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.aaindex
org.biojava.nbio.alignment.routines
org.biojava.nbio.alignment.template

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.
AlignedSequence Defines a data structure for a Sequence within an alignment.
AlignedSequence.Step Defines an alignment step in order to pass alignment information from an Aligner to a constructor.
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.
Profile Defines a data structure for the results of sequence alignment.
Profile.StringFormat List of output formats.
ProfilePair Defines a data structure for the results of the alignment of a pair of Profiles.
ProfileProfileAligner Defines an Aligner for a pair of Profiles.
ProfileProfileScorer Defines an algorithm which computes a score for a pairing of alignment profiles.
ProfileView Defines a data structure for a view of sequence alignment.
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.
SequencePair Defines a data structure for the results of pairwise sequence alignment.
SubstitutionMatrix 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.

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

Class and Description
SubstitutionMatrix 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.

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.
AlignedSequence.Step Defines an alignment step in order to pass alignment information from an Aligner to a constructor.
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.
SubstitutionMatrix 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.

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.
AlignedSequence Defines a data structure for a Sequence within an alignment.
AlignedSequence.Step Defines an alignment step in order to pass alignment information from an Aligner to a constructor.
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.
MutableProfile Defines a mutable (editable) data structure for a Profile.
PairwiseSequenceAligner Defines an Aligner for a pair of Sequences.
PairwiseSequenceScorer Defines an algorithm which computes a score for a pair of sequences.
Profile Defines a data structure for the results of sequence alignment.
Profile.StringFormat List of output formats.
ProfilePair Defines a data structure for the results of the alignment of a pair of Profiles.
ProfileProfileAligner Defines an Aligner for a pair of Profiles.
ProfileProfileScorer Defines an algorithm which computes a score for a pairing of alignment profiles.
ProfileView Defines a data structure for a view of sequence alignment.
Scorer Defines an algorithm which computes a score.
SequencePair Defines a data structure for the results of pairwise sequence alignment.
SubstitutionMatrix 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.