Uses of Class
compbio.metadata.JobSubmissionException

Packages that use JobSubmissionException

Package	Description
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

Methods in compbio.data.msa that throw JobSubmissionException

Modifier and Type	Method and Description
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

Methods in compbio.engine that throw JobSubmissionException

Modifier and Type	Method and Description
static <T> ConfiguredExecutable<T>	Configurator.configureExecutable(Executable<T> executable)
static <T> ConfiguredExecutable<T>	Configurator.configureExecutable(Executable<T> executable, Executable.ExecProvider provider)
static <T> ConfiguredExecutable<T>	Configurator.configureExecutable(Executable<T> executable, java.util.List<FastaSequence> dataSet)
void	SyncExecutor.executeJob() Execute the job
(package private) static Executable.ExecProvider	Configurator.getExecProvider(ConfiguredExecutable<?> executable, java.util.List<FastaSequence> dataSet) Depending on the values defined in the properties (engine.cluster.enable=true and engine.local.enable=true) return either Cluster job submission engine #JobRunner or local job submission engine #LocalRunner If both engines enabled than ask LoadBalancer for an engine.
static SyncExecutor	Configurator.getSyncEngine(ConfiguredExecutable<?> executable)
static SyncExecutor	Configurator.getSyncEngine(ConfiguredExecutable<?> executable, Executable.ExecProvider provider)
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

Methods in compbio.engine.client that throw JobSubmissionException

Modifier and Type	Method and Description
java.lang.String	ConfiguredExecutable.getCommand(Executable.ExecProvider provider)

Uses of JobSubmissionException in compbio.engine.cluster.drmaa

Methods in compbio.engine.cluster.drmaa that throw JobSubmissionException

Modifier and Type	Method and Description
void	JobRunner.executeJob()
void	ClusterRunner.executeJob()
static JobRunner	JobRunner.getInstance(ConfiguredExecutable<?> executable)
static ClusterRunner	ClusterRunner.getInstance(ConfiguredExecutable<?> executable)
(package private) java.lang.String	JobRunner.submitJob()
(package private) java.lang.String	ClusterRunner.submitJob()
java.lang.String	AsyncJobRunner.submitJob(ConfiguredExecutable<?> executable)
java.lang.String	AsyncClusterRunner.submitJob(ConfiguredExecutable<?> executable)

Constructors in compbio.engine.cluster.drmaa that throw JobSubmissionException

Constructor and Description
ClusterRunner(ConfiguredExecutable<?> confExec)
JobRunner(ConfiguredExecutable<?> confExec)

Uses of JobSubmissionException in compbio.engine.local

Methods in compbio.engine.local that throw JobSubmissionException

Modifier and Type	Method and Description
void	LocalRunner.executeJob()
java.lang.String	AsyncLocalRunner.submitJob(ConfiguredExecutable<?> executable)

Constructors in compbio.engine.local that throw JobSubmissionException

Constructor and Description
ExecutableWrapper(ConfiguredExecutable<?> executable, java.lang.String workDirectory)

Uses of JobSubmissionException in compbio.metadata

Subclasses of JobSubmissionException in compbio.metadata

Modifier and Type	Class and Description
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

Methods in compbio.runner that throw JobSubmissionException

Modifier and Type	Method and Description
static void	RunnerUtil.writeClustalInput(java.util.List<FastaSequence> sequences, ConfiguredExecutable<?> exec, char gapChar)
static void	Util.writeInput(java.util.List<FastaSequence> sequences, ConfiguredExecutable<?> exec)
static void	RunnerUtil.writeInput(java.util.List<FastaSequence> sequences, ConfiguredExecutable<?> exec)

Uses of JobSubmissionException in compbio.ws.server

Methods in compbio.ws.server that throw JobSubmissionException

Modifier and Type	Method and Description
java.lang.String	GLprobsWS.align(java.util.List<FastaSequence> sequences)
java.lang.String	MafftWS.align(java.util.List<FastaSequence> sequences)
java.lang.String	ClustalOWS.align(java.util.List<FastaSequence> sequences)
java.lang.String	MSAprobsWS.align(java.util.List<FastaSequence> sequences)
java.lang.String	MuscleWS.align(java.util.List<FastaSequence> sequences)
java.lang.String	ClustalWS.align(java.util.List<FastaSequence> sequences)
java.lang.String	TcoffeeWS.align(java.util.List<FastaSequence> sequences)
java.lang.String	ProbconsWS.align(java.util.List<FastaSequence> sequences)
static <T> java.lang.String	WSUtil.align(java.util.List<FastaSequence> sequences, ConfiguredExecutable<T> confExec, org.apache.log4j.Logger logger, java.lang.String callingMethod, Limit<T> limit)
java.lang.String	SequenceAnnotationService.analize(java.util.List<FastaSequence> sequences)
java.lang.String	AAConWS.analize(java.util.List<FastaSequence> sequences)
java.lang.String	RNAalifoldWS.analize(java.util.List<FastaSequence> sequences)
static <T> java.lang.String	WSUtil.analize(java.util.List<FastaSequence> sequences, ConfiguredExecutable<T> confExec, org.apache.log4j.Logger log, java.lang.String method, Limit<T> limit)
java.lang.String	ClustalOWS.customAlign(java.util.List<FastaSequence> sequences, java.util.List<Option<ClustalO>> options)
java.lang.String	ClustalWS.customAlign(java.util.List<FastaSequence> sequences, java.util.List<Option<ClustalW>> options)
java.lang.String	GLprobsWS.customAlign(java.util.List<FastaSequence> sequences, java.util.List<Option<GLprobs>> options)
java.lang.String	MafftWS.customAlign(java.util.List<FastaSequence> sequences, java.util.List<Option<Mafft>> options)
java.lang.String	MSAprobsWS.customAlign(java.util.List<FastaSequence> sequences, java.util.List<Option<MSAprobs>> options)
java.lang.String	MuscleWS.customAlign(java.util.List<FastaSequence> sequences, java.util.List<Option<Muscle>> options)
java.lang.String	ProbconsWS.customAlign(java.util.List<FastaSequence> sequences, java.util.List<Option<Probcons>> options)
java.lang.String	TcoffeeWS.customAlign(java.util.List<FastaSequence> sequences, java.util.List<Option<Tcoffee>> options)
java.lang.String	AAConWS.customAnalize(java.util.List<FastaSequence> sequences, java.util.List<Option<AACon>> options)
java.lang.String	DisemblWS.customAnalize(java.util.List<FastaSequence> sequences, java.util.List<Option<Disembl>> options)
java.lang.String	GlobPlotWS.customAnalize(java.util.List<FastaSequence> sequences, java.util.List<Option<GlobPlot>> options)
java.lang.String	RNAalifoldWS.customAnalize(java.util.List<FastaSequence> sequences, java.util.List<Option<RNAalifold>> options)
java.lang.String	SequenceAnnotationService.customAnalize(java.util.List<FastaSequence> sequences, java.util.List<Option<T>> options)
static <T> java.lang.String	WSUtil.fold(java.util.List<FastaSequence> sequences, ConfiguredExecutable<T> confExec, org.apache.log4j.Logger log, java.lang.String method, Limit<T> limit)
(package private) ConfiguredExecutable<T>	GenericMetadataService.init(java.util.List<FastaSequence> sequences)
(package private) ConfiguredExecutable<GLprobs>	GLprobsWS.init(java.util.List<FastaSequence> dataSet)
(package private) ConfiguredExecutable<Mafft>	MafftWS.init(java.util.List<FastaSequence> dataSet)
(package private) ConfiguredExecutable<ClustalO>	ClustalOWS.init(java.util.List<FastaSequence> dataSet)
(package private) ConfiguredExecutable<MSAprobs>	MSAprobsWS.init(java.util.List<FastaSequence> dataSet)
(package private) ConfiguredExecutable<Muscle>	MuscleWS.init(java.util.List<FastaSequence> sequences)
(package private) ConfiguredExecutable<ClustalW>	ClustalWS.init(java.util.List<FastaSequence> dataSet)
(package private) ConfiguredExecutable<Tcoffee>	TcoffeeWS.init(java.util.List<FastaSequence> sequences)
(package private) ConfiguredExecutable<Probcons>	ProbconsWS.init(java.util.List<FastaSequence> dataSet)
java.lang.String	ClustalOWS.presetAlign(java.util.List<FastaSequence> sequences, Preset<ClustalO> preset)
java.lang.String	ClustalWS.presetAlign(java.util.List<FastaSequence> sequences, Preset<ClustalW> preset)
java.lang.String	GLprobsWS.presetAlign(java.util.List<FastaSequence> sequences, Preset<GLprobs> preset)
java.lang.String	MafftWS.presetAlign(java.util.List<FastaSequence> sequences, Preset<Mafft> preset)
java.lang.String	MSAprobsWS.presetAlign(java.util.List<FastaSequence> sequences, Preset<MSAprobs> preset)
java.lang.String	MuscleWS.presetAlign(java.util.List<FastaSequence> sequences, Preset<Muscle> preset)
java.lang.String	ProbconsWS.presetAlign(java.util.List<FastaSequence> sequences, Preset<Probcons> preset)
java.lang.String	TcoffeeWS.presetAlign(java.util.List<FastaSequence> sequences, Preset<Tcoffee> preset)
java.lang.String	AAConWS.presetAnalize(java.util.List<FastaSequence> sequences, Preset<AACon> preset)
java.lang.String	DisemblWS.presetAnalize(java.util.List<FastaSequence> sequences, Preset<Disembl> preset)
java.lang.String	GlobPlotWS.presetAnalize(java.util.List<FastaSequence> sequences, Preset<GlobPlot> preset)
java.lang.String	IUPredWS.presetAnalize(java.util.List<FastaSequence> sequences, Preset<IUPred> preset)
java.lang.String	RNAalifoldWS.presetAnalize(java.util.List<FastaSequence> sequences, Preset<RNAalifold> preset)
java.lang.String	SequenceAnnotationService.presetAnalize(java.util.List<FastaSequence> sequences, Preset<T> preset)
static void	WSUtil.validateAAConInput(java.util.List<FastaSequence> sequences)
static void	WSUtil.validateFastaInput(java.util.List<FastaSequence> sequences)