- gapchar - Variable in class compbio.data.sequence.AlignmentMetadata
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- gapchar - Static variable in class compbio.data.sequence.ClustalAlignmentUtil
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Dash char to be used as gap char in the alignments
- getActualNumberofSequences() - Method in exception compbio.metadata.LimitExceededException
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- getAnnotationForSequence(String) - Method in class compbio.data.sequence.ScoreManager
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- getArgument(RunnerConfig<T>, String) - Method in class compbio.metadata.PresetManager
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- getArgument(String) - Method in class compbio.metadata.RunnerConfig
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Returns the argument by its name if found, NULL otherwise.
- getArgumentByOptionName(String) - Method in class compbio.metadata.RunnerConfig
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Returns the argument by option name, NULL if the argument is not found
- getArguments(RunnerConfig<T>) - Method in class compbio.metadata.Preset
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Converts list of options as String to type Option
- getArguments() - Method in class compbio.metadata.RunnerConfig
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- getAvgSeqLength() - Method in class compbio.metadata.Limit
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- getAvgSequenceLength(List<FastaSequence>) - Static method in class compbio.metadata.Limit
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Calculates an average sequence length of the dataset
- getBasicURL() - Method in class compbio.metadata.Option
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- getChunk() - Method in class compbio.metadata.ChunkHolder
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- getData() - Method in class compbio.data.sequence.RNAStructScoreManager
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- getDefaultLimit() - Method in class compbio.metadata.LimitsManager
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- getDefaultValue() - Method in interface compbio.metadata.Argument
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- getDefaultValue() - Method in class compbio.metadata.Option
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A default value of the option.
- getDescription() - Method in interface compbio.metadata.Argument
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- getDescription() - Method in class compbio.metadata.Option
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A long description of the Option
- getDescription() - Method in class compbio.metadata.Preset
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- getFormatedSequence(int) - Method in class compbio.data.sequence.FastaSequence
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Format sequence per width letter in one string.
- getFormattedFasta() - Method in class compbio.data.sequence.FastaSequence
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- getFurtherDetails() - Method in interface compbio.metadata.Argument
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- getFurtherDetails() - Method in class compbio.metadata.Option
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The URL where further details about the option can be found
- getGapchar() - Method in class compbio.data.sequence.AlignmentMetadata
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- getId() - Method in class compbio.data.sequence.FastaSequence
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Gets the value of id
- getLength() - Method in class compbio.data.sequence.FastaSequence
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- getLimitByName(String) - Method in class compbio.metadata.LimitsManager
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- getLimits() - Method in class compbio.metadata.LimitsManager
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- getMax() - Method in class compbio.metadata.ValueConstrain
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- getMetadata() - Method in class compbio.data.sequence.Alignment
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- getMethod(String) - Static method in enum compbio.data.sequence.ConservationMethod
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- getMethod() - Method in class compbio.data.sequence.Score
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Returns the ConservationMethod
- getMin() - Method in class compbio.metadata.ValueConstrain
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- getName() - Method in interface compbio.metadata.Argument
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- getName() - Method in class compbio.metadata.Option
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Human readable name of the option
- getName() - Method in class compbio.metadata.Preset
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- getName(String) - Method in class compbio.metadata.Preset
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- getNextPosition() - Method in class compbio.metadata.ChunkHolder
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- getNumberOfScores() - Method in class compbio.data.sequence.ScoreManager.ScoreHolder
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- getNumberOfSeq() - Method in class compbio.data.sequence.ScoreManager
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- getNumberOfSequencesAllowed() - Method in exception compbio.metadata.LimitExceededException
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- getOnelineFasta() - Method in class compbio.data.sequence.FastaSequence
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- getOptionName() - Method in class compbio.metadata.Parameter
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- getOptionNames() - Method in class compbio.metadata.Option
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- getOptions() - Method in class compbio.metadata.Preset
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- getOptions() - Method in class compbio.metadata.RunnerConfig
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Returns the list of the Options supported by the executable of type T
- getParameters() - Method in class compbio.metadata.RunnerConfig
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Returns the list of parameters supported executable of type T.
- getPossibleValues() - Method in interface compbio.metadata.Argument
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- getPossibleValues() - Method in class compbio.metadata.Option
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List of possible optionNames
- getPossibleValues() - Method in class compbio.metadata.Parameter
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List is more convenient to work with
- getPreset() - Method in class compbio.metadata.Limit
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- getPresetByName(String) - Method in class compbio.metadata.PresetManager
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- getPresets() - Method in class compbio.metadata.PresetManager
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- getPrmSeparator() - Method in class compbio.metadata.RunnerConfig
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- getProgram() - Method in class compbio.data.sequence.AlignmentMetadata
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- getRanges() - Method in class compbio.data.sequence.Score
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Return Ranges if any Collections.EMPTY_SET otherwise
- getRunnerClassName() - Method in class compbio.metadata.PresetManager
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- getRunnerClassName() - Method in class compbio.metadata.RunnerConfig
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- getScoreByMethod(Enum<?>) - Method in class compbio.data.sequence.ScoreManager.ScoreHolder
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- getScoreByMethod(String) - Method in class compbio.data.sequence.ScoreManager.ScoreHolder
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- getScores() - Method in class compbio.data.sequence.Score
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The column scores for the alignment
- getSeqNumber() - Method in class compbio.metadata.Limit
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- getSequence() - Method in class compbio.data.sequence.FastaSequence
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Gets the value of sequence
- getSequenceLenghtActual() - Method in exception compbio.metadata.LimitExceededException
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- getSequenceLenghtAllowed() - Method in exception compbio.metadata.LimitExceededException
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- getSequences() - Method in class compbio.data.sequence.Alignment
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- getSize() - Method in class compbio.data.sequence.Alignment
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- getSMERFSColumnScore(String) - Static method in enum compbio.data.sequence.SMERFSConstraints
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- getStructs() - Method in class compbio.data.sequence.RNAStructScoreManager
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- getType(File) - Static method in enum compbio.data.sequence.IUPredResult
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- getType() - Method in class compbio.metadata.ValueConstrain
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- getValidValue() - Method in class compbio.metadata.Parameter
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- getValue() - Method in class compbio.metadata.Parameter
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- getValue(String) - Method in class compbio.metadata.Preset
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- GlobProtResult - Enum in compbio.data.sequence
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- GlobProtResult() - Constructor for enum compbio.data.sequence.GlobProtResult
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