Inheritance diagram for umms.core.annotation.AnnotationList< T extends Annotation >:

Collaboration diagram for umms.core.annotation.AnnotationList< T extends Annotation >:

Public Member Functions
	AnnotationList ()

	AnnotationList (CoordinateSpace cs)

	AnnotationList (CoordinateSpace cs, Collection<?extends T > annotations)

	AnnotationList (CoordinateSpace cs, T...annotations)

int	size ()

double	getGlobalCount ()

double	getCount (Annotation region, boolean fullyContained)

double	getCountExcludingRegion (Annotation region, Annotation excluded)

int	getBasesCovered (Annotation region, boolean fullyContained)

CloseableIterator< T >	getOverlappingAnnotations (Annotation region, boolean fullyContained)

int	getNumOverlappingAnnotations (Annotation region)

CloseableIterator< T >	getPermutedAnnotations (Annotation region)

CloseableIterator< T >	iterator ()

void	addFilter (Predicate< T > filter)

void	addFilters (Collection< Predicate< T >> filters)

void	addAll (Iterable<?extends T > annotations)

void	addAll (AnnotationList<?extends T > otherSet)

void	add (T annotation)

void	removeAnnotation (T annotation)

void	collapse ()

AnnotationList< T >	intersect (AnnotationList<?extends Annotation > other)

AnnotationList< T >	minus (AnnotationList<?extends Annotation > other)

AnnotationList< T >	getOverlappingAnnotationList (AnnotationList<?extends Annotation > other)

boolean	hasAnnotationThatOverlaps (Annotation region)

boolean	hasAnnotationThatContains (Annotation region)

AnnotationList< T >	getOverlappingAnnotationList (AnnotationList<?extends Annotation > other, boolean fullyContained)

T	getClosest (final Annotation query)

T	getClosestNonOverlapping (final Annotation query)

T	getClosest (final Annotation query, boolean nonOverlapping)

T	getClosestUpstream (final Annotation query)

T	getClosestDownstream (final Annotation query)

Integer	getDistanceToClosest (final Annotation query)

List< T >	toList ()

CoordinateSpace	getCoordinateSpace ()

double	getRefSequenceLambda (String refname)

double	getCountStrandedExcludingRegion (Annotation region, Annotation excluded)

Static Public Attributes
static boolean	ENFORCE_REFERENCE = false

Protected Attributes
final CoordinateSpace	coordinateSpace

TreeMap< String, IntervalTree < T > >	annotations = new TreeMap<String, IntervalTree<T>>()

Detailed Description

Author: engreitz Class for storing and oeprating on a set of annotations in memory Allows multiple identical annotations. Iterators, counting, etc. always consider the filters present in the AnnotationList. TODO: Add a different class that will dynamically read BED files, perhaps by using an indexing system TODO: Add a global extension factor TODO: Integrate with modified reader classes that can populate an AnnotationList from a file (this class should not be responsible for parsing or reading - only for storing and manipulating) TODO: Alternative (faster?) implementation: remove all annotations that don't pass filters so you don't have to test every annotation every time you iterate. In this implementation, addFilter would apply the filter to all annotations upon addition, removing those that do not pass.

Parameters

<T>

Constructor & Destructor Documentation

umms.core.annotation.AnnotationList< T extends Annotation >.AnnotationList ( )

umms.core.annotation.AnnotationList< T extends Annotation >.AnnotationList ( CoordinateSpace cs )

Initializing with a coordinate space allows for some additional filtering and sanity checks

Parameters

cs

umms.core.annotation.AnnotationList< T extends Annotation >.AnnotationList	(	CoordinateSpace	cs,
		Collection<?extends T >	annotations
	)

umms.core.annotation.AnnotationList< T extends Annotation >.AnnotationList	(	CoordinateSpace	cs,
		T...	annotations
	)

Member Function Documentation

void umms.core.annotation.AnnotationList< T extends Annotation >.add ( T annotation )

Add an annotation

Parameters

annotation

void umms.core.annotation.AnnotationList< T extends Annotation >.addAll ( Iterable<?extends T > annotations )

Add a collection of annotations

Parameters

annotations

void umms.core.annotation.AnnotationList< T extends Annotation >.addAll ( AnnotationList<?extends T > otherSet )

Add another AnnotationList. Duplicates allowed

Parameters

otherSet

void umms.core.annotation.AnnotationList< T extends Annotation >.addFilter ( Predicate< T > filter )

void umms.core.annotation.AnnotationList< T extends Annotation >.addFilters ( Collection< Predicate< T >> filters )

void umms.core.annotation.AnnotationList< T extends Annotation >.collapse ( )

Collapse overlapping annotations.

int umms.core.annotation.AnnotationList< T extends Annotation >.getBasesCovered	(	Annotation	region,
		boolean	fullyContained
	)

T umms.core.annotation.AnnotationList< T extends Annotation >.getClosest ( final Annotation query )

Parameters

query

Returns: Closest annotation in the set, or null if there are no annotations on the same chromosome

T umms.core.annotation.AnnotationList< T extends Annotation >.getClosest	(	final Annotation	query,
		boolean	nonOverlapping
	)

Parameters

query

Returns: Closest (non-overlapping) annotation in the set, or null if there are no matches on the same chromosome

T umms.core.annotation.AnnotationList< T extends Annotation >.getClosestDownstream ( final Annotation query )

Returns the closest non-overlapping annotation 3-prime of the query, considering strand.

Parameters

query

Returns

T umms.core.annotation.AnnotationList< T extends Annotation >.getClosestNonOverlapping ( final Annotation query )

Parameters

query

Returns: Closest non-overlapping annotation in the set, or null if there are no non-overlapping annotations on the same chromosome

T umms.core.annotation.AnnotationList< T extends Annotation >.getClosestUpstream ( final Annotation query )

Returns the closest non-overlapping annotation 5-prime of the query, considering strand.

Parameters

query

Returns

CoordinateSpace umms.core.annotation.AnnotationList< T extends Annotation >.getCoordinateSpace ( )

double umms.core.annotation.AnnotationList< T extends Annotation >.getCount	(	Annotation	region,
		boolean	fullyContained
	)

double umms.core.annotation.AnnotationList< T extends Annotation >.getCountExcludingRegion	(	Annotation	region,
		Annotation	excluded
	)

double umms.core.annotation.AnnotationList< T extends Annotation >.getCountStrandedExcludingRegion	(	Annotation	region,
		Annotation	excluded
	)

Integer umms.core.annotation.AnnotationList< T extends Annotation >.getDistanceToClosest ( final Annotation query )

Parameters

query

Returns: distance in coordinate space between the query and the closest element in the set, or null if there are no others on the same chromosome

double umms.core.annotation.AnnotationList< T extends Annotation >.getGlobalCount ( )

int umms.core.annotation.AnnotationList< T extends Annotation >.getNumOverlappingAnnotations ( Annotation region )

AnnotationList<T> umms.core.annotation.AnnotationList< T extends Annotation >.getOverlappingAnnotationList ( AnnotationList<?extends Annotation > other )

Parameters

other

Returns: AnnotationList containing all annotations that overlap an annotation in other.

AnnotationList<T> umms.core.annotation.AnnotationList< T extends Annotation >.getOverlappingAnnotationList	(	AnnotationList<?extends Annotation >	other,
		boolean	fullyContained
	)

Parameters

other
fullyContained

Returns: AnnotationList containing all annotations that overlap (or contained by) an annotation in other.

CloseableIterator<T> umms.core.annotation.AnnotationList< T extends Annotation >.getOverlappingAnnotations	(	Annotation	region,
		boolean	fullyContained
	)

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CloseableIterator<T> umms.core.annotation.AnnotationList< T extends Annotation >.getPermutedAnnotations ( Annotation region )

double umms.core.annotation.AnnotationList< T extends Annotation >.getRefSequenceLambda ( String refname )

boolean umms.core.annotation.AnnotationList< T extends Annotation >.hasAnnotationThatContains ( Annotation region )

Parameters

region

Returns: true if this has any Annotations that fully contain region

boolean umms.core.annotation.AnnotationList< T extends Annotation >.hasAnnotationThatOverlaps ( Annotation region )

Parameters

region

Returns: true if this has any Annotations that overlap region

AnnotationList<T> umms.core.annotation.AnnotationList< T extends Annotation >.intersect ( AnnotationList<?extends Annotation > other )

Returns the intersection of this AnnotationList with another. Behaves like bedIntersect Different than getOverlappers

Parameters

other

Returns

CloseableIterator<T> umms.core.annotation.AnnotationList< T extends Annotation >.iterator ( )

AnnotationList<T> umms.core.annotation.AnnotationList< T extends Annotation >.minus ( AnnotationList<?extends Annotation > other )

Returns a new AnnotationList that does not contain any annotations that overlap annotations in other

Parameters

other

Returns

void umms.core.annotation.AnnotationList< T extends Annotation >.removeAnnotation ( T annotation )

int umms.core.annotation.AnnotationList< T extends Annotation >.size ( )

List<T> umms.core.annotation.AnnotationList< T extends Annotation >.toList ( )

Returns: A list of all annotations passing the filter

Member Data Documentation

TreeMap<String, IntervalTree<T> > umms.core.annotation.AnnotationList< T extends Annotation >.annotations = new TreeMap<String, IntervalTree<T>>()

protected

final CoordinateSpace umms.core.annotation.AnnotationList< T extends Annotation >.coordinateSpace

protected

boolean umms.core.annotation.AnnotationList< T extends Annotation >.ENFORCE_REFERENCE = false

static

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

java/umms/core/annotation/AnnotationList.java

Public Member Functions

Static Public Attributes

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation