public final class Aligner extends Object
| Modifier and Type | Method and Description |
|---|---|
static <S extends Sequence<S>> |
alignGlobal(AlignmentScoring<S> alignmentScoring,
S seq1,
S seq2)
Performs global alignment
|
static <S extends Sequence<S>> |
alignGlobal(AlignmentScoring<S> alignmentScoring,
S seq1,
S seq2,
int offset1,
int length1,
int offset2,
int length2) |
static <S extends Sequence<S>> |
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>> |
alignGlobalLinear(LinearGapAlignmentScoring scoring,
S seq1,
S seq2)
Performs global alignment using Linear scoring system (penalty exists only for gap)
|
static <S extends Sequence<S>> |
alignLocal(AlignmentScoring<S> alignmentScoring,
S seq1,
S seq2)
Performs local alignment
|
static <S extends Sequence<S>> |
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>> |
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>> |
alignOnlySubstitutions(S from,
S to) |
static <S extends Sequence<S>> |
alignOnlySubstitutions(S seq1,
S seq2,
int seq1From,
int seq1Length,
int seq2From,
int seq2Length,
AlignmentScoring<S> scoring) |
static <S extends Sequence<S>> |
alignOnlySubstitutions0(S seq1,
S seq2,
int seq1From,
int seq1Length,
int seq2From,
int seq2Length,
AlignmentScoring<S> scoring,
MutationsBuilder<S> builder) |
public static <S extends Sequence<S>> int alignOnlySubstitutions0(S seq1, S seq2, int seq1From, int seq1Length, int seq2From, int seq2Length, AlignmentScoring<S> scoring, MutationsBuilder<S> builder)
public static <S extends Sequence<S>> Alignment<S> alignOnlySubstitutions(S seq1, S seq2, int seq1From, int seq1Length, int seq2From, int seq2Length, AlignmentScoring<S> scoring)
public static <S extends Sequence<S>> Alignment<S> alignOnlySubstitutions(S from, S to)
public static <S extends Sequence<S>> Alignment<S> alignGlobal(AlignmentScoring<S> alignmentScoring, S seq1, S seq2, int offset1, int length1, int offset2, int length2)
public static <S extends Sequence<S>> Alignment<S> alignGlobal(AlignmentScoring<S> alignmentScoring, S seq1, S seq2)
alignmentScoring - scoring systemseq1 - first sequenceseq2 - second sequencepublic static <S extends Sequence<S>> Alignment<S> alignGlobalLinear(LinearGapAlignmentScoring scoring, S seq1, S seq2)
scoring - linear scoring systemseq1 - first sequenceseq2 - second sequencepublic static <S extends Sequence<S>> Alignment<S> alignGlobalAffine(AffineGapAlignmentScoring<S> scoring, S seq1, S seq2)
scoring - affine gap scoring systemseq1 - first sequenceseq2 - second sequencepublic static <S extends Sequence<S>> Alignment<S> alignLocal(AlignmentScoring<S> alignmentScoring, S seq1, S seq2)
alignmentScoring - scoring systemseq1 - first sequenceseq2 - second sequencepublic static <S extends Sequence<S>> Alignment<S> alignLocalLinear(LinearGapAlignmentScoring<S> scoring, S seq1, S seq2)
seq1 - first sequenceseq2 - second sequencepublic static <S extends Sequence<S>> Alignment<S> alignLocalAffine(AffineGapAlignmentScoring<S> scoring, S seq1, S seq2)
seq1 - first sequenceseq2 - second sequenceCopyright © 2018. All rights reserved.