Inheritance diagram for umms.core.annotation.BasicAnnotation:

Collaboration diagram for umms.core.annotation.BasicAnnotation:

Classes
class	Factory

Public Member Functions
	BasicAnnotation ()

	BasicAnnotation (SAMRecord samRecord)

	BasicAnnotation (String ucsc)

	BasicAnnotation (String referenceName, int start, int end, Strand orientation, String name)

	BasicAnnotation (String referenceName, Strand orientation, String name, Collection<?extends Annotation > blocks)

	BasicAnnotation (String referenceName, int start, int end)

	BasicAnnotation (String referenceName, int start, int end, Strand orientation)

	BasicAnnotation (String referenceName, int start, int end, String orientation)

	BasicAnnotation (BasicAnnotation other)

	BasicAnnotation (Annotation other)

	BasicAnnotation (Collection<?extends Annotation > blocks)

	BasicAnnotation (Collection<?extends Annotation > blocks, Strand orientation, String name)

	BasicAnnotation (Collection<?extends Annotation > blocks, String name)

	BasicAnnotation (String referenceName, CompoundInterval blocks, Strand orientation, String name)

	BasicAnnotation (String referenceName, CompoundInterval blocks, Strand orientation)

	BasicAnnotation (String referenceName, CompoundInterval blocks)

Annotation	copy ()

int	getStart ()

int	getEnd ()

int	getMidpoint ()

String	getReferenceName ()

String	getName ()

Strand	getOrientation ()

boolean	isUnoriented ()

List<?extends Annotation >	getBlocks ()

List<?extends Annotation >	getBlocks (boolean oriented)

Annotation[]	getFlankingBlocks (Annotation spliceJunction)

int	numBlocks ()

int	length ()

int	getReferenceCoordinateAtPosition (int positionInAnnotation, boolean ignoreOrientation)

int	getPositionAtReferenceCoordinate (int referenceCoordinate, boolean ignoreOrientation)

double	getScore ()

String	toString ()

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 n)

void	setScore (double s)

void	addBlocks (Annotation block)

void	addBlocks (Collection<?extends Annotation > blocks)

void	shift (int delta)

void	moveToCoordinate (int coordinateInReference)

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

boolean	overlaps (List<?extends Annotation > otherBlocks, int buffer)

int	getOverlap (Annotation other)

boolean	contains (Annotation other)

Annotation	union (Annotation other)

Annotation	intersect (Annotation other)

List< Annotation >	disect (Annotation a)

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

Annotation	minus (Annotation other)

Annotation	minus (Collection<?extends Annotation > others)

void	stitchTo (Annotation next)

Annotation	complement ()

Collection<?extends Annotation >	getSpliceConnections ()

Public Member Functions inherited from umms.core.annotation.AbstractAnnotation
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 ()

Static Public Member Functions
static Annotation	createFromUCSC (String ucsc)

static BasicAnnotation	fromFullInfoString (String fullInfoString)

static void	main (String[] args) throws IOException

Static Public Member Functions inherited from umms.core.annotation.AbstractAnnotation
static Strand	getStrand (String orientation)

static Strand	getStrand (char orientation)

Protected Attributes
CompoundInterval	blocks = new CompoundInterval()

Additional Inherited Members
Static Public Attributes inherited from umms.core.annotation.AbstractAnnotation
static final int	MAX_DISTANCE = 1000000000

Detailed Description

Author: engreitz Coordinate system: 0-based, including first base but not the last

Constructor & Destructor Documentation

umms.core.annotation.BasicAnnotation.BasicAnnotation ( )

For Berkeley DB only Do not use this constructor

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umms.core.annotation.BasicAnnotation.BasicAnnotation ( SAMRecord samRecord )

Create an annotation from a sam record The blocks are the mapped blocks This read only; does not consider the mate

Parameters

samRecord Annotation with name equal to the read name, orientation and blocks as specified in the alignment

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umms.core.annotation.BasicAnnotation.BasicAnnotation ( String ucsc )

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umms.core.annotation.BasicAnnotation.BasicAnnotation	(	String	referenceName,
		int	start,
		int	end,
		Strand	orientation,
		String	name
	)

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umms.core.annotation.BasicAnnotation.BasicAnnotation	(	String	referenceName,
		Strand	orientation,
		String	name,
		Collection<?extends Annotation >	blocks
	)

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umms.core.annotation.BasicAnnotation.BasicAnnotation	(	String	referenceName,
		int	start,
		int	end
	)

umms.core.annotation.BasicAnnotation.BasicAnnotation	(	String	referenceName,
		int	start,
		int	end,
		Strand	orientation
	)

umms.core.annotation.BasicAnnotation.BasicAnnotation	(	String	referenceName,
		int	start,
		int	end,
		String	orientation
	)

umms.core.annotation.BasicAnnotation.BasicAnnotation ( BasicAnnotation other )

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

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

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umms.core.annotation.BasicAnnotation.BasicAnnotation	(	Collection<?extends Annotation >	blocks,
		Strand	orientation,
		String	name
	)

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umms.core.annotation.BasicAnnotation.BasicAnnotation	(	Collection<?extends Annotation >	blocks,
		String	name
	)

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umms.core.annotation.BasicAnnotation.BasicAnnotation	(	String	referenceName,
		CompoundInterval	blocks,
		Strand	orientation,
		String	name
	)

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umms.core.annotation.BasicAnnotation.BasicAnnotation	(	String	referenceName,
		CompoundInterval	blocks,
		Strand	orientation
	)

umms.core.annotation.BasicAnnotation.BasicAnnotation	(	String	referenceName,
		CompoundInterval	blocks
	)

Member Function Documentation

void umms.core.annotation.BasicAnnotation.addBlocks ( Annotation block )

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void umms.core.annotation.BasicAnnotation.addBlocks ( Collection<?extends Annotation > blocks )

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

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

Implements umms.core.annotation.Annotation.

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

Parameters

other

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

Implements umms.core.annotation.Annotation.

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

Returns: A deep clone of this Annotation object

Implements umms.core.annotation.Annotation.

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static Annotation umms.core.annotation.BasicAnnotation.createFromUCSC ( String ucsc )

static

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

Implements umms.core.annotation.Annotation.

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List<Annotation> umms.core.annotation.BasicAnnotation.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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static BasicAnnotation umms.core.annotation.BasicAnnotation.fromFullInfoString ( String fullInfoString )

static

Create from string produced by AbstractAnnotation.getFullInfoString();

Parameters

fullInfoString Full info string

Returns: Corresponding annotation object

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

Returns unoriented blocks for this gene

Implements umms.core.annotation.Annotation.

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

Parameters

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

Returns

Implements umms.core.annotation.Annotation.

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

Returns: end of the annotation (exclusive)

Implements umms.core.annotation.Annotation.

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Annotation [] umms.core.annotation.BasicAnnotation.getFlankingBlocks ( Annotation spliceJunction )

This function returns the blocks on either ends of a given splicejunction

Parameters

spliceJunction

Returns

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int umms.core.annotation.BasicAnnotation.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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String umms.core.annotation.BasicAnnotation.getName ( )

Returns: the name of the annotation

Implements umms.core.annotation.Annotation.

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

Returns: orientation or strand

Implements umms.core.annotation.Annotation.

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

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

Parameters

other

Returns

Implements umms.core.annotation.Annotation.

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

Implements umms.core.annotation.Annotation.

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

Implements umms.core.annotation.Annotation.

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

Returns: name of the reference sequence

Implements umms.core.annotation.Annotation.

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

Implements umms.core.annotation.Annotation.

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

The BasicAnnotation will return the gaps themselves

Implements umms.core.annotation.Annotation.

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

Returns: start of the annotation (inclusive)

Implements umms.core.annotation.Annotation.

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

Returns the result of intersecting this instance with another

Parameters

other

Returns: returns null if there is no intersection

Implements umms.core.annotation.Annotation.

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

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

Implements umms.core.annotation.Annotation.

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

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

Implements umms.core.annotation.Annotation.

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static void umms.core.annotation.BasicAnnotation.main ( String[] args ) throws IOException

static

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Annotation umms.core.annotation.BasicAnnotation.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.

Implements umms.core.annotation.Annotation.

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Annotation umms.core.annotation.BasicAnnotation.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.

Implements umms.core.annotation.Annotation.

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

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

Parameters

coordinateInReference

Implements umms.core.annotation.Annotation.

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

Returns: number of blocks in the Annotation

Implements umms.core.annotation.Annotation.

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

Implements umms.core.annotation.Annotation.

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boolean umms.core.annotation.BasicAnnotation.overlaps	(	List<?extends Annotation >	otherBlocks,
		int	buffer
	)

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

Parameters

name	name of the annotation

Implements umms.core.annotation.Annotation.

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

Implements umms.core.annotation.Annotation.

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

Implements umms.core.annotation.Annotation.

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

Implements umms.core.annotation.Annotation.

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

Parameters

refName name of the reference sequence / chromosome

Implements umms.core.annotation.Annotation.

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void umms.core.annotation.BasicAnnotation.setScore ( double s )

Implements umms.core.annotation.Annotation.

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void umms.core.annotation.BasicAnnotation.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.

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void umms.core.annotation.BasicAnnotation.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.

Implements umms.core.annotation.Annotation.

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

Implements umms.core.annotation.Annotation.

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String umms.core.annotation.BasicAnnotation.toString ( )

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Annotation umms.core.annotation.BasicAnnotation.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

Implements umms.core.annotation.Annotation.

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Member Data Documentation

CompoundInterval umms.core.annotation.BasicAnnotation.blocks = new CompoundInterval()

protected

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

java/umms/core/annotation/BasicAnnotation.java

Classes

Public Member Functions

Static Public Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation