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

Score - Class in compbio.data.sequence

A value class for AACon annotation results storage.

Score(Enum<?>, ArrayList<Float>) - Constructor for class compbio.data.sequence.Score

Instantiate the Score

Score(Enum<?>, ArrayList<Float>, TreeSet<Range>) - Constructor for class compbio.data.sequence.Score

Score(Enum<?>, TreeSet<Range>) - Constructor for class compbio.data.sequence.Score

Score(Enum<?>, float[]) - Constructor for class compbio.data.sequence.Score

ScoreManager - Class in compbio.data.sequence

ScoreManager.ScoreHolder - Class in compbio.data.sequence

scores - Variable in class compbio.data.sequence.ScoreManager.ScoreHolder

SequenceAnnotation<T> - Interface in compbio.data.msa

Interface for tools that results to one or more annotation to sequence(s) Single, multiple sequences their groups or alignments can be annotated

SequenceAnnotationService<T> - Class in compbio.ws.server

Common methods for all SequenceAnnotation web services

SequenceUtil - Class in compbio.data.sequence

Utility class for operations on sequences

SERVICE_NAMESPACE - Static variable in interface compbio.data.msa.JABAService

Services - Enum in compbio.ws.client

List of web services currently supported by JABAWS version 2

ServiceStatus - Class in compbio.stat.servlet

Use cases: Test web services and display results on the web page

ServiceStatus() - Constructor for class compbio.stat.servlet.ServiceStatus

ServicesUtil - Class in compbio.ws.client

ServicesUtil() - Constructor for class compbio.ws.client.ServicesUtil

ServiceTestResult - Class in compbio.stat.servlet

Value class for test results.

ServiceTestResult(Services) - Constructor for class compbio.stat.servlet.ServiceTestResult

setActualNumberofSequences(int) - Method in class compbio.data.msa.jaxws.LimitExceededExceptionBean

setArg0(Services) - Method in class compbio.data.msa.jaxws.GetLastTested

setArg0(Services) - Method in class compbio.data.msa.jaxws.GetLastTestedOn

setArg0(Services) - Method in class compbio.data.msa.jaxws.GetServiceDescription

setArg0(Services) - Method in class compbio.data.msa.jaxws.IsOperating

setArg0(Services) - Method in class compbio.data.msa.jaxws.TestService

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

Deprecated.

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

SetExecutableFlag - Class in compbio.ws.server

Run setexecflag.sh script if executable flag is not set

SetExecutableFlag() - Constructor for class compbio.ws.server.SetExecutableFlag

setFastaSequences(List<FastaSequence>) - Method in class compbio.data.msa.jaxws.Align

setFastaSequences(List<FastaSequence>) - Method in class compbio.data.msa.jaxws.Analize

setFastaSequences(List<FastaSequence>) - Method in class compbio.data.msa.jaxws.CustomAlign

setFastaSequences(List<FastaSequence>) - Method in class compbio.data.msa.jaxws.CustomAnalize

setFastaSequences(List<FastaSequence>) - Method in class compbio.data.msa.jaxws.PresetAlign

setFastaSequences(List<FastaSequence>) - Method in class compbio.data.msa.jaxws.PresetAnalize

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.conservation.AACon

setInput(String) - Method in class compbio.runner.disorder.Disembl

setInput(String) - Method in class compbio.runner.disorder.GlobPlot

setInput(String) - Method in class compbio.runner.disorder.IUPred

setInput(String) - Method in class compbio.runner.disorder.Jronn

setInput(String) - Method in class compbio.runner.msa.ClustalO

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.GetAnnotation

setJobId(String) - Method in class compbio.data.msa.jaxws.GetJobStatus

setJobId(String) - Method in class compbio.data.msa.jaxws.GetResult

setJobId(String) - Method in class compbio.data.msa.jaxws.PullExecStatistics

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.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

Deprecated.

setNCore(int) - Method in class compbio.runner.conservation.AACon

setNCore(int) - Method in class compbio.runner.disorder.Jronn

setNCore(int) - Method in class compbio.runner.msa.ClustalO

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<Option>) - Method in class compbio.data.msa.jaxws.CustomAnalize

setOptions(List<String>) - Method in class compbio.metadata.Preset

setOptions(List<Option<T>>) - Method in class compbio.metadata.RunnerConfig

Adds the list of options or parameters to the internal list of options

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.conservation.AACon

setOutput(String) - Method in class compbio.runner.disorder.IUPred

setOutput(String) - Method in class compbio.runner.disorder.Jronn

setOutput(String) - Method in class compbio.runner.msa.ClustalO

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

Sets the list of parameters as internal list

setParams(List<String>) - Method in class compbio.engine.client.CommandBuilder

setPosition(long) - Method in class compbio.data.msa.jaxws.PullExecStatistics

setPossibleValues(Set<String>) - Method in class compbio.metadata.Parameter

setPreset(Preset) - Method in class compbio.data.msa.jaxws.PresetAlign

setPreset(Preset) - Method in class compbio.data.msa.jaxws.PresetAnalize

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

Sets name value separator character

setQueue(String) - Method in class compbio.runner._NativeSpecHelper

Deprecated.

setRanges(TreeSet<Range>) - Method in class compbio.data.sequence.Score

setRequired(boolean) - Method in class compbio.metadata.Option

setRequiredMemory(int) - Method in class compbio.runner._NativeSpecHelper

Deprecated.

setReturn(String) - Method in class compbio.data.msa.jaxws.AlignResponse

setReturn(String) - Method in class compbio.data.msa.jaxws.AnalizeResponse

setReturn(boolean) - Method in class compbio.data.msa.jaxws.CancelJobResponse

setReturn(String) - Method in class compbio.data.msa.jaxws.CustomAlignResponse

setReturn(String) - Method in class compbio.data.msa.jaxws.CustomAnalizeResponse

setReturn(ScoreManager) - Method in class compbio.data.msa.jaxws.GetAnnotationResponse

setReturn(JobStatus) - Method in class compbio.data.msa.jaxws.GetJobStatusResponse

setReturn(Date) - Method in class compbio.data.msa.jaxws.GetLastTestedOnResponse

setReturn(int) - Method in class compbio.data.msa.jaxws.GetLastTestedResponse

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(Alignment) - Method in class compbio.data.msa.jaxws.GetResultResponse

setReturn(RunnerConfig) - Method in class compbio.data.msa.jaxws.GetRunnerOptionsResponse

setReturn(Set<Category>) - Method in class compbio.data.msa.jaxws.GetServiceCategoriesResponse

setReturn(String) - Method in class compbio.data.msa.jaxws.GetServiceDescriptionResponse

setReturn(Set<Services>) - Method in class compbio.data.msa.jaxws.GetSupportedServicesResponse

setReturn(boolean) - Method in class compbio.data.msa.jaxws.IsOperatingResponse

setReturn(String) - Method in class compbio.data.msa.jaxws.PresetAlignResponse

setReturn(String) - Method in class compbio.data.msa.jaxws.PresetAnalizeResponse

setReturn(ChunkHolder) - Method in class compbio.data.msa.jaxws.PullExecStatisticsResponse

setReturn(String) - Method in class compbio.data.msa.jaxws.TestAllServicesResponse

setReturn(String) - Method in class compbio.data.msa.jaxws.TestServiceResponse

setRunnerClassName(String) - Method in class compbio.metadata.PresetManager

setRunnerClassName(String) - Method in class compbio.metadata.RunnerConfig

Set the name of a runner class

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

shutDown() - Static method in class compbio.engine.local.LocalExecutorService

This stops all executing processes via interruption.

shutdownDBServer() - Static method in class compbio.stat.collector.StatDB

ShutdownEngines - Class in compbio.ws.server

Switch off engines if JABAWS web application is undeployed, or web server is shutdown

ShutdownEngines() - Constructor for class compbio.ws.server.ShutdownEngines

shutdownService() - Static method in class compbio.engine.local.ExecutableWrapper

Stops internal executor service which captures streams of native executables.

SimpleWSPublisher - Class in compbio.ws.server

Deprecated.

SimpleWSPublisher(Object, String) - Constructor for class compbio.ws.server.SimpleWSPublisher

Deprecated.

SINGLE_ENTRY_KEY - Static variable in class compbio.data.sequence.ScoreManager

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

SMERFSConstraints - Enum in compbio.data.sequence

Enumeration defining two constraints for SMERFS columns score calculation.

sortByResultSize() - Method in class compbio.stat.collector.StatProcessor

sortByRuntime() - Method in class compbio.stat.collector.StatProcessor

sortByStartTime() - Method in class compbio.stat.collector.StatProcessor

SPACE - Static variable in class compbio.runner.Util

STAT_FILE - Static variable in class compbio.runner.conservation.AACon

STAT_FILE - Static variable in class compbio.runner.disorder.Jronn

StatCollection - Class in compbio.stat.servlet.util

StatCollection() - Constructor for class compbio.stat.servlet.util.StatCollection

StatCollection.Stattype - Enum in compbio.stat.servlet.util

Total number of requests incomplete abandoned cancelled

StatDB - Class in compbio.stat.collector

The database must be stored in the application root directory and called "ExecutionStatistic"

StatDB() - Constructor for class compbio.stat.collector.StatDB

StatisticCollector - Class in compbio.stat.servlet

StatisticCollector() - Constructor for class compbio.stat.servlet.StatisticCollector

StatisticManager - Class in compbio.engine.cluster.drmaa

StatisticManager(JobInfo) - Constructor for class compbio.engine.cluster.drmaa.StatisticManager

StatProcessor - Class in compbio.stat.collector

StatProcessor(List<JobStat>) - Constructor for class compbio.stat.collector.StatProcessor

StreamGobbler - Class in compbio.engine.local

SubmissionManager - Class in compbio.engine

Submit jobs for execution

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

sumOfTotals(Map<Date, Totals>) - Static method in class compbio.stat.servlet.util.Totals

sumStats(Map<Services, StatProcessor>) - Static method in class compbio.stat.servlet.util.Totals

SyncExecutor - Interface in compbio.engine

Synchronous executor, is an engine to run the Executable synchronously.