Package org.biojava3.alignment

Class Summary

Class	Description
Alignments	Static utility to easily run alignment routines.
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.
FractionalIdentityScorer<S extends Sequence<C>,C extends Compound>	Implements an algorithm which computes a score for a sequence alignment pair.
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.
FractionalSimilarityScorer<S extends Sequence<C>,C extends Compound>	Implements an algorithm which computes a score for a sequence alignment pair.
GuideTree<S extends Sequence<C>,C extends Compound>	Implements a data structure for a guide tree used during progressive multiple sequence alignment.
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).
SimpleAlignedSequence<S extends Sequence<C>,C extends Compound>	Implements a data structure for a Sequence within an alignment.
SimpleGapPenalty	Implements a data structure for the gap penalties used during a sequence alignment routine.
SimpleProfile<S extends Sequence<C>,C extends Compound>	Implements a data structure for the results of sequence alignment.
SimpleProfilePair<S extends Sequence<C>,C extends Compound>	Implements a data structure for the results of the alignment of a pair of Profiles.
SimpleProfileProfileAligner<S extends Sequence<C>,C extends Compound>	Implements a simple (naive) Aligner for a pair of Profiles.
SimpleSequencePair<S extends Sequence<C>,C extends Compound>	Implements a data structure for the results of pairwise sequence alignment.
SimpleSubstitutionMatrix<C extends Compound>	Implements a data structure which holds the score (penalty or bonus) given during alignment for the exchange of one Compound in a sequence for another.
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).
StandardRescoreRefiner<S extends Sequence<C>,C extends Compound>
SubstitutionMatrixHelper	Static utility to access substitution matrices that come bundled with BioJava.

Enum Summary

Enum	Description
Alignments.PairInProfileScorerType	List of implemented sequence pair in a profile scoring routines.
Alignments.PairwiseSequenceAlignerType	List of implemented pairwise sequence alignment routines.
Alignments.PairwiseSequenceScorerType	List of implemented pairwise sequence scoring routines.
Alignments.ProfileProfileAlignerType	List of implemented profile-profile alignment routines.
Alignments.RefinerType	List of implemented profile refinement routines.