| Package | Description |
|---|---|
| com.milaboratory.core.alignment | |
| com.milaboratory.core.alignment.batch |
| Modifier and Type | Class and Description |
|---|---|
class |
AbstractAlignmentScoring<S extends Sequence<S>>
AbstractAlignmentScoring - abstract scoring system class used for alignment procedure.
|
class |
AffineGapAlignmentScoring<S extends Sequence<S>>
AffineGapAlignmentScoring - scoring which uses different penalties for gap opening and gap extension
|
class |
LinearGapAlignmentScoring<S extends Sequence<S>>
LinearGapAlignmentScoring - scoring system which uses penalty for gap
|
| Modifier and Type | Method and Description |
|---|---|
AlignmentScoring<S> |
BandedAlignerParameters.getScoring()
Returns scoring used for alignment.
|
| Modifier and Type | Method and Description |
|---|---|
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.alignLocal(AlignmentScoring<S> alignmentScoring,
S seq1,
S seq2)
Performs local alignment
|
static <S extends Sequence<S>> |
Aligner.alignOnlySubstitutions(S seq1,
S seq2,
int seq1From,
int seq1Length,
int seq2From,
int seq2Length,
AlignmentScoring<S> scoring) |
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) |
int |
Alignment.calculateScore(AlignmentScoring<S> scoring)
Calculates score for this alignment using another scoring.
|
static <S extends Sequence<S>> |
AlignmentUtils.calculateScore(S seq1,
Mutations<S> mutations,
AlignmentScoring<S> scoring)
Calculates score of alignment
|
static <S extends Sequence<S>> |
AlignmentUtils.calculateScore(S seq1,
Range seq1Range,
Mutations<S> mutations,
AlignmentScoring<S> scoring)
Calculates score of alignment
|
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.rightTrimAlignment(Alignment<S> alignment,
AlignmentScoring<S> scoring)
Try increase total alignment score by partially (or fully) trimming it from right side.
|
BandedAlignerParameters |
BandedAlignerParameters.setScoring(AlignmentScoring<S> scoring)
Sets scoring used for alignment.
|
| Constructor and Description |
|---|
Alignment(S sequence1,
Mutations<S> mutations,
AlignmentScoring<S> scoring) |
Alignment(S sequence1,
Mutations<S> mutations,
Range sequence1Range,
Range sequence2Range,
AlignmentScoring<S> scoring) |
BandedAlignerParameters(AlignmentScoring<S> scoring,
int width,
int stopPenalty) |
| Modifier and Type | Method and Description |
|---|---|
AlignmentScoring<S> |
SimpleBatchAlignerParameters.getScoring() |
AlignmentScoring<NucleotideSequence> |
BatchAlignerWithBaseParameters.getScoring() |
| Modifier and Type | Method and Description |
|---|---|
void |
SimpleBatchAlignerParameters.setScoring(AlignmentScoring<S> scoring) |
| Constructor and Description |
|---|
SimpleBatchAlignerParameters(int maxHits,
float relativeMinScore,
float absoluteMinScore,
boolean global,
AlignmentScoring<S> scoring) |
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