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