+++ /dev/null
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- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>\r
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-<A NAME="_G_"><!-- --></A><H2>\r
-<B>G</B></H2>\r
-<DL>\r
-<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/ws/server/GenericMetadataService.html" title="class in compbio.ws.server"><B>GenericMetadataService</B></A><<A HREF="../compbio/ws/server/GenericMetadataService.html" title="type parameter in GenericMetadataService">T</A>> - Class in <A HREF="../compbio/ws/server/package-summary.html">compbio.ws.server</A><DD> <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> \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> \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> \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> \r
-<DT><A HREF="../compbio/metadata/LimitExceededException.html#getActualNumberofSequences()"><B>getActualNumberofSequences()</B></A> - \r
-Method in exception compbio.metadata.<A HREF="../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A>\r
-<DD> \r
-<DT><A HREF="../compbio/runner/OptionCombinator.html#getAllConstrainedParametersWithBorderValues(boolean)"><B>getAllConstrainedParametersWithBorderValues(boolean)</B></A> - \r
-Method in class compbio.runner.<A HREF="../compbio/runner/OptionCombinator.html" title="class in compbio.runner">OptionCombinator</A>\r
-<DD> \r
-<DT><A HREF="../compbio/runner/OptionCombinator.html#getAllConstrainedParametersWithRandomValues()"><B>getAllConstrainedParametersWithRandomValues()</B></A> - \r
-Method in class compbio.runner.<A HREF="../compbio/runner/OptionCombinator.html" title="class in compbio.runner">OptionCombinator</A>\r
-<DD> \r
-<DT><A HREF="../compbio/runner/OptionCombinator.html#getAllOptions()"><B>getAllOptions()</B></A> - \r
-Method in class compbio.runner.<A HREF="../compbio/runner/OptionCombinator.html" title="class in compbio.runner">OptionCombinator</A>\r
-<DD> \r
-<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> \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> \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> \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> <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> \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> \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> \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> \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> <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> \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> \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> \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> \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> \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> \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
-<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
-<DT><A HREF="../compbio/metadata/Preset.html#getArguments(compbio.metadata.RunnerConfig)"><B>getArguments(RunnerConfig<T>)</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>\r
-<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>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<?>, 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> \r
-<DT><A HREF="../compbio/engine/Configurator.html#getAsyncEngine(compbio.engine.client.ConfiguredExecutable)"><B>getAsyncEngine(ConfiguredExecutable<?>)</B></A> - \r
-Static method in class compbio.engine.<A HREF="../compbio/engine/Configurator.html" title="class in compbio.engine">Configurator</A>\r
-<DD> \r
-<DT><A HREF="../compbio/engine/Configurator.html#getAsyncEngine(java.lang.String)"><B>getAsyncEngine(String)</B></A> - \r
-Static method in class compbio.engine.<A HREF="../compbio/engine/Configurator.html" title="class in compbio.engine">Configurator</A>\r
-<DD> \r
-<DT><A HREF="../compbio/metadata/Limit.html#getAvgSeqLength()"><B>getAvgSeqLength()</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>\r
-<DD> \r
-<DT><A HREF="../compbio/metadata/Limit.html#getAvgSequenceLength(java.util.List)"><B>getAvgSequenceLength(List<FastaSequence>)</B></A> - \r
-Static method in class compbio.metadata.<A HREF="../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>\r
-<DD>Calculates an average sequence length of the dataset\r
-<DT><A HREF="../compbio/runner/_impl/Runners.html#getBlastAllRunnable(java.lang.String)"><B>getBlastAllRunnable(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> \r
-<DT><A HREF="../compbio/runner/_impl/Environment.html#getBlastBinDir()"><B>getBlastBinDir()</B></A> - \r
-Static method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Environment.html" title="class in compbio.runner._impl">Environment</A>\r
-<DD> \r
-<DT><A HREF="../compbio/runner/_impl/Environment.html#getBlastDatabasesDir()"><B>getBlastDatabasesDir()</B></A> - \r
-Static method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Environment.html" title="class in compbio.runner._impl">Environment</A>\r
-<DD> \r
-<DT><A HREF="../compbio/engine/Job.html#getByJobId(java.lang.String, java.util.List)"><B>getByJobId(String, List<Job>)</B></A> - \r
-Static method in class compbio.engine.<A HREF="../compbio/engine/Job.html" title="class in compbio.engine">Job</A>\r
-<DD> \r
-<DT><A HREF="../compbio/engine/Job.html#getByTaskId(java.lang.String, java.util.List)"><B>getByTaskId(String, List<Job>)</B></A> - \r
-Static method in class compbio.engine.<A HREF="../compbio/engine/Job.html" title="class in compbio.engine">Job</A>\r
-<DD> \r
-<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> \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> \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> \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> \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
-<DD> \r
-<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> \r
-<DT><A HREF="../compbio/engine/client/SkeletalExecutable.html#getClusterCpuNum(java.lang.Class)"><B>getClusterCpuNum(Class<? extends Executable<?>>)</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> \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> \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> \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> \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> \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> \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> \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> \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> \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> \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> \r
-<DT><A HREF="../compbio/engine/client/ConfiguredExecutable.html#getCommand(compbio.engine.client.Executable.ExecProvider)"><B>getCommand(Executable.ExecProvider)</B></A> - \r
-Method in interface compbio.engine.client.<A HREF="../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>\r
-<DD> \r
-<DT><A HREF="../compbio/engine/client/Util.html#getCommand(compbio.engine.client.Executable.ExecProvider, java.lang.Class)"><B>getCommand(Executable.ExecProvider, Class<?>)</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> \r
-<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> \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> \r
-<DT><A HREF="../compbio/runner/_impl/PSIBlast.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/PSIBlast.html" title="class in compbio.runner._impl">PSIBlast</A>\r
-<DD> \r
-<DT><A HREF="../compbio/runner/_impl/Ronn.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/Ronn.html" title="class in compbio.runner._impl">Ronn</A>\r
-<DD> \r
-<DT><A HREF="../compbio/runner/_impl/RPSBlast.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/RPSBlast.html" title="class in compbio.runner._impl">RPSBlast</A>\r
-<DD> \r
-<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> \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> \r
-<DT><A HREF="../compbio/runner/_impl/NetNglyc.html#getCommandName()"><B>getCommandName()</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> \r
-<DT><A HREF="../compbio/runner/_impl/PSIBlast.html#getCommandName()"><B>getCommandName()</B></A> - \r
-Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/PSIBlast.html" title="class in compbio.runner._impl">PSIBlast</A>\r
-<DD> \r
-<DT><A HREF="../compbio/runner/_impl/Ronn.html#getCommandName()"><B>getCommandName()</B></A> - \r
-Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Ronn.html" title="class in compbio.runner._impl">Ronn</A>\r
-<DD> \r
-<DT><A HREF="../compbio/runner/_impl/RPSBlast.html#getCommandName()"><B>getCommandName()</B></A> - \r
-Static method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/RPSBlast.html" title="class in compbio.runner._impl">RPSBlast</A>\r
-<DD> \r
-<DT><A HREF="../compbio/engine/client/CommandBuilder.html#getCommands()"><B>getCommands()</B></A> - \r
-Method in class compbio.engine.client.<A HREF="../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>\r
-<DD> \r
-<DT><A HREF="../compbio/ws/server/WSUtil.html#getCommands(java.util.List, java.lang.String)"><B>getCommands(List<Option<T>>, 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> \r
-<DT><A HREF="../compbio/engine/client/CommandBuilder.html#getCommandString()"><B>getCommandString()</B></A> - \r
-Method in class compbio.engine.client.<A HREF="../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>\r
-<DD> \r
-<DT><A HREF="../compbio/engine/Job.html#getConfExecutable()"><B>getConfExecutable()</B></A> - \r
-Method in class compbio.engine.<A HREF="../compbio/engine/Job.html" title="class in compbio.engine">Job</A>\r
-<DD> \r
-<DT><A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html#getCPUTimeStat()"><B>getCPUTimeStat()</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> \r
-<DT><A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html#getCPUUsageTime()"><B>getCPUUsageTime()</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> \r
-<DT><A HREF="../compbio/engine/client/ConfExecutable.html#getCreatedFiles()"><B>getCreatedFiles()</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> \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><B>Deprecated.</B> \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
- created or not.\r
-<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> \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> \r
-<DT><A HREF="../compbio/runner/_impl/NetNglyc.html#getCreatedFiles()"><B>getCreatedFiles()</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> \r
-<DT><A HREF="../compbio/runner/_impl/OB.html#getCreatedFiles()"><B>getCreatedFiles()</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> \r
-<DT><A HREF="../compbio/runner/_impl/PSIBlast.html#getCreatedFiles()"><B>getCreatedFiles()</B></A> - \r
-Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/PSIBlast.html" title="class in compbio.runner._impl">PSIBlast</A>\r
-<DD> \r
-<DT><A HREF="../compbio/runner/_impl/Ronn.html#getCreatedFiles()"><B>getCreatedFiles()</B></A> - \r
-Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Ronn.html" title="class in compbio.runner._impl">Ronn</A>\r
-<DD> \r
-<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> \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> \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> \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> \r
-<DT><A HREF="../compbio/runner/msa/Muscle.html#getCreatedFiles()"><B>getCreatedFiles()</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> \r
-<DT><A HREF="../compbio/runner/msa/Probcons.html#getCreatedFiles()"><B>getCreatedFiles()</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> \r
-<DT><A HREF="../compbio/runner/msa/Tcoffee.html#getCreatedFiles()"><B>getCreatedFiles()</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> \r
-<DT><A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html#getDataTransfered()"><B>getDataTransfered()</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> \r
-<DT><A HREF="../compbio/metadata/LimitsManager.html#getDefaultLimit()"><B>getDefaultLimit()</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>\r
-<DD> \r
-<DT><A HREF="../compbio/metadata/Argument.html#getDefaultValue()"><B>getDefaultValue()</B></A> - \r
-Method in interface compbio.metadata.<A HREF="../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</A>\r
-<DD> \r
-<DT><A HREF="../compbio/metadata/Option.html#getDefaultValue()"><B>getDefaultValue()</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
-<DD>A default value of the option.\r
-<DT><A HREF="../compbio/engine/FilePuller.html#getDelay(java.util.concurrent.TimeUnit)"><B>getDelay(TimeUnit)</B></A> - \r
-Method in class compbio.engine.<A HREF="../compbio/engine/FilePuller.html" title="class in compbio.engine">FilePuller</A>\r
-<DD> \r
-<DT><A HREF="../compbio/metadata/Argument.html#getDescription()"><B>getDescription()</B></A> - \r
-Method in interface compbio.metadata.<A HREF="../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</A>\r
-<DD> \r
-<DT><A HREF="../compbio/metadata/Option.html#getDescription()"><B>getDescription()</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
-<DD>A long description of the Option\r
-<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> \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> \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><B>Deprecated.</B> \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> \r
-<DT><A HREF="../compbio/engine/LoadBalancer.html#getEngine(compbio.engine.client.Executable)"><B>getEngine(Executable<?>)</B></A> - \r
-Static method in class compbio.engine.<A HREF="../compbio/engine/LoadBalancer.html" title="class in compbio.engine">LoadBalancer</A>\r
-<DD> \r
-<DT><A HREF="../compbio/engine/LoadBalancer.html#getEngine(compbio.engine.client.Executable, java.util.List)"><B>getEngine(Executable<V>, List<FastaSequence>)</B></A> - \r
-Static method in class compbio.engine.<A HREF="../compbio/engine/LoadBalancer.html" title="class in compbio.engine">LoadBalancer</A>\r
-<DD> \r
-<DT><A HREF="../compbio/ws/server/WSUtil.html#getEngine(compbio.engine.client.ConfiguredExecutable)"><B>getEngine(ConfiguredExecutable<?>)</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> \r
-<DT><A HREF="../compbio/engine/client/ConfExecutable.html#getEnvironment()"><B>getEnvironment()</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> \r
-<DT><A HREF="../compbio/engine/client/ConfiguredExecutable.html#getEnvironment()"><B>getEnvironment()</B></A> - \r
-Method in interface compbio.engine.client.<A HREF="../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>\r
-<DD> \r
-<DT><A HREF="../compbio/engine/client/EnvVariableProcessor.html#getEnvVariables(java.lang.String, java.lang.Class)"><B>getEnvVariables(String, Class<?>)</B></A> - \r
-Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/EnvVariableProcessor.html" title="class in compbio.engine.client">EnvVariableProcessor</A>\r
-<DD> \r
-<DT><A HREF="../compbio/engine/client/ConfExecutable.html#getError()"><B>getError()</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> \r
-<DT><A HREF="../compbio/engine/client/Executable.html#getError()"><B>getError()</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> \r
-<DT><A HREF="../compbio/engine/client/RunConfiguration.html#getError()"><B>getError()</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> \r
-<DT><A HREF="../compbio/engine/client/SkeletalExecutable.html#getError()"><B>getError()</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> \r
-<DT><A HREF="../compbio/runner/_impl/NetNglyc.html#getError()"><B>getError()</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> \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> \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> \r
-<DT><A HREF="../compbio/engine/client/Util.html#getExecProperty(java.lang.String, compbio.engine.client.Executable)"><B>getExecProperty(String, Executable<?>)</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> \r
-<DT><A HREF="../compbio/engine/client/Util.html#getExecProperty(java.lang.String, java.lang.Class)"><B>getExecProperty(String, Class<?>)</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> \r
-<DT><A HREF="../compbio/engine/client/ConfExecutable.html#getExecProvider()"><B>getExecProvider()</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> \r
-<DT><A HREF="../compbio/engine/client/ConfiguredExecutable.html#getExecProvider()"><B>getExecProvider()</B></A> - \r
-Method in interface compbio.engine.client.<A HREF="../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>\r
-<DD> \r
-<DT><A HREF="../compbio/engine/client/ConfExecutable.html#getExecutable()"><B>getExecutable()</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> \r
-<DT><A HREF="../compbio/engine/client/ConfiguredExecutable.html#getExecutable()"><B>getExecutable()</B></A> - \r
-Method in interface compbio.engine.client.<A HREF="../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>\r
-<DD> \r
-<DT><A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html#getExecutionStat()"><B>getExecutionStat()</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> \r
-<DT><A HREF="../compbio/engine/local/LocalExecutorService.html#getExecutor()"><B>getExecutor()</B></A> - \r
-Static method in class compbio.engine.local.<A HREF="../compbio/engine/local/LocalExecutorService.html" title="class in compbio.engine.local">LocalExecutorService</A>\r
-<DD>This method returns the single instance of CachedThreadPoolExecutor which
- it cashes internally\r
-<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> \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> \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> \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> \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> \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> \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> \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> \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> \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> \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
-<DT><A HREF="../compbio/data/sequence/FastaSequence.html#getFormattedFasta()"><B>getFormattedFasta()</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> \r
-<DT><A HREF="../compbio/engine/client/Util.html#getFullPath(java.lang.String, java.lang.String)"><B>getFullPath(String, String)</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> \r
-<DT><A HREF="../compbio/metadata/Argument.html#getFurtherDetails()"><B>getFurtherDetails()</B></A> - \r
-Method in interface compbio.metadata.<A HREF="../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</A>\r
-<DD> \r
-<DT><A HREF="../compbio/metadata/Option.html#getFurtherDetails()"><B>getFurtherDetails()</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
-<DD>The URL where further details about the option can be found\r
-<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> \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> \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> \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> \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
-<DT><A HREF="../compbio/engine/client/Executable.html#getInput()"><B>getInput()</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> \r
-<DT><A HREF="../compbio/engine/client/RunConfiguration.html#getInput()"><B>getInput()</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> \r
-<DT><A HREF="../compbio/engine/client/SkeletalExecutable.html#getInput()"><B>getInput()</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> \r
-<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> \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> \r
-<DT><A HREF="../compbio/runner/_impl/NetNglyc.html#getInput()"><B>getInput()</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> \r
-<DT><A HREF="../compbio/runner/_impl/OB.html#getInput()"><B>getInput()</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> \r
-<DT><A HREF="../compbio/runner/_impl/PSIBlast.html#getInput()"><B>getInput()</B></A> - \r
-Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/PSIBlast.html" title="class in compbio.runner._impl">PSIBlast</A>\r
-<DD> \r
-<DT><A HREF="../compbio/runner/_impl/Ronn.html#getInput()"><B>getInput()</B></A> - \r
-Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Ronn.html" title="class in compbio.runner._impl">Ronn</A>\r
-<DD> \r
-<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> \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> \r
-<DT><A HREF="../compbio/engine/cluster/drmaa/JobRunner.html#getInstance(compbio.engine.client.ConfiguredExecutable)"><B>getInstance(ConfiguredExecutable<?>)</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> \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> \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> \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> \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> \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> \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> \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> \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> \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> \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> \r
-<DT><A HREF="../compbio/engine/ClusterJobId.html#getJobId()"><B>getJobId()</B></A> - \r
-Method in class compbio.engine.<A HREF="../compbio/engine/ClusterJobId.html" title="class in compbio.engine">ClusterJobId</A>\r
-<DD> \r
-<DT><A HREF="../compbio/engine/Job.html#getJobId()"><B>getJobId()</B></A> - \r
-Method in class compbio.engine.<A HREF="../compbio/engine/Job.html" title="class in compbio.engine">Job</A>\r
-<DD> \r
-<DT><A HREF="../compbio/engine/cluster/drmaa/JobRunner.html#getJobInfo()"><B>getJobInfo()</B></A> - \r
-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> \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> \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> \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> \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> <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> \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
-<DD>Query the status of the job\r
-<DT><A HREF="../compbio/engine/cluster/drmaa/AsyncJobRunner.html#getJobStatus(java.lang.String)"><B>getJobStatus(String)</B></A> - \r
-Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/AsyncJobRunner.html" title="class in compbio.engine.cluster.drmaa">AsyncJobRunner</A>\r
-<DD>This will never return clust.engine.JobStatus.CANCELLED as for sun grid
- engine cancelled job is the same as failed.\r
-<DT><A HREF="../compbio/engine/cluster/drmaa/ClusterSession.html#getJobStatus(compbio.engine.ClusterJobId)"><B>getJobStatus(ClusterJobId)</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>Apparently completed jobs cannot be found! If this happened most likely
- that the job is not running any more and Most likely it has been
- cancelled, finished or failed.\r
-<DT><A HREF="../compbio/engine/cluster/drmaa/ClusterSession.html#getJobStatus(int)"><B>getJobStatus(int)</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><B>Deprecated.</B> \r
-<DT><A HREF="../compbio/engine/cluster/drmaa/JobRunner.html#getJobStatus()"><B>getJobStatus()</B></A> - \r
-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> \r
-<DT><A HREF="../compbio/engine/local/AsyncLocalRunner.html#getJobStatus(java.lang.String)"><B>getJobStatus(String)</B></A> - \r
-Method in class compbio.engine.local.<A HREF="../compbio/engine/local/AsyncLocalRunner.html" title="class in compbio.engine.local">AsyncLocalRunner</A>\r
-<DD> \r
-<DT><A HREF="../compbio/engine/local/LocalEngineUtil.html#getJobStatus(java.util.concurrent.Future)"><B>getJobStatus(Future<ConfiguredExecutable<?>>)</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> \r
-<DT><A HREF="../compbio/engine/local/LocalRunner.html#getJobStatus()"><B>getJobStatus()</B></A> - \r
-Method in class compbio.engine.local.<A HREF="../compbio/engine/local/LocalRunner.html" title="class in compbio.engine.local">LocalRunner</A>\r
-<DD> \r
-<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> \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> \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> \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> \r
-<DT><A HREF="../compbio/ws/server/MuscleWS.html#getJobStatus(java.lang.String)"><B>getJobStatus(String)</B></A> - \r
-Method in class compbio.ws.server.<A HREF="../compbio/ws/server/MuscleWS.html" title="class in compbio.ws.server">MuscleWS</A>\r
-<DD> \r
-<DT><A HREF="../compbio/ws/server/ProbconsWS.html#getJobStatus(java.lang.String)"><B>getJobStatus(String)</B></A> - \r
-Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ProbconsWS.html" title="class in compbio.ws.server">ProbconsWS</A>\r
-<DD> \r
-<DT><A HREF="../compbio/ws/server/TcoffeeWS.html#getJobStatus(java.lang.String)"><B>getJobStatus(String)</B></A> - \r
-Method in class compbio.ws.server.<A HREF="../compbio/ws/server/TcoffeeWS.html" title="class in compbio.ws.server">TcoffeeWS</A>\r
-<DD> \r
-<DT><A HREF="../compbio/ws/server/WSUtil.html#getJobStatus(java.lang.String)"><B>getJobStatus(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> \r
-<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> <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> \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> <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> \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> \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> <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> \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> <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> \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> <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> \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> \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> <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> \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
-<DD> \r
-<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> \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> \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> \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><B>Deprecated.</B> \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> \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> \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> \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> \r
-<DT><A HREF="../compbio/ws/server/MuscleWS.html#getLimit(java.lang.String)"><B>getLimit(String)</B></A> - \r
-Method in class compbio.ws.server.<A HREF="../compbio/ws/server/MuscleWS.html" title="class in compbio.ws.server">MuscleWS</A>\r
-<DD> \r
-<DT><A HREF="../compbio/ws/server/ProbconsWS.html#getLimit(java.lang.String)"><B>getLimit(String)</B></A> - \r
-Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ProbconsWS.html" title="class in compbio.ws.server">ProbconsWS</A>\r
-<DD> \r
-<DT><A HREF="../compbio/ws/server/TcoffeeWS.html#getLimit(java.lang.String)"><B>getLimit(String)</B></A> - \r
-Method in class compbio.ws.server.<A HREF="../compbio/ws/server/TcoffeeWS.html" title="class in compbio.ws.server">TcoffeeWS</A>\r
-<DD> \r
-<DT><A HREF="../compbio/metadata/LimitsManager.html#getLimitByName(java.lang.String)"><B>getLimitByName(String)</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>\r
-<DD> \r
-<DT><A HREF="../compbio/data/msa/jaxws/GetLimitResponse.html" title="class in compbio.data.msa.jaxws"><B>GetLimitResponse</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD> <DT><A HREF="../compbio/data/msa/jaxws/GetLimitResponse.html#GetLimitResponse()"><B>GetLimitResponse()</B></A> - \r
-Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetLimitResponse.html" title="class in compbio.data.msa.jaxws">GetLimitResponse</A>\r
-<DD> \r
-<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> <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> \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
-<DD> \r
-<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> \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> \r
-<DT><A HREF="../compbio/engine/client/Util.html#getLimits(java.lang.Class)"><B>getLimits(Class<T>)</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> \r
-<DT><A HREF="../compbio/runner/_impl/NetNglyc.html#getLimits()"><B>getLimits()</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> \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> \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> \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> \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> \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> \r
-<DT><A HREF="../compbio/ws/server/MuscleWS.html#getLimits()"><B>getLimits()</B></A> - \r
-Method in class compbio.ws.server.<A HREF="../compbio/ws/server/MuscleWS.html" title="class in compbio.ws.server">MuscleWS</A>\r
-<DD> \r
-<DT><A HREF="../compbio/ws/server/ProbconsWS.html#getLimits()"><B>getLimits()</B></A> - \r
-Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ProbconsWS.html" title="class in compbio.ws.server">ProbconsWS</A>\r
-<DD> \r
-<DT><A HREF="../compbio/ws/server/TcoffeeWS.html#getLimits()"><B>getLimits()</B></A> - \r
-Method in class compbio.ws.server.<A HREF="../compbio/ws/server/TcoffeeWS.html" title="class in compbio.ws.server">TcoffeeWS</A>\r
-<DD> \r
-<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> <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> \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> \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> \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> \r
-<DT><A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html#getMaxVMem()"><B>getMaxVMem()</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> \r
-<DT><A HREF="../compbio/runner/_impl/Runners.html#getMclRunnable(java.lang.String)"><B>getMclRunnable(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> \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><B>Deprecated.</B> 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> \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> \r
-<DT><A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html#getMessage()"><B>getMessage()</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> \r
-<DT><A HREF="../compbio/data/msa/jaxws/ResultNotAvailableExceptionBean.html#getMessage()"><B>getMessage()</B></A> - \r
-Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/ResultNotAvailableExceptionBean.html" title="class in compbio.data.msa.jaxws">ResultNotAvailableExceptionBean</A>\r
-<DD> \r
-<DT><A HREF="../compbio/data/msa/jaxws/UnsupportedRuntimeExceptionBean.html#getMessage()"><B>getMessage()</B></A> - \r
-Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/UnsupportedRuntimeExceptionBean.html" title="class in compbio.data.msa.jaxws">UnsupportedRuntimeExceptionBean</A>\r
-<DD> \r
-<DT><A HREF="../compbio/data/msa/jaxws/WrongParameterExceptionBean.html#getMessage()"><B>getMessage()</B></A> - \r
-Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/WrongParameterExceptionBean.html" title="class in compbio.data.msa.jaxws">WrongParameterExceptionBean</A>\r
-<DD> \r
-<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> \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> \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> \r
-<DT><A HREF="../compbio/metadata/Argument.html#getName()"><B>getName()</B></A> - \r
-Method in interface compbio.metadata.<A HREF="../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</A>\r
-<DD> \r
-<DT><A HREF="../compbio/metadata/Option.html#getName()"><B>getName()</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
-<DD>Human readable name of the option\r
-<DT><A HREF="../compbio/metadata/Preset.html#getName()"><B>getName()</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>\r
-<DD> \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><B>Deprecated.</B> \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><B>Deprecated.</B> \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> \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> \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> \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> \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> \r
-<DT><A HREF="../compbio/metadata/LimitExceededException.html#getNumberOfSequencesAllowed()"><B>getNumberOfSequencesAllowed()</B></A> - \r
-Method in exception compbio.metadata.<A HREF="../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A>\r
-<DD> \r
-<DT><A HREF="../compbio/runner/_impl/Runners.html#getOBRunnable(java.lang.String)"><B>getOBRunnable(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> \r
-<DT><A HREF="../compbio/data/sequence/FastaSequence.html#getOnelineFasta()"><B>getOnelineFasta()</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> \r
-<DT><A HREF="../compbio/metadata/Parameter.html#getOptionName()"><B>getOptionName()</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>\r
-<DD> \r
-<DT><A HREF="../compbio/metadata/Option.html#getOptionNames()"><B>getOptionNames()</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
-<DD> \r
-<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> \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> \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> \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>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> \r
-<DT><A HREF="../compbio/engine/client/ConfExecutable.html#getOutput()"><B>getOutput()</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> \r
-<DT><A HREF="../compbio/engine/client/Executable.html#getOutput()"><B>getOutput()</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> \r
-<DT><A HREF="../compbio/engine/client/RunConfiguration.html#getOutput()"><B>getOutput()</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> \r
-<DT><A HREF="../compbio/engine/client/SkeletalExecutable.html#getOutput()"><B>getOutput()</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> \r
-<DT><A HREF="../compbio/runner/_impl/NetNglyc.html#getOutput()"><B>getOutput()</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> \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> \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> \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
-<DD> \r
-<DT><A HREF="../compbio/engine/client/ConfExecutable.html#getParameters(compbio.engine.client.Executable.ExecProvider)"><B>getParameters(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> \r
-<DT><A HREF="../compbio/engine/client/ConfiguredExecutable.html#getParameters()"><B>getParameters()</B></A> - \r
-Method in interface compbio.engine.client.<A HREF="../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>\r
-<DD> \r
-<DT><A HREF="../compbio/engine/client/Executable.html#getParameters(compbio.engine.client.Executable.ExecProvider)"><B>getParameters(Executable.ExecProvider)</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> \r
-<DT><A HREF="../compbio/engine/client/RunConfiguration.html#getParameters()"><B>getParameters()</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> \r
-<DT><A HREF="../compbio/engine/client/SkeletalExecutable.html#getParameters(compbio.engine.client.Executable.ExecProvider)"><B>getParameters(Executable.ExecProvider)</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> \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>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> \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> \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> \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> \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> \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
-<DD> \r
-<DT><A HREF="../compbio/engine/client/CommandBuilder.html#getParamValue(java.lang.String)"><B>getParamValue(String)</B></A> - \r
-Method in class compbio.engine.client.<A HREF="../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>\r
-<DD> \r
-<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> \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> \r
-<DT><A HREF="../compbio/metadata/Option.html#getPossibleValues()"><B>getPossibleValues()</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
-<DD>List of possible optionNames\r
-<DT><A HREF="../compbio/metadata/Parameter.html#getPossibleValues()"><B>getPossibleValues()</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>\r
-<DD>List is more convenient to work with\r
-<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> \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> \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> \r
-<DT><A HREF="../compbio/metadata/PresetManager.html#getPresetByName(java.lang.String)"><B>getPresetByName(String)</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>\r
-<DD> \r
-<DT><A HREF="../compbio/data/msa/jaxws/GetLimit.html#getPresetName()"><B>getPresetName()</B></A> - \r
-Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetLimit.html" title="class in compbio.data.msa.jaxws">GetLimit</A>\r
-<DD> \r
-<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> <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> \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
-<DD> \r
-<DT><A HREF="../compbio/runner/Util.html#getPresets(java.lang.Class)"><B>getPresets(Class<? extends Executable<T>>)</B></A> - \r
-Static method in class compbio.runner.<A HREF="../compbio/runner/Util.html" title="class in compbio.runner">Util</A>\r
-<DD> \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> \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> \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> \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> \r
-<DT><A HREF="../compbio/ws/server/MuscleWS.html#getPresets()"><B>getPresets()</B></A> - \r
-Method in class compbio.ws.server.<A HREF="../compbio/ws/server/MuscleWS.html" title="class in compbio.ws.server">MuscleWS</A>\r
-<DD> \r
-<DT><A HREF="../compbio/ws/server/ProbconsWS.html#getPresets()"><B>getPresets()</B></A> - \r
-Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ProbconsWS.html" title="class in compbio.ws.server">ProbconsWS</A>\r
-<DD> \r
-<DT><A HREF="../compbio/ws/server/TcoffeeWS.html#getPresets()"><B>getPresets()</B></A> - \r
-Method in class compbio.ws.server.<A HREF="../compbio/ws/server/TcoffeeWS.html" title="class in compbio.ws.server">TcoffeeWS</A>\r
-<DD> \r
-<DT><A HREF="../compbio/data/msa/jaxws/GetPresetsResponse.html" title="class in compbio.data.msa.jaxws"><B>GetPresetsResponse</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD> <DT><A HREF="../compbio/data/msa/jaxws/GetPresetsResponse.html#GetPresetsResponse()"><B>GetPresetsResponse()</B></A> - \r
-Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetPresetsResponse.html" title="class in compbio.data.msa.jaxws">GetPresetsResponse</A>\r
-<DD> \r
-<DT><A HREF="../compbio/metadata/RunnerConfig.html#getPrmSeparator()"><B>getPrmSeparator()</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
-<DD> \r
-<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> \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> \r
-<DT><A HREF="../compbio/engine/ProgressGetter.html#getProgress(java.lang.String)"><B>getProgress(String)</B></A> - \r
-Static method in class compbio.engine.<A HREF="../compbio/engine/ProgressGetter.html" title="class in compbio.engine">ProgressGetter</A>\r
-<DD> \r
-<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> \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
- the path to a known class.\r
-<DT><A HREF="../compbio/runner/_impl/Runners.html#getPSIBlastRunnable(java.lang.String)"><B>getPSIBlastRunnable(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> \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><B>Deprecated.</B> \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><B>Deprecated.</B> \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><B>Deprecated.</B> \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><B>Deprecated.</B> \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> \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> \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> \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> <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> \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> \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> \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> \r
-<DT><A HREF="../compbio/ws/server/MafftWS.html#getResult(java.lang.String)"><B>getResult(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> \r
-<DT><A HREF="../compbio/ws/server/MuscleWS.html#getResult(java.lang.String)"><B>getResult(String)</B></A> - \r
-Method in class compbio.ws.server.<A HREF="../compbio/ws/server/MuscleWS.html" title="class in compbio.ws.server">MuscleWS</A>\r
-<DD> \r
-<DT><A HREF="../compbio/ws/server/ProbconsWS.html#getResult(java.lang.String)"><B>getResult(String)</B></A> - \r
-Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ProbconsWS.html" title="class in compbio.ws.server">ProbconsWS</A>\r
-<DD> \r
-<DT><A HREF="../compbio/ws/server/TcoffeeWS.html#getResult(java.lang.String)"><B>getResult(String)</B></A> - \r
-Method in class compbio.ws.server.<A HREF="../compbio/ws/server/TcoffeeWS.html" title="class in compbio.ws.server">TcoffeeWS</A>\r
-<DD> \r
-<DT><A HREF="../compbio/data/msa/jaxws/GetResultResponse.html" title="class in compbio.data.msa.jaxws"><B>GetResultResponse</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD> <DT><A HREF="../compbio/data/msa/jaxws/GetResultResponse.html#GetResultResponse()"><B>GetResultResponse()</B></A> - \r
-Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetResultResponse.html" title="class in compbio.data.msa.jaxws">GetResultResponse</A>\r
-<DD> \r
-<DT><A HREF="../compbio/engine/AsyncExecutor.html#getResults(java.lang.String)"><B>getResults(String)</B></A> - \r
-Method in interface compbio.engine.<A HREF="../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine">AsyncExecutor</A>\r
-<DD>Retrieve the results of the job.\r
-<DT><A HREF="../compbio/engine/client/ConfExecutable.html#getResults()"><B>getResults()</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> \r
-<DT><A HREF="../compbio/engine/client/ConfExecutable.html#getResults(java.lang.String)"><B>getResults(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
-<DD> \r
-<DT><A HREF="../compbio/engine/client/ConfiguredExecutable.html#getResults()"><B>getResults()</B></A> - \r
-Method in interface compbio.engine.client.<A HREF="../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>\r
-<DD> \r
-<DT><A HREF="../compbio/engine/client/Executable.html#getResults(java.lang.String)"><B>getResults(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> \r
-<DT><A HREF="../compbio/engine/cluster/drmaa/AsyncJobRunner.html#getResults(java.lang.String)"><B>getResults(String)</B></A> - \r
-Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/AsyncJobRunner.html" title="class in compbio.engine.cluster.drmaa">AsyncJobRunner</A>\r
-<DD> \r
-<DT><A HREF="../compbio/engine/cluster/drmaa/ClusterSession.html#getResults(java.lang.String)"><B>getResults(String)</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> \r
-<DT><A HREF="../compbio/engine/local/AsyncLocalRunner.html#getResults(java.lang.String)"><B>getResults(String)</B></A> - \r
-Method in class compbio.engine.local.<A HREF="../compbio/engine/local/AsyncLocalRunner.html" title="class in compbio.engine.local">AsyncLocalRunner</A>\r
-<DD> \r
-<DT><A HREF="../compbio/engine/local/LocalEngineUtil.html#getResults(java.util.concurrent.Future, java.lang.String)"><B>getResults(Future<ConfiguredExecutable<?>>, 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> \r
-<DT><A HREF="../compbio/runner/_impl/NetNglyc.html#getResults(java.lang.String)"><B>getResults(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> \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> \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> \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> \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> \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> \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> \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> \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
-<DD> \r
-<DT><A HREF="../compbio/runner/msa/Mafft.html#getResults(java.lang.String)"><B>getResults(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> \r
-<DT><A HREF="../compbio/runner/msa/Muscle.html#getResults(java.lang.String)"><B>getResults(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> \r
-<DT><A HREF="../compbio/runner/msa/Probcons.html#getResults(java.lang.String)"><B>getResults(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> \r
-<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> \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> \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> \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> \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> \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> \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> \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> \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> \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> \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> \r
-<DT><A HREF="../compbio/data/msa/jaxws/GetLimitsResponse.html#getReturn()"><B>getReturn()</B></A> - \r
-Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetLimitsResponse.html" title="class in compbio.data.msa.jaxws">GetLimitsResponse</A>\r
-<DD> \r
-<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> \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> \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> \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> \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> \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> \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> \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> \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> \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
-<DD> \r
-<DT><A HREF="../compbio/runner/_impl/Environment.html#getRPSBlastDatabasesDir()"><B>getRPSBlastDatabasesDir()</B></A> - \r
-Static method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Environment.html" title="class in compbio.runner._impl">Environment</A>\r
-<DD> \r
-<DT><A HREF="../compbio/runner/_impl/Runners.html#getRPSBlastRunnable(java.lang.String)"><B>getRPSBlastRunnable(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> \r
-<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> \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> \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> \r
-<DT><A HREF="../compbio/metadata/PresetManager.html#getRunnerClassName()"><B>getRunnerClassName()</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>\r
-<DD> \r
-<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> \r
-<DT><A HREF="../compbio/engine/client/ConfExecutable.html#getRunnerLimits(java.lang.Class)"><B>getRunnerLimits(Class<V>)</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> <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> \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<? extends Executable<V>>)</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> \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> \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> \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> \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> \r
-<DT><A HREF="../compbio/ws/server/MuscleWS.html#getRunnerOptions()"><B>getRunnerOptions()</B></A> - \r
-Method in class compbio.ws.server.<A HREF="../compbio/ws/server/MuscleWS.html" title="class in compbio.ws.server">MuscleWS</A>\r
-<DD> \r
-<DT><A HREF="../compbio/ws/server/ProbconsWS.html#getRunnerOptions()"><B>getRunnerOptions()</B></A> - \r
-Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ProbconsWS.html" title="class in compbio.ws.server">ProbconsWS</A>\r
-<DD> \r
-<DT><A HREF="../compbio/ws/server/TcoffeeWS.html#getRunnerOptions()"><B>getRunnerOptions()</B></A> - \r
-Method in class compbio.ws.server.<A HREF="../compbio/ws/server/TcoffeeWS.html" title="class in compbio.ws.server">TcoffeeWS</A>\r
-<DD> \r
-<DT><A HREF="../compbio/data/msa/jaxws/GetRunnerOptionsResponse.html" title="class in compbio.data.msa.jaxws"><B>GetRunnerOptionsResponse</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD> <DT><A HREF="../compbio/data/msa/jaxws/GetRunnerOptionsResponse.html#GetRunnerOptionsResponse()"><B>GetRunnerOptionsResponse()</B></A> - \r
-Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetRunnerOptionsResponse.html" title="class in compbio.data.msa.jaxws">GetRunnerOptionsResponse</A>\r
-<DD> \r
-<DT><A HREF="../compbio/engine/client/ConfExecutable.html#getRunnerPresets(java.lang.Class)"><B>getRunnerPresets(Class<? extends Executable<V>>)</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> \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> \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> \r
-<DT><A HREF="../compbio/data/sequence/ScoreManager.ScoreHolder.html#getScoreByMethod(java.lang.Enum)"><B>getScoreByMethod(Enum<?>)</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> \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> \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> \r
-<DT><A HREF="../compbio/data/sequence/FastaSequence.html#getSequence()"><B>getSequence()</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 sequence\r
-<DT><A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html#getSequenceLenghtActual()"><B>getSequenceLenghtActual()</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> \r
-<DT><A HREF="../compbio/metadata/LimitExceededException.html#getSequenceLenghtActual()"><B>getSequenceLenghtActual()</B></A> - \r
-Method in exception compbio.metadata.<A HREF="../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A>\r
-<DD> \r
-<DT><A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html#getSequenceLenghtAllowed()"><B>getSequenceLenghtAllowed()</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> \r
-<DT><A HREF="../compbio/metadata/LimitExceededException.html#getSequenceLenghtAllowed()"><B>getSequenceLenghtAllowed()</B></A> - \r
-Method in exception compbio.metadata.<A HREF="../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A>\r
-<DD> \r
-<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> \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> \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> \r
-<DT><A HREF="../compbio/ws/client/ServicesUtil.html#getServiceByRunner(java.lang.Class)"><B>getServiceByRunner(Class<Executable<?>>)</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> \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> \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> \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> \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> \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> \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> \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> \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> \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> \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> \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> \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> \r
-<DT><A HREF="../compbio/runner/msa/Muscle.html#getStatFile()"><B>getStatFile()</B></A> - \r
-Static method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>\r
-<DD> \r
-<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> \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> \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> \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> \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> \r
-<DT><A HREF="../compbio/runner/Util.html#getSupportedOptions(java.lang.Class)"><B>getSupportedOptions(Class<? extends Executable<T>>)</B></A> - \r
-Static method in class compbio.runner.<A HREF="../compbio/runner/Util.html" title="class in compbio.runner">Util</A>\r
-<DD> \r
-<DT><A HREF="../compbio/engine/client/ConfExecutable.html#getSupportedRuntimes()"><B>getSupportedRuntimes()</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> \r
-<DT><A HREF="../compbio/engine/client/ConfiguredExecutable.html#getSupportedRuntimes()"><B>getSupportedRuntimes()</B></A> - \r
-Method in interface compbio.engine.client.<A HREF="../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>\r
-<DD> \r
-<DT><A HREF="../compbio/engine/client/Util.html#getSupportedRuntimes(java.lang.Class)"><B>getSupportedRuntimes(Class<?>)</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> \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> <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> \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> \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> <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> \r
-<DT><A HREF="../compbio/engine/Configurator.html#getSyncEngine(compbio.engine.client.ConfiguredExecutable, compbio.engine.client.Executable.ExecProvider)"><B>getSyncEngine(ConfiguredExecutable<?>, 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> \r
-<DT><A HREF="../compbio/engine/Configurator.html#getSyncEngine(compbio.engine.client.ConfiguredExecutable)"><B>getSyncEngine(ConfiguredExecutable<?>)</B></A> - \r
-Static method in class compbio.engine.<A HREF="../compbio/engine/Configurator.html" title="class in compbio.engine">Configurator</A>\r
-<DD> \r
-<DT><A HREF="../compbio/engine/SubmissionManager.html#getTask(java.lang.String)"><B>getTask(String)</B></A> - \r
-Static method in class compbio.engine.<A HREF="../compbio/engine/SubmissionManager.html" title="class in compbio.engine">SubmissionManager</A>\r
-<DD> \r
-<DT><A HREF="../compbio/engine/conf/DirectoryManager.html#getTaskDirectory(java.lang.Class)"><B>getTaskDirectory(Class<?>)</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> \r
-<DT><A HREF="../compbio/engine/client/ConfExecutable.html#getTaskId()"><B>getTaskId()</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> \r
-<DT><A HREF="../compbio/engine/client/ConfiguredExecutable.html#getTaskId()"><B>getTaskId()</B></A> - \r
-Method in interface compbio.engine.client.<A HREF="../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>\r
-<DD> \r
-<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> \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> \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> \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> \r
-<DT><A HREF="../compbio/runner/_impl/NetNglyc.html#getTestCommand()"><B>getTestCommand()</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> \r
-<DT><A HREF="../compbio/runner/_impl/OB.html#getTestCommand()"><B>getTestCommand()</B></A> - \r
-Static method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/OB.html" title="class in compbio.runner._impl">OB</A>\r
-<DD> \r
-<DT><A HREF="../compbio/runner/_impl/Ronn.html#getTestCommand()"><B>getTestCommand()</B></A> - \r
-Static method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Ronn.html" title="class in compbio.runner._impl">Ronn</A>\r
-<DD> \r
-<DT><A HREF="../compbio/runner/_impl/RPSBlast.html#getTestCommand()"><B>getTestCommand()</B></A> - \r
-Static method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/RPSBlast.html" title="class in compbio.runner._impl">RPSBlast</A>\r
-<DD> \r
-<DT><A HREF="../compbio/runner/_impl/Mcl.html#getTestParams()"><B>getTestParams()</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> \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><B>Deprecated.</B> 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> \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> \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> \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> \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> \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> \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> \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> \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> \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> \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> \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> \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> \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> \r
-<DT><A HREF="../compbio/runner/msa/Mafft.html#getType()"><B>getType()</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> \r
-<DT><A HREF="../compbio/runner/msa/Muscle.html#getType()"><B>getType()</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> \r
-<DT><A HREF="../compbio/runner/msa/Probcons.html#getType()"><B>getType()</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> \r
-<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> \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> \r
-<DT><A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html#getUsedUserTime()"><B>getUsedUserTime()</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> \r
-<DT><A HREF="../compbio/engine/conf/RunnerConfigMarshaller.html#getValidator(java.lang.String)"><B>getValidator(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> \r
-<DT><A HREF="../compbio/engine/conf/RunnerConfigMarshaller.html#getValidator(javax.xml.validation.Schema)"><B>getValidator(Schema)</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> \r
-<DT><A HREF="../compbio/metadata/Parameter.html#getValidValue()"><B>getValidValue()</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>\r
-<DD> \r
-<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> \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> \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> \r
-<DT><A HREF="../compbio/engine/client/ConfExecutable.html#getWorkDirectory()"><B>getWorkDirectory()</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> \r
-<DT><A HREF="../compbio/engine/client/ConfiguredExecutable.html#getWorkDirectory()"><B>getWorkDirectory()</B></A> - \r
-Method in interface compbio.engine.client.<A HREF="../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>\r
-<DD> \r
-<DT><A HREF="../compbio/engine/cluster/drmaa/AsyncJobRunner.html#getWorkDirectory(java.lang.String)"><B>getWorkDirectory(String)</B></A> - \r
-Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/AsyncJobRunner.html" title="class in compbio.engine.cluster.drmaa">AsyncJobRunner</A>\r
-<DD> \r
-<DT><A HREF="../compbio/engine/cluster/drmaa/JobRunner.html#getWorkDirectory()"><B>getWorkDirectory()</B></A> - \r
-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> \r
-<DT><A HREF="../compbio/engine/Configurator.html#getWorkDirectory(java.lang.String)"><B>getWorkDirectory(String)</B></A> - \r
-Static method in class compbio.engine.<A HREF="../compbio/engine/Configurator.html" title="class in compbio.engine">Configurator</A>\r
-<DD> \r
-<DT><A HREF="../compbio/engine/local/AsyncLocalRunner.html#getWorkDirectory(java.lang.String)"><B>getWorkDirectory(String)</B></A> - \r
-Method in class compbio.engine.local.<A HREF="../compbio/engine/local/AsyncLocalRunner.html" title="class in compbio.engine.local">AsyncLocalRunner</A>\r
-<DD> \r
-<DT><A HREF="../compbio/engine/local/LocalRunner.html#getWorkDirectory()"><B>getWorkDirectory()</B></A> - \r
-Method in class compbio.engine.local.<A HREF="../compbio/engine/local/LocalRunner.html" title="class in compbio.engine.local">LocalRunner</A>\r
-<DD> \r
-<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> \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> \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> <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> \r
-</DL>\r
-<HR>\r
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-<A NAME="navbar_bottom"><!-- --></A>\r
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