Uses of Class
com.milaboratory.core.alignment.BandedSemiLocalResult

Packages that use BandedSemiLocalResult

Package	Description
com.milaboratory.core.alignment

Uses of BandedSemiLocalResult in com.milaboratory.core.alignment

Methods in com.milaboratory.core.alignment that return BandedSemiLocalResult

Modifier and Type	Method and Description
static BandedSemiLocalResult	BandedLinearAligner.alignLeftAdded0(LinearGapAlignmentScoring scoring, NucleotideSequence seq1, NucleotideSequence seq2, int offset1, int length1, int addedNucleotides1, int offset2, int length2, int addedNucleotides2, int width, MutationsBuilder<NucleotideSequence> mutations, CachedIntArray cachedArray) Semi-semi-global alignment with artificially added letters.
static BandedSemiLocalResult	BandedLinearAligner.alignRightAdded0(LinearGapAlignmentScoring scoring, NucleotideSequence seq1, NucleotideSequence seq2, int offset1, int length1, int addedNucleotides1, int offset2, int length2, int addedNucleotides2, int width, MutationsBuilder<NucleotideSequence> mutations, CachedIntArray cachedArray) Semi-semi-global alignment with artificially added letters.
static BandedSemiLocalResult	BandedLinearAligner.alignSemiLocalLeft0(LinearGapAlignmentScoring scoring, NucleotideSequence seq1, NucleotideSequence seq2, int offset1, int length1, int offset2, int length2, int width, int stopPenalty, MutationsBuilder<NucleotideSequence> mutations, CachedIntArray cachedArray) Alignment which identifies what is the highly similar part of the both sequences.
static BandedSemiLocalResult	BandedLinearAligner.alignSemiLocalRight0(LinearGapAlignmentScoring scoring, NucleotideSequence seq1, NucleotideSequence seq2, int offset1, int length1, int offset2, int length2, int width, int stopPenalty, MutationsBuilder<NucleotideSequence> mutations, CachedIntArray cachedArray) Alignment which identifies what is the highly similar part of the both sequences.
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)