Package org.biojava3.alignment.routines

Class Summary

AlignerHelper	Static utility to construct alignment routines from a common library of methods.
AlignerHelper.Cut	Defines a 'cut' row for divide-and-conquer alignment in which a new anchor is found.
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.
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).

Enum Summary

AlignerHelper.Last

Defines 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).