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S
saveRunConfiguration()
- Method in class compbio.engine.client.
ConfExecutable
saveRunConfiguration()
- Method in interface compbio.engine.client.
ConfiguredExecutable
SequenceUtil
- Class in
compbio.data.sequence
Utility class for operations on sequences
setActualNumberofSequences(int)
- Method in class compbio.data.msa.jaxws.
LimitExceededExceptionBean
setDefaultValue(String)
- Method in class compbio.metadata.
Option
Sets one of the values defined in optionList as default.
setDefaultValue(String)
- Method in class compbio.metadata.
Parameter
setDescription(String)
- Method in class compbio.metadata.
Option
setDescription(String)
- Method in class compbio.metadata.
Preset
setEmail(String)
- Method in class compbio.runner.
_SkeletalCommandBuilder
setError(String)
- Method in class compbio.engine.client.
RunConfiguration
setError(String)
- Method in class compbio.engine.client.
SkeletalExecutable
setExecProvider(Executable.ExecProvider)
- Method in class compbio.engine.client.
ConfExecutable
setFastaSequences(List<FastaSequence>)
- Method in class compbio.data.msa.jaxws.
Align
setFastaSequences(List<FastaSequence>)
- Method in class compbio.data.msa.jaxws.
CustomAlign
setFastaSequences(List<FastaSequence>)
- Method in class compbio.data.msa.jaxws.
PresetAlign
setFirst(String)
- Method in class compbio.engine.client.
CommandBuilder
setFurtherDetails(URL)
- Method in class compbio.metadata.
Option
setInput(String)
- Method in class compbio.engine.client.
RunConfiguration
setInput(String)
- Method in class compbio.engine.client.
SkeletalExecutable
setInput(String)
- Method in class compbio.runner.msa.
ClustalW
setInput(String)
- Method in class compbio.runner.msa.
Mafft
setInput(String)
- Method in class compbio.runner.msa.
Muscle
setInput(String)
- Method in class compbio.runner.msa.
Probcons
setInput(String)
- Method in class compbio.runner.msa.
Tcoffee
setJobId(String)
- Method in class compbio.data.msa.jaxws.
CancelJob
setJobId(String)
- Method in class compbio.data.msa.jaxws.
GetJobStatus
setJobId(String)
- Method in class compbio.data.msa.jaxws.
GetProgress
setJobId(String)
- Method in class compbio.data.msa.jaxws.
GetResult
setJobId(String)
- Method in class compbio.data.msa.jaxws.
PullExecStatistics
setJobId(String)
- Method in class compbio.data.msa.jaxws.
PullFile
setLast(String)
- Method in class compbio.engine.client.
CommandBuilder
setLast(String, String)
- Method in class compbio.engine.client.
CommandBuilder
setMax(String)
- Method in class compbio.metadata.
ValueConstrain
setMessage(String)
- Method in class compbio.data.msa.jaxws.
JobExecutionExceptionBean
setMessage(String)
- Method in class compbio.data.msa.jaxws.
JobSubmissionExceptionBean
setMessage(String)
- Method in class compbio.data.msa.jaxws.
LimitExceededExceptionBean
setMessage(String)
- Method in class compbio.data.msa.jaxws.
ResultNotAvailableExceptionBean
setMessage(String)
- Method in class compbio.data.msa.jaxws.
UnsupportedRuntimeExceptionBean
setMessage(String)
- Method in class compbio.data.msa.jaxws.
WrongParameterExceptionBean
setMin(String)
- Method in class compbio.metadata.
ValueConstrain
setName(String)
- Method in class compbio.metadata.
Option
setName(String)
- Method in class compbio.metadata.
Preset
setName(String)
- Method in class compbio.runner.
_SkeletalCommandBuilder
setNCore(int)
- Method in class compbio.runner.msa.
Tcoffee
setNumberOfSequencesAllowed(int)
- Method in class compbio.data.msa.jaxws.
LimitExceededExceptionBean
setOptionName(String)
- Method in class compbio.metadata.
Parameter
setOptionNames(Set<String>)
- Method in class compbio.metadata.
Option
setOptionNames(Set<String>)
- Method in class compbio.metadata.
Parameter
setOptions(List<Option>)
- Method in class compbio.data.msa.jaxws.
CustomAlign
setOptions(List<String>)
- Method in class compbio.metadata.
Preset
setOptions(List<Option<T>>)
- Method in class compbio.metadata.
RunnerConfig
setOutput(String)
- Method in class compbio.engine.client.
RunConfiguration
setOutput(String)
- Method in class compbio.engine.client.
SkeletalExecutable
setOutput(String)
- Method in class compbio.runner.msa.
ClustalW
setOutput(String)
- Method in class compbio.runner.msa.
Muscle
setParam(String)
- Method in class compbio.engine.client.
CommandBuilder
setParam(String, String)
- Method in class compbio.engine.client.
CommandBuilder
setParameter(String)
- Method in class compbio.engine.client.
SkeletalExecutable
setParameters(CommandBuilder<?>)
- Method in class compbio.engine.client.
RunConfiguration
setParameters(List<Parameter<T>>)
- Method in class compbio.metadata.
RunnerConfig
setParams(List<String>)
- Method in class compbio.engine.client.
CommandBuilder
setPosition(long)
- Method in class compbio.data.msa.jaxws.
PullExecStatistics
setPosition(long)
- Method in class compbio.data.msa.jaxws.
PullFile
setPossibleValues(Set<String>)
- Method in class compbio.metadata.
Parameter
setPreset(Preset)
- Method in class compbio.data.msa.jaxws.
PresetAlign
setPresetName(String)
- Method in class compbio.data.msa.jaxws.
GetLimit
setPresets(List<Preset<T>>)
- Method in class compbio.metadata.
PresetManager
setPrmSeparator(String)
- Method in class compbio.metadata.
RunnerConfig
setQueue(String)
- Method in class compbio.runner.
_NativeSpecHelper
setRequired(boolean)
- Method in class compbio.metadata.
Option
setRequiredMemory(int)
- Method in class compbio.runner.
_NativeSpecHelper
setReturn(String)
- Method in class compbio.data.msa.jaxws.
AlignResponse
setReturn(boolean)
- Method in class compbio.data.msa.jaxws.
CancelJobResponse
setReturn(String)
- Method in class compbio.data.msa.jaxws.
CustomAlignResponse
setReturn(JobStatus)
- Method in class compbio.data.msa.jaxws.
GetJobStatusResponse
setReturn(Limit)
- Method in class compbio.data.msa.jaxws.
GetLimitResponse
setReturn(LimitsManager)
- Method in class compbio.data.msa.jaxws.
GetLimitsResponse
setReturn(PresetManager)
- Method in class compbio.data.msa.jaxws.
GetPresetsResponse
setReturn(byte)
- Method in class compbio.data.msa.jaxws.
GetProgressResponse
setReturn(Alignment)
- Method in class compbio.data.msa.jaxws.
GetResultResponse
setReturn(RunnerConfig)
- Method in class compbio.data.msa.jaxws.
GetRunnerOptionsResponse
setReturn(String)
- Method in class compbio.data.msa.jaxws.
PresetAlignResponse
setReturn(ChunkHolder)
- Method in class compbio.data.msa.jaxws.
PullExecStatisticsResponse
setReturn(ChunkHolder)
- Method in class compbio.data.msa.jaxws.
PullFileResponse
setRunnerClassName(String)
- Method in class compbio.metadata.
PresetManager
setRunnerClassName(String)
- Method in class compbio.metadata.
RunnerConfig
setSequenceLenghtActual(int)
- Method in class compbio.data.msa.jaxws.
LimitExceededExceptionBean
setSequenceLenghtAllowed(int)
- Method in class compbio.data.msa.jaxws.
LimitExceededExceptionBean
setType(ValueConstrain.Type)
- Method in class compbio.metadata.
ValueConstrain
setValidValue(ValueConstrain)
- Method in class compbio.metadata.
Parameter
setValue(String)
- Method in interface compbio.metadata.
Argument
Set default values for the parameter or an option
setValue(String)
- Method in class compbio.metadata.
Option
setWorkDirectory(String)
- Method in class compbio.engine.client.
ConfExecutable
setWorkDirectory(String)
- Method in interface compbio.engine.client.
ConfiguredExecutable
SHORT_TIME_LIMIT
- Static variable in class compbio.engine.cluster.dundee.
_QueueConstraints
shutdown()
- Method in class compbio.engine.local.
_TrackingExecutor
shutDown()
- Static method in class compbio.engine.local.
LocalExecutorService
This stops all executing processes via interruption.
shutdownNow()
- Method in class compbio.engine.local.
_TrackingExecutor
SimpleWSPublisher
- Class in
compbio.ws.server
This class publish a web service.
SimpleWSPublisher(Object, String)
- Constructor for class compbio.ws.server.
SimpleWSPublisher
size()
- Method in class compbio.engine.client.
CommandBuilder
SkeletalExecutable
<
T
> - Class in
compbio.engine.client
SkeletalExecutable()
- Constructor for class compbio.engine.client.
SkeletalExecutable
SkeletalExecutable(String)
- Constructor for class compbio.engine.client.
SkeletalExecutable
SPACE
- Static variable in class compbio.runner.
Util
StatisticManager
- Class in
compbio.engine.cluster.drmaa
StatisticManager(JobInfo)
- Constructor for class compbio.engine.cluster.drmaa.
StatisticManager
StreamGobbler
- Class in
compbio.engine.local
SubmissionManager
- Class in
compbio.engine
Submit jobs for execution
submit(Callable<T>)
- Method in class compbio.engine.local.
_TrackingExecutor
submitJob(ConfiguredExecutable<?>)
- Method in interface compbio.engine.
AsyncExecutor
Submits job for the execution Immediate execution is not guaranteed, this method puts the job in the queue.
submitJob(ConfiguredExecutable<?>)
- Method in class compbio.engine.cluster.drmaa.
AsyncJobRunner
submitJob(ConfiguredExecutable<?>)
- Method in class compbio.engine.local.
AsyncLocalRunner
SyncExecutor
- Interface in
compbio.engine
Synchronous executor, is an engine to run the Executable synchronously.
Overview
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