| Package | Description |
|---|---|
| com.milaboratory.core | |
| com.milaboratory.core.alignment | |
| com.milaboratory.core.alignment.benchmark | |
| com.milaboratory.core.alignment.blast | |
| 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.io.sequence.fasta | |
| com.milaboratory.core.mutations | |
| com.milaboratory.core.mutations.generator | |
| com.milaboratory.core.sequence | |
| com.milaboratory.core.sequence.provider | |
| com.milaboratory.util |
| Modifier and Type | Field and Description |
|---|---|
static Comparator<Range> |
Range.COMPARATOR_BY_FROM |
| Modifier and Type | Method and Description |
|---|---|
Range |
Range.expand(int offset) |
Range |
Range.expand(int leftOffset,
int rightOffset) |
Range |
Range.getAbsoluteRangeFor(Range relativeRange)
Reverse operation for
getRelativeRangeOf(Range). |
Range |
Range.getRelativeRangeOf(Range absoluteRange) |
Range |
Range.intersection(Range other)
Returns intersection range with
other range. |
Range |
Range.intersectionWithTouch(Range other)
Returns intersection range with
other range. |
Range |
Range.inverse()
Returns reversed range.
|
Range |
Range.move(int offset)
Returns range moved using provided offset (e.g.
|
Range |
Range.reverse()
Return reversed range.
|
Range |
Range.tryMerge(Range other)
Returns union range with
other range. |
| Modifier and Type | Method and Description |
|---|---|
List<Range> |
Range.without(Range range)
Subtract provided range and return list of ranges contained in current range and not intersecting with other
range.
|
| Modifier and Type | Method and Description |
|---|---|
int |
Range.compareTo(Range o) |
boolean |
Range.contains(Range other)
Returns
true if range contains other range. |
Range |
Range.getAbsoluteRangeFor(Range relativeRange)
Reverse operation for
getRelativeRangeOf(Range). |
Range |
Range.getRelativeRangeOf(Range absoluteRange) |
boolean |
Range.hasSameDirection(Range other)
Returns true if two ranges has the same direction.
|
Range |
Range.intersection(Range other)
Returns intersection range with
other range. |
Range |
Range.intersectionWithTouch(Range other)
Returns intersection range with
other range. |
boolean |
Range.intersectsWith(Range other)
Returns
true if range intersects with other range. |
boolean |
Range.intersectsWithOrTouches(Range other)
Returns
true if range intersects with or touches other range. |
Range |
Range.tryMerge(Range other)
Returns union range with
other range. |
List<Range> |
Range.without(Range range)
Subtract provided range and return list of ranges contained in current range and not intersecting with other
range.
|
| Modifier and Type | Method and Description |
|---|---|
Range |
Alignment.convertToSeq1Range(Range rangeInSeq2)
Converts range in sequence2 to range in sequence1, or returns null if input range is not fully covered by
alignment
|
Range |
Alignment.convertToSeq2Range(Range rangeInSeq1)
Converts range in sequence1 to range in sequence2, or returns null if input range is not fully covered by
alignment
|
Range |
Alignment.getSequence1Range()
Returns aligned range of sequence1.
|
Range |
Alignment.getSequence2Range()
Returns aligned range of sequence2.
|
| 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.calculateScore(S seq1,
Range seq1Range,
Mutations<S> mutations,
AffineGapAlignmentScoring<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>> |
AlignmentUtils.calculateScore(S seq1,
Range seq1Range,
Mutations<S> mutations,
LinearGapAlignmentScoring<S> scoring)
Calculates score of alignment
|
Range |
Alignment.convertToSeq1Range(Range rangeInSeq2)
Converts range in sequence2 to range in sequence1, or returns null if input range is not fully covered by
alignment
|
Range |
Alignment.convertToSeq2Range(Range rangeInSeq1)
Converts range in sequence1 to range in sequence2, or returns null if input range is not fully covered by
alignment
|
| Constructor and Description |
|---|
Alignment(S sequence1,
Mutations<S> mutations,
Range sequence1Range,
Range sequence2Range,
AlignmentScoring<S> scoring) |
Alignment(S sequence1,
Mutations<S> mutations,
Range sequence1Range,
Range sequence2Range,
float score) |
AlignmentIteratorForward(Mutations<S> mutations,
Range seq1Range)
Create alignment iterator
|
AlignmentIteratorForward(Mutations<S> mutations,
Range seq1Range,
int seq2Position)
Create alignment iterator
|
AlignmentIteratorReverse(Mutations<S> mutations,
Range seq1Range)
Create alignment iterator
|
AlignmentIteratorReverse(Mutations<S> mutations,
Range seq1Range,
int seq2Position)
Create alignment iterator
|
| Modifier and Type | Field and Description |
|---|---|
List<Range> |
KAlignerQuery.queryClusters |
List<Range> |
KAlignerQuery.targetClusters |
| Constructor and Description |
|---|
KAlignerQuery(int targetId,
List<Range> queryClusters,
List<Range> targetClusters,
List<Mutations<NucleotideSequence>> mutationsInTarget,
NucleotideSequence query,
Alignment<NucleotideSequence> expectedAlignment) |
KAlignerQuery(int targetId,
List<Range> queryClusters,
List<Range> targetClusters,
List<Mutations<NucleotideSequence>> mutationsInTarget,
NucleotideSequence query,
Alignment<NucleotideSequence> expectedAlignment) |
| Modifier and Type | Method and Description |
|---|---|
Range |
BlastHit.getSubjectRange() |
| 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 NBlastHitExt |
NBlastAlignerExt.createHit(Alignment<NucleotideSequence> alignment,
double score,
double bitScore,
double eValue,
Range subjectRange,
String subjectId,
String subjectTitle) |
protected abstract H |
BlastAlignerExtAbstract.createHit(Alignment<S> alignment,
double score,
double bitScore,
double eValue,
Range subjectRange,
String subjectId,
String subjectTitle) |
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,
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,
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,
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 |
|---|---|
Range |
RangeSerializer.read(PrimitivI input) |
| Modifier and Type | Method and Description |
|---|---|
void |
RangeSerializer.write(PrimitivO output,
Range object) |
| Modifier and Type | Method and Description |
|---|---|
S |
RandomAccessFastaReader.getSequence(int id,
Range range) |
S |
RandomAccessFastaReader.getSequence(String id,
Range range) |
| Modifier and Type | Method and Description |
|---|---|
Range |
Mutations.getMutatedRange() |
| Modifier and Type | Method and Description |
|---|---|
void |
CoverageCounter.aggregate(Range r,
CoverageCounter.Provider provider) |
void |
CoverageCounter.aggregate(Range r,
int delta) |
Mutations<S> |
Mutations.extractAbsoluteMutationsForRange(Range range)
Extracts mutations for a range of positions in the original sequence.
|
Mutations<S> |
Mutations.extractRelativeMutationsForRange(Range range)
Extracts mutations for a range of positions in the original sequence and performs shift of corresponding
positions (moves them to
-range.from). |
Mutations<S> |
Mutations.removeMutationsInRange(Range range)
|
Mutations<S> |
Mutations.removeMutationsInRanges(Range... ranges)
|
| Constructor and Description |
|---|
CoverageCounter(Range seqRange) |
MutationConsensusBuilder(Range seqRange) |
| Modifier and Type | Method and Description |
|---|---|
static Mutations<NucleotideSequence> |
MutationsGenerator.generateMutations(NucleotideSequence sequence,
NucleotideMutationModel model,
Range range) |
| Modifier and Type | Method and Description |
|---|---|
SequenceQuality |
SequenceQuality.getRange(Range range)
Returns substring of current quality scores line.
|
S |
Seq.getRange(Range range)
Returns a subsequence of this bounded by specified
range. |
NucleotideSequence |
NucleotideSequence.getRange(Range range) |
NSequenceWithQuality |
NSequenceWithQuality.getRange(Range range) |
S |
AbstractSeq.getRange(Range range) |
SequenceWithQuality<S> |
SequenceWithQuality.getSubSequence(Range range)
Returns subsequence with its quality with starting (inclusive) and ending (exclusive) points defined by
range. |
| Modifier and Type | Method and Description |
|---|---|
Range |
SequenceProviderIndexOutOfBoundsException.getAvailableRange() |
| Modifier and Type | Method and Description |
|---|---|
Map.Entry<Range,S> |
CachedSequenceProvider.ensureEntry(Range range) |
Set<Map.Entry<Range,S>> |
CachedSequenceProvider.entrySet() |
| Modifier and Type | Method and Description |
|---|---|
Map.Entry<Range,S> |
CachedSequenceProvider.ensureEntry(Range range) |
S |
SequenceProviderUtils.LazySequenceProvider.getRegion(Range range) |
S |
SequenceProvider.getRegion(Range range)
Retrieves specified region of the sequence.
|
S |
CachedSequenceProvider.getRegion(Range range) |
void |
CachedSequenceProvider.setRegion(Range range,
S seq) |
static <S extends Sequence<S>> |
SequenceProviderUtils.subProvider(SequenceProvider<S> provider,
Range targetRange) |
| Constructor and Description |
|---|
SequenceProviderIndexOutOfBoundsException(Range availableRange) |
| Modifier and Type | Method and Description |
|---|---|
Range |
RangeMap.enclosingRange()
Return range enclosing all range-keys of this container.
|
| Modifier and Type | Method and Description |
|---|---|
Set<Map.Entry<Range,T>> |
RangeMap.entrySet() |
List<Map.Entry<Range,T>> |
RangeMap.findAllIntersecting(Range range) |
List<Map.Entry<Range,T>> |
RangeMap.findAllIntersectingOrTouching(Range range) |
Map.Entry<Range,T> |
RangeMap.findContaining(Range range) |
Map.Entry<Range,T> |
RangeMap.findSingleIntersection(Range range) |
| Modifier and Type | Method and Description |
|---|---|
boolean |
RangeMap.containIntersectingRanges(Range range) |
List<Map.Entry<Range,T>> |
RangeMap.findAllIntersecting(Range range) |
List<Map.Entry<Range,T>> |
RangeMap.findAllIntersectingOrTouching(Range range) |
Map.Entry<Range,T> |
RangeMap.findContaining(Range range) |
Map.Entry<Range,T> |
RangeMap.findSingleIntersection(Range range) |
void |
RangeMap.put(Range range,
T value) |
T |
RangeMap.remove(Range range) |
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