Uses of Class
com.milaboratory.core.Range

Packages that use Range

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

Uses of Range in com.milaboratory.core

Fields in com.milaboratory.core with type parameters of type Range

Modifier and Type	Field and Description
static Comparator<Range>	Range.COMPARATOR_BY_FROM

Methods in com.milaboratory.core that return Range

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.

Methods in com.milaboratory.core that return types with arguments of type 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.

Methods in com.milaboratory.core with parameters of type 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.

Uses of Range in com.milaboratory.core.alignment

Methods in com.milaboratory.core.alignment that return 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.

Methods in com.milaboratory.core.alignment with parameters of type Range

Modifier and Type	Method and Description
static <S extends Sequence<S>> MultiAlignmentHelper	MultiAlignmentHelper.build(MultiAlignmentHelper.Settings settings, Range subjectRange, Alignment<S>... alignments)
static <S extends Sequence<S>> MultiAlignmentHelper	MultiAlignmentHelper.build(MultiAlignmentHelper.Settings settings, Range subjectRange, S subject, Alignment<S>... alignments)
static <S extends Sequence<S>> int	AlignmentUtils.calculateScore(S seq1, Range seq1Range, Mutations<S> mutations, AffineGapAlignmentScoring<S> scoring) Calculates score of alignment
static <S extends Sequence<S>> int	AlignmentUtils.calculateScore(S seq1, Range seq1Range, Mutations<S> mutations, AlignmentScoring<S> scoring) Calculates score of alignment
static <S extends Sequence<S>> int	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

Constructors in com.milaboratory.core.alignment with parameters of type Range

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

Uses of Range in com.milaboratory.core.alignment.benchmark

Fields in com.milaboratory.core.alignment.benchmark with type parameters of type Range

Modifier and Type	Field and Description
List<Range>	KAlignerQuery.queryClusters
List<Range>	KAlignerQuery.targetClusters

Constructor parameters in com.milaboratory.core.alignment.benchmark with type arguments of type Range

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)

Uses of Range in com.milaboratory.core.alignment.blast

Methods in com.milaboratory.core.alignment.blast that return Range

Modifier and Type	Method and Description
Range	BlastHit.getSubjectRange()

Methods in com.milaboratory.core.alignment.blast with parameters of type Range

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)

Constructors in com.milaboratory.core.alignment.blast with parameters of type Range

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)

Uses of Range in com.milaboratory.core.io.binary

Methods in com.milaboratory.core.io.binary that return Range

Modifier and Type	Method and Description
Range	RangeSerializer.read(PrimitivI input)

Methods in com.milaboratory.core.io.binary with parameters of type Range

Modifier and Type	Method and Description
void	RangeSerializer.write(PrimitivO output, Range object)

Uses of Range in com.milaboratory.core.io.sequence.fasta

Methods in com.milaboratory.core.io.sequence.fasta with parameters of type Range

Modifier and Type	Method and Description
S	RandomAccessFastaReader.getSequence(int id, Range range)
S	RandomAccessFastaReader.getSequence(String id, Range range)

Uses of Range in com.milaboratory.core.mutations

Methods in com.milaboratory.core.mutations that return Range

Modifier and Type	Method and Description
Range	Mutations.getMutatedRange()

Methods in com.milaboratory.core.mutations with parameters of type Range

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) See Mutations.removeMutationsInRange(int, int).
Mutations<S>	Mutations.removeMutationsInRanges(Range... ranges) See Mutations.removeMutationsInRange(int, int).

Constructors in com.milaboratory.core.mutations with parameters of type Range

Constructor and Description
CoverageCounter(Range seqRange)
MutationConsensusBuilder(Range seqRange)

Uses of Range in com.milaboratory.core.mutations.generator

Methods in com.milaboratory.core.mutations.generator with parameters of type Range

Modifier and Type	Method and Description
static Mutations<NucleotideSequence>	MutationsGenerator.generateMutations(NucleotideSequence sequence, NucleotideMutationModel model, Range range)

Uses of Range in com.milaboratory.core.sequence

Methods in com.milaboratory.core.sequence with parameters of type 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.

Uses of Range in com.milaboratory.core.sequence.provider

Methods in com.milaboratory.core.sequence.provider that return Range

Modifier and Type	Method and Description
Range	SequenceProviderIndexOutOfBoundsException.getAvailableRange()

Methods in com.milaboratory.core.sequence.provider that return types with arguments of type Range

Modifier and Type	Method and Description
Map.Entry<Range,S>	CachedSequenceProvider.ensureEntry(Range range)
Set<Map.Entry<Range,S>>	CachedSequenceProvider.entrySet()

Methods in com.milaboratory.core.sequence.provider with parameters of type Range

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>> SequenceProvider<S>	SequenceProviderUtils.subProvider(SequenceProvider<S> provider, Range targetRange)

Constructors in com.milaboratory.core.sequence.provider with parameters of type Range

Constructor and Description
SequenceProviderIndexOutOfBoundsException(Range availableRange)

Uses of Range in com.milaboratory.util

Methods in com.milaboratory.util that return Range

Modifier and Type	Method and Description
Range	RangeMap.enclosingRange() Return range enclosing all range-keys of this container.

Methods in com.milaboratory.util that return types with arguments of type Range

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)

Methods in com.milaboratory.util with parameters of type 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)