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 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 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 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 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 org.biojava.nbio.core.sequence.template.Sequence<C>,C extends org.biojava.nbio.core.sequence.template.Compound>	Defines an algorithm which computes an alignment Profile from a list of Sequences.
interface	MatrixAligner<S extends org.biojava.nbio.core.sequence.template.Sequence<C>,C extends org.biojava.nbio.core.sequence.template.Compound>	Defines an Aligner which builds a score matrix during computation.
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.
interface	PairwiseSequenceScorer<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 pair of sequences.
interface	PartitionRefiner<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 new alignment Profile by splitting a current alignment and realigning.
interface	ProfileProfileAligner<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 Profiles.
interface	ProfileProfileScorer<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 pairing of alignment profiles.
interface	RescoreRefiner<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 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 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.
class	AbstractScorer	Implements common code for algorithms which compute a score.