Inheritance diagram for broad.core.annotation.BasicGenomicAnnotation:

Collaboration diagram for broad.core.annotation.BasicGenomicAnnotation:

Public Member Functions
	BasicGenomicAnnotation (String name)

	BasicGenomicAnnotation (String name, String chr, int start, int end)

	BasicGenomicAnnotation (String name, String chr, int start, int end, Strand strand)

	BasicGenomicAnnotation (LightweightGenomicAnnotation ga)

	BasicGenomicAnnotation (Annotation ga)

	BasicGenomicAnnotation (GenomicAnnotation ga)

	BasicGenomicAnnotation (String[] info)

int	getLength ()

String	toString ()

String	getId ()

void	setId (String id)

void	reduceToDifference (GenomicAnnotation other)

List< Annotation >	disect (Annotation a)

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

boolean	isFlankedBy (TwoSubjectAnnotation twoSubjectAnnotation, int buffer)

int	lastIdxWhereListSearchBroke ()

Sequence	getSequence ()

void	setSequence (Sequence sequence)

void	setOrientation (boolean orientation)

void	setThreePrimeBuffer (int bufferSize)

void	setFivePrimeBuffer (int bufferSize)

int	getFivePrimeBases ()

int	getThreePrimeBases ()

int	compareTo (GenomicAnnotation arg0)

int	getOrientedEnd ()

int	getOrientedStart ()

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

boolean	mayHaveBlocks ()

Public Member Functions inherited from broad.core.annotation.BasicLightweightAnnotation
	BasicLightweightAnnotation ()

	BasicLightweightAnnotation (String chr, int start, int end)

	BasicLightweightAnnotation (String chr, int start, int end, String orientation)

	BasicLightweightAnnotation (String chr, int start, int end, Strand orientation, String name)

	BasicLightweightAnnotation (String chr, int start, int end, String orientation, double Scr)

	BasicLightweightAnnotation (String chr, String start, String end)

	BasicLightweightAnnotation (LightweightGenomicAnnotation annotation)

	BasicLightweightAnnotation (Annotation annotation)

String	getChromosomeString ()

int	getDistanceTo (LightweightGenomicAnnotation other)

double	getExtraScore (int i)

List< Double >	getExtraScores ()

String	getLocationString ()

long	getMiddle ()

int	getOverlap (LightweightGenomicAnnotation other)

double	getScore ()

void	setReversedOrientation (boolean isInReversedOrientation)

void	setScore (double score)

boolean	almostEqual (LightweightGenomicAnnotation other, int fudge)

boolean	contains (LightweightGenomicAnnotation other)

boolean	inReversedOrientation ()

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

boolean	overlaps (Collection<?extends Annotation > others)

void	addExtraScore (double score)

void	removeExtraScores ()

void	setBoundariesFromAnnoations (List<?extends GenomicAnnotation > annotations)

void	stitchTo (LightweightGenomicAnnotation other)

void	takeIntersection (LightweightGenomicAnnotation other)

void	takeUnion (LightweightGenomicAnnotation other)

LightweightGenomicAnnotation	intersect (LightweightGenomicAnnotation other)

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

int	hashCode ()

int	length ()

String	toUCSC ()

String	toString ()

int	compareTo (LightweightGenomicAnnotation b)

void	setOrientation (String orientation)

String	getChromosome ()

void	setChromosome (String chr)

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

int	getEnd ()

String	getName ()

void	setName (String name)

void	setStart (int start)

void	setEnd (int end)

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 ()

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 (Annotation other)

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 ()

Public Member Functions inherited from broad.core.annotation.GenomicAnnotation
void	setReversedOrientation (boolean isInReversedOrientation)

void	setOrientation (String orientationString)

Strand	getOrientation ()

String	getLocationString ()

List<?extends Annotation >	getBlocks ()

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

double	getScore ()

Protected Member Functions
	BasicGenomicAnnotation ()

Protected Member Functions inherited from broad.core.annotation.BasicLightweightAnnotation
void	setStart (String data)

Additional Inherited Members
Static Public Member Functions inherited from broad.core.annotation.BasicLightweightAnnotation
static Collection < BasicLightweightAnnotation >	mergeAllOverlappers (TreeSet< BasicLightweightAnnotation > regions)

static LightweightGenomicAnnotation	createFromUCSC (String ucsc)

static List< Annotation >	stitchList (Collection<?extends Annotation > sortedList, int maxDistanceToStitch)

Constructor & Destructor Documentation

broad.core.annotation.BasicGenomicAnnotation.BasicGenomicAnnotation ( )

protected

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broad.core.annotation.BasicGenomicAnnotation.BasicGenomicAnnotation ( String name )

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broad.core.annotation.BasicGenomicAnnotation.BasicGenomicAnnotation	(	String	name,
		String	chr,
		int	start,
		int	end
	)

broad.core.annotation.BasicGenomicAnnotation.BasicGenomicAnnotation	(	String	name,
		String	chr,
		int	start,
		int	end,
		Strand	strand
	)

broad.core.annotation.BasicGenomicAnnotation.BasicGenomicAnnotation ( LightweightGenomicAnnotation ga )

broad.core.annotation.BasicGenomicAnnotation.BasicGenomicAnnotation ( Annotation ga )

broad.core.annotation.BasicGenomicAnnotation.BasicGenomicAnnotation ( GenomicAnnotation ga )

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broad.core.annotation.BasicGenomicAnnotation.BasicGenomicAnnotation ( String[] info )

A basic genomic annotation may be built from a raw string array where the first entry is the chromosome, the second the start and the third the end.

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Member Function Documentation

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

Adds a block to the annotation if it supports blocks

Implements broad.core.annotation.GenomicAnnotation.

int broad.core.annotation.BasicGenomicAnnotation.compareTo ( GenomicAnnotation arg0 )

Default compareTo method: If annotations are in the same chromosome their start/end locations are compared otherwise their chromosomes are.

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List<Annotation> broad.core.annotation.BasicGenomicAnnotation.disect ( Annotation a )

Fragments the current annotation if it overlaps the provided one. it returns an empty list if this annotation does not ovelap the one passed in.

Parameters

GenomicAnnotation annotation to disect the current one

Returns: List<GenomicAnnotation> of the disected annotations, an empty list is returned if the annotations do not overlap.

Implements umms.core.annotation.Annotation.

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List<Annotation> broad.core.annotation.BasicGenomicAnnotation.disect ( List<?extends Annotation > disectors )

Fragments the current annotation if it overlaps the provided ones. It returns a list with one component (this annotation) if no annotation in the provided list overlaps the discted annotaion.

Parameters

List<GenomicAnnotation> sorted annotations with which to disect the current one.

Returns: List<GenomicAnnotation> of the disected annotations, a list just this annotation is returned if the annotations do not overlap.

Implements umms.core.annotation.Annotation.

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

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

Implements broad.core.annotation.GenomicAnnotation.

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

Genomic annotation integer identification if such exists.

Implements broad.core.annotation.GenomicAnnotation.

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

Deprecated:

Use length() instead

Returns

Implements broad.core.annotation.GenomicAnnotation.

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

Gets the end of the annotation considering its orientation

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

Implements broad.core.annotation.GenomicAnnotation.

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

Gets the start of the annotation considering its orientation

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

Implements broad.core.annotation.GenomicAnnotation.

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

Implements broad.core.annotation.GenomicAnnotation.

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

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

Implements broad.core.annotation.GenomicAnnotation.

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

Checks whether a twoSubjectAnnotation flanks the instance

Implements broad.core.annotation.GenomicAnnotation.

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int broad.core.annotation.BasicGenomicAnnotation.lastIdxWhereListSearchBroke ( )

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

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

Implements broad.core.annotation.GenomicAnnotation.

void broad.core.annotation.BasicGenomicAnnotation.reduceToDifference ( GenomicAnnotation other )

Change the current instance to represent the difference of the instance with the other annotation

Parameters

other

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void broad.core.annotation.BasicGenomicAnnotation.setFivePrimeBuffer ( int bufferSize )

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

Implements broad.core.annotation.GenomicAnnotation.

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void broad.core.annotation.BasicGenomicAnnotation.setOrientation ( boolean orientation )

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void broad.core.annotation.BasicGenomicAnnotation.setSequence ( Sequence sequence )

Implements broad.core.annotation.GenomicAnnotation.

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void broad.core.annotation.BasicGenomicAnnotation.setThreePrimeBuffer ( int bufferSize )

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String broad.core.annotation.BasicGenomicAnnotation.toString ( )

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

java/broad/core/annotation/BasicGenomicAnnotation.java

Public Member Functions

Protected Member Functions

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation