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 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	SimpleProfileProfileAligner<S extends org.biojava.nbio.core.sequence.template.Sequence<C>,C extends org.biojava.nbio.core.sequence.template.Compound>	Implements a simple (naive) Aligner for a pair of Profiles.
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	StandardRescoreRefiner<S extends org.biojava.nbio.core.sequence.template.Sequence<C>,C extends org.biojava.nbio.core.sequence.template.Compound>
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.

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 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 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 org.biojava.nbio.core.sequence.template.Sequence<C>,C extends org.biojava.nbio.core.sequence.template.Compound>	Implements common code for an Aligner which builds a score matrix during computation.
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.
class	AbstractProfileProfileAligner<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 Profiles.