Uses of Interface
org.biojava.nbio.alignment.template.PairwiseSequenceAligner
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Packages that use PairwiseSequenceAligner Package Description org.biojava.nbio.alignment org.biojava.nbio.alignment.routines org.biojava.nbio.alignment.template -
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Uses of PairwiseSequenceAligner in org.biojava.nbio.alignment
Classes in org.biojava.nbio.alignment that implement PairwiseSequenceAligner Modifier and Type Class Description class
NeedlemanWunsch<S extends Sequence<C>,C extends Compound>
class
SmithWaterman<S extends Sequence<C>,C extends Compound>
Smith and Waterman defined an algorithm for pairwise local sequence alignments (best match of sections from eachSequence
).Methods in org.biojava.nbio.alignment that return PairwiseSequenceAligner Modifier and Type Method Description 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.Constructors in org.biojava.nbio.alignment with parameters of type PairwiseSequenceAligner Constructor Description FractionalIdentityScorer(PairwiseSequenceAligner<S,C> aligner)
Creates a fractional identity scorer for a pair of sequences aligned by the given pairwise sequence aligner.FractionalSimilarityScorer(PairwiseSequenceAligner<S,C> aligner)
Creates a fractional similarity scorer for a pair of sequences aligned by the given pairwise sequence aligner. -
Uses of PairwiseSequenceAligner in org.biojava.nbio.alignment.routines
Classes in org.biojava.nbio.alignment.routines that implement PairwiseSequenceAligner Modifier and Type Class Description class
AnchoredPairwiseSequenceAligner<S extends Sequence<C>,C extends Compound>
class
GuanUberbacher<S extends Sequence<C>,C extends Compound>
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Uses of PairwiseSequenceAligner in org.biojava.nbio.alignment.template
Classes in org.biojava.nbio.alignment.template that implement PairwiseSequenceAligner Modifier and Type Class Description class
AbstractPairwiseSequenceAligner<S extends Sequence<C>,C extends Compound>
Constructors in org.biojava.nbio.alignment.template with parameters of type PairwiseSequenceAligner Constructor Description CallablePairwiseSequenceAligner(PairwiseSequenceAligner<S,C> psa)
Creates a pairwise sequence alignment task for simplified parallel execution.
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