| Package | Description |
|---|---|
| com.milaboratory.core.alignment | |
| com.milaboratory.core.mutations |
| 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 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 <S extends Sequence<S>> |
Aligner.alignOnlySubstitutions0(S seq1,
S seq2,
int seq1From,
int seq1Length,
int seq2From,
int seq2Length,
AlignmentScoring<S> scoring,
MutationsBuilder<S> builder) |
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) |
| Modifier and Type | Method and Description |
|---|---|
MutationsBuilder<S> |
MutationsBuilder.append(int mutation) |
MutationsBuilder<S> |
MutationsBuilder.append(int[] other) |
MutationsBuilder<S> |
MutationsBuilder.append(Mutations<S> other) |
MutationsBuilder<S> |
MutationsBuilder.append(Mutations<S> other,
int otherFrom,
int length) |
MutationsBuilder<S> |
MutationsBuilder.append(MutationsBuilder<S> other) |
MutationsBuilder<S> |
MutationsBuilder.appendDeletion(int position,
int from) |
MutationsBuilder<S> |
MutationsBuilder.appendDeletion(int position,
int length,
S originalSequence) |
MutationsBuilder<S> |
MutationsBuilder.appendInsertion(int position,
int to) |
MutationsBuilder<S> |
MutationsBuilder.appendInsertion(int position,
S insert) |
MutationsBuilder<S> |
MutationsBuilder.appendSubstitution(int position,
int from,
int to) |
MutationsBuilder<S> |
MutationsBuilder.clone() |
MutationsBuilder<S> |
MutationsBuilder.ensureCapacity(int capacity) |
MutationsBuilder<S> |
MutationsBuilder.reverseRange(int from,
int to) |
| Modifier and Type | Method and Description |
|---|---|
MutationsBuilder<S> |
MutationsBuilder.append(MutationsBuilder<S> other) |
Copyright © 2018. All rights reserved.