Uses of Class
com.milaboratory.core.alignment.BandedAffineAligner.MatrixCache

Packages that use BandedAffineAligner.MatrixCache

Package	Description
com.milaboratory.core.alignment

Uses of BandedAffineAligner.MatrixCache in com.milaboratory.core.alignment

Methods in com.milaboratory.core.alignment with parameters of type BandedAffineAligner.MatrixCache

Modifier and Type	Method and Description
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.
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)