static int |
BandedAffineAligner.align0(AffineGapAlignmentScoring<NucleotideSequence> scoring,
NucleotideSequence seq1,
NucleotideSequence seq2,
int offset1,
int length1,
int offset2,
int length2,
int width,
MutationsBuilder<NucleotideSequence> mutations,
BandedAffineAligner.MatrixCache cache)
Classical Banded Alignment with affine gap scoring.
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static BandedSemiLocalResult |
BandedAffineAligner.semiGlobalLeft0(AffineGapAlignmentScoring<NucleotideSequence> scoring,
NucleotideSequence seq1,
NucleotideSequence seq2,
int offset1,
int length1,
int addedNucleotides1,
int offset2,
int length2,
int addedNucleotides2,
int width,
MutationsBuilder<NucleotideSequence> mutations,
BandedAffineAligner.MatrixCache cache) |
static BandedSemiLocalResult |
BandedAffineAligner.semiGlobalRight0(AffineGapAlignmentScoring<NucleotideSequence> scoring,
NucleotideSequence seq1,
NucleotideSequence seq2,
int offset1,
int length1,
int addedNucleotides1,
int offset2,
int length2,
int addedNucleotides2,
int width,
MutationsBuilder<NucleotideSequence> mutations,
BandedAffineAligner.MatrixCache cache) |
static BandedSemiLocalResult |
BandedAffineAligner.semiLocalLeft0(AffineGapAlignmentScoring<NucleotideSequence> scoring,
NucleotideSequence seq1,
NucleotideSequence seq2,
int offset1,
int length1,
int offset2,
int length2,
int width,
MutationsBuilder<NucleotideSequence> mutations,
BandedAffineAligner.MatrixCache cache) |
static BandedSemiLocalResult |
BandedAffineAligner.semiLocalRight0(AffineGapAlignmentScoring<NucleotideSequence> scoring,
NucleotideSequence seq1,
NucleotideSequence seq2,
int offset1,
int length1,
int offset2,
int length2,
int width,
MutationsBuilder<NucleotideSequence> mutations,
BandedAffineAligner.MatrixCache cache) |