GreedyTupleAligner< QueryType, ReferenceType, ReferenceIndex > Member List

This is the complete list of members for GreedyTupleAligner< QueryType, ReferenceType, ReferenceIndex >, including all inherited members.

Align(QueryType query, int queryLength, ReferenceType reference, ReferenceIndex searchStartIndex, int searchSize, CigarRoller &cigarRoller, ReferenceIndex &matchPosition)	GreedyTupleAligner< QueryType, ReferenceType, ReferenceIndex >	[inline]
GreedyTupleAligner(Weight &wt) (defined in GreedyTupleAligner< QueryType, ReferenceType, ReferenceIndex >)	GreedyTupleAligner< QueryType, ReferenceType, ReferenceIndex >	[inline]
MatchTuple(const QueryType query, const int queryLength, const ReferenceType reference, const ReferenceIndex searchStartIndex, const int searchSize, int &matchedLength, int &mismatch)	GreedyTupleAligner< QueryType, ReferenceType, ReferenceIndex >	[inline]