Uses of Package
org.biojava.nbio.alignment.template

Packages that use org.biojava.nbio.alignment.template

Package	Description
org.biojava.nbio.alignment
org.biojava.nbio.alignment.routines
org.biojava.nbio.alignment.template
org.biojava.nbio.structure.cluster

Classes in org.biojava.nbio.alignment.template used by org.biojava.nbio.alignment

Class	Description
AbstractMatrixAligner	Implements common code for an Aligner which builds a score matrix during computation.
AbstractPairwiseSequenceAligner	Implements common code for an Aligner for a pair of Sequences.
AbstractProfileProfileAligner	Implements common code for an Aligner for a pair of Profiles.
AbstractScorer	Implements common code for algorithms which compute a score.
Aligner	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.
GapPenalty.Type	Defines the possible types of gap penalties.
GuideTreeNode	Defines a data structure for the node in a guide tree used during progressive multiple sequence alignment.
MatrixAligner	Defines an Aligner which builds a score matrix during computation.
PairInProfileScorer	Defines an algorithm which computes a score for a sequence alignment pair picked from an alignment Profile.
PairwiseSequenceAligner	Defines an Aligner for a pair of Sequences.
PairwiseSequenceScorer	Defines an algorithm which computes a score for a pair of sequences.
ProfileProfileAligner	Defines an Aligner for a pair of Profiles.
ProfileProfileScorer	Defines an algorithm which computes a score for a pairing of alignment profiles.
RescoreRefiner	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.

Classes in org.biojava.nbio.alignment.template used by org.biojava.nbio.alignment.routines

Class	Description
AbstractMatrixAligner	Implements common code for an Aligner which builds a score matrix during computation.
AbstractPairwiseSequenceAligner	Implements common code for an Aligner for a pair of Sequences.
AbstractScorer	Implements common code for algorithms which compute a score.
Aligner	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.
MatrixAligner	Defines an Aligner which builds a score matrix during computation.
PairwiseSequenceAligner	Defines an Aligner for a pair of Sequences.
PairwiseSequenceScorer	Defines an algorithm which computes a score for a pair of sequences.
Scorer	Defines an algorithm which computes a score.

Classes in org.biojava.nbio.alignment.template used by org.biojava.nbio.alignment.template

Class	Description
AbstractMatrixAligner	Implements common code for an Aligner which builds a score matrix during computation.
AbstractScorer	Implements common code for algorithms which compute a score.
Aligner	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.
GapPenalty.Type	Defines the possible types of gap penalties.
GuideTreeNode	Defines a data structure for the node in a guide tree used during progressive multiple sequence alignment.
MatrixAligner	Defines an Aligner which builds a score matrix during computation.
PairwiseSequenceAligner	Defines an Aligner for a pair of Sequences.
PairwiseSequenceScorer	Defines an algorithm which computes a score for a pair of sequences.
ProfileProfileAligner	Defines an Aligner for a pair of Profiles.
ProfileProfileScorer	Defines an algorithm which computes a score for a pairing of alignment profiles.
Scorer	Defines an algorithm which computes a score.

Classes in org.biojava.nbio.alignment.template used by org.biojava.nbio.structure.cluster

Class	Description
GapPenalty	Defines a data structure for the gap penalties used during a sequence alignment routine.