Package org.biojava.nbio.alignment.template

Interface Summary

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>	Defines an algorithm which computes an alignment Profile from a list of Sequences.
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 Sequences.
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 Profiles.
ProfileProfileAligner<S extends Sequence<C>,C extends Compound>	Defines an Aligner for a pair of Profiles.
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 Summary

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>	Implements common code for an Aligner for a pair of Sequences.
AbstractProfileProfileAligner<S extends Sequence<C>,C extends Compound>	Implements common code for an Aligner for a pair of Profiles.
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 Summary

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.