-S-Index -

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=website%2Ffull_javadoc%2Findex-files%2Findex-18.html;fp=website%2Ffull_javadoc%2Findex-files%2Findex-18.html;h=0000000000000000000000000000000000000000;hb=0bbebf27d045b1345bc042bdf24ef2e6808df251;hp=813974dd403e5b36519e393de9508c5d24785164;hpb=5be600c3985aa7bcb8d8b51d77d773c76e6802bb;p=jabaws.git diff --git a/website/full_javadoc/index-files/index-18.html b/website/full_javadoc/index-files/index-18.html deleted file mode 100644 index 813974d..0000000 --- a/website/full_javadoc/index-files/index-18.html +++ /dev/null @@ -1,609 +0,0 @@ - - - - - - -S-Index - - - - - - - - - - - - -

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- - - -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
ServicesUtil - Class in compbio.ws.client
ServicesUtil() - -Constructor for class compbio.ws.client.ServicesUtil -: -
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.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 -: -
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<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.