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

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.