Class Summary Class Description AlignerHelperStatic utility to construct alignment routines from a common library of methods. AlignerHelper.AnchorCompounds in query and target sequences that must align AlignerHelper.Anchor.QueryIndexComparator AlignerHelper.CutDefines a 'cut' row for divide-and-conquer alignment in which a new anchor is found. AlignerHelper.SubproblemAlignment subproblem. AnchoredPairwiseSequenceAligner<S extends Sequence<C>,C extends Compound> GuanUberbacher<S extends Sequence<C>,C extends Compound>
Enum Summary Enum Description AlignerHelper.LastDefine 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).