Inheritance diagram for broad.core.annotation.LightweightGenomicAnnotation:

Collaboration diagram for broad.core.annotation.LightweightGenomicAnnotation:

Public Member Functions
int	getStart ()

int	getEnd ()

long	getMiddle ()

double	getScore ()

String	getName ()

void	setScore (double score)

void	setName (String name)

Strand	getOrientation ()

void	setOrientation (String orientation)

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 ()

List<?extends Annotation >	getBlocks (boolean oriented)

int	getSize ()

int	size ()

int	getLengthOnReference ()

int	getOrientedStart ()

int	getOrientedEnd ()

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.LightweightGenomicAnnotation.addExtraScore ( double score )

Adds a new extra score

Parameters

score

Implemented in broad.core.annotation.BasicLightweightAnnotation.

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

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

Parameters

other	The other annotation
fudge	Maximum difference at either end or start to consider similar

Returns

Implemented in broad.core.annotation.BasicLightweightAnnotation.

boolean broad.core.annotation.LightweightGenomicAnnotation.contains ( LightweightGenomicAnnotation other )

Implemented in broad.core.annotation.BasicLightweightAnnotation.

String broad.core.annotation.LightweightGenomicAnnotation.getChromosome ( )

Implemented in broad.core.annotation.BasicLightweightAnnotation.

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String broad.core.annotation.LightweightGenomicAnnotation.getChromosomeString ( )

Returns the usual way to write a chromosome: chrSymbol if a chromosome or the full name of the scaffold

Implemented in broad.core.annotation.BasicLightweightAnnotation.

int broad.core.annotation.LightweightGenomicAnnotation.getDistanceTo ( LightweightGenomicAnnotation other )

Calculates the distance to the another genomic annotation.

Returns: 0 if the annotations overlap or the minimum between the edges otherwise.

Implemented in broad.core.annotation.BasicLightweightAnnotation.

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int broad.core.annotation.LightweightGenomicAnnotation.getEnd ( )

Returns: end of the annotation (exclusive)

Implements umms.core.annotation.Annotation.

double broad.core.annotation.LightweightGenomicAnnotation.getExtraScore ( int i )

Returns the ith extra score

Implemented in broad.core.annotation.BasicLightweightAnnotation.

List<Double> broad.core.annotation.LightweightGenomicAnnotation.getExtraScores ( )

Returns: all extra scores

Implemented in broad.core.annotation.BasicLightweightAnnotation.

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long broad.core.annotation.LightweightGenomicAnnotation.getMiddle ( )

Implemented in broad.core.annotation.BasicLightweightAnnotation.

String broad.core.annotation.LightweightGenomicAnnotation.getName ( )

Returns: the name of the annotation

Implements umms.core.annotation.Annotation.

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

Returns: orientation or strand

Implements umms.core.annotation.Annotation.

Implemented in broad.core.annotation.GenomicAnnotation.

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int broad.core.annotation.LightweightGenomicAnnotation.getOverlap ( LightweightGenomicAnnotation other )

Parameters

other GenomicAnnotation to check of overlap

Returns: true if the current instance overlaps with the other one. Returns the number of bases that overlap between the two annotations.

Parameters

other

Returns

Implemented in broad.core.annotation.BasicLightweightAnnotation.

double broad.core.annotation.LightweightGenomicAnnotation.getScore ( )

Implements umms.core.annotation.Annotation.

Implemented in broad.core.annotation.BasicLightweightAnnotation, and broad.pda.datastructures.Alignments.

int broad.core.annotation.LightweightGenomicAnnotation.getStart ( )

Returns: start of the annotation (inclusive)

Implements umms.core.annotation.Annotation.

boolean broad.core.annotation.LightweightGenomicAnnotation.inReversedOrientation ( )

Implemented in broad.core.annotation.BasicLightweightAnnotation.

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int broad.core.annotation.LightweightGenomicAnnotation.length ( )

Returns: length of the Annotation; if it has blocks, the gaps between blocks are not included

Implements umms.core.annotation.Annotation.

Implemented in broad.core.annotation.BasicLightweightAnnotation, and broad.pda.datastructures.Alignments.

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void broad.core.annotation.LightweightGenomicAnnotation.removeExtraScores ( )

removes extra scores

Implemented in broad.core.annotation.BasicLightweightAnnotation.

void broad.core.annotation.LightweightGenomicAnnotation.setChromosome ( String chr )

Implemented in broad.core.annotation.BasicLightweightAnnotation.

void broad.core.annotation.LightweightGenomicAnnotation.setEnd ( int end )

Sets a new end position. Will delete and/or truncate blocks if the new end position is less than the old one. Will extend the last block if the new end position is greater than old one.

Parameters

new	end position (ignoring orientation) of the annotation

Implements umms.core.annotation.Annotation.

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void broad.core.annotation.LightweightGenomicAnnotation.setName ( String name )

Parameters

name	name of the annotation

Implements umms.core.annotation.Annotation.

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void broad.core.annotation.LightweightGenomicAnnotation.setOrientation ( String orientation )

Implemented in broad.core.annotation.BasicLightweightAnnotation, and broad.core.annotation.GenomicAnnotation.

void broad.core.annotation.LightweightGenomicAnnotation.setScore ( double score )

Implements umms.core.annotation.Annotation.

Implemented in broad.core.annotation.BasicLightweightAnnotation.

void broad.core.annotation.LightweightGenomicAnnotation.setStart ( int start )

Sets a new start position. Will delete and/or truncate blocks if the new start position is greater than the old one. Will extend the first block if the new start position is less than old one.

Parameters

new	start position (ignoring orientation) of the annotation

Implements umms.core.annotation.Annotation.

void broad.core.annotation.LightweightGenomicAnnotation.stitchTo ( LightweightGenomicAnnotation other )

Enlarges this annotation by

Parameters

other

Implemented in broad.core.annotation.BasicLightweightAnnotation.

void broad.core.annotation.LightweightGenomicAnnotation.takeIntersection ( LightweightGenomicAnnotation other )

Change the current instance to represent its intersection with the provided annotation

Parameters

other

Implemented in broad.core.annotation.BasicLightweightAnnotation.

void broad.core.annotation.LightweightGenomicAnnotation.takeUnion ( LightweightGenomicAnnotation other )

Change the current instance to represent its union with the provided annotation

Parameters

GenomicAnnotation other

Implemented in broad.core.annotation.BasicLightweightAnnotation.

String broad.core.annotation.LightweightGenomicAnnotation.toUCSC ( )

Similar to getLocationString()

See also: getLocationString and provided only for backwards compatibility.

Implements umms.core.annotation.Annotation.

Implemented in broad.core.annotation.BasicLightweightAnnotation, and broad.pda.datastructures.Alignments.

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

java/broad/core/annotation/LightweightGenomicAnnotation.java

Public Member Functions

Member Function Documentation