Inheritance diagram for umms.core.annotation.AbstractAnnotation:

Collaboration diagram for umms.core.annotation.AbstractAnnotation:

Public Member Functions
int	size ()

int	getSize ()

int	getMidpoint ()

Strand	getStrand ()

boolean	hasOrientation ()

boolean	isNegativeStrand ()

String	getChr ()

int	getOrientedStart ()

int	getOrientedEnd ()

int	getLengthOnReference ()

int	getReferenceCoordinateAtPosition (int positionInAnnotation)

int	getPositionAtReferenceCoordinate (int referenceCoordinate)

void	setOrientation (char orientation)

void	expand (int deltaStart, int deltaEnd)

Annotation	trim (int deltaStart, int deltaEnd)

boolean	fullyContains (Annotation other)

boolean	overlaps (Annotation other)

boolean	overlaps (Annotation other, int buffer)

boolean	overlapsStranded (Annotation other)

boolean	overlaps (Annotation other, boolean considerOrientation)

boolean	overlaps (Collection<?extends Annotation > others)

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

String	toUCSC ()

String	toBED ()

final String	getFullInfoString ()

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

String	toShortBED ()

String	toBEDGraph ()

int	getDistanceTo (Annotation other)

String	toCigar ()

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

int	compareTo (Annotation other)

int	compareToAnnotation (Annotation b)

int	compareToAnnotation (Annotation b, boolean useOrientation)

boolean	equals (Annotation a)

boolean	equals (Annotation a, boolean useOrientation)

int	getSAMStart ()

int	getSAMEnd ()

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

int	getEnd ()

String	getReferenceName ()

String	getName ()

Strand	getOrientation ()

int	numBlocks ()

List<?extends Annotation >	getBlocks ()

List<?extends Annotation >	getBlocks (boolean oriented)

int	length ()

double	getScore ()

boolean	isUnoriented ()

int	getReferenceCoordinateAtPosition (int positionInAnnotation, boolean ignoreOrientation)

int	getPositionAtReferenceCoordinate (int referenceCoordinate, boolean ignoreOrientation)

void	setStart (int start)

void	setEnd (int end)

void	setOrientation (Strand orientation)

void	setOrientedStart (int orientedStart)

void	setOrientedEnd (int orientedEnd)

void	setReferenceName (String refName)

void	setName (String name)

void	setScore (double score)

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)

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

int	getOverlap (Annotation other)

boolean	contains (Annotation other)

Annotation	union (Annotation other)

Annotation	intersect (Annotation other)

void	stitchTo (Annotation next)

Annotation	complement ()

Collection<?extends Annotation >	getSpliceConnections ()

Static Public Member Functions
static Strand	getStrand (String orientation)

static Strand	getStrand (char orientation)

Static Public Attributes
static final int	MAX_DISTANCE = 1000000000

Detailed Description

Author: engreitz This abstract class contains generic implementations of Annotation functions that rely only on other Annotation functions.

Member Function Documentation

int umms.core.annotation.AbstractAnnotation.compareTo ( Annotation other )

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int umms.core.annotation.AbstractAnnotation.compareToAnnotation ( Annotation b )

Should behave like compareTo for a basic annotation

Parameters

b

Returns

Implements umms.core.annotation.Annotation.

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int umms.core.annotation.AbstractAnnotation.compareToAnnotation	(	Annotation	b,
		boolean	useOrientation
	)

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boolean umms.core.annotation.AbstractAnnotation.equals ( Annotation a )

Implements umms.core.annotation.Annotation.

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boolean umms.core.annotation.AbstractAnnotation.equals	(	Annotation	other,
		boolean	useOrientation
	)

Test whether two annotations are equal regardless of whether the orientation are the same

Parameters

other	The annotation to test equality to
useOrientation	true=ensure strands match false=OK if strands dont match

Returns

Implements umms.core.annotation.Annotation.

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void umms.core.annotation.AbstractAnnotation.expand	(	int	deltaStart,
		int	deltaEnd
	)

Extends the annotation by delta on the unOriented Start and end.

Implements umms.core.annotation.Annotation.

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boolean umms.core.annotation.AbstractAnnotation.fullyContains ( Annotation annotation )

Test whether the annotation is fully contained in this

Parameters

annotation

Returns

Implements umms.core.annotation.Annotation.

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String umms.core.annotation.AbstractAnnotation.getChr ( )

Returns: name of the reference sequence

Implements umms.core.annotation.Annotation.

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int umms.core.annotation.AbstractAnnotation.getDistanceTo ( Annotation other )

Calculates the distance to the another genomic annotation.

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

Implements umms.core.annotation.Annotation.

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final String umms.core.annotation.AbstractAnnotation.getFullInfoString ( )

Returns: A string with no whitespace that includes all information about the annotation

Implements umms.core.annotation.Annotation.

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int umms.core.annotation.AbstractAnnotation.getLengthOnReference ( )

Returns: The distance between the start of the first block and end of the last on the reference sequence (including spaces between blocks)

Implements umms.core.annotation.Annotation.

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int umms.core.annotation.AbstractAnnotation.getMidpoint ( )

This will return the position in the center of this annotation taking into account the blocked structure

Returns

Implements umms.core.annotation.Annotation.

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int umms.core.annotation.AbstractAnnotation.getOrientedEnd ( )

Returns: the 3-prime end of the annotation, considering its orientation or strand

Implements umms.core.annotation.Annotation.

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int umms.core.annotation.AbstractAnnotation.getOrientedStart ( )

Returns: the 5-prime end of the annotation, considering its orientation or strand

Implements umms.core.annotation.Annotation.

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int umms.core.annotation.AbstractAnnotation.getPositionAtReferenceCoordinate ( int referenceCoordinate )

Parameters

referenceCoordinate 0-based reference coordinate

Returns: 0-based position in the Annotation, considering orientation

Implements umms.core.annotation.Annotation.

int umms.core.annotation.AbstractAnnotation.getReferenceCoordinateAtPosition ( int positionInAnnotation )

Parameters

positionInAnnotation 0-based position in the Annotation

Returns: 0-based reference coordinate at the specified position, considering orientation. NOTE: positionInAnnotation=0 for a negative-strand annotation will match getEnd()

Implements umms.core.annotation.Annotation.

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int umms.core.annotation.AbstractAnnotation.getSAMEnd ( )

Returns the start position of this window into SAM coordinate space SAM coordinates are 1-based and inclusive whereas all of our objects are 0-based exclusive

Returns

Implements umms.core.annotation.Annotation.

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int umms.core.annotation.AbstractAnnotation.getSAMStart ( )

Returns the start position of this window into SAM coordinate space SAM coordinates are 1-based and inclusive whereas all of our objects are 0-based exclusive

Returns

Implements umms.core.annotation.Annotation.

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int umms.core.annotation.AbstractAnnotation.getSize ( )

Returns: same as size();

Implements umms.core.annotation.Annotation.

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Strand umms.core.annotation.AbstractAnnotation.getStrand ( )

Returns: orientation or strand

Implements umms.core.annotation.Annotation.

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static Strand umms.core.annotation.AbstractAnnotation.getStrand ( String orientation )

static

static Strand umms.core.annotation.AbstractAnnotation.getStrand ( char orientation )

static

boolean umms.core.annotation.AbstractAnnotation.hasOrientation ( )

Returns: true if strand is known

Implements umms.core.annotation.Annotation.

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List<Annotation> umms.core.annotation.AbstractAnnotation.intersect ( List<?extends Annotation > annotations )

Returns the result of intersecting this instance with a list of annotations, with one (possibly blocked) intersection Annotation for each provided annotation

Parameters

other annotations

Returns: List of intersections or empty list if none

Implements umms.core.annotation.Annotation.

boolean umms.core.annotation.AbstractAnnotation.isNegativeStrand ( )

Returns true if the alignment is negative stranded

Returns

Implements umms.core.annotation.Annotation.

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boolean umms.core.annotation.AbstractAnnotation.overlaps ( Annotation other )

Parameters

other GenomicAnnotation to check of overlap

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

Implements umms.core.annotation.Annotation.

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boolean umms.core.annotation.AbstractAnnotation.overlaps	(	Annotation	other,
		int	buffer
	)

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, not considering orientation

Implements umms.core.annotation.Annotation.

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boolean umms.core.annotation.AbstractAnnotation.overlaps	(	Annotation	other,
		boolean	considerOrientation
	)

Implements umms.core.annotation.Annotation.

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boolean umms.core.annotation.AbstractAnnotation.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.

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

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.