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

Packages that use PairwiseSequenceScorer

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

Uses of PairwiseSequenceScorer in org.biojava.nbio.alignment

Classes in org.biojava.nbio.alignment that implement PairwiseSequenceScorer

Modifier and Type	Class	Description
class	FractionalIdentityInProfileScorer<S extends org.biojava.nbio.core.sequence.template.Sequence<C>,C extends org.biojava.nbio.core.sequence.template.Compound>	Implements an algorithm which computes a score for a sequence alignment pair picked from an alignment Profile.
class	FractionalIdentityScorer<S extends org.biojava.nbio.core.sequence.template.Sequence<C>,C extends org.biojava.nbio.core.sequence.template.Compound>	Implements an algorithm which computes a score for a sequence alignment pair.
class	FractionalSimilarityInProfileScorer<S extends org.biojava.nbio.core.sequence.template.Sequence<C>,C extends org.biojava.nbio.core.sequence.template.Compound>	Implements an algorithm which computes a score for a sequence alignment pair picked from an alignment Profile.
class	FractionalSimilarityScorer<S extends org.biojava.nbio.core.sequence.template.Sequence<C>,C extends org.biojava.nbio.core.sequence.template.Compound>	Implements an algorithm which computes a score for a sequence alignment pair.
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).
class	SubstitutionMatrixScorer<S extends org.biojava.nbio.core.sequence.template.Sequence<C>,C extends org.biojava.nbio.core.sequence.template.Compound>	Scores using a substitution matrix.

Methods in org.biojava.nbio.alignment that return types with arguments of type PairwiseSequenceScorer

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<PairwiseSequenceScorer<S,C>>	Alignments.getAllPairsScorers(List<S> sequences, Alignments.PairwiseSequenceScorerType type, GapPenalty gapPenalty, org.biojava.nbio.core.alignment.template.SubstitutionMatrix<C> subMatrix)	Factory method which sets up a sequence pair scorer for all Sequence pairs in the given List.

Method parameters in org.biojava.nbio.alignment with type arguments of type PairwiseSequenceScorer

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> double[]	Alignments.runPairwiseScorers(List<PairwiseSequenceScorer<S,C>> scorers)	Factory method to run a list of scorers concurrently.

Uses of PairwiseSequenceScorer in org.biojava.nbio.alignment.routines

Classes in org.biojava.nbio.alignment.routines that implement PairwiseSequenceScorer

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 PairwiseSequenceScorer in org.biojava.nbio.alignment.template

Subinterfaces of PairwiseSequenceScorer in org.biojava.nbio.alignment.template

Modifier and Type	Interface	Description
interface	PairInProfileScorer<S extends org.biojava.nbio.core.sequence.template.Sequence<C>,C extends org.biojava.nbio.core.sequence.template.Compound>	Defines an algorithm which computes a score for a sequence alignment pair picked from an alignment Profile.
interface	PairwiseSequenceAligner<S extends org.biojava.nbio.core.sequence.template.Sequence<C>,C extends org.biojava.nbio.core.sequence.template.Compound>	Defines an Aligner for a pair of Sequences.

Classes in org.biojava.nbio.alignment.template that implement PairwiseSequenceScorer

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 PairwiseSequenceScorer

Constructor	Description
CallablePairwiseSequenceScorer(PairwiseSequenceScorer<S,C> pss)	Creates a pairwise sequence scoring task for simplified parallel execution.