Inheritance diagram for broad.core.annotation.BasicLightweightAnnotation:

Collaboration diagram for broad.core.annotation.BasicLightweightAnnotation:

Public Member Functions
	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)

Strand	getOrientation ()

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 ()

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 (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 ()

Static Public Member Functions
static Collection < BasicLightweightAnnotation >	mergeAllOverlappers (TreeSet< BasicLightweightAnnotation > regions)

static LightweightGenomicAnnotation	createFromUCSC (String ucsc)

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

Protected Member Functions
void	setStart (String data)

Constructor & Destructor Documentation

broad.core.annotation.BasicLightweightAnnotation.BasicLightweightAnnotation ( )

Here is the caller graph for this function:

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

broad.core.annotation.BasicLightweightAnnotation.BasicLightweightAnnotation	(	String	chr,
		int	start,
		int	end,
		String	orientation
	)

broad.core.annotation.BasicLightweightAnnotation.BasicLightweightAnnotation	(	String	chr,
		int	start,
		int	end,
		Strand	orientation,
		String	name
	)

broad.core.annotation.BasicLightweightAnnotation.BasicLightweightAnnotation	(	String	chr,
		int	start,
		int	end,
		String	orientation,
		double	Scr
	)

broad.core.annotation.BasicLightweightAnnotation.BasicLightweightAnnotation	(	String	chr,
		String	start,
		String	end
	)

broad.core.annotation.BasicLightweightAnnotation.BasicLightweightAnnotation ( LightweightGenomicAnnotation annotation )

Here is the call graph for this function:

broad.core.annotation.BasicLightweightAnnotation.BasicLightweightAnnotation ( Annotation annotation )

Here is the call graph for this function:

Member Function Documentation

void broad.core.annotation.BasicLightweightAnnotation.addExtraScore ( double score )

Adds a new extra score

Parameters

score

Implements broad.core.annotation.LightweightGenomicAnnotation.

Here is the caller graph for this function:

boolean broad.core.annotation.BasicLightweightAnnotation.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

Implements broad.core.annotation.LightweightGenomicAnnotation.

Here is the call graph for this function:

int broad.core.annotation.BasicLightweightAnnotation.compareTo ( LightweightGenomicAnnotation b )

Here is the call graph for this function:

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

Implements broad.core.annotation.LightweightGenomicAnnotation.

Here is the call graph for this function:

Here is the caller graph for this function:

static LightweightGenomicAnnotation broad.core.annotation.BasicLightweightAnnotation.createFromUCSC ( String ucsc )

static

Here is the call graph for this function:

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

Implements broad.core.annotation.LightweightGenomicAnnotation.

Here is the call graph for this function:

Here is the caller graph for this function:

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

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

Implements broad.core.annotation.LightweightGenomicAnnotation.

Here is the call graph for this function:

Here is the caller graph for this function:

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

public void

Implements broad.core.annotation.LightweightGenomicAnnotation.

Here is the call graph for this function:

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

Returns the ith extra score

Implements broad.core.annotation.LightweightGenomicAnnotation.

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

Returns: all extra scores

Implements broad.core.annotation.LightweightGenomicAnnotation.

Here is the caller graph for this function:

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

Here is the call graph for this function:

Here is the caller graph for this function:

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

Implements broad.core.annotation.LightweightGenomicAnnotation.

Here is the call graph for this function:

int broad.core.annotation.BasicLightweightAnnotation.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

Implements broad.core.annotation.LightweightGenomicAnnotation.

Here is the call graph for this function:

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

Implements broad.core.annotation.LightweightGenomicAnnotation.

Here is the caller graph for this function:

int broad.core.annotation.BasicLightweightAnnotation.hashCode ( )

Here is the call graph for this function:

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

Implements broad.core.annotation.LightweightGenomicAnnotation.

Here is the call graph for this function:

Here is the caller graph for this function:

LightweightGenomicAnnotation broad.core.annotation.BasicLightweightAnnotation.intersect ( LightweightGenomicAnnotation other )

Change the current instance to represent its intersection with the provided annotation if they overlap

Parameters

other

Here is the call graph for this function:

Here is the caller graph for this function:

Collection<? extends Annotation> broad.core.annotation.BasicLightweightAnnotation.intersect ( Collection<?extends Annotation > annotations )

Here is the call graph for this function:

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

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

Implements broad.core.annotation.LightweightGenomicAnnotation.

Here is the call graph for this function:

Here is the caller graph for this function:

static Collection<BasicLightweightAnnotation> broad.core.annotation.BasicLightweightAnnotation.mergeAllOverlappers ( TreeSet< BasicLightweightAnnotation > regions )

static

Merge overlapping regions into a single region and leave singletons alone

Parameters

regions The regions to merge

Returns: The set of merged regions

Here is the call graph for this function:

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

Parameters

other GenomicAnnotation to check of overlap

Returns: true if the current instance overlaps with the other one.

Parameters

other	- other genomic annotation
buffer	if the overlap is within buffer they will be considered overlapping even if they do not overlap within their original boundaries.

Returns: true if they overlap in this extended definition

Implements umms.core.annotation.Annotation.

Here is the caller graph for this function:

boolean broad.core.annotation.BasicLightweightAnnotation.overlaps ( Collection<?extends Annotation > others )

Parameters

other GenomicAnnotations to check of overlap

Returns: true if the current instance overlaps with the other one, not considering orientation

Implements umms.core.annotation.Annotation.

Here is the call graph for this function:

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

removes extra scores

Implements broad.core.annotation.LightweightGenomicAnnotation.

void broad.core.annotation.BasicLightweightAnnotation.setBoundariesFromAnnoations ( List<?extends GenomicAnnotation > annotations )

Here is the call graph for this function:

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

Implements broad.core.annotation.LightweightGenomicAnnotation.

Here is the call graph for this function:

Here is the caller graph for this function:

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

Implements broad.core.annotation.LightweightGenomicAnnotation.

Here is the caller graph for this function:

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

Here is the call graph for this function:

Here is the caller graph for this function:

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

Implements broad.core.annotation.LightweightGenomicAnnotation.

Here is the caller graph for this function:

void broad.core.annotation.BasicLightweightAnnotation.setStart ( String data )

protected

Here is the caller graph for this function:

static List<Annotation> broad.core.annotation.BasicLightweightAnnotation.stitchList	(	Collection<?extends Annotation >	sortedList,
		int	maxDistanceToStitch
	)