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

Packages that use CachedIntArray

Package	Description
com.milaboratory.core.alignment

Uses of CachedIntArray in com.milaboratory.core.alignment

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

Modifier and Type	Method and Description
static CachedIntArray	AlignmentCache.get() Returns available CachedIntArray if AlignemntCache is on or creates new CachedIntArray otherwise

Methods in com.milaboratory.core.alignment with parameters of type CachedIntArray

Modifier and Type	Method and Description
static float	BandedLinearAligner.align0(LinearGapAlignmentScoring scoring, NucleotideSequence seq1, NucleotideSequence seq2, int offset1, int length1, int offset2, int length2, int width, MutationsBuilder<NucleotideSequence> mutations, CachedIntArray cachedArray) Classical Banded Alignment
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.

Constructors in com.milaboratory.core.alignment with parameters of type CachedIntArray

Constructor and Description
BandedMatrix(CachedIntArray cachedArray, int size1, int size2, int width)