Package org.biojava.nbio.alignment.routines

Class Summary

Class	Description
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.Subproblem	Alignment subproblem.
AnchoredPairwiseSequenceAligner<S extends org.biojava.nbio.core.sequence.template.Sequence<C>,C extends org.biojava.nbio.core.sequence.template.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.
GuanUberbacher<S extends org.biojava.nbio.core.sequence.template.Sequence<C>,C extends org.biojava.nbio.core.sequence.template.Compound>	Guan and Uberbacher defined an algorithm for pairwise global sequence alignments (from the first until the last Compound of each Sequence).

Enum Summary

Enum	Description
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).