A C D E F G H I J L M N O P R S T U V W

A

AA - Static variable in class compbio.data.sequence.SequenceUtil

Valid Amino acids

addOption(Option<T>) - Method in class compbio.metadata.RunnerConfig

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

addPossibleValues(String...) - Method in class compbio.metadata.Parameter

Alignment - Class in compbio.data.sequence

Multiple 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(Program, char) - Constructor for class compbio.data.sequence.AlignmentMetadata

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