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Packages that use JobSubmissionException | |
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compbio.data.msa | Web Service interfaces for JAva Bioinformatics Analysis Web Services. |
compbio.engine | |
compbio.engine.client | |
compbio.engine.cluster.drmaa | |
compbio.engine.local | |
compbio.metadata | A meta-data model for multiple sequence alignment web services Classes in this package have no dependencies to other sources in the project. |
compbio.runner | Utilities commonly used by all runners. |
compbio.ws.server |
Uses of JobSubmissionException in compbio.data.msa |
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Methods in compbio.data.msa that throw JobSubmissionException | |
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java.lang.String |
MsaWS.align(java.util.List<FastaSequence> sequences)
Align a list of sequences with default settings. |
java.lang.String |
SequenceAnnotation.analize(java.util.List<FastaSequence> sequences)
Analyse the sequences. |
java.lang.String |
MsaWS.customAlign(java.util.List<FastaSequence> sequences,
java.util.List<Option<T>> options)
Align a list of sequences with options. |
java.lang.String |
SequenceAnnotation.customAnalize(java.util.List<FastaSequence> sequences,
java.util.List<Option<T>> options)
Analyse the sequences according to custom settings defined in options list. |
java.lang.String |
MsaWS.presetAlign(java.util.List<FastaSequence> sequences,
Preset<T> preset)
Align a list of sequences with preset. |
java.lang.String |
SequenceAnnotation.presetAnalize(java.util.List<FastaSequence> sequences,
Preset<T> preset)
Analyse the sequences according to the preset settings. |
Uses of JobSubmissionException in compbio.engine |
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Methods in compbio.engine that throw JobSubmissionException | ||
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static
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Configurator.configureExecutable(Executable<T> executable)
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static
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Configurator.configureExecutable(Executable<T> executable,
Executable.ExecProvider provider)
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static
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Configurator.configureExecutable(Executable<T> executable,
java.util.List<FastaSequence> dataSet)
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void |
SyncExecutor.executeJob()
Execute the job |
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static SyncExecutor |
Configurator.getSyncEngine(ConfiguredExecutable<?> executable)
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static SyncExecutor |
Configurator.getSyncEngine(ConfiguredExecutable<?> executable,
Executable.ExecProvider provider)
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java.lang.String |
AsyncExecutor.submitJob(ConfiguredExecutable<?> executable)
Submits job for the execution Immediate execution is not guaranteed, this method puts the job in the queue. |
Uses of JobSubmissionException in compbio.engine.client |
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Methods in compbio.engine.client that throw JobSubmissionException | |
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java.lang.String |
ConfiguredExecutable.getCommand(Executable.ExecProvider provider)
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Uses of JobSubmissionException in compbio.engine.cluster.drmaa |
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Methods in compbio.engine.cluster.drmaa that throw JobSubmissionException | |
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void |
JobRunner.executeJob()
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static JobRunner |
JobRunner.getInstance(ConfiguredExecutable<?> executable)
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java.lang.String |
AsyncJobRunner.submitJob(ConfiguredExecutable<?> executable)
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Constructors in compbio.engine.cluster.drmaa that throw JobSubmissionException | |
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JobRunner(ConfiguredExecutable<?> confExec)
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Uses of JobSubmissionException in compbio.engine.local |
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Methods in compbio.engine.local that throw JobSubmissionException | |
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void |
LocalRunner.executeJob()
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java.lang.String |
AsyncLocalRunner.submitJob(ConfiguredExecutable<?> executable)
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Constructors in compbio.engine.local that throw JobSubmissionException | |
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ExecutableWrapper(ConfiguredExecutable<?> executable,
java.lang.String workDirectory)
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Uses of JobSubmissionException in compbio.metadata |
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Subclasses of JobSubmissionException in compbio.metadata | |
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class |
LimitExceededException
This exception is thrown if the task larger in size that the limit that applies to the calculation. |
class |
UnsupportedRuntimeException
Indicates that the server could not execute native executables. |
Uses of JobSubmissionException in compbio.runner |
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Methods in compbio.runner that throw JobSubmissionException | |
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static void |
Util.writeInput(java.util.List<FastaSequence> sequences,
ConfiguredExecutable<?> exec)
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Uses of JobSubmissionException in compbio.ws.server |
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Methods in compbio.ws.server that throw JobSubmissionException | ||
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java.lang.String |
MafftWS.align(java.util.List<FastaSequence> sequences)
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java.lang.String |
ClustalOWS.align(java.util.List<FastaSequence> sequences)
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java.lang.String |
ProbconsWS.align(java.util.List<FastaSequence> sequences)
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java.lang.String |
TcoffeeWS.align(java.util.List<FastaSequence> sequences)
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java.lang.String |
ClustalWS.align(java.util.List<FastaSequence> sequences)
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java.lang.String |
MuscleWS.align(java.util.List<FastaSequence> sequences)
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static
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WSUtil.align(java.util.List<FastaSequence> sequences,
ConfiguredExecutable<T> confExec,
org.apache.log4j.Logger logger,
java.lang.String callingMethod,
Limit<T> limit)
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java.lang.String |
AAConWS.analize(java.util.List<FastaSequence> sequences)
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java.lang.String |
SequenceAnnotationService.analize(java.util.List<FastaSequence> sequences)
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static
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WSUtil.analize(java.util.List<FastaSequence> sequences,
ConfiguredExecutable<T> confExec,
org.apache.log4j.Logger log,
java.lang.String method,
Limit<T> limit)
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java.lang.String |
ClustalOWS.customAlign(java.util.List<FastaSequence> sequences,
java.util.List<Option<ClustalO>> options)
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java.lang.String |
ClustalWS.customAlign(java.util.List<FastaSequence> sequences,
java.util.List<Option<ClustalW>> options)
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java.lang.String |
MafftWS.customAlign(java.util.List<FastaSequence> sequences,
java.util.List<Option<Mafft>> options)
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java.lang.String |
MuscleWS.customAlign(java.util.List<FastaSequence> sequences,
java.util.List<Option<Muscle>> options)
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java.lang.String |
ProbconsWS.customAlign(java.util.List<FastaSequence> sequences,
java.util.List<Option<Probcons>> options)
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java.lang.String |
TcoffeeWS.customAlign(java.util.List<FastaSequence> sequences,
java.util.List<Option<Tcoffee>> options)
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java.lang.String |
DisemblWS.customAnalize(java.util.List<FastaSequence> sequences,
java.util.List<Option<Disembl>> options)
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java.lang.String |
GlobPlotWS.customAnalize(java.util.List<FastaSequence> sequences,
java.util.List<Option<GlobPlot>> options)
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java.lang.String |
SequenceAnnotationService.customAnalize(java.util.List<FastaSequence> sequences,
java.util.List<Option<T>> options)
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java.lang.String |
ClustalOWS.presetAlign(java.util.List<FastaSequence> sequences,
Preset<ClustalO> preset)
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java.lang.String |
ClustalWS.presetAlign(java.util.List<FastaSequence> sequences,
Preset<ClustalW> preset)
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java.lang.String |
MafftWS.presetAlign(java.util.List<FastaSequence> sequences,
Preset<Mafft> preset)
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java.lang.String |
MuscleWS.presetAlign(java.util.List<FastaSequence> sequences,
Preset<Muscle> preset)
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java.lang.String |
ProbconsWS.presetAlign(java.util.List<FastaSequence> sequences,
Preset<Probcons> preset)
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java.lang.String |
TcoffeeWS.presetAlign(java.util.List<FastaSequence> sequences,
Preset<Tcoffee> preset)
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java.lang.String |
DisemblWS.presetAnalize(java.util.List<FastaSequence> sequences,
Preset<Disembl> preset)
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java.lang.String |
GlobPlotWS.presetAnalize(java.util.List<FastaSequence> sequences,
Preset<GlobPlot> preset)
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java.lang.String |
IUPredWS.presetAnalize(java.util.List<FastaSequence> sequences,
Preset<IUPred> preset)
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java.lang.String |
SequenceAnnotationService.presetAnalize(java.util.List<FastaSequence> sequences,
Preset<T> preset)
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static void |
WSUtil.validateAAConInput(java.util.List<FastaSequence> sequences)
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static void |
WSUtil.validateFastaInput(java.util.List<FastaSequence> sequences)
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