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Re-formatting the file
[jabaws.git] / website / full_javadoc / index-files / index-7.html
diff --git a/website/full_javadoc/index-files/index-7.html b/website/full_javadoc/index-files/index-7.html
index f2382f2..2a53e54 100644 (file)
--- a/website/full_javadoc/index-files/index-7.html
+++ b/website/full_javadoc/index-files/index-7.html
@@ -2,12 +2,12 @@
 <!--NewPage-->\r
 <HTML>\r
 <HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
+<!-- Generated by javadoc (build 1.6.0_24) on Wed Dec 07 12:30:43 GMT 2011 -->\r
 <TITLE>\r
 G-Index\r
 </TITLE>\r
 \r
-<META NAME="date" CONTENT="2010-02-17">\r
+<META NAME="date" CONTENT="2011-12-07">\r
 \r
 <LINK REL ="stylesheet" TYPE="text/css" HREF="../stylesheet.css" TITLE="Style">\r
 \r
@@ -85,9 +85,21 @@ function windowTitle()
 <DT><A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html#gapchar"><B>gapchar</B></A> - \r
 Static variable in class compbio.data.sequence.<A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence">ClustalAlignmentUtil</A>\r
 <DD>Dash char to be used as gap char in the alignments\r
-<DT><A HREF="../compbio/engine/PulledFileCache.html#get(java.lang.String)"><B>get(String)</B></A> - \r
+<DT><A HREF="../compbio/ws/server/GAUtils.html" title="class in compbio.ws.server"><B>GAUtils</B></A> - Class in <A HREF="../compbio/ws/server/package-summary.html">compbio.ws.server</A><DD>&nbsp;<DT><A HREF="../compbio/ws/server/GAUtils.html#GAUtils()"><B>GAUtils()</B></A> - \r
+Constructor for class compbio.ws.server.<A HREF="../compbio/ws/server/GAUtils.html" title="class in compbio.ws.server">GAUtils</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/ws/server/GenericMetadataService.html" title="class in compbio.ws.server"><B>GenericMetadataService</B></A>&lt;<A HREF="../compbio/ws/server/GenericMetadataService.html" title="type parameter in GenericMetadataService">T</A>&gt; - Class in <A HREF="../compbio/ws/server/package-summary.html">compbio.ws.server</A><DD>&nbsp;<DT><A HREF="../compbio/engine/PulledFileCache.html#get(java.lang.String)"><B>get(String)</B></A> - \r
 Static method in class compbio.engine.<A HREF="../compbio/engine/PulledFileCache.html" title="class in compbio.engine">PulledFileCache</A>\r
 <DD>&nbsp;\r
+<DT><A HREF="../compbio/stat/servlet/util/Totals.html#getAbandoned()"><B>getAbandoned()</B></A> - \r
+Method in class compbio.stat.servlet.util.<A HREF="../compbio/stat/servlet/util/Totals.html" title="class in compbio.stat.servlet.util">Totals</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/stat/collector/StatDB.html#getAbandonedCount(java.sql.Timestamp, java.sql.Timestamp)"><B>getAbandonedCount(Timestamp, Timestamp)</B></A> - \r
+Method in class compbio.stat.collector.<A HREF="../compbio/stat/collector/StatDB.html" title="class in compbio.stat.collector">StatDB</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/stat/collector/StatProcessor.html#getAbandonedJobs()"><B>getAbandonedJobs()</B></A> - \r
+Method in class compbio.stat.collector.<A HREF="../compbio/stat/collector/StatProcessor.html" title="class in compbio.stat.collector">StatProcessor</A>\r
+<DD>Not collected.\r
 <DT><A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html#getActualNumberofSequences()"><B>getActualNumberofSequences()</B></A> - \r
 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html" title="class in compbio.data.msa.jaxws">LimitExceededExceptionBean</A>\r
 <DD>&nbsp;\r
@@ -106,15 +118,51 @@ Method in class compbio.runner.<A HREF="../compbio/runner/OptionCombinator.html"
 <DT><A HREF="../compbio/runner/OptionCombinator.html#getAllParameters()"><B>getAllParameters()</B></A> - \r
 Method in class compbio.runner.<A HREF="../compbio/runner/OptionCombinator.html" title="class in compbio.runner">OptionCombinator</A>\r
 <DD>&nbsp;\r
+<DT><A HREF="../compbio/stat/servlet/util/StatCollection.html#getAllStat()"><B>getAllStat()</B></A> - \r
+Method in class compbio.stat.servlet.util.<A HREF="../compbio/stat/servlet/util/StatCollection.html" title="class in compbio.stat.servlet.util">StatCollection</A>\r
+<DD>&nbsp;\r
 <DT><A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html#getAllStats()"><B>getAllStats()</B></A> - \r
 Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</A>\r
 <DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/jaxws/GetAnnotation.html" title="class in compbio.data.msa.jaxws"><B>GetAnnotation</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/GetAnnotation.html#GetAnnotation()"><B>GetAnnotation()</B></A> - \r
+Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetAnnotation.html" title="class in compbio.data.msa.jaxws">GetAnnotation</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/SequenceAnnotation.html#getAnnotation(java.lang.String)"><B>getAnnotation(String)</B></A> - \r
+Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/SequenceAnnotation.html" title="interface in compbio.data.msa">SequenceAnnotation</A>\r
+<DD>Return the result of the job.\r
+<DT><A HREF="../compbio/ws/server/SequenceAnnotationService.html#getAnnotation(java.lang.String)"><B>getAnnotation(String)</B></A> - \r
+Method in class compbio.ws.server.<A HREF="../compbio/ws/server/SequenceAnnotationService.html" title="class in compbio.ws.server">SequenceAnnotationService</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/ws/server/WSUtil.html#getAnnotation(java.lang.String, org.apache.log4j.Logger)"><B>getAnnotation(String, Logger)</B></A> - \r
+Static method in class compbio.ws.server.<A HREF="../compbio/ws/server/WSUtil.html" title="class in compbio.ws.server">WSUtil</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/sequence/ScoreManager.html#getAnnotationForSequence(java.lang.String)"><B>getAnnotationForSequence(String)</B></A> - \r
+Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/jaxws/GetAnnotationResponse.html" title="class in compbio.data.msa.jaxws"><B>GetAnnotationResponse</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/GetAnnotationResponse.html#GetAnnotationResponse()"><B>GetAnnotationResponse()</B></A> - \r
+Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetAnnotationResponse.html" title="class in compbio.data.msa.jaxws">GetAnnotationResponse</A>\r
+<DD>&nbsp;\r
 <DT><A HREF="../compbio/runner/_NativeSpecHelper.html#getApproprieteQueue()"><B>getApproprieteQueue()</B></A> - \r
 Method in class compbio.runner.<A HREF="../compbio/runner/_NativeSpecHelper.html" title="class in compbio.runner">_NativeSpecHelper</A>\r
+<DD><B>Deprecated.</B>&nbsp;&nbsp;\r
+<DT><A HREF="../compbio/data/msa/jaxws/GetLastTested.html#getArg0()"><B>getArg0()</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetLastTested.html" title="class in compbio.data.msa.jaxws">GetLastTested</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/jaxws/GetLastTestedOn.html#getArg0()"><B>getArg0()</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetLastTestedOn.html" title="class in compbio.data.msa.jaxws">GetLastTestedOn</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/jaxws/GetServiceDescription.html#getArg0()"><B>getArg0()</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetServiceDescription.html" title="class in compbio.data.msa.jaxws">GetServiceDescription</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/jaxws/IsOperating.html#getArg0()"><B>getArg0()</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/IsOperating.html" title="class in compbio.data.msa.jaxws">IsOperating</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/jaxws/TestService.html#getArg0()"><B>getArg0()</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/TestService.html" title="class in compbio.data.msa.jaxws">TestService</A>\r
 <DD>&nbsp;\r
 <DT><A HREF="../compbio/metadata/RunnerConfig.html#getArgument(java.lang.String)"><B>getArgument(String)</B></A> - \r
 Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
-<DD>Returns the argument by its name if found, NULL otherwise\r
+<DD>Returns the argument by its name if found, NULL otherwise.\r
 <DT><A HREF="../compbio/metadata/RunnerConfig.html#getArgumentByOptionName(java.lang.String)"><B>getArgumentByOptionName(String)</B></A> - \r
 Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
 <DD>Returns the argument by option name, NULL if the argument is not found\r
@@ -123,7 +171,8 @@ Method in class compbio.metadata.<A HREF="../compbio/metadata/Preset.html" title
 <DD>Converts list of options as String to type Option\r
 <DT><A HREF="../compbio/metadata/RunnerConfig.html#getArguments()"><B>getArguments()</B></A> - \r
 Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
-<DD>&nbsp;\r
+<DD>Returns list of <A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata"><CODE>Parameter</CODE></A> and <A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata"><CODE>Option</CODE></A> supported by current
+ runner\r
 <DT><A HREF="../compbio/engine/Configurator.html#getAsyncEngine(compbio.engine.client.ConfiguredExecutable, compbio.engine.client.Executable.ExecProvider)"><B>getAsyncEngine(ConfiguredExecutable&lt;?&gt;, Executable.ExecProvider)</B></A> - \r
 Static method in class compbio.engine.<A HREF="../compbio/engine/Configurator.html" title="class in compbio.engine">Configurator</A>\r
 <DD>&nbsp;\r
@@ -157,8 +206,17 @@ Static method in class compbio.engine.<A HREF="../compbio/engine/Job.html" title
 <DT><A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html#getCalculationTime()"><B>getCalculationTime()</B></A> - \r
 Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</A>\r
 <DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/local/_TrackingExecutor.html#getCancelledTasks()"><B>getCancelledTasks()</B></A> - \r
-Method in class compbio.engine.local.<A HREF="../compbio/engine/local/_TrackingExecutor.html" title="class in compbio.engine.local">_TrackingExecutor</A>\r
+<DT><A HREF="../compbio/stat/servlet/util/Totals.html#getCancelled()"><B>getCancelled()</B></A> - \r
+Method in class compbio.stat.servlet.util.<A HREF="../compbio/stat/servlet/util/Totals.html" title="class in compbio.stat.servlet.util">Totals</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/stat/collector/StatDB.html#getCancelledCount(java.sql.Timestamp, java.sql.Timestamp)"><B>getCancelledCount(Timestamp, Timestamp)</B></A> - \r
+Method in class compbio.stat.collector.<A HREF="../compbio/stat/collector/StatDB.html" title="class in compbio.stat.collector">StatDB</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/stat/collector/StatProcessor.html#getCancelledJobs()"><B>getCancelledJobs()</B></A> - \r
+Method in class compbio.stat.collector.<A HREF="../compbio/stat/collector/StatProcessor.html" title="class in compbio.stat.collector">StatProcessor</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/Category.html#getCategories()"><B>getCategories()</B></A> - \r
+Static method in class compbio.data.msa.<A HREF="../compbio/data/msa/Category.html" title="class in compbio.data.msa">Category</A>\r
 <DD>&nbsp;\r
 <DT><A HREF="../compbio/metadata/ChunkHolder.html#getChunk()"><B>getChunk()</B></A> - \r
 Method in class compbio.metadata.<A HREF="../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A>\r
@@ -166,15 +224,36 @@ Method in class compbio.metadata.<A HREF="../compbio/metadata/ChunkHolder.html"
 <DT><A HREF="../compbio/engine/conf/DirectoryManager.html#getClass(java.lang.String)"><B>getClass(String)</B></A> - \r
 Static method in class compbio.engine.conf.<A HREF="../compbio/engine/conf/DirectoryManager.html" title="class in compbio.engine.conf">DirectoryManager</A>\r
 <DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/msa/Tcoffee.html#getClusterCpuNum()"><B>getClusterCpuNum()</B></A> - \r
-Static method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>\r
+<DT><A HREF="../compbio/engine/client/SkeletalExecutable.html#getClusterCpuNum(java.lang.Class)"><B>getClusterCpuNum(Class&lt;? extends Executable&lt;?&gt;&gt;)</B></A> - \r
+Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>\r
 <DD>&nbsp;\r
 <DT><A HREF="../compbio/engine/cluster/drmaa/ClusterSession.html#getClusterJobId(java.lang.String)"><B>getClusterJobId(String)</B></A> - \r
 Static method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/ClusterSession.html" title="class in compbio.engine.cluster.drmaa">ClusterSession</A>\r
 <DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/SkeletalExecutable.html#getClusterSettings()"><B>getClusterSettings()</B></A> - \r
+<DT><A HREF="../compbio/stat/collector/JobStat.html#getClusterJobId()"><B>getClusterJobId()</B></A> - \r
+Method in class compbio.stat.collector.<A HREF="../compbio/stat/collector/JobStat.html" title="class in compbio.stat.collector">JobStat</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/stat/collector/StatProcessor.html#getClusterJobs()"><B>getClusterJobs()</B></A> - \r
+Method in class compbio.stat.collector.<A HREF="../compbio/stat/collector/StatProcessor.html" title="class in compbio.stat.collector">StatProcessor</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/engine/client/ConfExecutable.html#getClusterJobSettings()"><B>getClusterJobSettings()</B></A> - \r
+Method in class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/engine/client/Executable.html#getClusterJobSettings()"><B>getClusterJobSettings()</B></A> - \r
+Method in interface compbio.engine.client.<A HREF="../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/engine/client/SkeletalExecutable.html#getClusterJobSettings()"><B>getClusterJobSettings()</B></A> - \r
 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>\r
 <DD>&nbsp;\r
+<DT><A HREF="../compbio/runner/_impl/NetNglyc.html#getClusterJobSettings()"><B>getClusterJobSettings()</B></A> - \r
+Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/runner/_SkeletalCommandBuilder.html#getClusterJobSettings()"><B>getClusterJobSettings()</B></A> - \r
+Method in class compbio.runner.<A HREF="../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>\r
+<DD><B>Deprecated.</B>&nbsp;&nbsp;\r
+<DT><A HREF="../compbio/stat/servlet/util/StatCollection.html#getClusterStat()"><B>getClusterStat()</B></A> - \r
+Method in class compbio.stat.servlet.util.<A HREF="../compbio/stat/servlet/util/StatCollection.html" title="class in compbio.stat.servlet.util">StatCollection</A>\r
+<DD>&nbsp;\r
 <DT><A HREF="../compbio/engine/client/ConfExecutable.html#getCommand(compbio.engine.client.Executable.ExecProvider)"><B>getCommand(Executable.ExecProvider)</B></A> - \r
 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>\r
 <DD>&nbsp;\r
@@ -187,9 +266,6 @@ Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/U
 <DT><A HREF="../compbio/runner/_impl/BlastAll.html#getCommand(compbio.engine.client.Executable.ExecProvider)"><B>getCommand(Executable.ExecProvider)</B></A> - \r
 Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/BlastAll.html" title="class in compbio.runner._impl">BlastAll</A>\r
 <DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/_impl/Disembl.html#getCommand(compbio.engine.client.Executable.ExecProvider)"><B>getCommand(Executable.ExecProvider)</B></A> - \r
-Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Disembl.html" title="class in compbio.runner._impl">Disembl</A>\r
-<DD>&nbsp;\r
 <DT><A HREF="../compbio/runner/_impl/Mcl.html#getCommand(compbio.engine.client.Executable.ExecProvider)"><B>getCommand(Executable.ExecProvider)</B></A> - \r
 Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Mcl.html" title="class in compbio.runner._impl">Mcl</A>\r
 <DD>&nbsp;\r
@@ -205,9 +281,6 @@ Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/RPSBlast.h
 <DT><A HREF="../compbio/runner/_impl/BlastAll.html#getCommandName()"><B>getCommandName()</B></A> - \r
 Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/BlastAll.html" title="class in compbio.runner._impl">BlastAll</A>\r
 <DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/_impl/Disembl.html#getCommandName()"><B>getCommandName()</B></A> - \r
-Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Disembl.html" title="class in compbio.runner._impl">Disembl</A>\r
-<DD>&nbsp;\r
 <DT><A HREF="../compbio/runner/_impl/Mcl.html#getCommandName()"><B>getCommandName()</B></A> - \r
 Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Mcl.html" title="class in compbio.runner._impl">Mcl</A>\r
 <DD>&nbsp;\r
@@ -246,7 +319,7 @@ Method in class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExec
 <DD>&nbsp;\r
 <DT><A HREF="../compbio/engine/client/Executable.html#getCreatedFiles()"><B>getCreatedFiles()</B></A> - \r
 Method in interface compbio.engine.client.<A HREF="../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>\r
-<DD>&nbsp;\r
+<DD><B>Deprecated.</B>&nbsp;\r
 <DT><A HREF="../compbio/engine/client/SkeletalExecutable.html#getCreatedFiles()"><B>getCreatedFiles()</B></A> - \r
 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>\r
 <DD>This method cannot really tell whether the files has actually been
@@ -254,9 +327,6 @@ Method in class compbio.engine.client.<A HREF="../compbio/engine/client/Skeletal
 <DT><A HREF="../compbio/runner/_impl/BlastAll.html#getCreatedFiles()"><B>getCreatedFiles()</B></A> - \r
 Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/BlastAll.html" title="class in compbio.runner._impl">BlastAll</A>\r
 <DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/_impl/Disembl.html#getCreatedFiles()"><B>getCreatedFiles()</B></A> - \r
-Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Disembl.html" title="class in compbio.runner._impl">Disembl</A>\r
-<DD>&nbsp;\r
 <DT><A HREF="../compbio/runner/_impl/Mcl.html#getCreatedFiles()"><B>getCreatedFiles()</B></A> - \r
 Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Mcl.html" title="class in compbio.runner._impl">Mcl</A>\r
 <DD>&nbsp;\r
@@ -275,6 +345,12 @@ Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Ronn.html"
 <DT><A HREF="../compbio/runner/_impl/RPSBlast.html#getCreatedFiles()"><B>getCreatedFiles()</B></A> - \r
 Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/RPSBlast.html" title="class in compbio.runner._impl">RPSBlast</A>\r
 <DD>&nbsp;\r
+<DT><A HREF="../compbio/runner/conservation/AACon.html#getCreatedFiles()"><B>getCreatedFiles()</B></A> - \r
+Method in class compbio.runner.conservation.<A HREF="../compbio/runner/conservation/AACon.html" title="class in compbio.runner.conservation">AACon</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/runner/disorder/Jronn.html#getCreatedFiles()"><B>getCreatedFiles()</B></A> - \r
+Method in class compbio.runner.disorder.<A HREF="../compbio/runner/disorder/Jronn.html" title="class in compbio.runner.disorder">Jronn</A>\r
+<DD>&nbsp;\r
 <DT><A HREF="../compbio/runner/msa/ClustalW.html#getCreatedFiles()"><B>getCreatedFiles()</B></A> - \r
 Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>\r
 <DD>&nbsp;\r
@@ -311,12 +387,15 @@ Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title
 <DT><A HREF="../compbio/metadata/Preset.html#getDescription()"><B>getDescription()</B></A> - \r
 Method in class compbio.metadata.<A HREF="../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>\r
 <DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/_impl/Runners.html#getDisemblRunnable(java.lang.String)"><B>getDisemblRunnable(String)</B></A> - \r
-Static method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Runners.html" title="class in compbio.runner._impl">Runners</A>\r
+<DT><A HREF="../compbio/stat/servlet/ServiceTestResult.html#getDetails()"><B>getDetails()</B></A> - \r
+Method in class compbio.stat.servlet.<A HREF="../compbio/stat/servlet/ServiceTestResult.html" title="class in compbio.stat.servlet">ServiceTestResult</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/stat/collector/StatDB.html#getEarliestRecord()"><B>getEarliestRecord()</B></A> - \r
+Method in class compbio.stat.collector.<A HREF="../compbio/stat/collector/StatDB.html" title="class in compbio.stat.collector">StatDB</A>\r
 <DD>&nbsp;\r
 <DT><A HREF="../compbio/runner/_SkeletalCommandBuilder.html#getEmail()"><B>getEmail()</B></A> - \r
 Method in class compbio.runner.<A HREF="../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>\r
-<DD>&nbsp;\r
+<DD><B>Deprecated.</B>&nbsp;&nbsp;\r
 <DT><A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html#getEndTime()"><B>getEndTime()</B></A> - \r
 Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</A>\r
 <DD>&nbsp;\r
@@ -355,6 +434,9 @@ Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/NetNglyc.h
 <DD>&nbsp;\r
 <DT><A HREF="../compbio/runner/_SkeletalCommandBuilder.html#getError()"><B>getError()</B></A> - \r
 Method in class compbio.runner.<A HREF="../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>\r
+<DD><B>Deprecated.</B>&nbsp;&nbsp;\r
+<DT><A HREF="../compbio/stat/collector/JobStat.html#getEscJobname()"><B>getEscJobname()</B></A> - \r
+Method in class compbio.stat.collector.<A HREF="../compbio/stat/collector/JobStat.html" title="class in compbio.stat.collector">JobStat</A>\r
 <DD>&nbsp;\r
 <DT><A HREF="../compbio/engine/client/Util.html#getExecProperty(java.lang.String, compbio.engine.client.Executable)"><B>getExecProperty(String, Executable&lt;?&gt;)</B></A> - \r
 Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/Util.html" title="class in compbio.engine.client">Util</A>\r
@@ -384,18 +466,36 @@ Static method in class compbio.engine.local.<A HREF="../compbio/engine/local/Loc
 <DT><A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html#getExitStatus()"><B>getExitStatus()</B></A> - \r
 Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</A>\r
 <DD>&nbsp;\r
+<DT><A HREF="../compbio/stat/servlet/util/Totals.html#getFailed()"><B>getFailed()</B></A> - \r
+Method in class compbio.stat.servlet.util.<A HREF="../compbio/stat/servlet/util/Totals.html" title="class in compbio.stat.servlet.util">Totals</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/stat/collector/StatProcessor.html#getFailedJobs()"><B>getFailedJobs()</B></A> - \r
+Method in class compbio.stat.collector.<A HREF="../compbio/stat/collector/StatProcessor.html" title="class in compbio.stat.collector">StatProcessor</A>\r
+<DD>Started & finished but did not produce result\r
 <DT><A HREF="../compbio/data/msa/jaxws/Align.html#getFastaSequences()"><B>getFastaSequences()</B></A> - \r
 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/Align.html" title="class in compbio.data.msa.jaxws">Align</A>\r
 <DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/jaxws/Analize.html#getFastaSequences()"><B>getFastaSequences()</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/Analize.html" title="class in compbio.data.msa.jaxws">Analize</A>\r
+<DD>&nbsp;\r
 <DT><A HREF="../compbio/data/msa/jaxws/CustomAlign.html#getFastaSequences()"><B>getFastaSequences()</B></A> - \r
 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/CustomAlign.html" title="class in compbio.data.msa.jaxws">CustomAlign</A>\r
 <DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/jaxws/CustomAnalize.html#getFastaSequences()"><B>getFastaSequences()</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/CustomAnalize.html" title="class in compbio.data.msa.jaxws">CustomAnalize</A>\r
+<DD>&nbsp;\r
 <DT><A HREF="../compbio/data/msa/jaxws/PresetAlign.html#getFastaSequences()"><B>getFastaSequences()</B></A> - \r
 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/PresetAlign.html" title="class in compbio.data.msa.jaxws">PresetAlign</A>\r
 <DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/jaxws/PresetAnalize.html#getFastaSequences()"><B>getFastaSequences()</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/PresetAnalize.html" title="class in compbio.data.msa.jaxws">PresetAnalize</A>\r
+<DD>&nbsp;\r
 <DT><A HREF="../compbio/engine/FilePuller.html#getFile()"><B>getFile()</B></A> - \r
 Method in class compbio.engine.<A HREF="../compbio/engine/FilePuller.html" title="class in compbio.engine">FilePuller</A>\r
 <DD>&nbsp;\r
+<DT><A HREF="../compbio/stat/collector/JobStat.html#getFinish()"><B>getFinish()</B></A> - \r
+Method in class compbio.stat.collector.<A HREF="../compbio/stat/collector/JobStat.html" title="class in compbio.stat.collector">JobStat</A>\r
+<DD>&nbsp;\r
 <DT><A HREF="../compbio/data/sequence/FastaSequence.html#getFormatedSequence(int)"><B>getFormatedSequence(int)</B></A> - \r
 Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>\r
 <DD>Format sequence per width letter in one string.\r
@@ -414,12 +514,18 @@ Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title
 <DT><A HREF="../compbio/data/sequence/AlignmentMetadata.html#getGapchar()"><B>getGapchar()</B></A> - \r
 Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence">AlignmentMetadata</A>\r
 <DD>&nbsp;\r
-<DT><A HREF="../compbio/ws/client/Jws2Client.html#getHost(java.lang.String[])"><B>getHost(String[])</B></A> - \r
-Static method in class compbio.ws.client.<A HREF="../compbio/ws/client/Jws2Client.html" title="class in compbio.ws.client">Jws2Client</A>\r
-<DD>Extracts host name from the command line\r
 <DT><A HREF="../compbio/data/sequence/FastaSequence.html#getId()"><B>getId()</B></A> - \r
 Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>\r
 <DD>Gets the value of id\r
+<DT><A HREF="../compbio/stat/servlet/util/Totals.html#getIncomplete()"><B>getIncomplete()</B></A> - \r
+Method in class compbio.stat.servlet.util.<A HREF="../compbio/stat/servlet/util/Totals.html" title="class in compbio.stat.servlet.util">Totals</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/stat/collector/StatDB.html#getIncompleteCount(java.sql.Timestamp, java.sql.Timestamp)"><B>getIncompleteCount(Timestamp, Timestamp)</B></A> - \r
+Method in class compbio.stat.collector.<A HREF="../compbio/stat/collector/StatDB.html" title="class in compbio.stat.collector">StatDB</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/stat/collector/StatProcessor.html#getIncompleteJobs()"><B>getIncompleteJobs()</B></A> - \r
+Method in class compbio.stat.collector.<A HREF="../compbio/stat/collector/StatProcessor.html" title="class in compbio.stat.collector">StatProcessor</A>\r
+<DD>&nbsp;\r
 <DT><A HREF="../compbio/engine/client/ConfExecutable.html#getInput()"><B>getInput()</B></A> - \r
 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>\r
 <DD>Not all input paths are relative! Input path could be absolute!\r
@@ -435,9 +541,6 @@ Method in class compbio.engine.client.<A HREF="../compbio/engine/client/Skeletal
 <DT><A HREF="../compbio/runner/_impl/BlastAll.html#getInput()"><B>getInput()</B></A> - \r
 Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/BlastAll.html" title="class in compbio.runner._impl">BlastAll</A>\r
 <DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/_impl/Disembl.html#getInput()"><B>getInput()</B></A> - \r
-Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Disembl.html" title="class in compbio.runner._impl">Disembl</A>\r
-<DD>&nbsp;\r
 <DT><A HREF="../compbio/runner/_impl/Mcl.html#getInput()"><B>getInput()</B></A> - \r
 Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Mcl.html" title="class in compbio.runner._impl">Mcl</A>\r
 <DD>&nbsp;\r
@@ -456,30 +559,42 @@ Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Ronn.html"
 <DT><A HREF="../compbio/runner/_impl/RPSBlast.html#getInput()"><B>getInput()</B></A> - \r
 Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/RPSBlast.html" title="class in compbio.runner._impl">RPSBlast</A>\r
 <DD>&nbsp;\r
+<DT><A HREF="../compbio/stat/collector/JobStat.html#getInputSize()"><B>getInputSize()</B></A> - \r
+Method in class compbio.stat.collector.<A HREF="../compbio/stat/collector/JobStat.html" title="class in compbio.stat.collector">JobStat</A>\r
+<DD>&nbsp;\r
 <DT><A HREF="../compbio/engine/cluster/drmaa/JobRunner.html#getInstance(compbio.engine.client.ConfiguredExecutable)"><B>getInstance(ConfiguredExecutable&lt;?&gt;)</B></A> - \r
 Static method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/JobRunner.html" title="class in compbio.engine.cluster.drmaa">JobRunner</A>\r
 <DD>&nbsp;\r
 <DT><A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html#getIOWait()"><B>getIOWait()</B></A> - \r
 Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</A>\r
 <DD>&nbsp;\r
+<DT><A HREF="../compbio/stat/collector/JobStat.html#getIsCancelled()"><B>getIsCancelled()</B></A> - \r
+Method in class compbio.stat.collector.<A HREF="../compbio/stat/collector/JobStat.html" title="class in compbio.stat.collector">JobStat</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/stat/collector/JobStat.html#getIsCollected()"><B>getIsCollected()</B></A> - \r
+Method in class compbio.stat.collector.<A HREF="../compbio/stat/collector/JobStat.html" title="class in compbio.stat.collector">JobStat</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/stat/collector/JobStat.html#getIsFinished()"><B>getIsFinished()</B></A> - \r
+Method in class compbio.stat.collector.<A HREF="../compbio/stat/collector/JobStat.html" title="class in compbio.stat.collector">JobStat</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/engine/client/Util.html#getJava()"><B>getJava()</B></A> - \r
+Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/Util.html" title="class in compbio.engine.client">Util</A>\r
+<DD>Returns the absolute path to the Java executable from JAVA_HOME\r
 <DT><A HREF="../compbio/data/msa/jaxws/CancelJob.html#getJobId()"><B>getJobId()</B></A> - \r
 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/CancelJob.html" title="class in compbio.data.msa.jaxws">CancelJob</A>\r
 <DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/jaxws/GetAnnotation.html#getJobId()"><B>getJobId()</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetAnnotation.html" title="class in compbio.data.msa.jaxws">GetAnnotation</A>\r
+<DD>&nbsp;\r
 <DT><A HREF="../compbio/data/msa/jaxws/GetJobStatus.html#getJobId()"><B>getJobId()</B></A> - \r
 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetJobStatus.html" title="class in compbio.data.msa.jaxws">GetJobStatus</A>\r
 <DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/jaxws/GetProgress.html#getJobId()"><B>getJobId()</B></A> - \r
-Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetProgress.html" title="class in compbio.data.msa.jaxws">GetProgress</A>\r
-<DD>&nbsp;\r
 <DT><A HREF="../compbio/data/msa/jaxws/GetResult.html#getJobId()"><B>getJobId()</B></A> - \r
 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetResult.html" title="class in compbio.data.msa.jaxws">GetResult</A>\r
 <DD>&nbsp;\r
 <DT><A HREF="../compbio/data/msa/jaxws/PullExecStatistics.html#getJobId()"><B>getJobId()</B></A> - \r
 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/PullExecStatistics.html" title="class in compbio.data.msa.jaxws">PullExecStatistics</A>\r
 <DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/jaxws/PullFile.html#getJobId()"><B>getJobId()</B></A> - \r
-Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/PullFile.html" title="class in compbio.data.msa.jaxws">PullFile</A>\r
-<DD>&nbsp;\r
 <DT><A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html#getJobId()"><B>getJobId()</B></A> - \r
 Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</A>\r
 <DD>&nbsp;\r
@@ -493,14 +608,23 @@ Method in class compbio.engine.<A HREF="../compbio/engine/Job.html" title="class
 Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/JobRunner.html" title="class in compbio.engine.cluster.drmaa">JobRunner</A>\r
 <DD>This method will block before the calculation has completed and then
  return the object containing a job execution statistics\r
+<DT><A HREF="../compbio/stat/collector/JobStat.html#getJobname()"><B>getJobname()</B></A> - \r
+Method in class compbio.stat.collector.<A HREF="../compbio/stat/collector/JobStat.html" title="class in compbio.stat.collector">JobStat</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/stat/collector/StatProcessor.html#getJobNumber()"><B>getJobNumber()</B></A> - \r
+Method in class compbio.stat.collector.<A HREF="../compbio/stat/collector/StatProcessor.html" title="class in compbio.stat.collector">StatProcessor</A>\r
+<DD>&nbsp;\r
 <DT><A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html#getJobPriority()"><B>getJobPriority()</B></A> - \r
 Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</A>\r
 <DD>&nbsp;\r
+<DT><A HREF="../compbio/stat/collector/StatProcessor.html#getJobs()"><B>getJobs()</B></A> - \r
+Method in class compbio.stat.collector.<A HREF="../compbio/stat/collector/StatProcessor.html" title="class in compbio.stat.collector">StatProcessor</A>\r
+<DD>&nbsp;\r
 <DT><A HREF="../compbio/data/msa/jaxws/GetJobStatus.html" title="class in compbio.data.msa.jaxws"><B>GetJobStatus</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/GetJobStatus.html#GetJobStatus()"><B>GetJobStatus()</B></A> - \r
 Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetJobStatus.html" title="class in compbio.data.msa.jaxws">GetJobStatus</A>\r
 <DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/MsaWS.html#getJobStatus(java.lang.String)"><B>getJobStatus(String)</B></A> - \r
-Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>\r
+<DT><A HREF="../compbio/data/msa/JManagement.html#getJobStatus(java.lang.String)"><B>getJobStatus(String)</B></A> - \r
+Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/JManagement.html" title="interface in compbio.data.msa">JManagement</A>\r
 <DD>Return the status of the job.\r
 <DT><A HREF="../compbio/engine/AsyncExecutor.html#getJobStatus(java.lang.String)"><B>getJobStatus(String)</B></A> - \r
 Method in interface compbio.engine.<A HREF="../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine">AsyncExecutor</A>\r
@@ -532,9 +656,15 @@ Method in class compbio.engine.local.<A HREF="../compbio/engine/local/LocalRunne
 <DT><A HREF="../compbio/engine/SyncExecutor.html#getJobStatus()"><B>getJobStatus()</B></A> - \r
 Method in interface compbio.engine.<A HREF="../compbio/engine/SyncExecutor.html" title="interface in compbio.engine">SyncExecutor</A>\r
 <DD>Query the status of the job by its id.\r
+<DT><A HREF="../compbio/ws/server/ClustalOWS.html#getJobStatus(java.lang.String)"><B>getJobStatus(String)</B></A> - \r
+Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ClustalOWS.html" title="class in compbio.ws.server">ClustalOWS</A>\r
+<DD>&nbsp;\r
 <DT><A HREF="../compbio/ws/server/ClustalWS.html#getJobStatus(java.lang.String)"><B>getJobStatus(String)</B></A> - \r
 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ClustalWS.html" title="class in compbio.ws.server">ClustalWS</A>\r
 <DD>&nbsp;\r
+<DT><A HREF="../compbio/ws/server/GenericMetadataService.html#getJobStatus(java.lang.String)"><B>getJobStatus(String)</B></A> - \r
+Method in class compbio.ws.server.<A HREF="../compbio/ws/server/GenericMetadataService.html" title="class in compbio.ws.server">GenericMetadataService</A>\r
+<DD>&nbsp;\r
 <DT><A HREF="../compbio/ws/server/MafftWS.html#getJobStatus(java.lang.String)"><B>getJobStatus(String)</B></A> - \r
 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/MafftWS.html" title="class in compbio.ws.server">MafftWS</A>\r
 <DD>&nbsp;\r
@@ -553,14 +683,38 @@ Static method in class compbio.ws.server.<A HREF="../compbio/ws/server/WSUtil.ht
 <DT><A HREF="../compbio/data/msa/jaxws/GetJobStatusResponse.html" title="class in compbio.data.msa.jaxws"><B>GetJobStatusResponse</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/GetJobStatusResponse.html#GetJobStatusResponse()"><B>GetJobStatusResponse()</B></A> - \r
 Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetJobStatusResponse.html" title="class in compbio.data.msa.jaxws">GetJobStatusResponse</A>\r
 <DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/jaxws/GetLastTested.html" title="class in compbio.data.msa.jaxws"><B>GetLastTested</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/GetLastTested.html#GetLastTested()"><B>GetLastTested()</B></A> - \r
+Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetLastTested.html" title="class in compbio.data.msa.jaxws">GetLastTested</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/RegistryWS.html#getLastTested(compbio.ws.client.Services)"><B>getLastTested(Services)</B></A> - \r
+Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/RegistryWS.html" title="interface in compbio.data.msa">RegistryWS</A>\r
+<DD>Number of seconds since the last test.\r
+<DT><A HREF="../compbio/ws/server/RegistryWS.html#getLastTested(compbio.ws.client.Services)"><B>getLastTested(Services)</B></A> - \r
+Method in class compbio.ws.server.<A HREF="../compbio/ws/server/RegistryWS.html" title="class in compbio.ws.server">RegistryWS</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/jaxws/GetLastTestedOn.html" title="class in compbio.data.msa.jaxws"><B>GetLastTestedOn</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/GetLastTestedOn.html#GetLastTestedOn()"><B>GetLastTestedOn()</B></A> - \r
+Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetLastTestedOn.html" title="class in compbio.data.msa.jaxws">GetLastTestedOn</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/RegistryWS.html#getLastTestedOn(compbio.ws.client.Services)"><B>getLastTestedOn(Services)</B></A> - \r
+Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/RegistryWS.html" title="interface in compbio.data.msa">RegistryWS</A>\r
+<DD>The date and time the service has been verified to work last time\r
+<DT><A HREF="../compbio/ws/server/RegistryWS.html#getLastTestedOn(compbio.ws.client.Services)"><B>getLastTestedOn(Services)</B></A> - \r
+Method in class compbio.ws.server.<A HREF="../compbio/ws/server/RegistryWS.html" title="class in compbio.ws.server">RegistryWS</A>\r
+<DD>Can potentially return null if the service has not been tested yet.\r
+<DT><A HREF="../compbio/data/msa/jaxws/GetLastTestedOnResponse.html" title="class in compbio.data.msa.jaxws"><B>GetLastTestedOnResponse</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/GetLastTestedOnResponse.html#GetLastTestedOnResponse()"><B>GetLastTestedOnResponse()</B></A> - \r
+Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetLastTestedOnResponse.html" title="class in compbio.data.msa.jaxws">GetLastTestedOnResponse</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/jaxws/GetLastTestedResponse.html" title="class in compbio.data.msa.jaxws"><B>GetLastTestedResponse</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/GetLastTestedResponse.html#GetLastTestedResponse()"><B>GetLastTestedResponse()</B></A> - \r
+Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetLastTestedResponse.html" title="class in compbio.data.msa.jaxws">GetLastTestedResponse</A>\r
+<DD>&nbsp;\r
 <DT><A HREF="../compbio/data/sequence/FastaSequence.html#getLength()"><B>getLength()</B></A> - \r
 Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>\r
 <DD>&nbsp;\r
 <DT><A HREF="../compbio/data/msa/jaxws/GetLimit.html" title="class in compbio.data.msa.jaxws"><B>GetLimit</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/GetLimit.html#GetLimit()"><B>GetLimit()</B></A> - \r
 Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetLimit.html" title="class in compbio.data.msa.jaxws">GetLimit</A>\r
 <DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/MsaWS.html#getLimit(java.lang.String)"><B>getLimit(String)</B></A> - \r
-Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>\r
+<DT><A HREF="../compbio/data/msa/Metadata.html#getLimit(java.lang.String)"><B>getLimit(String)</B></A> - \r
+Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/Metadata.html" title="interface in compbio.data.msa">Metadata</A>\r
 <DD>Get a Limit for a preset.\r
 <DT><A HREF="../compbio/engine/client/ConfExecutable.html#getLimit(java.lang.String)"><B>getLimit(String)</B></A> - \r
 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>\r
@@ -568,33 +722,24 @@ Method in class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExec
 <DT><A HREF="../compbio/engine/client/Executable.html#getLimit(java.lang.String)"><B>getLimit(String)</B></A> - \r
 Method in interface compbio.engine.client.<A HREF="../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>\r
 <DD>&nbsp;\r
+<DT><A HREF="../compbio/engine/client/SkeletalExecutable.html#getLimit(java.lang.String)"><B>getLimit(String)</B></A> - \r
+Method in class compbio.engine.client.<A HREF="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>\r
+<DD>&nbsp;\r
 <DT><A HREF="../compbio/runner/_impl/NetNglyc.html#getLimit(java.lang.String)"><B>getLimit(String)</B></A> - \r
 Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>\r
 <DD>&nbsp;\r
 <DT><A HREF="../compbio/runner/_SkeletalCommandBuilder.html#getLimit(java.lang.String)"><B>getLimit(String)</B></A> - \r
 Method in class compbio.runner.<A HREF="../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/msa/ClustalW.html#getLimit(java.lang.String)"><B>getLimit(String)</B></A> - \r
-Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/msa/Mafft.html#getLimit(java.lang.String)"><B>getLimit(String)</B></A> - \r
-Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/msa/Muscle.html#getLimit(java.lang.String)"><B>getLimit(String)</B></A> - \r
-Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/msa/Probcons.html#getLimit(java.lang.String)"><B>getLimit(String)</B></A> - \r
-Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/msa/Tcoffee.html#getLimit(java.lang.String)"><B>getLimit(String)</B></A> - \r
-Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/psiblast/PsiBlast.html#getLimit(java.lang.String)"><B>getLimit(String)</B></A> - \r
-Method in class compbio.runner.psiblast.<A HREF="../compbio/runner/psiblast/PsiBlast.html" title="class in compbio.runner.psiblast">PsiBlast</A>\r
+<DD><B>Deprecated.</B>&nbsp;&nbsp;\r
+<DT><A HREF="../compbio/ws/server/ClustalOWS.html#getLimit(java.lang.String)"><B>getLimit(String)</B></A> - \r
+Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ClustalOWS.html" title="class in compbio.ws.server">ClustalOWS</A>\r
 <DD>&nbsp;\r
 <DT><A HREF="../compbio/ws/server/ClustalWS.html#getLimit(java.lang.String)"><B>getLimit(String)</B></A> - \r
 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ClustalWS.html" title="class in compbio.ws.server">ClustalWS</A>\r
 <DD>&nbsp;\r
+<DT><A HREF="../compbio/ws/server/GenericMetadataService.html#getLimit(java.lang.String)"><B>getLimit(String)</B></A> - \r
+Method in class compbio.ws.server.<A HREF="../compbio/ws/server/GenericMetadataService.html" title="class in compbio.ws.server">GenericMetadataService</A>\r
+<DD>&nbsp;\r
 <DT><A HREF="../compbio/ws/server/MafftWS.html#getLimit(java.lang.String)"><B>getLimit(String)</B></A> - \r
 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/MafftWS.html" title="class in compbio.ws.server">MafftWS</A>\r
 <DD>&nbsp;\r
@@ -616,8 +761,8 @@ Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/
 <DT><A HREF="../compbio/data/msa/jaxws/GetLimits.html" title="class in compbio.data.msa.jaxws"><B>GetLimits</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/GetLimits.html#GetLimits()"><B>GetLimits()</B></A> - \r
 Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetLimits.html" title="class in compbio.data.msa.jaxws">GetLimits</A>\r
 <DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/MsaWS.html#getLimits()"><B>getLimits()</B></A> - \r
-Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>\r
+<DT><A HREF="../compbio/data/msa/Metadata.html#getLimits()"><B>getLimits()</B></A> - \r
+Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/Metadata.html" title="interface in compbio.data.msa">Metadata</A>\r
 <DD>List Limits supported by a web service.\r
 <DT><A HREF="../compbio/engine/client/ConfExecutable.html#getLimits()"><B>getLimits()</B></A> - \r
 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>\r
@@ -625,6 +770,13 @@ Method in class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExec
 <DT><A HREF="../compbio/engine/client/Executable.html#getLimits()"><B>getLimits()</B></A> - \r
 Method in interface compbio.engine.client.<A HREF="../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>\r
 <DD>&nbsp;\r
+<DT><A HREF="../compbio/engine/client/SkeletalExecutable.html#getLimits()"><B>getLimits()</B></A> - \r
+Method in class compbio.engine.client.<A HREF="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/engine/client/Util.html#getLimits(java.lang.Class)"><B>getLimits(Class&lt;T&gt;)</B></A> - \r
+Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/Util.html" title="class in compbio.engine.client">Util</A>\r
+<DD>For now just assume that all parameters which came in needs setting it
+ will be a client responsibility to prepare RunnerConfig object then\r
 <DT><A HREF="../compbio/metadata/LimitsManager.html#getLimits()"><B>getLimits()</B></A> - \r
 Method in class compbio.metadata.<A HREF="../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>\r
 <DD>&nbsp;\r
@@ -633,32 +785,16 @@ Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/NetNglyc.h
 <DD>&nbsp;\r
 <DT><A HREF="../compbio/runner/_SkeletalCommandBuilder.html#getLimits()"><B>getLimits()</B></A> - \r
 Method in class compbio.runner.<A HREF="../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>\r
+<DD><B>Deprecated.</B>&nbsp;&nbsp;\r
+<DT><A HREF="../compbio/ws/server/ClustalOWS.html#getLimits()"><B>getLimits()</B></A> - \r
+Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ClustalOWS.html" title="class in compbio.ws.server">ClustalOWS</A>\r
 <DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/msa/ClustalW.html#getLimits()"><B>getLimits()</B></A> - \r
-Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/msa/Mafft.html#getLimits()"><B>getLimits()</B></A> - \r
-Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/msa/Muscle.html#getLimits()"><B>getLimits()</B></A> - \r
-Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/msa/Probcons.html#getLimits()"><B>getLimits()</B></A> - \r
-Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/msa/Tcoffee.html#getLimits()"><B>getLimits()</B></A> - \r
-Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/psiblast/PsiBlast.html#getLimits()"><B>getLimits()</B></A> - \r
-Method in class compbio.runner.psiblast.<A HREF="../compbio/runner/psiblast/PsiBlast.html" title="class in compbio.runner.psiblast">PsiBlast</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/Util.html#getLimits(java.lang.Class)"><B>getLimits(Class&lt;? extends Executable&lt;T&gt;&gt;)</B></A> - \r
-Static method in class compbio.runner.<A HREF="../compbio/runner/Util.html" title="class in compbio.runner">Util</A>\r
-<DD>For now just assume that all parameters which came in needs setting it
- will be a client responsibility to prepare RunnerConfig object then\r
 <DT><A HREF="../compbio/ws/server/ClustalWS.html#getLimits()"><B>getLimits()</B></A> - \r
 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ClustalWS.html" title="class in compbio.ws.server">ClustalWS</A>\r
 <DD>&nbsp;\r
+<DT><A HREF="../compbio/ws/server/GenericMetadataService.html#getLimits()"><B>getLimits()</B></A> - \r
+Method in class compbio.ws.server.<A HREF="../compbio/ws/server/GenericMetadataService.html" title="class in compbio.ws.server">GenericMetadataService</A>\r
+<DD>&nbsp;\r
 <DT><A HREF="../compbio/ws/server/MafftWS.html#getLimits()"><B>getLimits()</B></A> - \r
 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/MafftWS.html" title="class in compbio.ws.server">MafftWS</A>\r
 <DD>&nbsp;\r
@@ -674,9 +810,15 @@ Method in class compbio.ws.server.<A HREF="../compbio/ws/server/TcoffeeWS.html"
 <DT><A HREF="../compbio/data/msa/jaxws/GetLimitsResponse.html" title="class in compbio.data.msa.jaxws"><B>GetLimitsResponse</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/GetLimitsResponse.html#GetLimitsResponse()"><B>GetLimitsResponse()</B></A> - \r
 Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetLimitsResponse.html" title="class in compbio.data.msa.jaxws">GetLimitsResponse</A>\r
 <DD>&nbsp;\r
+<DT><A HREF="../compbio/stat/collector/StatProcessor.html#getLocalJobs()"><B>getLocalJobs()</B></A> - \r
+Method in class compbio.stat.collector.<A HREF="../compbio/stat/collector/StatProcessor.html" title="class in compbio.stat.collector">StatProcessor</A>\r
+<DD>&nbsp;\r
 <DT><A HREF="../compbio/engine/conf/PropertyHelperManager.html#getLocalPath()"><B>getLocalPath()</B></A> - \r
 Static method in class compbio.engine.conf.<A HREF="../compbio/engine/conf/PropertyHelperManager.html" title="class in compbio.engine.conf">PropertyHelperManager</A>\r
 <DD>Method return the absolute path to the project root directory.\r
+<DT><A HREF="../compbio/stat/servlet/util/StatCollection.html#getLocalStat()"><B>getLocalStat()</B></A> - \r
+Method in class compbio.stat.servlet.util.<A HREF="../compbio/stat/servlet/util/StatCollection.html" title="class in compbio.stat.servlet.util">StatCollection</A>\r
+<DD>&nbsp;\r
 <DT><A HREF="../compbio/metadata/ValueConstrain.html#getMax()"><B>getMax()</B></A> - \r
 Method in class compbio.metadata.<A HREF="../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A>\r
 <DD>&nbsp;\r
@@ -688,13 +830,10 @@ Static method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Run
 <DD>&nbsp;\r
 <DT><A HREF="../compbio/engine/cluster/dundee/_Queue.html#getMemoryLimit()"><B>getMemoryLimit()</B></A> - \r
 Method in enum compbio.engine.cluster.dundee.<A HREF="../compbio/engine/cluster/dundee/_Queue.html" title="enum in compbio.engine.cluster.dundee">_Queue</A>\r
-<DD>return max memory limit in Mb\r
+<DD><B>Deprecated.</B>&nbsp;return max memory limit in Mb\r
 <DT><A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html#getMemoryStat()"><B>getMemoryStat()</B></A> - \r
 Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</A>\r
 <DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/jaxws/JobExecutionExceptionBean.html#getMessage()"><B>getMessage()</B></A> - \r
-Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/JobExecutionExceptionBean.html" title="class in compbio.data.msa.jaxws">JobExecutionExceptionBean</A>\r
-<DD>&nbsp;\r
 <DT><A HREF="../compbio/data/msa/jaxws/JobSubmissionExceptionBean.html#getMessage()"><B>getMessage()</B></A> - \r
 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/JobSubmissionExceptionBean.html" title="class in compbio.data.msa.jaxws">JobSubmissionExceptionBean</A>\r
 <DD>&nbsp;\r
@@ -713,6 +852,12 @@ Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/WrongP
 <DT><A HREF="../compbio/data/sequence/Alignment.html#getMetadata()"><B>getMetadata()</B></A> - \r
 Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A>\r
 <DD>&nbsp;\r
+<DT><A HREF="../compbio/data/sequence/ConservationMethod.html#getMethod(java.lang.String)"><B>getMethod(String)</B></A> - \r
+Static method in enum compbio.data.sequence.<A HREF="../compbio/data/sequence/ConservationMethod.html" title="enum in compbio.data.sequence">ConservationMethod</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/sequence/Score.html#getMethod()"><B>getMethod()</B></A> - \r
+Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>\r
+<DD>Returns the ConservationMethod\r
 <DT><A HREF="../compbio/metadata/ValueConstrain.html#getMin()"><B>getMin()</B></A> - \r
 Method in class compbio.metadata.<A HREF="../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A>\r
 <DD>&nbsp;\r
@@ -727,22 +872,22 @@ Method in class compbio.metadata.<A HREF="../compbio/metadata/Preset.html" title
 <DD>&nbsp;\r
 <DT><A HREF="../compbio/runner/_SkeletalCommandBuilder.html#getName()"><B>getName()</B></A> - \r
 Method in class compbio.runner.<A HREF="../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>\r
-<DD>&nbsp;\r
+<DD><B>Deprecated.</B>&nbsp;&nbsp;\r
 <DT><A HREF="../compbio/runner/_NativeSpecHelper.html#getNativeSpec()"><B>getNativeSpec()</B></A> - \r
 Method in class compbio.runner.<A HREF="../compbio/runner/_NativeSpecHelper.html" title="class in compbio.runner">_NativeSpecHelper</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/ClusterNativeSpecExecutable.html#getNativeSpecs()"><B>getNativeSpecs()</B></A> - \r
-Method in interface compbio.engine.client.<A HREF="../compbio/engine/client/ClusterNativeSpecExecutable.html" title="interface in compbio.engine.client">ClusterNativeSpecExecutable</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/msa/Tcoffee.html#getNativeSpecs()"><B>getNativeSpecs()</B></A> - \r
-Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>\r
-<DD>&nbsp;\r
+<DD><B>Deprecated.</B>&nbsp;&nbsp;\r
 <DT><A HREF="../compbio/runner/_impl/Runners.html#getNetNglycRunnable(java.lang.String)"><B>getNetNglycRunnable(String)</B></A> - \r
 Static method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Runners.html" title="class in compbio.runner._impl">Runners</A>\r
 <DD>&nbsp;\r
 <DT><A HREF="../compbio/metadata/ChunkHolder.html#getNextPosition()"><B>getNextPosition()</B></A> - \r
 Method in class compbio.metadata.<A HREF="../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A>\r
 <DD>&nbsp;\r
+<DT><A HREF="../compbio/data/sequence/ScoreManager.ScoreHolder.html#getNumberOfScores()"><B>getNumberOfScores()</B></A> - \r
+Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/ScoreManager.ScoreHolder.html" title="class in compbio.data.sequence">ScoreManager.ScoreHolder</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/sequence/ScoreManager.html#getNumberOfSeq()"><B>getNumberOfSeq()</B></A> - \r
+Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</A>\r
+<DD>&nbsp;\r
 <DT><A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html#getNumberOfSequencesAllowed()"><B>getNumberOfSequencesAllowed()</B></A> - \r
 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html" title="class in compbio.data.msa.jaxws">LimitExceededExceptionBean</A>\r
 <DD>&nbsp;\r
@@ -764,12 +909,15 @@ Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title
 <DT><A HREF="../compbio/data/msa/jaxws/CustomAlign.html#getOptions()"><B>getOptions()</B></A> - \r
 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/CustomAlign.html" title="class in compbio.data.msa.jaxws">CustomAlign</A>\r
 <DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/jaxws/CustomAnalize.html#getOptions()"><B>getOptions()</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/CustomAnalize.html" title="class in compbio.data.msa.jaxws">CustomAnalize</A>\r
+<DD>&nbsp;\r
 <DT><A HREF="../compbio/metadata/Preset.html#getOptions()"><B>getOptions()</B></A> - \r
 Method in class compbio.metadata.<A HREF="../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>\r
 <DD>&nbsp;\r
 <DT><A HREF="../compbio/metadata/RunnerConfig.html#getOptions()"><B>getOptions()</B></A> - \r
 Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
-<DD>&nbsp;\r
+<DD>Returns the list of the Options supported by the executable of type T\r
 <DT><A HREF="../compbio/runner/OptionCombinator.html#getOptionsAtRandom()"><B>getOptionsAtRandom()</B></A> - \r
 Method in class compbio.runner.<A HREF="../compbio/runner/OptionCombinator.html" title="class in compbio.runner">OptionCombinator</A>\r
 <DD>&nbsp;\r
@@ -790,6 +938,9 @@ Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/NetNglyc.h
 <DD>&nbsp;\r
 <DT><A HREF="../compbio/runner/_SkeletalCommandBuilder.html#getOutput()"><B>getOutput()</B></A> - \r
 Method in class compbio.runner.<A HREF="../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>\r
+<DD><B>Deprecated.</B>&nbsp;&nbsp;\r
+<DT><A HREF="../compbio/runner/disorder/IUPred.html#getOutput()"><B>getOutput()</B></A> - \r
+Method in class compbio.runner.disorder.<A HREF="../compbio/runner/disorder/IUPred.html" title="class in compbio.runner.disorder">IUPred</A>\r
 <DD>&nbsp;\r
 <DT><A HREF="../compbio/engine/client/ConfExecutable.html#getParameters()"><B>getParameters()</B></A> - \r
 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>\r
@@ -811,12 +962,21 @@ Method in class compbio.engine.client.<A HREF="../compbio/engine/client/Skeletal
 <DD>&nbsp;\r
 <DT><A HREF="../compbio/metadata/RunnerConfig.html#getParameters()"><B>getParameters()</B></A> - \r
 Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
-<DD>&nbsp;\r
+<DD>Returns the list of parameters supported executable of type T.\r
 <DT><A HREF="../compbio/runner/_impl/NetNglyc.html#getParameters(compbio.engine.client.Executable.ExecProvider)"><B>getParameters(Executable.ExecProvider)</B></A> - \r
 Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>\r
 <DD>&nbsp;\r
 <DT><A HREF="../compbio/runner/_SkeletalCommandBuilder.html#getParameters(compbio.engine.client.Executable.ExecProvider)"><B>getParameters(Executable.ExecProvider)</B></A> - \r
 Method in class compbio.runner.<A HREF="../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>\r
+<DD><B>Deprecated.</B>&nbsp;&nbsp;\r
+<DT><A HREF="../compbio/runner/conservation/AACon.html#getParameters(compbio.engine.client.Executable.ExecProvider)"><B>getParameters(Executable.ExecProvider)</B></A> - \r
+Method in class compbio.runner.conservation.<A HREF="../compbio/runner/conservation/AACon.html" title="class in compbio.runner.conservation">AACon</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/runner/disorder/Jronn.html#getParameters(compbio.engine.client.Executable.ExecProvider)"><B>getParameters(Executable.ExecProvider)</B></A> - \r
+Method in class compbio.runner.disorder.<A HREF="../compbio/runner/disorder/Jronn.html" title="class in compbio.runner.disorder">Jronn</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/runner/msa/ClustalO.html#getParameters(compbio.engine.client.Executable.ExecProvider)"><B>getParameters(Executable.ExecProvider)</B></A> - \r
+Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</A>\r
 <DD>&nbsp;\r
 <DT><A HREF="../compbio/runner/msa/Tcoffee.html#getParameters(compbio.engine.client.Executable.ExecProvider)"><B>getParameters(Executable.ExecProvider)</B></A> - \r
 Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>\r
@@ -827,9 +987,6 @@ Method in class compbio.engine.client.<A HREF="../compbio/engine/client/CommandB
 <DT><A HREF="../compbio/data/msa/jaxws/PullExecStatistics.html#getPosition()"><B>getPosition()</B></A> - \r
 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/PullExecStatistics.html" title="class in compbio.data.msa.jaxws">PullExecStatistics</A>\r
 <DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/jaxws/PullFile.html#getPosition()"><B>getPosition()</B></A> - \r
-Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/PullFile.html" title="class in compbio.data.msa.jaxws">PullFile</A>\r
-<DD>&nbsp;\r
 <DT><A HREF="../compbio/metadata/Argument.html#getPossibleValues()"><B>getPossibleValues()</B></A> - \r
 Method in interface compbio.metadata.<A HREF="../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</A>\r
 <DD>&nbsp;\r
@@ -842,6 +999,9 @@ Method in class compbio.metadata.<A HREF="../compbio/metadata/Parameter.html" ti
 <DT><A HREF="../compbio/data/msa/jaxws/PresetAlign.html#getPreset()"><B>getPreset()</B></A> - \r
 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/PresetAlign.html" title="class in compbio.data.msa.jaxws">PresetAlign</A>\r
 <DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/jaxws/PresetAnalize.html#getPreset()"><B>getPreset()</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/PresetAnalize.html" title="class in compbio.data.msa.jaxws">PresetAnalize</A>\r
+<DD>&nbsp;\r
 <DT><A HREF="../compbio/metadata/Limit.html#getPreset()"><B>getPreset()</B></A> - \r
 Method in class compbio.metadata.<A HREF="../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>\r
 <DD>&nbsp;\r
@@ -854,8 +1014,8 @@ Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetLim
 <DT><A HREF="../compbio/data/msa/jaxws/GetPresets.html" title="class in compbio.data.msa.jaxws"><B>GetPresets</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/GetPresets.html#GetPresets()"><B>GetPresets()</B></A> - \r
 Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetPresets.html" title="class in compbio.data.msa.jaxws">GetPresets</A>\r
 <DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/MsaWS.html#getPresets()"><B>getPresets()</B></A> - \r
-Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>\r
+<DT><A HREF="../compbio/data/msa/Metadata.html#getPresets()"><B>getPresets()</B></A> - \r
+Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/Metadata.html" title="interface in compbio.data.msa">Metadata</A>\r
 <DD>Get presets supported by a web service\r
 <DT><A HREF="../compbio/metadata/PresetManager.html#getPresets()"><B>getPresets()</B></A> - \r
 Method in class compbio.metadata.<A HREF="../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>\r
@@ -863,9 +1023,15 @@ Method in class compbio.metadata.<A HREF="../compbio/metadata/PresetManager.html
 <DT><A HREF="../compbio/runner/Util.html#getPresets(java.lang.Class)"><B>getPresets(Class&lt;? extends Executable&lt;T&gt;&gt;)</B></A> - \r
 Static method in class compbio.runner.<A HREF="../compbio/runner/Util.html" title="class in compbio.runner">Util</A>\r
 <DD>&nbsp;\r
+<DT><A HREF="../compbio/ws/server/ClustalOWS.html#getPresets()"><B>getPresets()</B></A> - \r
+Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ClustalOWS.html" title="class in compbio.ws.server">ClustalOWS</A>\r
+<DD>&nbsp;\r
 <DT><A HREF="../compbio/ws/server/ClustalWS.html#getPresets()"><B>getPresets()</B></A> - \r
 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ClustalWS.html" title="class in compbio.ws.server">ClustalWS</A>\r
 <DD>&nbsp;\r
+<DT><A HREF="../compbio/ws/server/GenericMetadataService.html#getPresets()"><B>getPresets()</B></A> - \r
+Method in class compbio.ws.server.<A HREF="../compbio/ws/server/GenericMetadataService.html" title="class in compbio.ws.server">GenericMetadataService</A>\r
+<DD>&nbsp;\r
 <DT><A HREF="../compbio/ws/server/MafftWS.html#getPresets()"><B>getPresets()</B></A> - \r
 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/MafftWS.html" title="class in compbio.ws.server">MafftWS</A>\r
 <DD>&nbsp;\r
@@ -887,9 +1053,6 @@ Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html"
 <DT><A HREF="../compbio/data/sequence/AlignmentMetadata.html#getProgram()"><B>getProgram()</B></A> - \r
 Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence">AlignmentMetadata</A>\r
 <DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/jaxws/GetProgress.html" title="class in compbio.data.msa.jaxws"><B>GetProgress</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/GetProgress.html#GetProgress()"><B>GetProgress()</B></A> - \r
-Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetProgress.html" title="class in compbio.data.msa.jaxws">GetProgress</A>\r
-<DD>&nbsp;\r
 <DT><A HREF="../compbio/engine/FilePuller.html#getProgress()"><B>getProgress()</B></A> - \r
 Method in class compbio.engine.<A HREF="../compbio/engine/FilePuller.html" title="class in compbio.engine">FilePuller</A>\r
 <DD>&nbsp;\r
@@ -899,9 +1062,6 @@ Static method in class compbio.engine.<A HREF="../compbio/engine/ProgressGetter.
 <DT><A HREF="../compbio/ws/server/WSUtil.html#getProgress(java.lang.String)"><B>getProgress(String)</B></A> - \r
 Static method in class compbio.ws.server.<A HREF="../compbio/ws/server/WSUtil.html" title="class in compbio.ws.server">WSUtil</A>\r
 <DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/jaxws/GetProgressResponse.html" title="class in compbio.data.msa.jaxws"><B>GetProgressResponse</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/GetProgressResponse.html#GetProgressResponse()"><B>GetProgressResponse()</B></A> - \r
-Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetProgressResponse.html" title="class in compbio.data.msa.jaxws">GetProgressResponse</A>\r
-<DD>&nbsp;\r
 <DT><A HREF="../compbio/engine/conf/PropertyHelperManager.html#getPropertyHelper()"><B>getPropertyHelper()</B></A> - \r
 Static method in class compbio.engine.conf.<A HREF="../compbio/engine/conf/PropertyHelperManager.html" title="class in compbio.engine.conf">PropertyHelperManager</A>\r
 <DD>Ways to fix path problem: 1) find a path to WEB-INF directory based on
@@ -911,31 +1071,40 @@ Static method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Run
 <DD>&nbsp;\r
 <DT><A HREF="../compbio/engine/cluster/dundee/_Queue.html#getQueue(int, int)"><B>getQueue(int, int)</B></A> - \r
 Static method in enum compbio.engine.cluster.dundee.<A HREF="../compbio/engine/cluster/dundee/_Queue.html" title="enum in compbio.engine.cluster.dundee">_Queue</A>\r
-<DD>&nbsp;\r
+<DD><B>Deprecated.</B>&nbsp;&nbsp;\r
 <DT><A HREF="../compbio/engine/cluster/dundee/_Queue.html#getQueue(java.lang.String)"><B>getQueue(String)</B></A> - \r
 Method in enum compbio.engine.cluster.dundee.<A HREF="../compbio/engine/cluster/dundee/_Queue.html" title="enum in compbio.engine.cluster.dundee">_Queue</A>\r
-<DD>&nbsp;\r
+<DD><B>Deprecated.</B>&nbsp;&nbsp;\r
 <DT><A HREF="../compbio/runner/_NativeSpecHelper.html#getQueue()"><B>getQueue()</B></A> - \r
 Method in class compbio.runner.<A HREF="../compbio/runner/_NativeSpecHelper.html" title="class in compbio.runner">_NativeSpecHelper</A>\r
-<DD>&nbsp;\r
+<DD><B>Deprecated.</B>&nbsp;&nbsp;\r
 <DT><A HREF="../compbio/engine/cluster/dundee/_Queue.html#getQueueByMemoryRequirements(int)"><B>getQueueByMemoryRequirements(int)</B></A> - \r
 Static method in enum compbio.engine.cluster.dundee.<A HREF="../compbio/engine/cluster/dundee/_Queue.html" title="enum in compbio.engine.cluster.dundee">_Queue</A>\r
-<DD>&nbsp;\r
+<DD><B>Deprecated.</B>&nbsp;&nbsp;\r
+<DT><A HREF="../compbio/data/sequence/Score.html#getRanges()"><B>getRanges()</B></A> - \r
+Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>\r
+<DD>Return Ranges if any Collections.EMPTY_SET otherwise\r
 <DT><A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html#getRawUsage()"><B>getRawUsage()</B></A> - \r
 Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</A>\r
 <DD>&nbsp;\r
 <DT><A HREF="../compbio/engine/local/LocalEngineUtil.html#getRecordedJobStatus(java.lang.String)"><B>getRecordedJobStatus(String)</B></A> - \r
 Static method in class compbio.engine.local.<A HREF="../compbio/engine/local/LocalEngineUtil.html" title="class in compbio.engine.local">LocalEngineUtil</A>\r
 <DD>&nbsp;\r
-<DT><A HREF="../compbio/ws/server/WSUtil.html#getRemoteAddress(javax.xml.ws.WebServiceContext)"><B>getRemoteAddress(WebServiceContext)</B></A> - \r
-Static method in class compbio.ws.server.<A HREF="../compbio/ws/server/WSUtil.html" title="class in compbio.ws.server">WSUtil</A>\r
-<DD>&nbsp;\r
+<DT><A HREF="../compbio/ws/server/_WSLogger.html#getRemoteAddress()"><B>getRemoteAddress()</B></A> - \r
+Method in class compbio.ws.server.<A HREF="../compbio/ws/server/_WSLogger.html" title="class in compbio.ws.server">_WSLogger</A>\r
+<DD><B>Deprecated.</B>&nbsp;&nbsp;\r
 <DT><A HREF="../compbio/data/msa/jaxws/GetResult.html" title="class in compbio.data.msa.jaxws"><B>GetResult</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/GetResult.html#GetResult()"><B>GetResult()</B></A> - \r
 Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetResult.html" title="class in compbio.data.msa.jaxws">GetResult</A>\r
 <DD>&nbsp;\r
 <DT><A HREF="../compbio/data/msa/MsaWS.html#getResult(java.lang.String)"><B>getResult(String)</B></A> - \r
 Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>\r
 <DD>Return the result of the job.\r
+<DT><A HREF="../compbio/ws/server/_MsaService.html#getResult(java.lang.String)"><B>getResult(String)</B></A> - \r
+Method in class compbio.ws.server.<A HREF="../compbio/ws/server/_MsaService.html" title="class in compbio.ws.server">_MsaService</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/ws/server/ClustalOWS.html#getResult(java.lang.String)"><B>getResult(String)</B></A> - \r
+Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ClustalOWS.html" title="class in compbio.ws.server">ClustalOWS</A>\r
+<DD>&nbsp;\r
 <DT><A HREF="../compbio/ws/server/ClustalWS.html#getResult(java.lang.String)"><B>getResult(String)</B></A> - \r
 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ClustalWS.html" title="class in compbio.ws.server">ClustalWS</A>\r
 <DD>&nbsp;\r
@@ -986,6 +1155,24 @@ Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/NetNglyc.h
 <DD>&nbsp;\r
 <DT><A HREF="../compbio/runner/_SkeletalCommandBuilder.html#getResults(java.lang.String)"><B>getResults(String)</B></A> - \r
 Method in class compbio.runner.<A HREF="../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>\r
+<DD><B>Deprecated.</B>&nbsp;&nbsp;\r
+<DT><A HREF="../compbio/runner/conservation/AACon.html#getResults(java.lang.String)"><B>getResults(String)</B></A> - \r
+Method in class compbio.runner.conservation.<A HREF="../compbio/runner/conservation/AACon.html" title="class in compbio.runner.conservation">AACon</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/runner/disorder/Disembl.html#getResults(java.lang.String)"><B>getResults(String)</B></A> - \r
+Method in class compbio.runner.disorder.<A HREF="../compbio/runner/disorder/Disembl.html" title="class in compbio.runner.disorder">Disembl</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/runner/disorder/GlobPlot.html#getResults(java.lang.String)"><B>getResults(String)</B></A> - \r
+Method in class compbio.runner.disorder.<A HREF="../compbio/runner/disorder/GlobPlot.html" title="class in compbio.runner.disorder">GlobPlot</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/runner/disorder/IUPred.html#getResults(java.lang.String)"><B>getResults(String)</B></A> - \r
+Method in class compbio.runner.disorder.<A HREF="../compbio/runner/disorder/IUPred.html" title="class in compbio.runner.disorder">IUPred</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/runner/disorder/Jronn.html#getResults(java.lang.String)"><B>getResults(String)</B></A> - \r
+Method in class compbio.runner.disorder.<A HREF="../compbio/runner/disorder/Jronn.html" title="class in compbio.runner.disorder">Jronn</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/runner/msa/ClustalO.html#getResults(java.lang.String)"><B>getResults(String)</B></A> - \r
+Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</A>\r
 <DD>&nbsp;\r
 <DT><A HREF="../compbio/runner/msa/ClustalW.html#getResults(java.lang.String)"><B>getResults(String)</B></A> - \r
 Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>\r
@@ -1002,18 +1189,33 @@ Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/Probcons.html"
 <DT><A HREF="../compbio/runner/msa/Tcoffee.html#getResults(java.lang.String)"><B>getResults(String)</B></A> - \r
 Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>\r
 <DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/psiblast/PsiBlast.html#getResults(java.lang.String)"><B>getResults(String)</B></A> - \r
-Method in class compbio.runner.psiblast.<A HREF="../compbio/runner/psiblast/PsiBlast.html" title="class in compbio.runner.psiblast">PsiBlast</A>\r
+<DT><A HREF="../compbio/stat/collector/JobStat.html#getResultSize()"><B>getResultSize()</B></A> - \r
+Method in class compbio.stat.collector.<A HREF="../compbio/stat/collector/JobStat.html" title="class in compbio.stat.collector">JobStat</A>\r
 <DD>&nbsp;\r
 <DT><A HREF="../compbio/data/msa/jaxws/AlignResponse.html#getReturn()"><B>getReturn()</B></A> - \r
 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/AlignResponse.html" title="class in compbio.data.msa.jaxws">AlignResponse</A>\r
 <DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/jaxws/AnalizeResponse.html#getReturn()"><B>getReturn()</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/AnalizeResponse.html" title="class in compbio.data.msa.jaxws">AnalizeResponse</A>\r
+<DD>&nbsp;\r
 <DT><A HREF="../compbio/data/msa/jaxws/CustomAlignResponse.html#getReturn()"><B>getReturn()</B></A> - \r
 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/CustomAlignResponse.html" title="class in compbio.data.msa.jaxws">CustomAlignResponse</A>\r
 <DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/jaxws/CustomAnalizeResponse.html#getReturn()"><B>getReturn()</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/CustomAnalizeResponse.html" title="class in compbio.data.msa.jaxws">CustomAnalizeResponse</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/jaxws/GetAnnotationResponse.html#getReturn()"><B>getReturn()</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetAnnotationResponse.html" title="class in compbio.data.msa.jaxws">GetAnnotationResponse</A>\r
+<DD>&nbsp;\r
 <DT><A HREF="../compbio/data/msa/jaxws/GetJobStatusResponse.html#getReturn()"><B>getReturn()</B></A> - \r
 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetJobStatusResponse.html" title="class in compbio.data.msa.jaxws">GetJobStatusResponse</A>\r
 <DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/jaxws/GetLastTestedOnResponse.html#getReturn()"><B>getReturn()</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetLastTestedOnResponse.html" title="class in compbio.data.msa.jaxws">GetLastTestedOnResponse</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/jaxws/GetLastTestedResponse.html#getReturn()"><B>getReturn()</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetLastTestedResponse.html" title="class in compbio.data.msa.jaxws">GetLastTestedResponse</A>\r
+<DD>&nbsp;\r
 <DT><A HREF="../compbio/data/msa/jaxws/GetLimitResponse.html#getReturn()"><B>getReturn()</B></A> - \r
 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetLimitResponse.html" title="class in compbio.data.msa.jaxws">GetLimitResponse</A>\r
 <DD>&nbsp;\r
@@ -1023,23 +1225,35 @@ Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetLim
 <DT><A HREF="../compbio/data/msa/jaxws/GetPresetsResponse.html#getReturn()"><B>getReturn()</B></A> - \r
 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetPresetsResponse.html" title="class in compbio.data.msa.jaxws">GetPresetsResponse</A>\r
 <DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/jaxws/GetProgressResponse.html#getReturn()"><B>getReturn()</B></A> - \r
-Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetProgressResponse.html" title="class in compbio.data.msa.jaxws">GetProgressResponse</A>\r
-<DD>&nbsp;\r
 <DT><A HREF="../compbio/data/msa/jaxws/GetResultResponse.html#getReturn()"><B>getReturn()</B></A> - \r
 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetResultResponse.html" title="class in compbio.data.msa.jaxws">GetResultResponse</A>\r
 <DD>&nbsp;\r
 <DT><A HREF="../compbio/data/msa/jaxws/GetRunnerOptionsResponse.html#getReturn()"><B>getReturn()</B></A> - \r
 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetRunnerOptionsResponse.html" title="class in compbio.data.msa.jaxws">GetRunnerOptionsResponse</A>\r
 <DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/jaxws/GetServiceCategoriesResponse.html#getReturn()"><B>getReturn()</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetServiceCategoriesResponse.html" title="class in compbio.data.msa.jaxws">GetServiceCategoriesResponse</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/jaxws/GetServiceDescriptionResponse.html#getReturn()"><B>getReturn()</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetServiceDescriptionResponse.html" title="class in compbio.data.msa.jaxws">GetServiceDescriptionResponse</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/jaxws/GetSupportedServicesResponse.html#getReturn()"><B>getReturn()</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetSupportedServicesResponse.html" title="class in compbio.data.msa.jaxws">GetSupportedServicesResponse</A>\r
+<DD>&nbsp;\r
 <DT><A HREF="../compbio/data/msa/jaxws/PresetAlignResponse.html#getReturn()"><B>getReturn()</B></A> - \r
 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/PresetAlignResponse.html" title="class in compbio.data.msa.jaxws">PresetAlignResponse</A>\r
 <DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/jaxws/PresetAnalizeResponse.html#getReturn()"><B>getReturn()</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/PresetAnalizeResponse.html" title="class in compbio.data.msa.jaxws">PresetAnalizeResponse</A>\r
+<DD>&nbsp;\r
 <DT><A HREF="../compbio/data/msa/jaxws/PullExecStatisticsResponse.html#getReturn()"><B>getReturn()</B></A> - \r
 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/PullExecStatisticsResponse.html" title="class in compbio.data.msa.jaxws">PullExecStatisticsResponse</A>\r
 <DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/jaxws/PullFileResponse.html#getReturn()"><B>getReturn()</B></A> - \r
-Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/PullFileResponse.html" title="class in compbio.data.msa.jaxws">PullFileResponse</A>\r
+<DT><A HREF="../compbio/data/msa/jaxws/TestAllServicesResponse.html#getReturn()"><B>getReturn()</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/TestAllServicesResponse.html" title="class in compbio.data.msa.jaxws">TestAllServicesResponse</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/jaxws/TestServiceResponse.html#getReturn()"><B>getReturn()</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/TestServiceResponse.html" title="class in compbio.data.msa.jaxws">TestServiceResponse</A>\r
 <DD>&nbsp;\r
 <DT><A HREF="../compbio/runner/_impl/Runners.html#getRonnRunnable(java.lang.String)"><B>getRonnRunnable(String)</B></A> - \r
 Static method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Runners.html" title="class in compbio.runner._impl">Runners</A>\r
@@ -1053,6 +1267,9 @@ Static method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Run
 <DT><A HREF="../compbio/engine/client/ConfExecutable.html#getRunConfiguration()"><B>getRunConfiguration()</B></A> - \r
 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>\r
 <DD>&nbsp;\r
+<DT><A HREF="../compbio/ws/client/ServicesUtil.html#getRunnerByJobDirectory(java.io.File)"><B>getRunnerByJobDirectory(File)</B></A> - \r
+Static method in class compbio.ws.client.<A HREF="../compbio/ws/client/ServicesUtil.html" title="class in compbio.ws.client">ServicesUtil</A>\r
+<DD>&nbsp;\r
 <DT><A HREF="../compbio/engine/client/RunConfiguration.html#getRunnerClassName()"><B>getRunnerClassName()</B></A> - \r
 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>\r
 <DD>&nbsp;\r
@@ -1062,21 +1279,27 @@ Method in class compbio.metadata.<A HREF="../compbio/metadata/PresetManager.html
 <DT><A HREF="../compbio/metadata/RunnerConfig.html#getRunnerClassName()"><B>getRunnerClassName()</B></A> - \r
 Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
 <DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/ConfExecutable.html#getRunnerLimits(java.lang.Class)"><B>getRunnerLimits(Class&lt;? extends Executable&lt;V&gt;&gt;)</B></A> - \r
+<DT><A HREF="../compbio/engine/client/ConfExecutable.html#getRunnerLimits(java.lang.Class)"><B>getRunnerLimits(Class&lt;V&gt;)</B></A> - \r
 Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>\r
 <DD>This method should be executed once and result of its execution reused.\r
 <DT><A HREF="../compbio/data/msa/jaxws/GetRunnerOptions.html" title="class in compbio.data.msa.jaxws"><B>GetRunnerOptions</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/GetRunnerOptions.html#GetRunnerOptions()"><B>GetRunnerOptions()</B></A> - \r
 Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetRunnerOptions.html" title="class in compbio.data.msa.jaxws">GetRunnerOptions</A>\r
 <DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/MsaWS.html#getRunnerOptions()"><B>getRunnerOptions()</B></A> - \r
-Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>\r
+<DT><A HREF="../compbio/data/msa/Metadata.html#getRunnerOptions()"><B>getRunnerOptions()</B></A> - \r
+Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/Metadata.html" title="interface in compbio.data.msa">Metadata</A>\r
 <DD>Get options supported by a web service\r
 <DT><A HREF="../compbio/engine/client/ConfExecutable.html#getRunnerOptions(java.lang.Class)"><B>getRunnerOptions(Class&lt;? extends Executable&lt;V&gt;&gt;)</B></A> - \r
 Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>\r
 <DD>&nbsp;\r
+<DT><A HREF="../compbio/ws/server/ClustalOWS.html#getRunnerOptions()"><B>getRunnerOptions()</B></A> - \r
+Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ClustalOWS.html" title="class in compbio.ws.server">ClustalOWS</A>\r
+<DD>&nbsp;\r
 <DT><A HREF="../compbio/ws/server/ClustalWS.html#getRunnerOptions()"><B>getRunnerOptions()</B></A> - \r
 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ClustalWS.html" title="class in compbio.ws.server">ClustalWS</A>\r
 <DD>&nbsp;\r
+<DT><A HREF="../compbio/ws/server/GenericMetadataService.html#getRunnerOptions()"><B>getRunnerOptions()</B></A> - \r
+Method in class compbio.ws.server.<A HREF="../compbio/ws/server/GenericMetadataService.html" title="class in compbio.ws.server">GenericMetadataService</A>\r
+<DD>&nbsp;\r
 <DT><A HREF="../compbio/ws/server/MafftWS.html#getRunnerOptions()"><B>getRunnerOptions()</B></A> - \r
 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/MafftWS.html" title="class in compbio.ws.server">MafftWS</A>\r
 <DD>&nbsp;\r
@@ -1095,9 +1318,21 @@ Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/
 <DT><A HREF="../compbio/engine/client/ConfExecutable.html#getRunnerPresets(java.lang.Class)"><B>getRunnerPresets(Class&lt;? extends Executable&lt;V&gt;&gt;)</B></A> - \r
 Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>\r
 <DD>&nbsp;\r
+<DT><A HREF="../compbio/stat/collector/JobStat.html#getRuntime()"><B>getRuntime()</B></A> - \r
+Method in class compbio.stat.collector.<A HREF="../compbio/stat/collector/JobStat.html" title="class in compbio.stat.collector">JobStat</A>\r
+<DD>&nbsp;\r
 <DT><A HREF="../compbio/engine/conf/RunnerConfigMarshaller.html#getSchema(java.lang.String)"><B>getSchema(String)</B></A> - \r
 Static method in class compbio.engine.conf.<A HREF="../compbio/engine/conf/RunnerConfigMarshaller.html" title="class in compbio.engine.conf">RunnerConfigMarshaller</A>\r
 <DD>&nbsp;\r
+<DT><A HREF="../compbio/data/sequence/ScoreManager.ScoreHolder.html#getScoreByMethod(java.lang.Enum)"><B>getScoreByMethod(Enum&lt;?&gt;)</B></A> - \r
+Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/ScoreManager.ScoreHolder.html" title="class in compbio.data.sequence">ScoreManager.ScoreHolder</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/sequence/ScoreManager.ScoreHolder.html#getScoreByMethod(java.lang.String)"><B>getScoreByMethod(String)</B></A> - \r
+Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/ScoreManager.ScoreHolder.html" title="class in compbio.data.sequence">ScoreManager.ScoreHolder</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/sequence/Score.html#getScores()"><B>getScores()</B></A> - \r
+Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>\r
+<DD>The column scores for the alignment\r
 <DT><A HREF="../compbio/metadata/Limit.html#getSeqNumber()"><B>getSeqNumber()</B></A> - \r
 Method in class compbio.metadata.<A HREF="../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>\r
 <DD>&nbsp;\r
@@ -1119,18 +1354,81 @@ Method in exception compbio.metadata.<A HREF="../compbio/metadata/LimitExceededE
 <DT><A HREF="../compbio/data/sequence/Alignment.html#getSequences()"><B>getSequences()</B></A> - \r
 Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A>\r
 <DD>&nbsp;\r
-<DT><A HREF="../compbio/ws/client/Jws2Client.html#getServiceName(java.lang.String[])"><B>getServiceName(String[])</B></A> - \r
+<DT><A HREF="../compbio/stat/servlet/ServiceTestResult.html#getService()"><B>getService()</B></A> - \r
+Method in class compbio.stat.servlet.<A HREF="../compbio/stat/servlet/ServiceTestResult.html" title="class in compbio.stat.servlet">ServiceTestResult</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/ws/client/Services.html#getService(java.lang.String)"><B>getService(String)</B></A> - \r
+Static method in enum compbio.ws.client.<A HREF="../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/ws/client/ServicesUtil.html#getServiceByJobDirectory(java.io.File)"><B>getServiceByJobDirectory(File)</B></A> - \r
+Static method in class compbio.ws.client.<A HREF="../compbio/ws/client/ServicesUtil.html" title="class in compbio.ws.client">ServicesUtil</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/ws/client/ServicesUtil.html#getServiceByRunner(java.lang.Class)"><B>getServiceByRunner(Class&lt;? extends Executable&gt;)</B></A> - \r
+Static method in class compbio.ws.client.<A HREF="../compbio/ws/client/ServicesUtil.html" title="class in compbio.ws.client">ServicesUtil</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/jaxws/GetServiceCategories.html" title="class in compbio.data.msa.jaxws"><B>GetServiceCategories</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/GetServiceCategories.html#GetServiceCategories()"><B>GetServiceCategories()</B></A> - \r
+Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetServiceCategories.html" title="class in compbio.data.msa.jaxws">GetServiceCategories</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/RegistryWS.html#getServiceCategories()"><B>getServiceCategories()</B></A> - \r
+Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/RegistryWS.html" title="interface in compbio.data.msa">RegistryWS</A>\r
+<DD>Gets the list of services per category.\r
+<DT><A HREF="../compbio/ws/server/RegistryWS.html#getServiceCategories()"><B>getServiceCategories()</B></A> - \r
+Method in class compbio.ws.server.<A HREF="../compbio/ws/server/RegistryWS.html" title="class in compbio.ws.server">RegistryWS</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/jaxws/GetServiceCategoriesResponse.html" title="class in compbio.data.msa.jaxws"><B>GetServiceCategoriesResponse</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/GetServiceCategoriesResponse.html#GetServiceCategoriesResponse()"><B>GetServiceCategoriesResponse()</B></A> - \r
+Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetServiceCategoriesResponse.html" title="class in compbio.data.msa.jaxws">GetServiceCategoriesResponse</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/jaxws/GetServiceDescription.html" title="class in compbio.data.msa.jaxws"><B>GetServiceDescription</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/GetServiceDescription.html#GetServiceDescription()"><B>GetServiceDescription()</B></A> - \r
+Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetServiceDescription.html" title="class in compbio.data.msa.jaxws">GetServiceDescription</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/RegistryWS.html#getServiceDescription(compbio.ws.client.Services)"><B>getServiceDescription(Services)</B></A> - \r
+Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/RegistryWS.html" title="interface in compbio.data.msa">RegistryWS</A>\r
+<DD>Gives the description of the service.\r
+<DT><A HREF="../compbio/ws/server/RegistryWS.html#getServiceDescription(compbio.ws.client.Services)"><B>getServiceDescription(Services)</B></A> - \r
+Method in class compbio.ws.server.<A HREF="../compbio/ws/server/RegistryWS.html" title="class in compbio.ws.server">RegistryWS</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/jaxws/GetServiceDescriptionResponse.html" title="class in compbio.data.msa.jaxws"><B>GetServiceDescriptionResponse</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/GetServiceDescriptionResponse.html#GetServiceDescriptionResponse()"><B>GetServiceDescriptionResponse()</B></A> - \r
+Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetServiceDescriptionResponse.html" title="class in compbio.data.msa.jaxws">GetServiceDescriptionResponse</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/ws/client/ServicesUtil.html#getServiceImpl(compbio.ws.client.Services)"><B>getServiceImpl(Services)</B></A> - \r
+Static method in class compbio.ws.client.<A HREF="../compbio/ws/client/ServicesUtil.html" title="class in compbio.ws.client">ServicesUtil</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/ws/client/Services.html#getServiceInfo()"><B>getServiceInfo()</B></A> - \r
+Method in enum compbio.ws.client.<A HREF="../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/Category.html#getServices()"><B>getServices()</B></A> - \r
+Method in class compbio.data.msa.<A HREF="../compbio/data/msa/Category.html" title="class in compbio.data.msa">Category</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/ws/client/Jws2Client.html#getServices(java.lang.String)"><B>getServices(String)</B></A> - \r
 Static method in class compbio.ws.client.<A HREF="../compbio/ws/client/Jws2Client.html" title="class in compbio.ws.client">Jws2Client</A>\r
-<DD>Extracts service name from the command line\r
+<DD>&nbsp;\r
 <DT><A HREF="../compbio/engine/cluster/drmaa/ClusterSession.html#getSession()"><B>getSession()</B></A> - \r
 Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/ClusterSession.html" title="class in compbio.engine.cluster.drmaa">ClusterSession</A>\r
 <DD>&nbsp;\r
+<DT><A HREF="../compbio/stat/collector/StatProcessor.html#getSingleWSStat(compbio.ws.client.Services)"><B>getSingleWSStat(Services)</B></A> - \r
+Method in class compbio.stat.collector.<A HREF="../compbio/stat/collector/StatProcessor.html" title="class in compbio.stat.collector">StatProcessor</A>\r
+<DD>&nbsp;\r
 <DT><A HREF="../compbio/data/sequence/Alignment.html#getSize()"><B>getSize()</B></A> - \r
 Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A>\r
 <DD>&nbsp;\r
+<DT><A HREF="../compbio/data/sequence/SMERFSConstraints.html#getSMERFSColumnScore(java.lang.String)"><B>getSMERFSColumnScore(String)</B></A> - \r
+Static method in enum compbio.data.sequence.<A HREF="../compbio/data/sequence/SMERFSConstraints.html" title="enum in compbio.data.sequence">SMERFSConstraints</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/stat/collector/JobStat.html#getStart()"><B>getStart()</B></A> - \r
+Method in class compbio.stat.collector.<A HREF="../compbio/stat/collector/JobStat.html" title="class in compbio.stat.collector">JobStat</A>\r
+<DD>&nbsp;\r
 <DT><A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html#getStartTime()"><B>getStartTime()</B></A> - \r
 Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</A>\r
 <DD>&nbsp;\r
+<DT><A HREF="../compbio/runner/conservation/AACon.html#getStatFile()"><B>getStatFile()</B></A> - \r
+Static method in class compbio.runner.conservation.<A HREF="../compbio/runner/conservation/AACon.html" title="class in compbio.runner.conservation">AACon</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/runner/disorder/Jronn.html#getStatFile()"><B>getStatFile()</B></A> - \r
+Static method in class compbio.runner.disorder.<A HREF="../compbio/runner/disorder/Jronn.html" title="class in compbio.runner.disorder">Jronn</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/runner/msa/ClustalO.html#getStatFile()"><B>getStatFile()</B></A> - \r
+Static method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</A>\r
+<DD>&nbsp;\r
 <DT><A HREF="../compbio/runner/msa/ClustalW.html#getStatFile()"><B>getStatFile()</B></A> - \r
 Static method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>\r
 <DD>&nbsp;\r
@@ -1140,6 +1438,18 @@ Static method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/Muscle.
 <DT><A HREF="../compbio/engine/cluster/drmaa/ClusterSession.html#getStatistics(org.ggf.drmaa.JobInfo)"><B>getStatistics(JobInfo)</B></A> - \r
 Static method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/ClusterSession.html" title="class in compbio.engine.cluster.drmaa">ClusterSession</A>\r
 <DD>&nbsp;\r
+<DT><A HREF="../compbio/ws/server/_WSLogger.html#getStatLogger(compbio.ws.client.Services, javax.xml.ws.WebServiceContext)"><B>getStatLogger(Services, WebServiceContext)</B></A> - \r
+Static method in class compbio.ws.server.<A HREF="../compbio/ws/server/_WSLogger.html" title="class in compbio.ws.server">_WSLogger</A>\r
+<DD><B>Deprecated.</B>&nbsp;&nbsp;\r
+<DT><A HREF="../compbio/stat/servlet/util/StatCollection.html#getStats(int)"><B>getStats(int)</B></A> - \r
+Static method in class compbio.stat.servlet.util.<A HREF="../compbio/stat/servlet/util/StatCollection.html" title="class in compbio.stat.servlet.util">StatCollection</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/stat/servlet/util/StatCollection.html#getStats(java.util.Date)"><B>getStats(Date)</B></A> - \r
+Static method in class compbio.stat.servlet.util.<A HREF="../compbio/stat/servlet/util/StatCollection.html" title="class in compbio.stat.servlet.util">StatCollection</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/stat/servlet/ServiceTestResult.html#getStatus()"><B>getStatus()</B></A> - \r
+Method in class compbio.stat.servlet.<A HREF="../compbio/stat/servlet/ServiceTestResult.html" title="class in compbio.stat.servlet">ServiceTestResult</A>\r
+<DD>&nbsp;\r
 <DT><A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html#getSubmissionTime()"><B>getSubmissionTime()</B></A> - \r
 Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</A>\r
 <DD>&nbsp;\r
@@ -1155,6 +1465,18 @@ Method in interface compbio.engine.client.<A HREF="../compbio/engine/client/Conf
 <DT><A HREF="../compbio/engine/client/Util.html#getSupportedRuntimes(java.lang.Class)"><B>getSupportedRuntimes(Class&lt;?&gt;)</B></A> - \r
 Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/Util.html" title="class in compbio.engine.client">Util</A>\r
 <DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/jaxws/GetSupportedServices.html" title="class in compbio.data.msa.jaxws"><B>GetSupportedServices</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/GetSupportedServices.html#GetSupportedServices()"><B>GetSupportedServices()</B></A> - \r
+Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetSupportedServices.html" title="class in compbio.data.msa.jaxws">GetSupportedServices</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/RegistryWS.html#getSupportedServices()"><B>getSupportedServices()</B></A> - \r
+Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/RegistryWS.html" title="interface in compbio.data.msa">RegistryWS</A>\r
+<DD>List of services that are functioning on the server.\r
+<DT><A HREF="../compbio/ws/server/RegistryWS.html#getSupportedServices()"><B>getSupportedServices()</B></A> - \r
+Method in class compbio.ws.server.<A HREF="../compbio/ws/server/RegistryWS.html" title="class in compbio.ws.server">RegistryWS</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/jaxws/GetSupportedServicesResponse.html" title="class in compbio.data.msa.jaxws"><B>GetSupportedServicesResponse</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/GetSupportedServicesResponse.html#GetSupportedServicesResponse()"><B>GetSupportedServicesResponse()</B></A> - \r
+Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetSupportedServicesResponse.html" title="class in compbio.data.msa.jaxws">GetSupportedServicesResponse</A>\r
+<DD>&nbsp;\r
 <DT><A HREF="../compbio/engine/Configurator.html#getSyncEngine(compbio.engine.client.ConfiguredExecutable, compbio.engine.client.Executable.ExecProvider)"><B>getSyncEngine(ConfiguredExecutable&lt;?&gt;, Executable.ExecProvider)</B></A> - \r
 Static method in class compbio.engine.<A HREF="../compbio/engine/Configurator.html" title="class in compbio.engine">Configurator</A>\r
 <DD>&nbsp;\r
@@ -1176,18 +1498,12 @@ Method in interface compbio.engine.client.<A HREF="../compbio/engine/client/Conf
 <DT><A HREF="../compbio/engine/Job.html#getTaskId()"><B>getTaskId()</B></A> - \r
 Method in class compbio.engine.<A HREF="../compbio/engine/Job.html" title="class in compbio.engine">Job</A>\r
 <DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/_impl/Disembl.html#getTestArgs()"><B>getTestArgs()</B></A> - \r
-Static method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Disembl.html" title="class in compbio.runner._impl">Disembl</A>\r
-<DD>&nbsp;\r
 <DT><A HREF="../compbio/runner/_impl/NetNglyc.html#getTestArgs()"><B>getTestArgs()</B></A> - \r
 Static method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>\r
 <DD>&nbsp;\r
 <DT><A HREF="../compbio/runner/_impl/OB.html#getTestArgs()"><B>getTestArgs()</B></A> - \r
 Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/OB.html" title="class in compbio.runner._impl">OB</A>\r
 <DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/_impl/Disembl.html#getTestCommand()"><B>getTestCommand()</B></A> - \r
-Static method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Disembl.html" title="class in compbio.runner._impl">Disembl</A>\r
-<DD>&nbsp;\r
 <DT><A HREF="../compbio/runner/_impl/Mcl.html#getTestCommand()"><B>getTestCommand()</B></A> - \r
 Static method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Mcl.html" title="class in compbio.runner._impl">Mcl</A>\r
 <DD>&nbsp;\r
@@ -1208,19 +1524,46 @@ Static method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Mcl
 <DD>&nbsp;\r
 <DT><A HREF="../compbio/engine/cluster/dundee/_Queue.html#getTimeLimit()"><B>getTimeLimit()</B></A> - \r
 Method in enum compbio.engine.cluster.dundee.<A HREF="../compbio/engine/cluster/dundee/_Queue.html" title="enum in compbio.engine.cluster.dundee">_Queue</A>\r
-<DD>0 - unlimited\r
+<DD><B>Deprecated.</B>&nbsp;0 - unlimited\r
 <DT><A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html#getTimeStat()"><B>getTimeStat()</B></A> - \r
 Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</A>\r
 <DD>&nbsp;\r
 <DT><A HREF="../compbio/runner/_impl/Runners.html#getTmhmm2Runnable(java.lang.String)"><B>getTmhmm2Runnable(String)</B></A> - \r
 Static method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Runners.html" title="class in compbio.runner._impl">Runners</A>\r
 <DD>&nbsp;\r
+<DT><A HREF="../compbio/stat/servlet/util/Totals.html#getTotal()"><B>getTotal()</B></A> - \r
+Method in class compbio.stat.servlet.util.<A HREF="../compbio/stat/servlet/util/Totals.html" title="class in compbio.stat.servlet.util">Totals</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/stat/collector/StatDB.html#getTotalJobsCount(java.sql.Timestamp, java.sql.Timestamp)"><B>getTotalJobsCount(Timestamp, Timestamp)</B></A> - \r
+Method in class compbio.stat.collector.<A HREF="../compbio/stat/collector/StatDB.html" title="class in compbio.stat.collector">StatDB</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/stat/collector/StatProcessor.html#getTotalRuntime()"><B>getTotalRuntime()</B></A> - \r
+Method in class compbio.stat.collector.<A HREF="../compbio/stat/collector/StatProcessor.html" title="class in compbio.stat.collector">StatProcessor</A>\r
+<DD>&nbsp;\r
 <DT><A HREF="../compbio/engine/client/SkeletalExecutable.html#getType()"><B>getType()</B></A> - \r
 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>\r
 <DD>&nbsp;\r
 <DT><A HREF="../compbio/metadata/ValueConstrain.html#getType()"><B>getType()</B></A> - \r
 Method in class compbio.metadata.<A HREF="../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A>\r
 <DD>&nbsp;\r
+<DT><A HREF="../compbio/runner/conservation/AACon.html#getType()"><B>getType()</B></A> - \r
+Method in class compbio.runner.conservation.<A HREF="../compbio/runner/conservation/AACon.html" title="class in compbio.runner.conservation">AACon</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/runner/disorder/Disembl.html#getType()"><B>getType()</B></A> - \r
+Method in class compbio.runner.disorder.<A HREF="../compbio/runner/disorder/Disembl.html" title="class in compbio.runner.disorder">Disembl</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/runner/disorder/GlobPlot.html#getType()"><B>getType()</B></A> - \r
+Method in class compbio.runner.disorder.<A HREF="../compbio/runner/disorder/GlobPlot.html" title="class in compbio.runner.disorder">GlobPlot</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/runner/disorder/IUPred.html#getType()"><B>getType()</B></A> - \r
+Method in class compbio.runner.disorder.<A HREF="../compbio/runner/disorder/IUPred.html" title="class in compbio.runner.disorder">IUPred</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/runner/disorder/Jronn.html#getType()"><B>getType()</B></A> - \r
+Method in class compbio.runner.disorder.<A HREF="../compbio/runner/disorder/Jronn.html" title="class in compbio.runner.disorder">Jronn</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/runner/msa/ClustalO.html#getType()"><B>getType()</B></A> - \r
+Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</A>\r
+<DD>&nbsp;\r
 <DT><A HREF="../compbio/runner/msa/ClustalW.html#getType()"><B>getType()</B></A> - \r
 Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>\r
 <DD>&nbsp;\r
@@ -1236,9 +1579,6 @@ Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/Probcons.html"
 <DT><A HREF="../compbio/runner/msa/Tcoffee.html#getType()"><B>getType()</B></A> - \r
 Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>\r
 <DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/psiblast/PsiBlast.html#getType()"><B>getType()</B></A> - \r
-Method in class compbio.runner.psiblast.<A HREF="../compbio/runner/psiblast/PsiBlast.html" title="class in compbio.runner.psiblast">PsiBlast</A>\r
-<DD>&nbsp;\r
 <DT><A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html#getUsedSysTime()"><B>getUsedSysTime()</B></A> - \r
 Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</A>\r
 <DD>&nbsp;\r
@@ -1257,6 +1597,9 @@ Method in class compbio.metadata.<A HREF="../compbio/metadata/Parameter.html" ti
 <DT><A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html#getVMem()"><B>getVMem()</B></A> - \r
 Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</A>\r
 <DD>&nbsp;\r
+<DT><A HREF="../compbio/stat/collector/JobStat.html#getWebService()"><B>getWebService()</B></A> - \r
+Method in class compbio.stat.collector.<A HREF="../compbio/stat/collector/JobStat.html" title="class in compbio.stat.collector">JobStat</A>\r
+<DD>&nbsp;\r
 <DT><A HREF="../compbio/engine/AsyncExecutor.html#getWorkDirectory(java.lang.String)"><B>getWorkDirectory(String)</B></A> - \r
 Method in interface compbio.engine.<A HREF="../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine">AsyncExecutor</A>\r
 <DD>&nbsp;\r
@@ -1284,6 +1627,20 @@ Method in class compbio.engine.local.<A HREF="../compbio/engine/local/LocalRunne
 <DT><A HREF="../compbio/engine/SyncExecutor.html#getWorkDirectory()"><B>getWorkDirectory()</B></A> - \r
 Method in interface compbio.engine.<A HREF="../compbio/engine/SyncExecutor.html" title="interface in compbio.engine">SyncExecutor</A>\r
 <DD>&nbsp;\r
+<DT><A HREF="../compbio/runner/disorder/GlobPlot.html" title="class in compbio.runner.disorder"><B>GlobPlot</B></A> - Class in <A HREF="../compbio/runner/disorder/package-summary.html">compbio.runner.disorder</A><DD>./GlobPipe.py SmoothFrame DOMjoinFrame DOMpeakFrame DISjoinFrame DISpeakFrame
+ 
+ FASTAfile' Optimised for ELM: ./GlobPlot.py 10 8 75 8 8 sequence_file'
+ Webserver settings: ./GlobPlot.py 10 15 74 4 5 sequence_file'
+ 
+ Hard-coded values are 10 15 74 4 5.<DT><A HREF="../compbio/runner/disorder/GlobPlot.html#GlobPlot()"><B>GlobPlot()</B></A> - \r
+Constructor for class compbio.runner.disorder.<A HREF="../compbio/runner/disorder/GlobPlot.html" title="class in compbio.runner.disorder">GlobPlot</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/ws/client/Services.html#GLOBPLOT_INFO"><B>GLOBPLOT_INFO</B></A> - \r
+Static variable in enum compbio.ws.client.<A HREF="../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/ws/server/GlobPlotWS.html" title="class in compbio.ws.server"><B>GlobPlotWS</B></A> - Class in <A HREF="../compbio/ws/server/package-summary.html">compbio.ws.server</A><DD>&nbsp;<DT><A HREF="../compbio/ws/server/GlobPlotWS.html#GlobPlotWS()"><B>GlobPlotWS()</B></A> - \r
+Constructor for class compbio.ws.server.<A HREF="../compbio/ws/server/GlobPlotWS.html" title="class in compbio.ws.server">GlobPlotWS</A>\r
+<DD>&nbsp;\r
 </DL>\r
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