umms.core.alignment.SmithWatermanAlignment Member List

This is the complete list of members for umms.core.alignment.SmithWatermanAlignment, including all inherited members.

align(String seq)	umms.core.alignment.SmithWatermanAlignment
align(String seq1, String seq2, float matchScore, float mismatchScore, float gapOpenPenalty, float gapExtendPenalty)	umms.core.alignment.SmithWatermanAlignment	static
containsFullLengthUngappedMatch(String seq1, String seq2, int seq1start, int maxMismatches)	umms.core.alignment.SmithWatermanAlignment	static
containsFullLengthUngappedMatch(String seq1, String seq2, int seq1start, float matchScore, float mismatchScore, int maxMismatches)	umms.core.alignment.SmithWatermanAlignment	static
containsFullLengthUngappedMatch(String seq1, String seq2, int maxMismatches)	umms.core.alignment.SmithWatermanAlignment	static
containsFullLengthUngappedMatch(String seq1, String seq2, float matchScore, float mismatchScore, int maxMismatches)	umms.core.alignment.SmithWatermanAlignment	static
DEFAULT_GAP_EXTEND_PENALTY	umms.core.alignment.SmithWatermanAlignment	static
DEFAULT_GAP_OPEN_PENALTY	umms.core.alignment.SmithWatermanAlignment	static
DEFAULT_MATCH_SCORE	umms.core.alignment.SmithWatermanAlignment	static
DEFAULT_MISMATCH_SCORE	umms.core.alignment.SmithWatermanAlignment	static
getFullPrintableAlignment(jaligner.Alignment alignment)	umms.core.alignment.SmithWatermanAlignment	static
matchStartOnFirstSequence(String seq1, String seq2, float matchScore, float mismatchScore, float gapOpenPenalty, float gapExtendPenalty, float minPctIdentity)	umms.core.alignment.SmithWatermanAlignment	static
SmithWatermanAlignment(String seq)	umms.core.alignment.SmithWatermanAlignment
SmithWatermanAlignment(String seq, float matchScore, float mismatchScore, float gapOpenPenalty, float gapExtendPenalty)	umms.core.alignment.SmithWatermanAlignment
ungappedMatchStartOnFirstSequence(String seq1, String seq2, float matchScore, float mismatchScore, float minPctIdentity)	umms.core.alignment.SmithWatermanAlignment	static