impl/Environment.html" title="class in compbio.runner._impl"><B>Environment</B></A><LI TYPE="circle">compbio.engine.client.<A HREF="compbio/engine/client/EnvVariableProcessor.html" title="class in compbio.engine.client"><B>EnvVariableProcessor</B></A><LI TYPE="circle">compbio.engine.local.<A HREF="compbio/engine/local/ExecutableWrapper.html" title="class in compbio.engine.local"><B>ExecutableWrapper</B></A> (implements java.util.concurrent.<A HREF="http://java.sun.com/javase/6/docs/api/java/util/concurrent/Callable.html?is-external=true" title="class or interface in java.util.concurrent">Callable</A>&lt;V&gt;)\r
 <LI TYPE="circle">compbio.stat.collector.<A HREF="compbio/stat/collector/ExecutionStatCollector.html" title="class in compbio.stat.collector"><B>ExecutionStatCollector</B></A> (implements java.lang.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Runnable.html?is-external=true" title="class or interface in java.lang">Runnable</A>)\r
 <LI TYPE="circle">compbio.data.sequence.<A HREF="compbio/data/sequence/FastaReader.html" title="class in compbio.data.sequence"><B>FastaReader</B></A> (implements java.util.<A HREF="http://java.sun.com/javase/6/docs/api/java/util/Iterator.html?is-external=true" title="class or interface in java.util">Iterator</A>&lt;E&gt;)\r
 <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.engine.<A HREF="compbio/engine/FilePuller.html" title="class in compbio.engine"><B>FilePuller</B></A> (implements java.util.concurrent.<A HREF="http://java.sun.com/javase/6/docs/api/java/util/concurrent/Delayed.html?is-external=true" title="class or interface in java.util.concurrent">Delayed</A>)\r
-<LI TYPE="circle">compbio.ws.server.<A HREF="compbio/ws/server/GenericMetadataService.html" title="class in compbio.ws.server"><B>GenericMetadataService</B></A>&lt;T&gt;<UL>\r
+<LI TYPE="circle">compbio.ws.server.<A HREF="compbio/ws/server/GAUtils.html" title="class in compbio.ws.server"><B>GAUtils</B></A><LI TYPE="circle">compbio.ws.server.<A HREF="compbio/ws/server/GenericMetadataService.html" title="class in compbio.ws.server"><B>GenericMetadataService</B></A>&lt;T&gt;<UL>\r
 <LI TYPE="circle">compbio.ws.server.<A HREF="compbio/ws/server/_MsaService.html" title="class in compbio.ws.server"><B>_MsaService</B></A>&lt;T&gt;<LI TYPE="circle">compbio.ws.server.<A HREF="compbio/ws/server/SequenceAnnotationService.html" title="class in compbio.ws.server"><B>SequenceAnnotationService</B></A>&lt;T&gt;<UL>\r
 <LI TYPE="circle">compbio.ws.server.<A HREF="compbio/ws/server/AAConWS.html" title="class in compbio.ws.server"><B>AAConWS</B></A> (implements compbio.data.msa.<A HREF="compbio/data/msa/SequenceAnnotation.html" title="interface in compbio.data.msa">SequenceAnnotation</A>&lt;T&gt;)\r
 <LI TYPE="circle">compbio.ws.server.<A HREF="compbio/ws/server/DisemblWS.html" title="class in compbio.ws.server"><B>DisemblWS</B></A> (implements compbio.data.msa.<A HREF="compbio/data/msa/SequenceAnnotation.html" title="interface in compbio.data.msa">SequenceAnnotation</A>&lt;T&gt;)\r
@@ -121,11 +121,11 @@ Class Hierarchy
 <UL>\r
 <LI TYPE="circle">javax.servlet.http.HttpServlet (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">compbio.stat.servlet.<A HREF="compbio/stat/servlet/AnnualStat.html" title="class in compbio.stat.servlet"><B>AnnualStat</B></A><LI TYPE="circle">compbio.stat.servlet.<A HREF="compbio/stat/servlet/DisplayStat.html" title="class in compbio.stat.servlet"><B>DisplayStat</B></A><LI TYPE="circle">compbio.stat.servlet.<A HREF="compbio/stat/servlet/Joblist.html" title="class in compbio.stat.servlet"><B>Joblist</B></A></UL>\r
+<LI TYPE="circle">compbio.stat.servlet.<A HREF="compbio/stat/servlet/AnnualStat.html" title="class in compbio.stat.servlet"><B>AnnualStat</B></A><LI TYPE="circle">compbio.stat.servlet.<A HREF="compbio/stat/servlet/DisplayStat.html" title="class in compbio.stat.servlet"><B>DisplayStat</B></A><LI TYPE="circle">compbio.stat.servlet.<A HREF="compbio/stat/servlet/DownloadRedirector.html" title="class in compbio.stat.servlet"><B>DownloadRedirector</B></A><LI TYPE="circle">compbio.stat.servlet.<A HREF="compbio/stat/servlet/HttpCodeResponseServiceStatus.html" title="class in compbio.stat.servlet"><B>HttpCodeResponseServiceStatus</B></A><LI TYPE="circle">compbio.stat.servlet.<A HREF="compbio/stat/servlet/Joblist.html" title="class in compbio.stat.servlet"><B>Joblist</B></A><LI TYPE="circle">compbio.stat.servlet.<A HREF="compbio/stat/servlet/ServiceStatus.html" title="class in compbio.stat.servlet"><B>ServiceStatus</B></A></UL>\r
 </UL>\r
-<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/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.pipeline._jpred.<A HREF="compbio/pipeline/_jpred/Hit.html" title="class in compbio.pipeline._jpred"><B>Hit</B></A><LI TYPE="circle">compbio.pipeline._jpred.<A HREF="compbio/pipeline/_jpred/Hit.EvalueComporator.html" title="class in compbio.pipeline._jpred"><B>Hit.EvalueComporator</B></A> (implements java.util.<A HREF="http://java.sun.com/javase/6/docs/api/java/util/Comparator.html?is-external=true" title="class or interface in java.util">Comparator</A>&lt;T&gt;)\r
+<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.pipeline._jpred.<A HREF="compbio/pipeline/_jpred/Hit.html" title="class in compbio.pipeline._jpred"><B>Hit</B></A><LI TYPE="circle">compbio.pipeline._jpred.<A HREF="compbio/pipeline/_jpred/Hit.EvalueComporator.html" title="class in compbio.pipeline._jpred"><B>Hit.EvalueComporator</B></A> (implements java.util.<A HREF="http://java.sun.com/javase/6/docs/api/java/util/Comparator.html?is-external=true" title="class or interface in java.util">Comparator</A>&lt;T&gt;)\r
 <LI TYPE="circle">compbio.pipeline._jpred.<A HREF="compbio/pipeline/_jpred/Hit.NumberComporator.html" title="class in compbio.pipeline._jpred"><B>Hit.NumberComporator</B></A> (implements java.util.<A HREF="http://java.sun.com/javase/6/docs/api/java/util/Comparator.html?is-external=true" title="class or interface in java.util">Comparator</A>&lt;T&gt;)\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.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.pipeline._jpred.<A HREF="compbio/pipeline/_jpred/JackHmmerHitParser.html" title="class in compbio.pipeline._jpred"><B>JackHmmerHitParser</B></A><LI TYPE="circle">compbio.engine.<A HREF="compbio/engine/Job.html" title="class in compbio.engine"><B>Job</B></A><LI TYPE="circle">compbio.engine.cluster.drmaa.<A HREF="compbio/engine/cluster/drmaa/JobRunner.html" title="class in compbio.engine.cluster.drmaa"><B>JobRunner</B></A> (implements compbio.engine.<A HREF="compbio/engine/SyncExecutor.html" title="interface in compbio.engine">SyncExecutor</A>)\r
+<LI TYPE="circle">compbio.stat.collector.<A HREF="compbio/stat/collector/InputFilter.html" title="class in compbio.stat.collector"><B>InputFilter</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.pipeline._jpred.<A HREF="compbio/pipeline/_jpred/JackHmmerHitParser.html" title="class in compbio.pipeline._jpred"><B>JackHmmerHitParser</B></A><LI TYPE="circle">compbio.engine.<A HREF="compbio/engine/Job.html" title="class in compbio.engine"><B>Job</B></A><LI TYPE="circle">compbio.engine.cluster.drmaa.<A HREF="compbio/engine/cluster/drmaa/JobRunner.html" title="class in compbio.engine.cluster.drmaa"><B>JobRunner</B></A> (implements compbio.engine.<A HREF="compbio/engine/SyncExecutor.html" title="interface in compbio.engine">SyncExecutor</A>)\r
 <LI TYPE="circle">compbio.stat.collector.<A HREF="compbio/stat/collector/JobStat.html" title="class in compbio.stat.collector"><B>JobStat</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.pipeline._jpred.<A HREF="compbio/pipeline/_jpred/Jpred4.html" title="class in compbio.pipeline._jpred"><B>Jpred4</B></A><LI TYPE="circle">compbio.data._structure.<A HREF="compbio/data/_structure/JpredResult.html" title="class in compbio.data._structure"><B>JpredResult</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.engine.<A HREF="compbio/engine/LoadBalancer.html" title="class in compbio.engine"><B>LoadBalancer</B></A><LI TYPE="circle">compbio.engine.local.<A HREF="compbio/engine/local/LocalEngineUtil.html" title="class in compbio.engine.local"><B>LocalEngineUtil</B></A><LI TYPE="circle">compbio.engine.local.<A HREF="compbio/engine/local/LocalRunner.html" title="class in compbio.engine.local"><B>LocalRunner</B></A> (implements compbio.engine.<A HREF="compbio/engine/SyncExecutor.html" title="interface in compbio.engine">SyncExecutor</A>)\r
 <LI TYPE="circle">compbio.ws.server.<A HREF="compbio/ws/server/MafftWS.html" title="class in compbio.ws.server"><B>MafftWS</B></A> (implements compbio.data.msa.<A HREF="compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>&lt;T&gt;)\r
 <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.ws.server.<A HREF="compbio/ws/server/MuscleWS.html" title="class in compbio.ws.server"><B>MuscleWS</B></A> (implements compbio.data.msa.<A HREF="compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>&lt;T&gt;)\r
@@ -137,7 +137,8 @@ Class Hierarchy
 <LI TYPE="circle">compbio.engine.<A HREF="compbio/engine/ProgressGetter.html" title="class in compbio.engine"><B>ProgressGetter</B></A><LI TYPE="circle">compbio.engine.conf.<A HREF="compbio/engine/conf/PropertyHelperManager.html" title="class in compbio.engine.conf"><B>PropertyHelperManager</B></A><LI TYPE="circle">compbio.pipeline._jpred.<A HREF="compbio/pipeline/_jpred/PScore.html" title="class in compbio.pipeline._jpred"><B>PScore</B></A><LI TYPE="circle">compbio.engine.<A HREF="compbio/engine/PulledFileCache.html" title="class in compbio.engine"><B>PulledFileCache</B></A><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.<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;)\r
 <LI TYPE="circle">compbio.ws.server.<A HREF="compbio/ws/server/RegistryWS.html" title="class in compbio.ws.server"><B>RegistryWS</B></A> (implements 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/RegistryWS.html" title="interface in compbio.data.msa">RegistryWS</A>)\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.engine.client.<A HREF="compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client"><B>RunConfiguration</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.engine.conf.<A HREF="compbio/engine/conf/RunnerConfigMarshaller.html" title="class in compbio.engine.conf"><B>RunnerConfigMarshaller</B></A>&lt;T&gt;<LI TYPE="circle">compbio.runner._impl.<A HREF="compbio/runner/_impl/Runners.html" title="class in compbio.runner._impl"><B>Runners</B></A><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.<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;)\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.ws.server.<A HREF="compbio/ws/server/ShutdownEngines.html" title="class in compbio.ws.server"><B>ShutdownEngines</B></A> (implements javax.servlet.ServletContextListener)\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.stat.servlet.<A HREF="compbio/stat/servlet/ServiceTestResult.html" title="class in compbio.stat.servlet"><B>ServiceTestResult</B></A><LI TYPE="circle">compbio.ws.server.<A HREF="compbio/ws/server/SetExecutableFlag.html" title="class in compbio.ws.server"><B>SetExecutableFlag</B></A> (implements javax.servlet.ServletContextListener)\r
+<LI TYPE="circle">compbio.ws.server.<A HREF="compbio/ws/server/ShutdownEngines.html" title="class in compbio.ws.server"><B>ShutdownEngines</B></A> (implements javax.servlet.ServletContextListener)\r
 <LI TYPE="circle">compbio.ws.server.<A HREF="compbio/ws/server/SimpleWSPublisher.html" title="class in compbio.ws.server"><B>SimpleWSPublisher</B></A><LI TYPE="circle">compbio.engine.client.<A HREF="compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client"><B>SkeletalExecutable</B></A>&lt;T&gt; (implements compbio.engine.client.<A HREF="compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;T&gt;)\r
 <UL>\r
 <LI TYPE="circle">compbio.runner.conservation.<A HREF="compbio/runner/conservation/AACon.html" title="class in compbio.runner.conservation"><B>AACon</B></A><LI TYPE="circle">compbio.runner.msa.<A HREF="compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa"><B>ClustalO</B></A><LI TYPE="circle">compbio.runner.msa.<A HREF="compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa"><B>ClustalW</B></A><LI TYPE="circle">compbio.runner.disorder.<A HREF="compbio/runner/disorder/Disembl.html" title="class in compbio.runner.disorder"><B>Disembl</B></A> (implements compbio.engine.client.<A HREF="compbio/engine/client/PipedExecutable.html" title="interface in compbio.engine.client">PipedExecutable</A>&lt;T&gt;)\r