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.