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A

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