Interface | Description |
---|---|
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> | |
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> | |
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> | |
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. |
Class | Description |
---|---|
AbstractMatrixAligner<S extends Sequence<C>,C extends Compound> |
Implements common code for an
Aligner which builds a score matrix during computation. |
AbstractPairwiseSequenceAligner<S extends Sequence<C>,C extends Compound> | |
AbstractProfileProfileAligner<S extends Sequence<C>,C extends Compound> | |
AbstractScorer |
Implements common code for algorithms which compute a score.
|
CallablePairwiseSequenceAligner<S extends Sequence<C>,C extends Compound> |
Implements a concurrency wrapper for a
PairwiseSequenceAligner . |
CallablePairwiseSequenceScorer<S extends Sequence<C>,C extends Compound> |
Implements a concurrency wrapper for a
PairwiseSequenceScorer . |
CallableProfileProfileAligner<S extends Sequence<C>,C extends Compound> |
Implements a concurrency wrapper for a
ProfileProfileAligner . |
Enum | Description |
---|---|
AlignedSequence.Step |
Defines an alignment step in order to pass alignment information from an
Aligner to a constructor. |
GapPenalty.Type |
Defines the possible types of gap penalties.
|
Profile.StringFormat |
List of output formats.
|