| Package | Description |
|---|---|
| com.milaboratory.core.alignment | |
| com.milaboratory.core.alignment.kaligner1 | |
| com.milaboratory.core.tree |
| Modifier and Type | Method and Description |
|---|---|
static LinearGapAlignmentScoring<AminoAcidSequence> |
LinearGapAlignmentScoring.getAminoAcidBLASTScoring(BLASTMatrix matrix)
Returns standard amino acid BLAST scoring with
#gapPenalty=5 |
static LinearGapAlignmentScoring<AminoAcidSequence> |
LinearGapAlignmentScoring.getAminoAcidBLASTScoring(BLASTMatrix matrix,
int gapPenalty)
Returns standard amino acid BLAST scoring
|
static LinearGapAlignmentScoring<NucleotideSequence> |
LinearGapAlignmentScoring.getNucleotideBLASTScoring()
Returns standard Nucleotide BLAST scoring with
#gapPenalty=5 |
static LinearGapAlignmentScoring<NucleotideSequence> |
LinearGapAlignmentScoring.getNucleotideBLASTScoring(int gapPenalty)
Returns standard Nucleotide BLAST scoring
|
| Modifier and Type | Method and Description |
|---|---|
static Alignment<NucleotideSequence> |
BandedLinearAligner.align(LinearGapAlignmentScoring scoring,
NucleotideSequence seq1,
NucleotideSequence seq2,
int width)
Classical Banded Alignment
|
static Alignment<NucleotideSequence> |
BandedLinearAligner.align(LinearGapAlignmentScoring scoring,
NucleotideSequence seq1,
NucleotideSequence seq2,
int offset1,
int length1,
int offset2,
int length2,
int width)
Classical Banded Alignment
|
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 <S extends Sequence<S>> |
Aligner.alignGlobalLinear(LinearGapAlignmentScoring scoring,
S seq1,
S seq2)
Performs global alignment using Linear scoring system (penalty exists only for gap)
|
static Alignment<NucleotideSequence> |
BandedLinearAligner.alignLeftAdded(LinearGapAlignmentScoring scoring,
NucleotideSequence seq1,
NucleotideSequence seq2,
int offset1,
int length1,
int addedNucleotides1,
int offset2,
int length2,
int addedNucleotides2,
int width)
Semi-semi-global alignment with artificially added letters.
|
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 <S extends Sequence<S>> |
AlignerCustom.alignLinearSemiLocalLeft0(LinearGapAlignmentScoring<S> scoring,
S seq1,
S seq2,
int offset1,
int length1,
int offset2,
int length2,
boolean boundSeq1,
boolean boundSeq2,
Alphabet<S> alphabet,
AlignerCustom.LinearMatrixCache cache)
Align two sequences from left to right; left edges of both sequences considered to be already aligned.
|
static <S extends Sequence<S>> |
AlignerCustom.alignLinearSemiLocalRight0(LinearGapAlignmentScoring<S> scoring,
S seq1,
S seq2,
int offset1,
int length1,
int offset2,
int length2,
boolean boundSeq1,
boolean boundSeq2,
Alphabet<S> alphabet,
AlignerCustom.LinearMatrixCache cache) |
static <S extends Sequence<S>> |
Aligner.alignLocalLinear(LinearGapAlignmentScoring<S> scoring,
S seq1,
S seq2)
Performs local alignment using Linear scoring system (penalty exists only for gap)
|
static Alignment<NucleotideSequence> |
BandedLinearAligner.alignRightAdded(LinearGapAlignmentScoring scoring,
NucleotideSequence seq1,
NucleotideSequence seq2,
int offset1,
int length1,
int addedNucleotides1,
int offset2,
int length2,
int addedNucleotides2,
int width)
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 Alignment<NucleotideSequence> |
BandedLinearAligner.alignSemiLocalLeft(LinearGapAlignmentScoring scoring,
NucleotideSequence seq1,
NucleotideSequence seq2,
int width,
int stopPenalty)
Alignment which identifies what is the highly similar part of the both sequences.
|
static Alignment<NucleotideSequence> |
BandedLinearAligner.alignSemiLocalLeft(LinearGapAlignmentScoring scoring,
NucleotideSequence seq1,
NucleotideSequence seq2,
int offset1,
int length1,
int offset2,
int length2,
int width,
int stopPenalty)
Alignment which identifies what is the highly similar part of the both sequences.
|
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 Alignment<NucleotideSequence> |
BandedLinearAligner.alignSemiLocalRight(LinearGapAlignmentScoring scoring,
NucleotideSequence seq1,
NucleotideSequence seq2,
int width,
int stopPenalty)
Alignment which identifies what is the highly similar part of the both sequences.
|
static Alignment<NucleotideSequence> |
BandedLinearAligner.alignSemiLocalRight(LinearGapAlignmentScoring scoring,
NucleotideSequence seq1,
NucleotideSequence seq2,
int offset1,
int length1,
int offset2,
int length2,
int width,
int stopPenalty)
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 <S extends Sequence<S>> |
AlignmentUtils.calculateScore(S seq1,
Range seq1Range,
Mutations<S> mutations,
LinearGapAlignmentScoring<S> scoring)
Calculates score of alignment
|
static <S extends Sequence<S>> |
AlignmentTrimmer.leftTrimAlignment(Alignment<S> alignment,
LinearGapAlignmentScoring<S> scoring)
Try increase total alignment score by partially (or fully) trimming it from left side.
|
static <S extends Sequence<S>> |
AlignmentTrimmer.rightTrimAlignment(Alignment<S> alignment,
LinearGapAlignmentScoring<S> scoring)
Try increase total alignment score by partially (or fully) trimming it from right side.
|
| Modifier and Type | Method and Description |
|---|---|
LinearGapAlignmentScoring<NucleotideSequence> |
KAlignerParameters.getScoring()
Returns scoring system used for building alignments
|
| Modifier and Type | Method and Description |
|---|---|
KAlignerParameters |
KAlignerParameters.setScoring(LinearGapAlignmentScoring scoring)
Sets scoring system used for building alignments
|
| Constructor and Description |
|---|
KAlignerParameters(int mapperKValue,
boolean floatingLeftBound,
boolean floatingRightBound,
float mapperAbsoluteMinScore,
float mapperRelativeMinScore,
float mapperMatchScore,
float mapperMismatchPenalty,
float mapperOffsetShiftPenalty,
int mapperMinSeedsDistance,
int mapperMaxSeedsDistance,
int minAlignmentLength,
int maxAdjacentIndels,
int alignmentStopPenalty,
float absoluteMinScore,
float relativeMinScore,
int maxHits,
LinearGapAlignmentScoring<NucleotideSequence> scoring)
Creates new KAligner
|
| Modifier and Type | Method and Description |
|---|---|
Alignment<S> |
NeighborhoodIterator.getCurrentAlignment(LinearGapAlignmentScoring<S> scoring) |
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