A B C D E F G H I J K L M N O P R S T U V W _

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.