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

Packages that use Alignments.PairwiseSequenceAlignerType

Package	Description
org.biojava.nbio.alignment

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

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

Modifier and Type	Method	Description
static Alignments.PairwiseSequenceAlignerType	Alignments.PairwiseSequenceAlignerType.valueOf(String name)	Returns the enum constant of this type with the specified name.
static Alignments.PairwiseSequenceAlignerType[]	Alignments.PairwiseSequenceAlignerType.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.PairwiseSequenceAlignerType

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<org.biojava.nbio.core.alignment.template.SequencePair<S,C>>	Alignments.getAllPairsAlignments(List<S> sequences, Alignments.PairwiseSequenceAlignerType type, GapPenalty gapPenalty, org.biojava.nbio.core.alignment.template.SubstitutionMatrix<C> subMatrix)	Factory method which computes a sequence alignment 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> PairwiseSequenceAligner<S,C>	Alignments.getPairwiseAligner(S query, S target, Alignments.PairwiseSequenceAlignerType type, GapPenalty gapPenalty, org.biojava.nbio.core.alignment.template.SubstitutionMatrix<C> subMatrix)	Factory method which constructs a pairwise sequence aligner.
static <S extends org.biojava.nbio.core.sequence.template.Sequence<C>,C extends org.biojava.nbio.core.sequence.template.Compound> org.biojava.nbio.core.alignment.template.SequencePair<S,C>	Alignments.getPairwiseAlignment(S query, S target, Alignments.PairwiseSequenceAlignerType type, GapPenalty gapPenalty, org.biojava.nbio.core.alignment.template.SubstitutionMatrix<C> subMatrix)	Factory method which computes a sequence alignment for the given Sequence pair.