| Package | Description |
|---|---|
| com.milaboratory.core.alignment | |
| com.milaboratory.core.alignment.batch | |
| com.milaboratory.core.alignment.benchmark | |
| com.milaboratory.core.alignment.blast | |
| com.milaboratory.core.alignment.kaligner1 | |
| com.milaboratory.core.alignment.kaligner2 | |
| com.milaboratory.core.io.binary |
Contains
PrimitivIO (see com.milaboratory.primitivio) serializers for MiLib classes that don't need
access to package only constructors and fields. |
| com.milaboratory.core.mutations | |
| com.milaboratory.core.tree |
| Modifier and Type | Method and Description |
|---|---|
static Alignment<NucleotideSequence> |
BandedAffineAligner.align(AffineGapAlignmentScoring<NucleotideSequence> scoring,
NucleotideSequence seq1,
NucleotideSequence seq2,
int width) |
static Alignment<NucleotideSequence> |
BandedAffineAligner.align(AffineGapAlignmentScoring<NucleotideSequence> scoring,
NucleotideSequence seq1,
NucleotideSequence seq2,
int offset1,
int length1,
int offset2,
int length2,
int width) |
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 <S extends Sequence<S>> |
AlignerCustom.alignAffineSemiLocalLeft0(AffineGapAlignmentScoring<S> scoring,
S seq1,
S seq2,
int offset1,
int length1,
int offset2,
int length2,
boolean boundSeq1,
boolean boundSeq2,
Alphabet<S> alphabet,
AlignerCustom.AffineMatrixCache cache) |
static Alignment<NucleotideSequence> |
BandedAligner.alignGlobal(AlignmentScoring<NucleotideSequence> scoring,
NucleotideSequence seq1,
NucleotideSequence seq2,
int offset1,
int length1,
int offset2,
int length2,
int width)
Classical Banded Alignment.
|
static <S extends Sequence<S>> |
Aligner.alignGlobal(AlignmentScoring<S> alignmentScoring,
S seq1,
S seq2)
Performs global alignment
|
static <S extends Sequence<S>> |
Aligner.alignGlobal(AlignmentScoring<S> alignmentScoring,
S seq1,
S seq2,
int offset1,
int length1,
int offset2,
int length2) |
static <S extends Sequence<S>> |
Aligner.alignGlobalAffine(AffineGapAlignmentScoring<S> scoring,
S seq1,
S seq2)
Performs global alignment using affine gap scoring system (different penalties exist for gap opening and gap
extension)
|
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 <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.alignLocal(AlignmentScoring<S> alignmentScoring,
S seq1,
S seq2)
Performs local alignment
|
static <S extends Sequence<S>> |
Aligner.alignLocalAffine(AffineGapAlignmentScoring<S> scoring,
S seq1,
S seq2)
Performs local alignment using Affine gap scoring system (different penalties exist for gap opening and gap
extension)
|
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 <S extends Sequence<S>> |
Aligner.alignOnlySubstitutions(S from,
S to) |
static <S extends Sequence<S>> |
Aligner.alignOnlySubstitutions(S seq1,
S seq2,
int seq1From,
int seq1Length,
int seq2From,
int seq2Length,
AlignmentScoring<S> scoring) |
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 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 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.
|
Alignment<S> |
Alignment.invert(S sequence2)
Having sequence2 creates alignment from sequence2 to sequence1
|
static <S extends Sequence<S>> |
AlignmentTrimmer.leftTrimAlignment(Alignment<S> alignment,
AffineGapAlignmentScoring<S> scoring)
Try increase total alignment score by partially (or fully) trimming it from left side.
|
static <S extends Sequence<S>> |
AlignmentTrimmer.leftTrimAlignment(Alignment<S> alignment,
AlignmentScoring<S> scoring)
Try increase total alignment score by partially (or fully) trimming it from left side.
|
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.
|
Alignment<S> |
Alignment.move(int offset)
Returns alignment with seq2range = seq2Range.move(offset), and everything else inherited from this alignment.
|
static <S extends Sequence<S>> |
AlignmentTrimmer.rightTrimAlignment(Alignment<S> alignment,
AffineGapAlignmentScoring<S> scoring)
Try increase total alignment score by partially (or fully) trimming it from right side.
|
static <S extends Sequence<S>> |
AlignmentTrimmer.rightTrimAlignment(Alignment<S> alignment,
AlignmentScoring<S> scoring)
Try increase total alignment score by partially (or fully) trimming it from right 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.
|
static Alignment<NucleotideSequence> |
BandedAffineAligner.semiGlobalLeft(AffineGapAlignmentScoring<NucleotideSequence> scoring,
NucleotideSequence seq1,
NucleotideSequence seq2,
int offset1,
int length1,
int addedNucleotides1,
int offset2,
int length2,
int addedNucleotides2,
int width) |
static Alignment<NucleotideSequence> |
BandedAffineAligner.semiGlobalRight(AffineGapAlignmentScoring<NucleotideSequence> scoring,
NucleotideSequence seq1,
NucleotideSequence seq2,
int offset1,
int length1,
int addedNucleotides1,
int offset2,
int length2,
int addedNucleotides2,
int width) |
static Alignment<NucleotideSequence> |
BandedAffineAligner.semiLocalLeft(AffineGapAlignmentScoring<NucleotideSequence> scoring,
NucleotideSequence seq1,
NucleotideSequence seq2,
int width) |
static Alignment<NucleotideSequence> |
BandedAffineAligner.semiLocalLeft(AffineGapAlignmentScoring<NucleotideSequence> scoring,
NucleotideSequence seq1,
NucleotideSequence seq2,
int offset1,
int length1,
int offset2,
int length2,
int width) |
static Alignment<NucleotideSequence> |
BandedAffineAligner.semiLocalRight(AffineGapAlignmentScoring<NucleotideSequence> scoring,
NucleotideSequence seq1,
NucleotideSequence seq2,
int width) |
static Alignment<NucleotideSequence> |
BandedAffineAligner.semiLocalRight(AffineGapAlignmentScoring<NucleotideSequence> scoring,
NucleotideSequence seq1,
NucleotideSequence seq2,
int offset1,
int length1,
int offset2,
int length2,
int width) |
static <S extends Sequence<S>> |
AlignmentUtils.shiftIndelsAtHomopolymers(Alignment<S> alignment)
Shifts indels to the left at homopolymer regions
|
| Modifier and Type | Method and Description |
|---|---|
static <S extends Sequence<S>> |
MultiAlignmentHelper.build(MultiAlignmentHelper.Settings settings,
Range subjectRange,
Alignment<S>... alignments) |
static <S extends Sequence<S>> |
MultiAlignmentHelper.build(MultiAlignmentHelper.Settings settings,
Range subjectRange,
S subject,
Alignment<S>... alignments) |
static <S extends Sequence<S>> |
AlignmentUtils.getAlignedSequence2Part(Alignment<S> alignment) |
static <S extends Sequence<S>> |
AlignmentTrimmer.leftTrimAlignment(Alignment<S> alignment,
AffineGapAlignmentScoring<S> scoring)
Try increase total alignment score by partially (or fully) trimming it from left side.
|
static <S extends Sequence<S>> |
AlignmentTrimmer.leftTrimAlignment(Alignment<S> alignment,
AlignmentScoring<S> scoring)
Try increase total alignment score by partially (or fully) trimming it from left side.
|
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,
AffineGapAlignmentScoring<S> scoring)
Try increase total alignment score by partially (or fully) trimming it from right side.
|
static <S extends Sequence<S>> |
AlignmentTrimmer.rightTrimAlignment(Alignment<S> alignment,
AlignmentScoring<S> scoring)
Try increase total alignment score by partially (or fully) trimming it from right 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.
|
static <S extends Sequence<S>> |
AlignmentUtils.shiftIndelsAtHomopolymers(Alignment<S> alignment)
Shifts indels to the left at homopolymer regions
|
| Modifier and Type | Method and Description |
|---|---|
Alignment<S> |
AlignmentHitImpl.getAlignment() |
Alignment<S> |
AlignmentHit.getAlignment() |
| Constructor and Description |
|---|
AlignmentHitImpl(Alignment<S> alignment,
P recordPayload) |
| Modifier and Type | Field and Description |
|---|---|
Alignment<NucleotideSequence> |
KAlignerQuery.expectedAlignment |
| Constructor and Description |
|---|
KAlignerQuery(int targetId,
List<Range> queryClusters,
List<Range> targetClusters,
List<Mutations<NucleotideSequence>> mutationsInTarget,
NucleotideSequence query,
Alignment<NucleotideSequence> expectedAlignment) |
| Modifier and Type | Method and Description |
|---|---|
protected AABlastHitExt |
AABlastAlignerExt.createHit(Alignment<AminoAcidSequence> alignment,
double score,
double bitScore,
double eValue,
Range subjectRange,
String subjectId,
String subjectTitle) |
protected AABlastHit<P> |
AABlastAligner.createHit(Alignment<AminoAcidSequence> alignment,
P recordPayload,
BlastHit<AminoAcidSequence,?> hit) |
protected NBlastHitExt |
NBlastAlignerExt.createHit(Alignment<NucleotideSequence> alignment,
double score,
double bitScore,
double eValue,
Range subjectRange,
String subjectId,
String subjectTitle) |
protected NBlastHit<P> |
NBlastAligner.createHit(Alignment<NucleotideSequence> alignment,
P recordPayload,
BlastHit<NucleotideSequence,?> hit) |
protected abstract H |
BlastAlignerExtAbstract.createHit(Alignment<S> alignment,
double score,
double bitScore,
double eValue,
Range subjectRange,
String subjectId,
String subjectTitle) |
protected abstract H |
BlastAlignerAbstract.createHit(Alignment<S> alignment,
P recordPayload,
BlastHit<S,?> hit) |
protected BlastHit<S,P> |
BlastAligner.createHit(Alignment<S> alignment,
P recordPayload,
BlastHit<S,?> hit) |
protected BlastHitExt<S> |
BlastAlignerExt.createHit(Alignment alignment,
double score,
double bitScore,
double eValue,
Range subjectRange,
String subjectId,
String subjectTitle) |
| Constructor and Description |
|---|
AABlastHit(Alignment<AminoAcidSequence> alignment,
P recordPayload,
BlastHit<AminoAcidSequence,?> hit) |
AABlastHit(Alignment<AminoAcidSequence> alignment,
P recordPayload,
double score,
double bitScore,
double eValue,
Range subjectRange,
String subjectId,
String subjectTitle) |
AABlastHitExt(Alignment<AminoAcidSequence> alignment,
double score,
double bitScore,
double eValue,
Range subjectRange,
String subjectId,
String subjectTitle) |
BlastHit(Alignment<S> alignment,
P recordPayload,
BlastHit<S,?> hit) |
BlastHit(Alignment<S> alignment,
P recordPayload,
double score,
double bitScore,
double eValue,
Range subjectRange,
String subjectId,
String subjectTitle) |
BlastHitExt(Alignment<S> alignment,
double score,
double bitScore,
double eValue,
Range subjectRange,
String subjectId,
String subjectTitle) |
NBlastHit(Alignment<NucleotideSequence> alignment,
P recordPayload,
BlastHit<NucleotideSequence,?> hit) |
NBlastHit(Alignment<NucleotideSequence> alignment,
P recordPayload,
double score,
double bitScore,
double eValue,
Range subjectRange,
String subjectId,
String subjectTitle) |
NBlastHitExt(Alignment<NucleotideSequence> alignment,
double score,
double bitScore,
double eValue,
Range subjectRange,
String subjectId,
String subjectTitle) |
| Modifier and Type | Method and Description |
|---|---|
Alignment<NucleotideSequence> |
KAlignmentHit.getAlignment() |
| Modifier and Type | Method and Description |
|---|---|
Alignment<NucleotideSequence> |
KAlignmentHit2.getAlignment() |
| Constructor and Description |
|---|
KAlignmentHit2(KAlignmentResult2<P> result,
int indexOfMappingHit,
Alignment<NucleotideSequence> alignment,
P payload) |
| Modifier and Type | Method and Description |
|---|---|
Alignment |
AlignmentSerializer.read(PrimitivI input) |
| Modifier and Type | Method and Description |
|---|---|
void |
AlignmentSerializer.write(PrimitivO output,
Alignment object) |
| Modifier and Type | Method and Description |
|---|---|
void |
MutationConsensusBuilder.aggregate(Alignment<?> alignment,
CoverageCounter.Provider coverageFunction) |
| Modifier and Type | Method and Description |
|---|---|
Alignment<S> |
NeighborhoodIterator.getCurrentAlignment() |
Alignment<S> |
NeighborhoodIterator.getCurrentAlignment(LinearGapAlignmentScoring<S> scoring) |
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