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

Packages that use Alignments.PairwiseSequenceAlignerType

Package	Description
org.biojava.nbio.alignment
org.biojava.nbio.structure.cluster

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(java.lang.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 Sequence<C>,C extends Compound> java.util.List<SequencePair<S,C>>	Alignments.getAllPairsAlignments(java.util.List<S> sequences, Alignments.PairwiseSequenceAlignerType type, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix)	Factory method which computes a sequence alignment for all Sequence pairs in the given List.
static <S extends Sequence<C>,C extends Compound> PairwiseSequenceAligner<S,C>	Alignments.getPairwiseAligner(S query, S target, Alignments.PairwiseSequenceAlignerType type, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix)	Factory method which constructs a pairwise sequence aligner.
static <S extends Sequence<C>,C extends Compound> SequencePair<S,C>	Alignments.getPairwiseAlignment(S query, S target, Alignments.PairwiseSequenceAlignerType type, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix)	Factory method which computes a sequence alignment for the given Sequence pair.

Uses of Alignments.PairwiseSequenceAlignerType in org.biojava.nbio.structure.cluster

Methods in org.biojava.nbio.structure.cluster with parameters of type Alignments.PairwiseSequenceAlignerType

Modifier and Type	Method	Description
boolean	SubunitCluster.mergeSequence(SubunitCluster other, SubunitClustererParameters params, Alignments.PairwiseSequenceAlignerType alignerType, GapPenalty gapPenalty, SubstitutionMatrix<AminoAcidCompound> subsMatrix)	Merges the other SubunitCluster into this one if their representatives sequences are similar (according to the criteria in params).