+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.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 +: +
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<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 +: +
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.