| Modifier and Type | Field and Description |
|---|---|
protected BitArray |
AlignmentHelper.match |
| Constructor and Description |
|---|
AlignmentHelper(String seq1String,
String seq2String,
int[] seq1Position,
int[] seq2Position,
BitArray match) |
AlignmentHelper(String seq1String,
String seq2String,
int[] seq1Position,
int[] seq2Position,
BitArray match,
int offset) |
| Modifier and Type | Method and Description |
|---|---|
BitArray |
BatchAlignerWithBaseWithFilter.createFilter(cc.redberry.primitives.Filter<P> filter) |
| Modifier and Type | Method and Description |
|---|---|
AlignmentResult<H> |
BatchAlignerWithBaseWithFilter.align(S sequence,
int from,
int to,
BitArray filter) |
| Modifier and Type | Method and Description |
|---|---|
BitArray |
KAligner.createFilter(cc.redberry.primitives.Filter<P> filter) |
| Modifier and Type | Method and Description |
|---|---|
KMappingResult |
KMapper.align(NucleotideSequence sequence,
int from,
int to,
BitArray filter)
Performs an alignment for a part of the target sequence.
|
AlignmentResult<KAlignmentHit<P>> |
KAligner.align(NucleotideSequence sequence,
int from,
int to,
BitArray filter) |
KAlignmentResult<P> |
KAligner.align(NucleotideSequence sequence,
int from,
int to,
boolean restrictToRange,
BitArray filter)
Performs a comprehensive alignment of a sequence.
|
| Modifier and Type | Method and Description |
|---|---|
BitArray |
KAligner2.createFilter(cc.redberry.primitives.Filter<P> filter) |
| Modifier and Type | Method and Description |
|---|---|
KMappingResult2 |
KMapper2.align(NucleotideSequence sequence,
int from,
int to,
BitArray filter)
Performs an alignment for a part of the target sequence.
|
KAlignmentResult2<P> |
KAligner2.align(NucleotideSequence query,
int from,
int to,
BitArray filter) |
| Modifier and Type | Method and Description |
|---|---|
BitArray |
BitArray.clone() |
static BitArray |
BitArray.construct(byte[] data,
int size) |
BitArray |
BitArray.getRange(int from,
int to) |
| Modifier and Type | Method and Description |
|---|---|
void |
BitArray.and(BitArray bitArray) |
static byte[] |
BitArray.extractRawDataArray(BitArray array) |
boolean |
BitArray.intersects(BitArray bitArray) |
void |
BitArray.loadValueFrom(BitArray bitArray) |
void |
BitArray.or(BitArray bitArray) |
void |
BitArray.set(BitArray ba) |
void |
BitArray.xor(BitArray bitArray) |
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