| Package | Description |
|---|---|
| com.milaboratory.core.alignment |
| Modifier and Type | Method and Description |
|---|---|
static CachedIntArray |
AlignmentCache.get()
Returns available CachedIntArray if AlignemntCache is on or creates new CachedIntArray otherwise
|
| 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.
|
| Constructor and Description |
|---|
BandedMatrix(CachedIntArray cachedArray,
int size1,
int size2,
int width) |
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