Inheritance diagram for umms.core.annotation.Annotation:

Collaboration diagram for umms.core.annotation.Annotation:

Classes
enum	Strand

Public Member Functions
int	getStart ()

int	getSAMStart ()

int	getEnd ()

int	getSAMEnd ()

String	getReferenceName ()

String	getChr ()

String	getName ()

Strand	getOrientation ()

Strand	getStrand ()

boolean	hasOrientation ()

boolean	isNegativeStrand ()

int	numBlocks ()

List<?extends Annotation >	getBlocks ()

List<?extends Annotation >	getBlocks (boolean oriented)

int	length ()

int	getSize ()

int	size ()

int	getLengthOnReference ()

int	getOrientedStart ()

int	getOrientedEnd ()

double	getScore ()

boolean	isUnoriented ()

int	getReferenceCoordinateAtPosition (int positionInAnnotation)

int	getPositionAtReferenceCoordinate (int referenceCoordinate)

int	getReferenceCoordinateAtPosition (int positionInAnnotation, boolean ignoreOrientation)

int	getPositionAtReferenceCoordinate (int referenceCoordinate, boolean ignoreOrientation)

void	setStart (int start)

void	setEnd (int end)

void	setOrientation (char orientation)

void	setOrientation (Strand orientation)

void	setOrientedStart (int orientedStart)

void	setOrientedEnd (int orientedEnd)

void	setReferenceName (String refName)

void	setName (String name)

void	setScore (double score)

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	toUCSC ()

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

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

Should behave like compareTo for a basic annotation

Parameters

b

Returns

Implemented in umms.core.annotation.AbstractAnnotation.

Annotation umms.core.annotation.Annotation.complement ( )

Returns: a new CompoundInterval containing the gaps between the blocks in this annotation

Implemented in umms.core.annotation.BasicAnnotation.

boolean umms.core.annotation.Annotation.contains ( Annotation other )

Parameters

other

Returns: true if the blocks of other are fully contained within the blocks of this object

Implemented in umms.core.annotation.BasicAnnotation.

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Annotation umms.core.annotation.Annotation.copy ( )

Returns: A deep clone of this Annotation object

Implemented in umms.core.annotation.Gene, and umms.core.annotation.BasicAnnotation.

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List<Annotation> umms.core.annotation.Annotation.disect ( Annotation a )

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

Parameters

Annotation annotation to disect the current one

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

Implemented in umms.core.annotation.BasicAnnotation, and broad.core.annotation.BasicGenomicAnnotation.

List<Annotation> umms.core.annotation.Annotation.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.

Implemented in umms.core.annotation.BasicAnnotation, and broad.core.annotation.BasicGenomicAnnotation.

boolean umms.core.annotation.Annotation.equals ( Annotation other )

Implemented in umms.core.alignment.SingleEndAlignment, and umms.core.annotation.AbstractAnnotation.

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boolean umms.core.annotation.Annotation.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

Implemented in umms.core.annotation.AbstractAnnotation.

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

Expand annotation by a set number of bases, taking into account blocks

Parameters

deltaStart	positive extends the gene.
deltaEnd	positive extends the gene.

Implemented in umms.core.annotation.AbstractAnnotation.

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

Test whether the annotation is fully contained in this

Parameters

annotation

Returns

Implemented in umms.core.annotation.AbstractAnnotation.

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

Returns: list of blocks in coordinate order

Implemented in umms.core.annotation.BasicAnnotation, broad.core.annotation.BED, and broad.core.annotation.GenomicAnnotation.

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List<? extends Annotation> umms.core.annotation.Annotation.getBlocks ( boolean oriented )

Parameters

oriented set to true if the list should be ordered according to the annotation orientation and by position

Returns

Implemented in umms.core.annotation.BasicAnnotation.

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

Returns: name of the reference sequence

Implemented in umms.core.alignment.AbstractPairedEndAlignment, umms.core.alignment.SingleEndAlignment, umms.core.alignment.Alignment, and umms.core.annotation.AbstractAnnotation.

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

Calculates the distance to the another genomic annotation.

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

Implemented in umms.core.annotation.AbstractAnnotation.

int umms.core.annotation.Annotation.getEnd ( )

Returns: end of the annotation (exclusive)

Implemented in umms.core.alignment.AbstractPairedEndAlignment, umms.core.annotation.BasicAnnotation, umms.core.alignment.Alignment, and broad.core.annotation.LightweightGenomicAnnotation.

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String umms.core.annotation.Annotation.getFullInfoString ( )

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

Implemented in umms.core.annotation.AbstractAnnotation.

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

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

Implemented in umms.core.annotation.AbstractAnnotation.

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

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

Returns

Implemented in umms.core.annotation.BasicAnnotation, and umms.core.annotation.AbstractAnnotation.

String umms.core.annotation.Annotation.getName ( )

Returns: the name of the annotation

Implemented in umms.core.annotation.BasicAnnotation, and broad.core.annotation.LightweightGenomicAnnotation.

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Strand umms.core.annotation.Annotation.getOrientation ( )

Returns: orientation or strand

Implemented in umms.core.alignment.AbstractPairedEndAlignment, umms.core.annotation.BasicAnnotation, broad.core.annotation.LightweightGenomicAnnotation, and broad.core.annotation.GenomicAnnotation.

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

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

Implemented in broad.core.annotation.BasicGenomicAnnotation, umms.core.annotation.AbstractAnnotation, and broad.core.annotation.GenomicAnnotation.

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

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

Implemented in broad.core.annotation.BasicGenomicAnnotation, umms.core.annotation.AbstractAnnotation, and broad.core.annotation.GenomicAnnotation.

int umms.core.annotation.Annotation.getOverlap ( Annotation other )

Returns the number of bases that overlap between the two annotations.

Parameters

other

Returns

Implemented in umms.core.annotation.BasicAnnotation.

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

Parameters

referenceCoordinate 0-based reference coordinate

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

Implemented in umms.core.annotation.AbstractAnnotation.

int umms.core.annotation.Annotation.getPositionAtReferenceCoordinate	(	int	referenceCoordinate,
		boolean	ignoreOrientation
	)

Implemented in umms.core.annotation.BasicAnnotation.

int umms.core.annotation.Annotation.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()

Implemented in umms.core.annotation.AbstractAnnotation.

int umms.core.annotation.Annotation.getReferenceCoordinateAtPosition	(	int	positionInAnnotation,
		boolean	ignoreOrientation
	)

Implemented in umms.core.annotation.BasicAnnotation.

String umms.core.annotation.Annotation.getReferenceName ( )

Returns: name of the reference sequence

Implemented in umms.core.annotation.BasicAnnotation.

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int umms.core.annotation.Annotation.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

Implemented in umms.core.annotation.AbstractAnnotation.

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

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

Returns

Implemented in umms.core.annotation.AbstractAnnotation.

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double umms.core.annotation.Annotation.getScore ( )

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

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

Returns: same as size();

Implemented in umms.core.annotation.Gene, umms.core.feature.GeneWindow, and umms.core.annotation.AbstractAnnotation.

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Collection<? extends Annotation> umms.core.annotation.Annotation.getSpliceConnections ( )

This will return a collection of splice junctions This is not the same as all gaps, it will only return splice junctions

Returns: A collection of splice junctions

Implemented in umms.core.annotation.BasicAnnotation, umms.core.alignment.SingleEndAlignment, and umms.core.alignment.Alignment.

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int umms.core.annotation.Annotation.getStart ( )

Returns: start of the annotation (inclusive)

Implemented in umms.core.alignment.AbstractPairedEndAlignment, umms.core.annotation.BasicAnnotation, umms.core.alignment.Alignment, and broad.core.annotation.LightweightGenomicAnnotation.

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

Returns: orientation or strand

Implemented in broad.core.annotation.GFF, and umms.core.annotation.AbstractAnnotation.

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

Returns: true if strand is known

Implemented in umms.core.annotation.AbstractAnnotation.

Annotation umms.core.annotation.Annotation.intersect ( Annotation other )

Returns the result of intersecting this instance with another

Parameters

other

Returns: returns null if there is no intersection

Implemented in umms.core.annotation.BasicAnnotation.

List<Annotation> umms.core.annotation.Annotation.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

Implemented in umms.core.annotation.AbstractAnnotation.

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

Implemented in umms.core.annotation.Gene, umms.core.alignment.AbstractPairedEndAlignment, umms.core.alignment.Alignment, and umms.core.annotation.AbstractAnnotation.

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boolean umms.core.annotation.Annotation.isUnoriented ( )

Returns: false if the annotation is not in either negative or positive orientation

Implemented in umms.core.annotation.BasicAnnotation.

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int umms.core.annotation.Annotation.length ( )

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

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

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Annotation umms.core.annotation.Annotation.minus ( Annotation other )

Returns the difference (all regions in this genomic annotation not in the given other annotation) between this genomic annotation and the one

Parameters

other - the annotations to take the difference against

Returns: A blocked annotation of the resulting difference.

Implemented in umms.core.annotation.BasicAnnotation.

Annotation umms.core.annotation.Annotation.minus ( Collection<?extends Annotation > others )

Returns the difference (all regions in this genomic annotation not in the given list) between this genomic annotation and the given list

Parameters

others - the annotations to take the difference against

Returns: A blocked annotation of the resulting difference.

Implemented in umms.core.annotation.BasicAnnotation.

void umms.core.annotation.Annotation.moveToCoordinate ( int coordinateInReference )

Move an annotation, preserving the relationships between its blocks, to a new coordinate.

Parameters

coordinateInReference

Implemented in umms.core.annotation.BasicAnnotation, and umms.core.alignment.AbstractPairedEndAlignment.

int umms.core.annotation.Annotation.numBlocks ( )

Returns: number of blocks in the Annotation

Implemented in umms.core.annotation.BasicAnnotation.

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boolean umms.core.annotation.Annotation.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

Implemented in umms.core.annotation.AbstractAnnotation.

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boolean umms.core.annotation.Annotation.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.

Returns: true if they overlap in this extended definition, not considering orientation

Implemented in broad.core.annotation.BasicLightweightAnnotation, and umms.core.annotation.AbstractAnnotation.

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

Parameters

other GenomicAnnotation to check of overlap

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

Implemented in umms.core.annotation.AbstractAnnotation.

boolean umms.core.annotation.Annotation.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

Implemented in broad.core.annotation.BasicLightweightAnnotation, and umms.core.annotation.AbstractAnnotation.

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

Implemented in umms.core.annotation.BasicAnnotation.

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

Implemented in umms.core.annotation.AbstractAnnotation.

boolean umms.core.annotation.Annotation.overlapsStranded ( Annotation other )

Implemented in umms.core.annotation.AbstractAnnotation.

void umms.core.annotation.Annotation.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

Implemented in umms.core.annotation.BasicAnnotation, and broad.core.annotation.LightweightGenomicAnnotation.

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void umms.core.annotation.Annotation.setName ( String name )

Parameters

name	name of the annotation

Implemented in umms.core.annotation.BasicAnnotation, and broad.core.annotation.LightweightGenomicAnnotation.

void umms.core.annotation.Annotation.setOrientation ( char orientation )

Implemented in umms.core.annotation.AbstractAnnotation.

void umms.core.annotation.Annotation.setOrientation ( Strand orientation )

Implemented in umms.core.annotation.BasicAnnotation.

void umms.core.annotation.Annotation.setOrientedEnd ( int orientedEnd )

Implemented in umms.core.annotation.BasicAnnotation.

void umms.core.annotation.Annotation.setOrientedStart ( int orientedStart )

Implemented in umms.core.annotation.BasicAnnotation.

void umms.core.annotation.Annotation.setReferenceName ( String refName )

Parameters

refName name of the reference sequence / chromosome

Implemented in umms.core.annotation.BasicAnnotation.

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void umms.core.annotation.Annotation.setScore ( double score )

Implemented in umms.core.annotation.BasicAnnotation, broad.core.annotation.BasicLightweightAnnotation, and broad.core.annotation.LightweightGenomicAnnotation.

void umms.core.annotation.Annotation.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

Implemented in umms.core.annotation.BasicAnnotation, and broad.core.annotation.LightweightGenomicAnnotation.

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void umms.core.annotation.Annotation.shift ( int delta )

Shift the positioning of the annotation by a given number of base pairs.

Parameters

delta

Positive or negative shift to apply to all blocks in the annotation.

delta=0

leaves the annotation unchanged.

Implemented in umms.core.annotation.BasicAnnotation, and umms.core.alignment.AbstractPairedEndAlignment.

int umms.core.annotation.Annotation.size ( )

Returns: same as length()

Implemented in umms.core.annotation.AbstractAnnotation.

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void umms.core.annotation.Annotation.stitchTo ( Annotation next )

Implemented in umms.core.annotation.BasicAnnotation.

String umms.core.annotation.Annotation.toBED ( )

Implemented in umms.core.annotation.Gene, broad.core.annotation.BED, and umms.core.annotation.AbstractAnnotation.

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String umms.core.annotation.Annotation.toBED	(	int	r,
		int	g,
		int	b
	)

Implemented in umms.core.annotation.Gene, broad.core.annotation.BED, and umms.core.annotation.AbstractAnnotation.

String umms.core.annotation.Annotation.toBEDGraph ( )

Implemented in umms.core.annotation.AbstractAnnotation.

String umms.core.annotation.Annotation.toCigar ( )

Implemented in umms.core.annotation.AbstractAnnotation.

String umms.core.annotation.Annotation.toShortBED ( )

Implemented in umms.core.annotation.AbstractAnnotation.

String umms.core.annotation.Annotation.toUCSC ( )

Returns: chrX:start-end

Implemented in umms.core.annotation.Gene, broad.core.annotation.BasicLightweightAnnotation, umms.core.annotation.AbstractAnnotation, broad.pda.datastructures.Alignments, and broad.core.annotation.LightweightGenomicAnnotation.

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Annotation umms.core.annotation.Annotation.trim	(	int	deltaStart,
		int	deltaEnd
	)

Trim annotation by a set number of bases, taking into account blocks.

Parameters

deltaStart	(Positive) The number of bases to remove from the beginning of gene. e.g. deltaStart=1 removes one base from the front
deltaEnd	(Positive) The number of bases to remove from the end of gene. e.g. deltaStart=1 removes one base fromt he end

Returns

Implemented in umms.core.annotation.AbstractAnnotation.

Annotation umms.core.annotation.Annotation.union ( Annotation other )

Parameters

other

Returns: union of current instance and other object. If strands agree, then strand is set to that. If the strands conflict, strand is set to UNKNOWN

Implemented in umms.core.annotation.BasicAnnotation.

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

java/umms/core/annotation/Annotation.java

Classes

Public Member Functions

Member Function Documentation