Inheritance diagram for broad.core.sequence.SequenceRegion:

Collaboration diagram for broad.core.sequence.SequenceRegion:

Public Member Functions
	SequenceRegion (String containingSequenceId)

	SequenceRegion (String containingSequenceId, String chr, int start, int end)

	SequenceRegion (String containingSequenceId, Annotation annotation)

int	getRegionEnd ()

void	setRegionEnd (int regionEnd)

int	getRegionStart ()

void	setRegionStart (int regionStart)

WindowSlider	getSlider (int windowSize, int overlap)

int	length ()

Strand	getOrientation ()

void	setReversedOrientation (boolean reversed)

String	getContainingSequenceId ()

String	getId ()

int	getStart ()

int	getEnd ()

double	getScore ()

void	setScore (double score)

double	getExtraScore (int i)

String	getName ()

void	setId (String id)

void	setName (String name)

boolean	inReversedOrientation ()

long	getMiddle ()

void	setStart (int start)

void	setEnd (int end)

Sequence	getSequence ()

void	setSequence (Sequence seq)

String	getChromosome ()

void	setChromosome (String chr)

boolean	overlaps (LightweightGenomicAnnotation other, int buffer)

boolean	overlaps (LightweightGenomicAnnotation other)

int	getOverlap (LightweightGenomicAnnotation other)

Annotation	minus (Annotation other)

Annotation	minus (List<?extends Annotation > others)

void	takeIntersection (LightweightGenomicAnnotation other)

void	takeUnion (LightweightGenomicAnnotation other)

void	stitchTo (LightweightGenomicAnnotation other)

boolean	isFlankedBy (TwoSubjectAnnotation twoSubjectAnnotation, int buffer)

int	getFivePrimeBases ()

int	getThreePrimeBases ()

String	toString ()

int	getAbsoluteStart (int absoluteStart)

int	getAbsoluteEnd (int absoluteStart)

String	getLocationString ()

String	getChromosomeString ()

SequenceRegion	extractRegionBasedOnGC (float targetGC, int size, int buffer)

boolean	contains (LightweightGenomicAnnotation other)

int	getDistanceTo (LightweightGenomicAnnotation other)

void	setOrientation (String orientation)

int	compareTo (GenomicAnnotation arg0)

List< Annotation >	disect (Annotation a)

List< Annotation >	disect (List<?extends Annotation > disectors)

SequenceRegion	getRegion (int start, int end)

int	getOrientedEnd ()

int	getOrientedStart ()

boolean	isUnoriented ()

void	addBlock (String name, int start, int end)

List<?extends Annotation >	getBlocks ()

List<?extends Annotation >	getBlocks (boolean oriented)

boolean	mayHaveBlocks ()

String	toUCSC ()

int	getLength ()

boolean	overlaps (Collection<?extends Annotation > others, int buffer)

boolean	overlaps (Collection<?extends Annotation > others)

void	removeExtraScores ()

int	compareTo (LightweightGenomicAnnotation b)

LightweightGenomicAnnotation	intersect (LightweightGenomicAnnotation other)

List< Annotation >	intersect (List<?extends Annotation > annotations)

double	percentGC ()

void	addExtraScore (double score)

List< Double >	getExtraScores ()

boolean	almostEqual (LightweightGenomicAnnotation other, int fudge)

int	getSAMStart ()

int	getSAMEnd ()

String	getReferenceName ()

String	getChr ()

Strand	getStrand ()

boolean	hasOrientation ()

int	numBlocks ()

int	getSize ()

int	size ()

int	getLengthOnReference ()

int	getReferenceCoordinateAtPosition (int positionInAnnotation)

int	getPositionAtReferenceCoordinate (int referenceCoordinate)

int	getReferenceCoordinateAtPosition (int positionInAnnotation, boolean ignoreOrientation)

int	getPositionAtReferenceCoordinate (int referenceCoordinate, boolean ignoreOrientation)

void	setOrientation (char orientation)

void	setOrientation (Strand orientation)

void	setOrientedStart (int orientedStart)

void	setOrientedEnd (int orientedEnd)

void	setReferenceName (String refName)

boolean	equals (Annotation other)

void	expand (int deltaStart, int deltaEnd)

Annotation	trim (int deltaStart, int deltaEnd)

Annotation	copy ()

int	getDistanceTo (Annotation other)

String	toBED ()

String	toShortBED ()

String	toBEDGraph ()

boolean	overlaps (Annotation other, int buffer)

boolean	overlaps (Annotation other)

boolean	overlaps (Annotation other, int buffer, boolean considerStrand)

boolean	overlapsStranded (Annotation other)

int	getOverlap (Annotation other)

boolean	contains (Annotation other)

Annotation	union (Annotation other)

Annotation	intersect (Annotation other)

int	compareToAnnotation (Annotation b)

void	stitchTo (Annotation next)

String	toCigar ()

boolean	fullyContains (Annotation annotation)

int	compareTo (Annotation arg0)

void	moveToCoordinate (int i)

void	shift (int delta)

boolean	isNegativeStrand ()

Annotation	complement ()

Annotation	minus (Collection<?extends Annotation > others)

boolean	equals (Annotation other, boolean useOrientation)

Collection<?extends Annotation >	getSpliceConnections ()

String	toBED (int r, int g, int b)

boolean	overlaps (Annotation other, boolean considerOrientation)

int	getMidpoint ()

String	getFullInfoString ()

Public Member Functions inherited from broad.core.sequence.Sequence
	Sequence (String id)

	Sequence (String id, boolean isLarge)

	Sequence (String id, int expectedSize)

String	getId ()

void	setForwardStrand (boolean isForwardStrand)

void	setId (String id)

void	unloadSequence ()

void	unloadEncodedSequence ()

void	unloadAllSequences ()

int	getLength ()

void	setCharAt (int position, char newCharacter) throws IllegalAccessException

String	getSequenceBases ()

void	setSequenceBases (String sequence)

void	append (String partialSequence)

Sequence	shuffle ()

void	append (char c)

boolean	isGap (int position)

List< GenomicAnnotation >	getSoftmaskedRegions ()

int	countSoftMaskedBases ()

void	maskSoftmaskedRegions ()

short[]	getEncodedSequence ()

Matrix	getVectorEncodedSequence ()

Matrix	encodeSequenceAsVector ()

short[]	encodeSequence ()

short[]	encodeSequenceIgnoreCase ()

short[]	encodeSequenceIgnoreCase (boolean distinguishMissingSequence)

List< Short >	compute454Flow (char[] flowOrder)

List< Short >	compute454Flow (char[] flowOrder, int start, int end)

float	gcContent ()

boolean	contains (String motif)

void	reverse ()

void	uppercase ()

void	mask (Annotation region, boolean softmask)

SequenceRegion	getRegion (int start, int end)

void	getRegion (SequenceRegion region)

void	getRegion (SequenceRegion region, boolean softmask)

void	getRegion (SequenceRegion region, boolean softmask, Map< String, IntervalTree< Alignments >> okRepeats)

void	getRegions (List<?extends SequenceRegion > regions)

SequenceRegion	extractRegionBasedOnGC (float targetGC, int size, int buffer)

boolean	isForwardStrand ()

StringBuilder	getSequenceBuilder ()

int	getGapsSize ()

WindowSlider	getSlider (int windowSize, int overlap)

List< SequenceRegion >	chunk (int chunkSize, int chunkOverlap)

int	getEnd ()

List< int[]>	findUngappedSequenceChunks ()

Collection< Annotation >	getMatches (String s, int windowStart, int windowEnd, boolean includeRC)

Sequence	getSubSequence (SequenceRegion region, int extension)

Sequence	getSubSequence (String name, int start, int end, int extension)

Sequence	getSubSequence (String name, int start, int end)

Sequence	getSubsequence (Gene annot)

Sequence	getSubsequence (Annotation annot)

void	setCapacity (int size)

Sequence	scramble ()

Sequence	getAntisense ()

String	getRefseqGeneName ()

String	getRefseqSpeciesName ()

String	getRefseqRnaClassName ()

Map< String, KmerInfo >	buildKmerMap (int kmer)

Static Public Attributes
static final int	INF = Integer.MAX_VALUE

Static Public Attributes inherited from broad.core.sequence.Sequence
static final char[]	SHORT_READ_FLOW = {'T','A','C','G'}

static final char[]	LONG_READ_FLOW = {'G','A','T','C'}

static final short	SHORT_ENCODED_A = 0

static final short	SHORT_ENCODED_C = 1

static final short	SHORT_ENCODED_G = 2

static final short	SHORT_ENCODED_T = 3

static final short	SHORT_ENCODED_GAP = 4

static final short	SHORT_ENCODED_a = 5

static final short	SHORT_ENCODED_c = 6

static final short	SHORT_ENCODED_g = 7

static final short	SHORT_ENCODED_t = 8

static final short	SHORT_ENCODED_N = 9

Additional Inherited Members
Static Public Member Functions inherited from broad.core.sequence.Sequence
static short[]	encodeSequence (StringBuilder bases)

static short[]	encodeSequenceIgnoreCase (StringBuilder sequence)

static short[]	encodeSequenceIgnoreCase (StringBuilder sequence, boolean distinguishMissingSequence)

static float	computeGCContent (String dnaString)

static float[]	computeSequenceComposition (String dnaString)

static Sequence	reverseSequence (Sequence seq)

static String	reverseSequence (String seq)

static String	decode (short[] shortEncodedSequence)

static String	generateRandomSequence (int oligoSize)

static String	get3Prime (String seq, int numBases)

static Collection< String >	generateAll5Mers ()

static Collection< String >	generateAllKmers (int k)

static String	complement (String seq)

Constructor & Destructor Documentation

broad.core.sequence.SequenceRegion.SequenceRegion ( String containingSequenceId )

broad.core.sequence.SequenceRegion.SequenceRegion	(	String	containingSequenceId,
		String	chr,
		int	start,
		int	end
	)

broad.core.sequence.SequenceRegion.SequenceRegion	(	String	containingSequenceId,
		Annotation	annotation
	)

Member Function Documentation

void broad.core.sequence.SequenceRegion.addBlock	(	String	name,
		int	start,
		int	end
	)

void broad.core.sequence.SequenceRegion.addExtraScore ( double score )

boolean broad.core.sequence.SequenceRegion.almostEqual	(	LightweightGenomicAnnotation	other,
		int	fudge
	)

Checks whether two annotations differ by a small (fudge) factor

Parameters

fudge Maximum difference at either end or start to consider similar

Returns

int broad.core.sequence.SequenceRegion.compareTo ( GenomicAnnotation arg0 )

int broad.core.sequence.SequenceRegion.compareTo ( LightweightGenomicAnnotation b )

int broad.core.sequence.SequenceRegion.compareTo ( Annotation arg0 )

int broad.core.sequence.SequenceRegion.compareToAnnotation ( Annotation b )

Annotation broad.core.sequence.SequenceRegion.complement ( )

boolean broad.core.sequence.SequenceRegion.contains ( LightweightGenomicAnnotation other )

boolean broad.core.sequence.SequenceRegion.contains ( Annotation other )

Annotation broad.core.sequence.SequenceRegion.copy ( )

List<Annotation> broad.core.sequence.SequenceRegion.disect ( Annotation a )

List<Annotation> broad.core.sequence.SequenceRegion.disect ( List<?extends Annotation > disectors )

boolean broad.core.sequence.SequenceRegion.equals ( Annotation other )

boolean broad.core.sequence.SequenceRegion.equals	(	Annotation	other,
		boolean	useOrientation
	)

void broad.core.sequence.SequenceRegion.expand	(	int	deltaStart,
		int	deltaEnd
	)

SequenceRegion broad.core.sequence.SequenceRegion.extractRegionBasedOnGC	(	float	targetGC,
		int	size,
		int	buffer
	)

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boolean broad.core.sequence.SequenceRegion.fullyContains ( Annotation annotation )

int broad.core.sequence.SequenceRegion.getAbsoluteEnd ( int absoluteStart )

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int broad.core.sequence.SequenceRegion.getAbsoluteStart ( int absoluteStart )

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List<? extends Annotation> broad.core.sequence.SequenceRegion.getBlocks ( )

List<? extends Annotation> broad.core.sequence.SequenceRegion.getBlocks ( boolean oriented )

String broad.core.sequence.SequenceRegion.getChr ( )

String broad.core.sequence.SequenceRegion.getChromosome ( )

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String broad.core.sequence.SequenceRegion.getChromosomeString ( )

String broad.core.sequence.SequenceRegion.getContainingSequenceId ( )

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int broad.core.sequence.SequenceRegion.getDistanceTo ( LightweightGenomicAnnotation other )

int broad.core.sequence.SequenceRegion.getDistanceTo ( Annotation other )

int broad.core.sequence.SequenceRegion.getEnd ( )

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double broad.core.sequence.SequenceRegion.getExtraScore ( int i )

List<Double> broad.core.sequence.SequenceRegion.getExtraScores ( )

int broad.core.sequence.SequenceRegion.getFivePrimeBases ( )

String broad.core.sequence.SequenceRegion.getFullInfoString ( )

String broad.core.sequence.SequenceRegion.getId ( )

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int broad.core.sequence.SequenceRegion.getLength ( )

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int broad.core.sequence.SequenceRegion.getLengthOnReference ( )

String broad.core.sequence.SequenceRegion.getLocationString ( )

long broad.core.sequence.SequenceRegion.getMiddle ( )

int broad.core.sequence.SequenceRegion.getMidpoint ( )

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String broad.core.sequence.SequenceRegion.getName ( )

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Strand broad.core.sequence.SequenceRegion.getOrientation ( )

int broad.core.sequence.SequenceRegion.getOrientedEnd ( )

int broad.core.sequence.SequenceRegion.getOrientedStart ( )

int broad.core.sequence.SequenceRegion.getOverlap ( LightweightGenomicAnnotation other )

int broad.core.sequence.SequenceRegion.getOverlap ( Annotation other )

int broad.core.sequence.SequenceRegion.getPositionAtReferenceCoordinate ( int referenceCoordinate )

int broad.core.sequence.SequenceRegion.getPositionAtReferenceCoordinate	(	int	referenceCoordinate,
		boolean	ignoreOrientation
	)

int broad.core.sequence.SequenceRegion.getReferenceCoordinateAtPosition ( int positionInAnnotation )

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int broad.core.sequence.SequenceRegion.getReferenceCoordinateAtPosition	(	int	positionInAnnotation,
		boolean	ignoreOrientation
	)

String broad.core.sequence.SequenceRegion.getReferenceName ( )

SequenceRegion broad.core.sequence.SequenceRegion.getRegion	(	int	start,
		int	end
	)

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int broad.core.sequence.SequenceRegion.getRegionEnd ( )

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int broad.core.sequence.SequenceRegion.getRegionStart ( )

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int broad.core.sequence.SequenceRegion.getSAMEnd ( )

int broad.core.sequence.SequenceRegion.getSAMStart ( )

double broad.core.sequence.SequenceRegion.getScore ( )

Sequence broad.core.sequence.SequenceRegion.getSequence ( )

int broad.core.sequence.SequenceRegion.getSize ( )

WindowSlider broad.core.sequence.SequenceRegion.getSlider	(	int	windowSize,
		int	overlap
	)

Collection<? extends Annotation> broad.core.sequence.SequenceRegion.getSpliceConnections ( )

int broad.core.sequence.SequenceRegion.getStart ( )

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Strand broad.core.sequence.SequenceRegion.getStrand ( )

int broad.core.sequence.SequenceRegion.getThreePrimeBases ( )

boolean broad.core.sequence.SequenceRegion.hasOrientation ( )

boolean broad.core.sequence.SequenceRegion.inReversedOrientation ( )

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LightweightGenomicAnnotation broad.core.sequence.SequenceRegion.intersect ( LightweightGenomicAnnotation other )

List<Annotation> broad.core.sequence.SequenceRegion.intersect ( List<?extends Annotation > annotations )

Annotation broad.core.sequence.SequenceRegion.intersect ( Annotation other )

boolean broad.core.sequence.SequenceRegion.isFlankedBy	(	TwoSubjectAnnotation	twoSubjectAnnotation,
		int	buffer
	)

boolean broad.core.sequence.SequenceRegion.isNegativeStrand ( )

boolean broad.core.sequence.SequenceRegion.isUnoriented ( )

int broad.core.sequence.SequenceRegion.length ( )

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boolean broad.core.sequence.SequenceRegion.mayHaveBlocks ( )

Annotation broad.core.sequence.SequenceRegion.minus ( Annotation other )

Annotation broad.core.sequence.SequenceRegion.minus ( List<?extends Annotation > others )

Annotation broad.core.sequence.SequenceRegion.minus ( Collection<?extends Annotation > others )

void broad.core.sequence.SequenceRegion.moveToCoordinate ( int i )

int broad.core.sequence.SequenceRegion.numBlocks ( )

boolean broad.core.sequence.SequenceRegion.overlaps	(	LightweightGenomicAnnotation	other,
		int	buffer
	)

boolean broad.core.sequence.SequenceRegion.overlaps ( LightweightGenomicAnnotation other )

boolean broad.core.sequence.SequenceRegion.overlaps	(	Collection<?extends Annotation >	others,
		int	buffer
	)

boolean broad.core.sequence.SequenceRegion.overlaps ( Collection<?extends Annotation > others )

boolean broad.core.sequence.SequenceRegion.overlaps	(	Annotation	other,
		int	buffer
	)

boolean broad.core.sequence.SequenceRegion.overlaps ( Annotation other )

boolean broad.core.sequence.SequenceRegion.overlaps	(	Annotation	other,
		int	buffer,
		boolean	considerStrand
	)

boolean broad.core.sequence.SequenceRegion.overlaps	(	Annotation	other,
		boolean	considerOrientation
	)

boolean broad.core.sequence.SequenceRegion.overlapsStranded ( Annotation other )

double broad.core.sequence.SequenceRegion.percentGC ( )

void broad.core.sequence.SequenceRegion.removeExtraScores ( )

void broad.core.sequence.SequenceRegion.setChromosome ( String chr )

void broad.core.sequence.SequenceRegion.setEnd ( int end )

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void broad.core.sequence.SequenceRegion.setId ( String id )

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void broad.core.sequence.SequenceRegion.setName ( String name )

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void broad.core.sequence.SequenceRegion.setOrientation ( String orientation )

void broad.core.sequence.SequenceRegion.setOrientation ( char orientation )

void broad.core.sequence.SequenceRegion.setOrientation ( Strand orientation )

void broad.core.sequence.SequenceRegion.setOrientedEnd ( int orientedEnd )

void broad.core.sequence.SequenceRegion.setOrientedStart ( int orientedStart )

void broad.core.sequence.SequenceRegion.setReferenceName ( String refName )

void broad.core.sequence.SequenceRegion.setRegionEnd ( int regionEnd )

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void broad.core.sequence.SequenceRegion.setRegionStart ( int regionStart )

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void broad.core.sequence.SequenceRegion.setReversedOrientation ( boolean reversed )

void broad.core.sequence.SequenceRegion.setScore ( double score )

void broad.core.sequence.SequenceRegion.setSequence ( Sequence seq )

void broad.core.sequence.SequenceRegion.setStart ( int start )

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void broad.core.sequence.SequenceRegion.shift ( int delta )

int broad.core.sequence.SequenceRegion.size ( )

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void broad.core.sequence.SequenceRegion.stitchTo ( LightweightGenomicAnnotation other )

void broad.core.sequence.SequenceRegion.stitchTo ( Annotation next )

void broad.core.sequence.SequenceRegion.takeIntersection ( LightweightGenomicAnnotation other )

void broad.core.sequence.SequenceRegion.takeUnion ( LightweightGenomicAnnotation other )

String broad.core.sequence.SequenceRegion.toBED ( )

String broad.core.sequence.SequenceRegion.toBED	(	int	r,
		int	g,
		int	b
	)

String broad.core.sequence.SequenceRegion.toBEDGraph ( )

String broad.core.sequence.SequenceRegion.toCigar ( )

String broad.core.sequence.SequenceRegion.toShortBED ( )

String broad.core.sequence.SequenceRegion.toString ( )

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String broad.core.sequence.SequenceRegion.toUCSC ( )

Annotation broad.core.sequence.SequenceRegion.trim	(	int	deltaStart,
		int	deltaEnd
	)

Annotation broad.core.sequence.SequenceRegion.union ( Annotation other )

Member Data Documentation

final int broad.core.sequence.SequenceRegion.INF = Integer.MAX_VALUE

static

The documentation for this class was generated from the following file:

java/broad/core/sequence/SequenceRegion.java

Public Member Functions

Static Public Attributes

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation