Inheritance diagram for broad.core.annotation.GenomicAnnotation:

Collaboration diagram for broad.core.annotation.GenomicAnnotation:

Public Member Functions
void	setReversedOrientation (boolean isInReversedOrientation)

int	getLength ()

Sequence	getSequence ()

void	setSequence (Sequence seq)

void	setOrientation (String orientationString)

Strand	getOrientation ()

String	getId ()

void	setId (String id)

int	getFivePrimeBases ()

int	getThreePrimeBases ()

boolean	isFlankedBy (TwoSubjectAnnotation twoSubjectAnnotation, int buffer)

int	getOrientedStart ()

int	getOrientedEnd ()

String	getLocationString ()

boolean	mayHaveBlocks ()

List<?extends Annotation >	getBlocks ()

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

Public Member Functions inherited from broad.core.annotation.Feature
String	getName ()

double	getScore ()

Public Member Functions inherited from broad.core.annotation.LightweightGenomicAnnotation
int	getStart ()

int	getEnd ()

long	getMiddle ()

double	getScore ()

String	getName ()

void	setScore (double score)

void	setName (String name)

int	length ()

void	setStart (int start)

void	setEnd (int end)

String	getChromosome ()

void	setChromosome (String chr)

boolean	inReversedOrientation ()

int	getDistanceTo (LightweightGenomicAnnotation other)

String	toUCSC ()

int	getOverlap (LightweightGenomicAnnotation other)

boolean	contains (LightweightGenomicAnnotation other)

void	takeIntersection (LightweightGenomicAnnotation other)

void	takeUnion (LightweightGenomicAnnotation other)

void	stitchTo (LightweightGenomicAnnotation other)

String	getChromosomeString ()

double	getExtraScore (int i)

void	addExtraScore (double score)

List< Double >	getExtraScores ()

void	removeExtraScores ()

boolean	almostEqual (LightweightGenomicAnnotation other, int fudge)

Public Member Functions inherited from umms.core.annotation.Annotation
int	getSAMStart ()

int	getSAMEnd ()

String	getReferenceName ()

String	getChr ()

Strand	getStrand ()

boolean	hasOrientation ()

boolean	isNegativeStrand ()

int	numBlocks ()

List<?extends Annotation >	getBlocks (boolean oriented)

int	getSize ()

int	size ()

int	getLengthOnReference ()

boolean	isUnoriented ()

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)

void	shift (int delta)

void	moveToCoordinate (int coordinateInReference)

Annotation	copy ()

List< Annotation >	disect (Annotation a)

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

Annotation	minus (Annotation other)

Annotation	minus (Collection<?extends Annotation > others)

int	getDistanceTo (Annotation other)

String	toBED ()

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

String	toShortBED ()

String	toBEDGraph ()

String	getFullInfoString ()

boolean	overlaps (Annotation other, int buffer)

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

boolean	overlaps (Annotation other)

boolean	overlaps (Collection<?extends Annotation > others)

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

boolean	overlaps (Annotation other, boolean considerOrientation)

boolean	overlapsStranded (Annotation other)

int	getOverlap (Annotation other)

boolean	contains (Annotation other)

Annotation	union (Annotation other)

Annotation	intersect (Annotation other)

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

int	compareToAnnotation (Annotation b)

void	stitchTo (Annotation next)

String	toCigar ()

boolean	fullyContains (Annotation annotation)

Annotation	complement ()

boolean	equals (Annotation other, boolean useOrientation)

Collection<?extends Annotation >	getSpliceConnections ()

int	getMidpoint ()

Member Function Documentation

void broad.core.annotation.GenomicAnnotation.addBlock	(	String	name,
		int	start,
		int	end
	)

Adds a block to the annotation if it supports blocks

Implemented in broad.core.annotation.BasicGenomicAnnotation, and broad.core.annotation.BED.

List<? extends Annotation> broad.core.annotation.GenomicAnnotation.getBlocks ( )

Returns a list of blocks if the annotations has any (

See also: containsBlocks)

Implements umms.core.annotation.Annotation.

Implemented in broad.core.annotation.BED.

int broad.core.annotation.GenomicAnnotation.getFivePrimeBases ( )

Returns: int - the five prime buffer (i.e. bases not belonging to the annotation proper).

Implemented in broad.core.annotation.BasicGenomicAnnotation.

String broad.core.annotation.GenomicAnnotation.getId ( )

Genomic annotation integer identification if such exists.

Implemented in broad.core.annotation.BasicGenomicAnnotation.

int broad.core.annotation.GenomicAnnotation.getLength ( )

Deprecated:

Use length() instead

Returns

Implemented in broad.core.annotation.BasicGenomicAnnotation.

String broad.core.annotation.GenomicAnnotation.getLocationString ( )

Returns a string of the form chr<chromosome>:start-end

Returns

Strand broad.core.annotation.GenomicAnnotation.getOrientation ( )

Returns: orientation or strand

Implements broad.core.annotation.LightweightGenomicAnnotation.

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int broad.core.annotation.GenomicAnnotation.getOrientedEnd ( )

Gets the end of the annotation considering its orientation

Returns: getEnd() if the feature is in direct orientation or getStart() otherwise

Implements umms.core.annotation.Annotation.

Implemented in broad.core.annotation.BasicGenomicAnnotation.

int broad.core.annotation.GenomicAnnotation.getOrientedStart ( )

Gets the start of the annotation considering its orientation

Returns: getStart() if the feature is in direct orientation or getEnd() otherwise

Implements umms.core.annotation.Annotation.

Implemented in broad.core.annotation.BasicGenomicAnnotation.

Sequence broad.core.annotation.GenomicAnnotation.getSequence ( )

Implemented in broad.core.annotation.BasicGenomicAnnotation.

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int broad.core.annotation.GenomicAnnotation.getThreePrimeBases ( )

Returns: int - the three prime buffer (i.e. bases not belonging to the annotation proper).

Implemented in broad.core.annotation.BasicGenomicAnnotation.

boolean broad.core.annotation.GenomicAnnotation.isFlankedBy	(	TwoSubjectAnnotation	twoSubjectAnnotation,
		int	buffer
	)

Checks whether a twoSubjectAnnotation flanks the instance

Implemented in broad.core.annotation.BasicGenomicAnnotation.

boolean broad.core.annotation.GenomicAnnotation.mayHaveBlocks ( )

Returns true if the annotation (like a full BED or a RefSeq) has sub annotations like exons or blocks

Implemented in broad.core.annotation.BasicGenomicAnnotation, and broad.core.annotation.BED.

void broad.core.annotation.GenomicAnnotation.setId ( String id )

Implemented in broad.core.annotation.BasicGenomicAnnotation.

void broad.core.annotation.GenomicAnnotation.setOrientation ( String orientationString )

Implements broad.core.annotation.LightweightGenomicAnnotation.

void broad.core.annotation.GenomicAnnotation.setReversedOrientation ( boolean isInReversedOrientation )

void broad.core.annotation.GenomicAnnotation.setSequence ( Sequence seq )

Implemented in broad.core.annotation.BasicGenomicAnnotation.

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

java/broad/core/annotation/GenomicAnnotation.java

Public Member Functions

Member Function Documentation