All Classes and Interfaces

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.
Aligner<S extends Sequence<C>,C extends Compound>	Defines an algorithm which computes an alignment Profile from a list of Sequences.
AlignerHelper	Static utility to construct alignment routines from a common library of methods.
AlignerHelper.Anchor	Compounds in query and target sequences that must align
AlignerHelper.Anchor.QueryIndexComparator
AlignerHelper.Cut	Defines a 'cut' row for divide-and-conquer alignment in which a new anchor is found.
AlignerHelper.Last	Define a traceback pointer for the three edit operations: substitution (match/replacement of a query compound with a target compound), deletion (removal of a query compound leaving a gap in the target sequence), and insertion (addition of a target compound opening a gap in the query sequence).
AlignerHelper.Subproblem	Alignment subproblem.
Alignments	Static utility to easily run alignment routines.
Alignments.PairInProfileScorerType	List of implemented sequence pair in a profile scoring routines.
Alignments.PairwiseSequenceAlignerType	List of implemented pairwise sequence alignment routines.
Alignments.PairwiseSequenceScorerType	List of implemented pairwise sequence scoring routines.
Alignments.ProfileProfileAlignerType	List of implemented profile-profile alignment routines.
Alignments.RefinerType	List of implemented profile refinement routines.
AnchoredPairwiseSequenceAligner<S extends Sequence<C>,C extends Compound>	This algorithm uses a divide-and-conquer approach to find optimal pairwise global sequence alignments (from the first until the last Compound of each Sequence) with the restriction that any alignment produced will connect the query sequence to the target sequence at the anchors.
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.
Comparison	This class provides static methods for the calculation of the percentage of identity between two aligned sequences.
CookbookMSA
DemoAlignProteins
DemoDistanceTree	This demo contains the CookBook example to create a phylogenetic tree from a multiple sequence alignment (MSA).
DemoLoadSubstMax
DistanceMatrixCalculator	The DistanceMatrixCalculator methods generate a DistanceMatrix from a MultipleSequenceAlignment or other indirect distance infomation (RMSD).
DistanceTreeEvaluator	Check the accuracy of a Distance Tree by least squares error (LSE) of the Tree branch lengths and the original Distance Matrix.
ForesterWrapper	This class contains wrapper methods for communication between BioJava and forester (e.g, Data Structure conversion).
FractionalIdentityInProfileScorer<S extends Sequence<C>,C extends Compound>	Implements an algorithm which computes a score for a sequence alignment pair picked from an alignment Profile.
FractionalIdentityScorer<S extends Sequence<C>,C extends Compound>	Implements an algorithm which computes a score for a sequence alignment pair.
FractionalSimilarityInProfileScorer<S extends Sequence<C>,C extends Compound>	Implements an algorithm which computes a score for a sequence alignment pair picked from an alignment Profile.
FractionalSimilarityScorer<S extends Sequence<C>,C extends Compound>	Implements an algorithm which computes a score for a sequence alignment pair.
GapPenalty	Defines a data structure for the gap penalties used during a sequence alignment routine.
GapPenalty.Type	Defines the possible types of gap penalties.
GuanUberbacher<S extends Sequence<C>,C extends Compound>	Guan and Uberbacher defined an algorithm for pairwise global sequence alignments (from the first until the last Compound of each Sequence).
GuideTree<S extends Sequence<C>,C extends Compound>	Implements a data structure for a guide tree used during progressive multiple sequence alignment.
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.
NeedlemanWunsch<S extends Sequence<C>,C extends Compound>	Needleman and Wunsch defined an algorithm for pairwise global sequence alignments (from the first until the last Compound of each Sequence).
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.
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.
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.
SimpleGapPenalty	Implements a data structure for the gap penalties used during a sequence alignment routine.
SimpleProfileProfileAligner<S extends Sequence<C>,C extends Compound>	Implements a simple (naive) Aligner for a pair of Profiles.
SmithWaterman<S extends Sequence<C>,C extends Compound>	Smith and Waterman defined an algorithm for pairwise local sequence alignments (best match of sections from each Sequence).
StandardRescoreRefiner<S extends Sequence<C>,C extends Compound>
StockholmFileAnnotation	Stores all the content parsed from the #=GF lines
StockholmFileAnnotation.StockholmFileAnnotationReference
StockholmFileParser	Stockholm file parser. for more information about the format refer to ftp://ftp.sanger.ac.uk/pub/databases /Pfam/current_release/userman.txt. ftp://ftp.sanger.ac.uk/pub/databases/Rfam/CURRENT /USERMAN. http://sonnhammer.sbc.su.se/Stockholm.html.
StockholmStructure	Stores all the content of a Stockholm file.
StockholmStructure.DatabaseReference
SubstitutionMatrixScorer<S extends Sequence<C>,C extends Compound>	Scores using a substitution matrix.
TestDNANeedlemanWunsch
TreeConstructor	The TreeConstructor uses the forester library to build different types of phylogenetic trees.
TreeConstructorType	The TreeConstructorType specifies the aligorithm used to construct the tree (clustering algorithm).
TreeType	The TreeType specifies the optimization criteria used to generate the tree.