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

Packages that use Scorer

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

Uses of Scorer in org.biojava.nbio.alignment

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

Modifier and Type	Class	Description
class	FractionalIdentityInProfileScorer<S extends Sequence<C>,C extends Compound>	Implements an algorithm which computes a score for a sequence alignment pair picked from an alignment Profile.
class	FractionalIdentityScorer<S extends Sequence<C>,C extends Compound>	Implements an algorithm which computes a score for a sequence alignment pair.
class	FractionalSimilarityInProfileScorer<S extends Sequence<C>,C extends Compound>	Implements an algorithm which computes a score for a sequence alignment pair picked from an alignment Profile.
class	FractionalSimilarityScorer<S extends Sequence<C>,C extends Compound>	Implements an algorithm which computes a score for a sequence alignment pair.
class	NeedlemanWunsch<S extends Sequence<C>,C extends Compound>	Needleman and Wunsch defined an algorithm for pairwise global sequence alignments (from the first until the last Compound of each Sequence).
class	SimpleProfileProfileAligner<S extends Sequence<C>,C extends Compound>	Implements a simple (naive) Aligner for a pair of Profiles.
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 each Sequence).
class	StandardRescoreRefiner<S extends Sequence<C>,C extends Compound>
class	SubstitutionMatrixScorer<S extends Sequence<C>,C extends Compound>	Scores using a substitution matrix.

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

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

Modifier and Type	Class	Description
class	AnchoredPairwiseSequenceAligner<S extends Sequence<C>,C extends 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 Sequence<C>,C extends Compound>	Guan and Uberbacher defined an algorithm for pairwise global sequence alignments (from the first until the last Compound of each Sequence).

Uses of Scorer in org.biojava.nbio.alignment.template

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

Modifier and Type	Interface	Description
interface	Aligner<S extends Sequence<C>,C extends Compound>	Defines an algorithm which computes an alignment Profile from a list of Sequences.
interface	MatrixAligner<S extends Sequence<C>,C extends Compound>	Defines an Aligner which builds a score matrix during computation.
interface	PairInProfileScorer<S extends Sequence<C>,C extends Compound>	Defines an algorithm which computes a score for a sequence alignment pair picked from an alignment Profile.
interface	PairwiseSequenceAligner<S extends Sequence<C>,C extends Compound>	Defines an Aligner for a pair of Sequences.
interface	PairwiseSequenceScorer<S extends Sequence<C>,C extends Compound>	Defines an algorithm which computes a score for a pair of sequences.
interface	PartitionRefiner<S extends Sequence<C>,C extends Compound>	Defines an algorithm which computes a new alignment Profile by splitting a current alignment and realigning.
interface	ProfileProfileAligner<S extends Sequence<C>,C extends Compound>	Defines an Aligner for a pair of Profiles.
interface	ProfileProfileScorer<S extends Sequence<C>,C extends Compound>	Defines an algorithm which computes a score for a pairing of alignment profiles.
interface	RescoreRefiner<S extends Sequence<C>,C extends Compound>	Defines an algorithm which computes a new alignment Profile by rescoring all pairs in an alignment and realigning.

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

Modifier and Type	Class	Description
class	AbstractMatrixAligner<S extends Sequence<C>,C extends Compound>	Implements common code for an Aligner which builds a score matrix during computation.
class	AbstractPairwiseSequenceAligner<S extends Sequence<C>,C extends Compound>	Implements common code for an Aligner for a pair of Sequences.
class	AbstractProfileProfileAligner<S extends Sequence<C>,C extends Compound>	Implements common code for an Aligner for a pair of Profiles.
class	AbstractScorer	Implements common code for algorithms which compute a score.