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> | |
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
Profile s. |
SimpleProfileProfileAligner<S extends Sequence<C>,C extends Compound> | |
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 | 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.
|