Uses of Interface
org.biojava.nbio.alignment.template.PairwiseSequenceAligner

Packages that use PairwiseSequenceAligner

Package	Description
org.biojava.nbio.alignment
org.biojava.nbio.alignment.routines
org.biojava.nbio.alignment.template

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 org.biojava.nbio.core.sequence.template.Sequence<C>,C extends org.biojava.nbio.core.sequence.template.Compound>	Needleman and Wunsch defined an algorithm for pairwise global sequence alignments (from the first until the last Compound of each Sequence).
class	SmithWaterman<S extends org.biojava.nbio.core.sequence.template.Sequence<C>,C extends org.biojava.nbio.core.sequence.template.Compound>	Smith and Waterman defined an algorithm for pairwise local sequence alignments (best match of sections from each Sequence).

Methods in org.biojava.nbio.alignment that return PairwiseSequenceAligner

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> 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.

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 org.biojava.nbio.core.sequence.template.Sequence<C>,C extends org.biojava.nbio.core.sequence.template.Compound>	This algorithm uses a divide-and-conquer approach to find optimal pairwise global sequence alignments (from the first until the last Compound of each Sequence) with the restriction that any alignment produced will connect the query sequence to the target sequence at the anchors.
class	GuanUberbacher<S extends org.biojava.nbio.core.sequence.template.Sequence<C>,C extends org.biojava.nbio.core.sequence.template.Compound>	Guan and Uberbacher defined an algorithm for pairwise global sequence alignments (from the first until the last Compound of each Sequence).

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 org.biojava.nbio.core.sequence.template.Sequence<C>,C extends org.biojava.nbio.core.sequence.template.Compound>	Implements common code for an Aligner for a pair of Sequences.

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.