- AA - Static variable in class compbio.data.sequence.SequenceUtil
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Valid Amino acids
- actualNumberofSequences - Variable in exception compbio.metadata.LimitExceededException
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- addOption(Option<T>) - Method in class compbio.metadata.RunnerConfig
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Adds Option to the internal list of options
- addOptionNames(String...) - Method in class compbio.metadata.Option
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Adds an option to the optionName list
- addOptionNames(String...) - Method in class compbio.metadata.Parameter
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- addParameter(Parameter<T>) - Method in class compbio.metadata.RunnerConfig
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Adds parameter to the internal parameter list
- addPossibleValues(String...) - Method in class compbio.metadata.Parameter
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- AlifoldLine(String) - Constructor for enum compbio.data.sequence.RNAStructReader.AlifoldLine
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- AlifoldResult() - Constructor for enum compbio.data.sequence.RNAStructReader.AlifoldResult
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- Alignment - Class in compbio.data.sequence
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Multiple sequence alignment.
- Alignment() - Constructor for class compbio.data.sequence.Alignment
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- Alignment(List<FastaSequence>, Program, char) - Constructor for class compbio.data.sequence.Alignment
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- Alignment(List<FastaSequence>, AlignmentMetadata) - Constructor for class compbio.data.sequence.Alignment
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- AlignmentMetadata - Class in compbio.data.sequence
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Alignment metadata e.g.
- AlignmentMetadata() - Constructor for class compbio.data.sequence.AlignmentMetadata
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- AlignmentMetadata(Program, char) - Constructor for class compbio.data.sequence.AlignmentMetadata
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- alignmentP - Static variable in class compbio.data.sequence.RNAStructReader
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- AMBIGUOUS_AA - Static variable in class compbio.data.sequence.SequenceUtil
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Same as AA pattern but with two additional letters - XU
- AMBIGUOUS_NUCLEOTIDE - Static variable in class compbio.data.sequence.SequenceUtil
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Ambiguous nucleotide
- Argument<T> - Interface in compbio.metadata
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An unmodifiable view for the options and parameters, with one exception - it
allows to set a value
- arguments - Variable in class compbio.metadata.RunnerConfig
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- aSequenceLenghtActual - Variable in exception compbio.metadata.LimitExceededException
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- aSequenceLenghtAllowed - Variable in exception compbio.metadata.LimitExceededException
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- asMap() - Method in class compbio.data.sequence.ScoreManager
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- asSet() - Method in class compbio.data.sequence.ScoreManager
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