Uses of Enum Class
org.biojava.nbio.alignment.Alignments.PairwiseSequenceAlignerType
Packages that use Alignments.PairwiseSequenceAlignerType
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Uses of Alignments.PairwiseSequenceAlignerType in org.biojava.nbio.alignment
Methods in org.biojava.nbio.alignment that return Alignments.PairwiseSequenceAlignerTypeModifier and TypeMethodDescriptionReturns the enum constant of this class with the specified name.Alignments.PairwiseSequenceAlignerType.values()
Returns an array containing the constants of this enum class, in the order they are declared.Methods in org.biojava.nbio.alignment with parameters of type Alignments.PairwiseSequenceAlignerTypeModifier and TypeMethodDescriptionstatic <S extends Sequence<C>,
C extends Compound>
List<SequencePair<S, C>> Alignments.getAllPairsAlignments
(List<S> sequences, Alignments.PairwiseSequenceAlignerType type, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix) 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 givenSequence
pair. -
Uses of Alignments.PairwiseSequenceAlignerType in org.biojava.nbio.structure.cluster
Methods in org.biojava.nbio.structure.cluster with parameters of type Alignments.PairwiseSequenceAlignerTypeModifier and TypeMethodDescriptionboolean
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).