Uses of Class
org.biojava.nbio.alignment.Alignments.PairwiseSequenceScorerType

Packages that use Alignments.PairwiseSequenceScorerType

Package	Description
org.biojava.nbio.alignment

Uses of Alignments.PairwiseSequenceScorerType in org.biojava.nbio.alignment

Methods in org.biojava.nbio.alignment that return Alignments.PairwiseSequenceScorerType

Modifier and Type	Method	Description
static Alignments.PairwiseSequenceScorerType	Alignments.PairwiseSequenceScorerType.valueOf(String name)	Returns the enum constant of this type with the specified name.
static Alignments.PairwiseSequenceScorerType[]	Alignments.PairwiseSequenceScorerType.values()	Returns an array containing the constants of this enum type, in the order they are declared.

Methods in org.biojava.nbio.alignment with parameters of type Alignments.PairwiseSequenceScorerType

Modifier and Type	Method	Description
static <S extends org.biojava.nbio.core.sequence.template.Sequence<C>,C extends org.biojava.nbio.core.sequence.template.Compound> List<PairwiseSequenceScorer<S,C>>	Alignments.getAllPairsScorers(List<S> sequences, Alignments.PairwiseSequenceScorerType type, GapPenalty gapPenalty, org.biojava.nbio.core.alignment.template.SubstitutionMatrix<C> subMatrix)	Factory method which sets up a sequence pair scorer for all Sequence pairs in the given List.
static <S extends org.biojava.nbio.core.sequence.template.Sequence<C>,C extends org.biojava.nbio.core.sequence.template.Compound> double[]	Alignments.getAllPairsScores(List<S> sequences, Alignments.PairwiseSequenceScorerType type, GapPenalty gapPenalty, org.biojava.nbio.core.alignment.template.SubstitutionMatrix<C> subMatrix)	Factory method which computes a sequence pair score for all Sequence pairs in the given List.