Uses of Class
org.biojava.nbio.alignment.template.AbstractMatrixAligner

Packages that use AbstractMatrixAligner

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

Uses of AbstractMatrixAligner in org.biojava.nbio.alignment

Subclasses of AbstractMatrixAligner in org.biojava.nbio.alignment

Modifier and Type	Class	Description
class	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).
class	SimpleProfileProfileAligner<S extends Sequence<C>,C extends Compound>	Implements a simple (naive) Aligner for a pair of Profiles.
class	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).

Uses of AbstractMatrixAligner in org.biojava.nbio.alignment.routines

Subclasses of AbstractMatrixAligner in org.biojava.nbio.alignment.routines

Modifier and Type	Class	Description
class	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.
class	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).

Uses of AbstractMatrixAligner in org.biojava.nbio.alignment.template

Subclasses of AbstractMatrixAligner in org.biojava.nbio.alignment.template

Modifier and Type	Class	Description
class	AbstractPairwiseSequenceAligner<S extends Sequence<C>,C extends Compound>	Implements common code for an Aligner for a pair of Sequences.
class	AbstractProfileProfileAligner<S extends Sequence<C>,C extends Compound>	Implements common code for an Aligner for a pair of Profiles.