Uses of Class
org.biojava.nbio.alignment.template.AbstractScorer

Packages that use AbstractScorer

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

Uses of AbstractScorer in org.biojava.nbio.alignment

Subclasses of AbstractScorer in org.biojava.nbio.alignment

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 AbstractScorer in org.biojava.nbio.alignment.routines

Subclasses of AbstractScorer in org.biojava.nbio.alignment.routines

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 AbstractScorer in org.biojava.nbio.alignment.template

Subclasses of AbstractScorer in org.biojava.nbio.alignment.template

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.