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 and Description
static Alignments.PairwiseSequenceScorerType	Alignments.PairwiseSequenceScorerType.valueOf(java.lang.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 and Description
static <S extends Sequence<C>,C extends Compound> java.util.List<PairwiseSequenceScorer<S,C>>	Alignments.getAllPairsScorers(java.util.List<S> sequences, Alignments.PairwiseSequenceScorerType type, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix) Factory method which sets up a sequence pair scorer for all Sequence pairs in the given List.
static <S extends Sequence<C>,C extends Compound> double[]	Alignments.getAllPairsScores(java.util.List<S> sequences, Alignments.PairwiseSequenceScorerType type, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix) Factory method which computes a sequence pair score for all Sequence pairs in the given List.