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

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

setFurtherDetails(URL) - Method in class compbio.metadata.Option

setMax(String) - Method in class compbio.metadata.ValueConstrain

setMin(String) - Method in class compbio.metadata.ValueConstrain

setName(String) - Method in class compbio.metadata.Option

setName(String) - Method in class compbio.metadata.Preset

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<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

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

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

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

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

Set the name of a runner class

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.