Interface Summary |
AlignedSequence<S extends Sequence<C>,C extends Compound> |
Defines a data structure for a Sequence within an alignment. |
Aligner<S extends Sequence<C>,C extends Compound> |
Defines an algorithm which computes an alignment Profile from a list of Sequence s. |
GapPenalty |
Defines a data structure for the gap penalties used during a sequence alignment routine. |
GuideTreeNode<S extends Sequence<C>,C extends Compound> |
Defines a data structure for the node in a guide tree used during progressive multiple sequence alignment. |
HierarchicalClusterer<S extends Sequence<C>,C extends Compound> |
Defines a clustering algorithm that converts a distance matrix into a tree. |
MatrixAligner<S extends Sequence<C>,C extends Compound> |
Defines an Aligner which builds a score matrix during computation. |
MutableAlignedSequence<S extends Sequence<C>,C extends Compound> |
Defines a mutable (editable) data structure for an AlignedSequence . |
MutableProfile<S extends Sequence<C>,C extends Compound> |
Defines a mutable (editable) data structure for a Profile . |
MutableProfilePair<S extends Sequence<C>,C extends Compound> |
Defines a mutable (editable) data structure for a ProfilePair . |
MutableSequencePair<S extends Sequence<C>,C extends Compound> |
Defines a mutable (editable) data structure for the results of pairwise sequence alignment. |
PairInProfileScorer<S extends Sequence<C>,C extends Compound> |
Defines an algorithm which computes a score for a sequence alignment pair picked from an alignment Profile . |
PairwiseSequenceAligner<S extends Sequence<C>,C extends Compound> |
Defines an Aligner for a pair of Sequence s. |
PairwiseSequenceScorer<S extends Sequence<C>,C extends Compound> |
Defines an algorithm which computes a score for a pair of sequences. |
PartitionRefiner<S extends Sequence<C>,C extends Compound> |
Defines an algorithm which computes a new alignment Profile by splitting a current alignment and realigning. |
Profile<S extends Sequence<C>,C extends Compound> |
Defines a data structure for the results of sequence alignment. |
ProfilePair<S extends Sequence<C>,C extends Compound> |
Defines a data structure for the results of the alignment of a pair of Profile s. |
ProfileProfileAligner<S extends Sequence<C>,C extends Compound> |
Defines an Aligner for a pair of Profile s. |
ProfileProfileScorer<S extends Sequence<C>,C extends Compound> |
Defines an algorithm which computes a score for a pairing of alignment profiles. |
ProfileView<S extends Sequence<C>,C extends Compound> |
Defines a data structure for a view of sequence alignment. |
RescoreRefiner<S extends Sequence<C>,C extends Compound> |
Defines an algorithm which computes a new alignment Profile by rescoring all pairs in an alignment and
realigning. |
Scorer |
Defines an algorithm which computes a score. |
SequencePair<S extends Sequence<C>,C extends Compound> |
Defines a data structure for the results of pairwise sequence alignment. |
SubstitutionMatrix<C extends Compound> |
Defines a data structure which holds the score (penalty or bonus) given during alignment for the exchange of one
Compound in a sequence for another. |