-S-Index -

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

-S

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
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 -: -
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 -: -
setFurtherDetails(URL) - -Method in class compbio.metadata.Option -: -
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 -: -
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 -: -
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 -
setParameters(List<Parameter<T>>) - -Method in class compbio.metadata.RunnerConfig -: Sets the list of parameters as internal list -
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 -
setRanges(TreeSet<Range>) - -Method in class compbio.data.sequence.Score -: -
setRequired(boolean) - -Method in class compbio.metadata.Option -: -
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 -: -
SINGLE_ENTRY_KEY - -Static variable in class compbio.data.sequence.ScoreManager -: -
SMERFSConstraints - Enum in compbio.data.sequence: Enumeration defining two constraints for SMERFS columns score calculation.