-Uses of Class compbio.metadata.JobSubmissionException -

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-Uses of Class
compbio.metadata.JobSubmissionException

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-Packages that use JobSubmissionException
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

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-Uses of JobSubmissionException in compbio.data.msa
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Methods in compbio.data.msa that throw JobSubmissionException
- String MsaWS.align(List<FastaSequence> sequences) - -
-          Align a list of sequences with default settings.
- String SequenceAnnotation.analize(List<FastaSequence> sequences) - -
-          Analyse the sequences.
- String MsaWS.customAlign(List<FastaSequence> sequences, - List<Option<T>> options) - -
-          Align a list of sequences with options.
- String SequenceAnnotation.customAnalize(List<FastaSequence> sequences, - List<Option<T>> options) - -
-          Analyse the sequences according to custom settings defined in options - list.
- String MsaWS.presetAlign(List<FastaSequence> sequences, - Preset<T> preset) - -
-          Align a list of sequences with preset.
- String SequenceAnnotation.presetAnalize(List<FastaSequence> sequences, - Preset<T> preset) - -
-          Analyse the sequences according to the preset settings.
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Methods in compbio.data.msa that throw JobSubmissionException
- `String`	`MsaWS.align(List<FastaSequence> sequences)` - - - Align a list of sequences with default settings.
- `String`	`SequenceAnnotation.analize(List<FastaSequence> sequences)` - - - Analyse the sequences.
- `String`	`MsaWS.customAlign(List<FastaSequence> sequences, - List<Option<T>> options)` - - - Align a list of sequences with options.
- `String`	`SequenceAnnotation.customAnalize(List<FastaSequence> sequences, - List<Option<T>> options)` - - - Analyse the sequences according to custom settings defined in options - list.
- `String`	`MsaWS.presetAlign(List<FastaSequence> sequences, - Preset<T> preset)` - - - Align a list of sequences with preset.
- `String`	`SequenceAnnotation.presetAnalize(List<FastaSequence> sequences, - Preset<T> preset)` - - - Analyse the sequences according to the preset settings.

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-Uses of JobSubmissionException in compbio.engine
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Methods in compbio.engine that throw JobSubmissionException
-static - - - - - -<T> ConfiguredExecutable<T> - Configurator.configureExecutable(Executable<T> executable) - -
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-static - - - - - -<T> ConfiguredExecutable<T> - Configurator.configureExecutable(Executable<T> executable, - Executable.ExecProvider provider) - -
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-static - - - - - -<T> ConfiguredExecutable<T> - Configurator.configureExecutable(Executable<T> executable, - List<FastaSequence> dataSet) - -
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- void SyncExecutor.executeJob() - -
-          Execute the job
-static SyncExecutor Configurator.getSyncEngine(ConfiguredExecutable<?> executable) - -
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-static SyncExecutor Configurator.getSyncEngine(ConfiguredExecutable<?> executable, - Executable.ExecProvider provider) - -
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- String AsyncExecutor.submitJob(ConfiguredExecutable<?> executable) - -
-          Submits job for the execution - Immediate execution is not guaranteed, this method puts the job in the queue.
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-Uses of JobSubmissionException in compbio.engine.client
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Methods in compbio.engine.client that throw JobSubmissionException
- String ConfiguredExecutable.getCommand(Executable.ExecProvider provider) - -
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Methods in compbio.engine.client that throw JobSubmissionException
- `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
- void JobRunner.executeJob() - -
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-static JobRunner JobRunner.getInstance(ConfiguredExecutable<?> executable) - -
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- String AsyncJobRunner.submitJob(ConfiguredExecutable<?> executable) - -
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Methods in compbio.engine.cluster.drmaa that throw JobSubmissionException
- `void`	`JobRunner.executeJob()` - - -
-`static JobRunner`	`JobRunner.getInstance(ConfiguredExecutable<?> executable)` - - -
- `String`	`AsyncJobRunner.submitJob(ConfiguredExecutable<?> executable)` - - -

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Constructors in compbio.engine.cluster.drmaa that throw JobSubmissionException
JobRunner(ConfiguredExecutable<?> confExec) - -
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Constructors in compbio.engine.cluster.drmaa that throw JobSubmissionException
`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
- void LocalRunner.executeJob() - -
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- String AsyncLocalRunner.submitJob(ConfiguredExecutable<?> executable) - -
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Methods in compbio.engine.local that throw JobSubmissionException
- `void`	`LocalRunner.executeJob()` - - -
- `String`	`AsyncLocalRunner.submitJob(ConfiguredExecutable<?> executable)` - - -

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Constructors in compbio.engine.local that throw JobSubmissionException
ExecutableWrapper(ConfiguredExecutable<?> executable, - String workDirectory) - -
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Constructors in compbio.engine.local that throw JobSubmissionException
`ExecutableWrapper(ConfiguredExecutable<?> executable, - String workDirectory)` - - -

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-Uses of JobSubmissionException in compbio.metadata
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Subclasses of JobSubmissionException in compbio.metadata
- 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.
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Subclasses of JobSubmissionException in compbio.metadata
- `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.

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-Uses of JobSubmissionException in compbio.runner
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Methods in compbio.runner that throw JobSubmissionException
-static void Util.writeInput(List<FastaSequence> sequences, - ConfiguredExecutable<?> exec) - -
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Methods in compbio.runner that throw JobSubmissionException
-`static void`	`Util.writeInput(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
- String ClustalWS.align(List<FastaSequence> sequences) - -
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- String _MsaService.align(List<FastaSequence> sequences) - -
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- String MuscleWS.align(List<FastaSequence> sequences) - -
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- String MafftWS.align(List<FastaSequence> sequences) - -
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- String TcoffeeWS.align(List<FastaSequence> sequences) - -
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- String ProbconsWS.align(List<FastaSequence> sequences) - -
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- String ClustalOWS.align(List<FastaSequence> sequences) - -
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-static - - - - - -<T> String - WSUtil.align(List<FastaSequence> sequences, - ConfiguredExecutable<T> confExec, - org.apache.log4j.Logger logger, - String callingMethod, - Limit<T> limit) - -
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- String AAConWS.analize(List<FastaSequence> sequences) - -
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- String SequenceAnnotationService.analize(List<FastaSequence> sequences) - -
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-static - - - - - -<T> String - WSUtil.analize(List<FastaSequence> sequences, - ConfiguredExecutable<T> confExec, - org.apache.log4j.Logger log, - String method, - Limit<T> limit) - -
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- String ClustalOWS.customAlign(List<FastaSequence> sequences, - List<Option<ClustalO>> options) - -
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- String ClustalWS.customAlign(List<FastaSequence> sequences, - List<Option<ClustalW>> options) - -
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- String MafftWS.customAlign(List<FastaSequence> sequences, - List<Option<Mafft>> options) - -
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- String MuscleWS.customAlign(List<FastaSequence> sequences, - List<Option<Muscle>> options) - -
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- String ProbconsWS.customAlign(List<FastaSequence> sequences, - List<Option<Probcons>> options) - -
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- String _MsaService.customAlign(List<FastaSequence> sequences, - List<Option<T>> options) - -
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- String TcoffeeWS.customAlign(List<FastaSequence> sequences, - List<Option<Tcoffee>> options) - -
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- String DisemblWS.customAnalize(List<FastaSequence> sequences, - List<Option<Disembl>> options) - -
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- String GlobPlotWS.customAnalize(List<FastaSequence> sequences, - List<Option<GlobPlot>> options) - -
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- String SequenceAnnotationService.customAnalize(List<FastaSequence> sequences, - List<Option<T>> options) - -
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- String ClustalOWS.presetAlign(List<FastaSequence> sequences, - Preset<ClustalO> preset) - -
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- String ClustalWS.presetAlign(List<FastaSequence> sequences, - Preset<ClustalW> preset) - -
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- String MafftWS.presetAlign(List<FastaSequence> sequences, - Preset<Mafft> preset) - -
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- String MuscleWS.presetAlign(List<FastaSequence> sequences, - Preset<Muscle> preset) - -
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- String ProbconsWS.presetAlign(List<FastaSequence> sequences, - Preset<Probcons> preset) - -
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- String _MsaService.presetAlign(List<FastaSequence> sequences, - Preset<T> preset) - -
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- String TcoffeeWS.presetAlign(List<FastaSequence> sequences, - Preset<Tcoffee> preset) - -
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- String DisemblWS.presetAnalize(List<FastaSequence> sequences, - Preset<Disembl> preset) - -
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- String GlobPlotWS.presetAnalize(List<FastaSequence> sequences, - Preset<GlobPlot> preset) - -
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- String IUPredWS.presetAnalize(List<FastaSequence> sequences, - Preset<IUPred> preset) - -
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- String SequenceAnnotationService.presetAnalize(List<FastaSequence> sequences, - Preset<T> preset) - -
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-static void WSUtil.validateAAConInput(List<FastaSequence> sequences) - -
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-static void WSUtil.validateFastaInput(List<FastaSequence> sequences) - -
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