- s - Static variable in class compbio.data.sequence.RNAStructReader
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- Score - Class in compbio.data.sequence
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A value class for AACon annotation results storage.
- Score() - Constructor for class compbio.data.sequence.Score
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- Score(Enum<?>, ArrayList<Float>) - Constructor for class compbio.data.sequence.Score
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Instantiate the Score
- Score(Enum<?>, ArrayList<Float>, TreeSet<Range>) - Constructor for class compbio.data.sequence.Score
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- Score(Enum<?>, TreeSet<Range>) - Constructor for class compbio.data.sequence.Score
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- Score(Enum<?>, float[]) - Constructor for class compbio.data.sequence.Score
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- ScoreHolder() - Constructor for class compbio.data.sequence.ScoreManager.ScoreHolder
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- ScoreHolder(String, Set<Score>) - Constructor for class compbio.data.sequence.ScoreManager.ScoreHolder
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- ScoreManager - Class in compbio.data.sequence
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- ScoreManager() - Constructor for class compbio.data.sequence.ScoreManager
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- ScoreManager(String, Set<Score>) - Constructor for class compbio.data.sequence.ScoreManager
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- ScoreManager(Map<String, Set<Score>>) - Constructor for class compbio.data.sequence.ScoreManager
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- ScoreManager.ScoreHolder - Class in compbio.data.sequence
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- scores - Variable in class compbio.data.sequence.Score
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- scores - Variable in class compbio.data.sequence.ScoreManager.ScoreHolder
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- seqLength - Variable in class compbio.metadata.Limit
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- seqNumber - Variable in class compbio.metadata.Limit
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- seqP - Static variable in class compbio.data.sequence.RNAStructReader
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- seqScores - Variable in class compbio.data.sequence.ScoreManager
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- sequence - Variable in class compbio.data.sequence.FastaSequence
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Returns the string representation of sequence
- sequences - Variable in class compbio.data.sequence.Alignment
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- SequenceUtil - Class in compbio.data.sequence
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Utility class for operations on sequences
- SequenceUtil() - Constructor for class compbio.data.sequence.SequenceUtil
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- serialVersionUID - Static variable in exception compbio.data.sequence.UnknownFileFormatException
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- serialVersionUID - Static variable in exception compbio.metadata.JobExecutionException
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Default stable serial for serialization
- serialVersionUID - Static variable in exception compbio.metadata.JobSubmissionException
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- serialVersionUID - Static variable in exception compbio.metadata.LimitExceededException
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- serialVersionUID - Static variable in exception compbio.metadata.ResultNotAvailableException
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Default stable serial for serialization
- serialVersionUID - Static variable in exception compbio.metadata.UnsupportedRuntimeException
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- serialVersionUID - Static variable in exception compbio.metadata.WrongParameterException
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Default stable serial for serialization
- setBasicURL(URL) - Method in class compbio.metadata.Option
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- setDefaultValue(String) - Method in class compbio.metadata.Option
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Sets one of the values defined in optionList as default.
- setDefaultValue(String) - Method in class compbio.metadata.Parameter
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- setDescription(String) - Method in class compbio.metadata.Option
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- setDescription(String) - Method in class compbio.metadata.Preset
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- setFurtherDetails(String) - Method in class compbio.metadata.Option
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- setMax(String) - Method in class compbio.metadata.ValueConstrain
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- setMin(String) - Method in class compbio.metadata.ValueConstrain
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- setName(String) - Method in class compbio.metadata.Option
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- setName(String) - Method in class compbio.metadata.Preset
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- setOptionName(String) - Method in class compbio.metadata.Parameter
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- setOptionNames(Set<String>) - Method in class compbio.metadata.Option
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- setOptionNames(Set<String>) - Method in class compbio.metadata.Parameter
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- setOptions(List<String>) - Method in class compbio.metadata.Preset
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- setOptions(List<Option<T>>) - Method in class compbio.metadata.RunnerConfig
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Adds the list of options or parameters to the internal list of options
- setParameters(List<Parameter<T>>) - Method in class compbio.metadata.RunnerConfig
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Sets the list of parameters as internal list
- setPossibleValues(Set<String>) - Method in class compbio.metadata.Parameter
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- setPresets(List<Preset<T>>) - Method in class compbio.metadata.PresetManager
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- setPrmSeparator(String) - Method in class compbio.metadata.RunnerConfig
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Sets name value separator character
- setRanges(TreeSet<Range>) - Method in class compbio.data.sequence.Score
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- setRequired(boolean) - Method in class compbio.metadata.Option
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- setRunnerClassName(String) - Method in class compbio.metadata.PresetManager
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- setRunnerClassName(String) - Method in class compbio.metadata.RunnerConfig
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Set the name of a runner class
- setType(ValueConstrain.Type) - Method in class compbio.metadata.ValueConstrain
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- setValidValue(ValueConstrain) - Method in class compbio.metadata.Parameter
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- setValue(String) - Method in interface compbio.metadata.Argument
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Set default values for the parameter or an option
- setValue(String) - Method in class compbio.metadata.Option
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- SINGLE_ENTRY_KEY - Static variable in class compbio.data.sequence.ScoreManager
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- SMERFSConstraints - Enum in compbio.data.sequence
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Enumeration defining two constraints for SMERFS columns score calculation.
- SMERFSConstraints() - Constructor for enum compbio.data.sequence.SMERFSConstraints
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- SPACE - Static variable in class compbio.metadata.Preset
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- spacer - Static variable in class compbio.data.sequence.ClustalAlignmentUtil
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- stochBTStructP - Static variable in class compbio.data.sequence.RNAStructReader
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- structP - Static variable in class compbio.data.sequence.RNAStructReader
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