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

addAnnotation(T, ArrayList<Float>) - Method in class compbio.data.sequence.MultiAnnotatedSequence

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

align(List<FastaSequence>) - Method in interface compbio.data.msa.MsaWS

Align a list of sequences with default settings.

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

analize(List<FastaSequence>) - Method in interface compbio.data.msa.Annotation

Analyse the sequences.

AnnotatedSequence - Class in compbio.data.sequence

AnnotatedSequence(String, String, float[]) - Constructor for class compbio.data.sequence.AnnotatedSequence

AnnotatedSequence(FastaSequence, float[]) - Constructor for class compbio.data.sequence.AnnotatedSequence

Annotation<T> - Interface in compbio.data.msa

Interface for tools that results to one or more annotation to sequence(s)

Argument<T> - Interface in compbio.metadata

An unmodifiable view for the options and parameters, with one exception - it allows to set a value