Public Member Functions
int	size ()

double	getGlobalCount ()

double	getCount (Annotation region, boolean fullyContained)

double	getCount (Annotation region)

double	getCount (AnnotationList<?extends Annotation > set)

double	getCount (AnnotationList<?extends Annotation > set, boolean fullyContained)

int	getBasesCovered (Annotation region, boolean fullyContained)

int	getBasesCovered (Annotation region)

double	getTotalCoverage (Annotation region)

double	getAverageCoverage (Annotation region)

Annotation	collapse (Annotation region, boolean fullyContained)

CloseableIterator< T >	getOverlappingAnnotations (Annotation region)

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

CloseableIterator< T >	iterator ()

void	addFilter (Predicate< T > filter)

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

CloseableIterator< T >	getPermutedAnnotations (Annotation region)

double	getCountExcludingRegion (Annotation region, Annotation excluded)

double	getCountStrandedExcludingRegion (Annotation region, Annotation excluded)

CoordinateSpace	getCoordinateSpace ()

WindowScoreIterator< CountScore >	scan (int windowSize, int overlap)

public< W extends WindowScore > WindowScoreIterator< W >	scan (int windowSize, int overlap, WindowProcessor< W > processor)

public< W extends WindowScore > WindowScoreIterator< W >	scan (Annotation region, int windowSize, int overlap, WindowProcessor< W > processor)

WindowScoreIterator< CountScore >	scan (Annotation region, int windowSize, int overlap)

double	getRefSequenceLambda (String refname)

Detailed Description

Author: engreitz Interface to allow for counting over both AnnotationReader and ReadCollection.

Member Function Documentation

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

Adds a filter to use to decide whether an alignment is valid

Parameters

filter the filter to use

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

Add a set of filters to decide whether an alignment is valid

Parameters

filters Collection of filters to add

Annotation umms.core.annotation.AnnotationCollection< T extends Annotation >.collapse	(	Annotation	region,
		boolean	fullyContained
	)

Collapse all reads within the defined region into the overlapping set

Parameters

region	The region to determine overlap
fullyContained	Whether to count only fully contained reads

Returns: null if there are no Annotations that overlap

double umms.core.annotation.AnnotationCollection< T extends Annotation >.getAverageCoverage ( Annotation region )

Returns the average base-level coverage for the given region.

Parameters

region

Returns

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

This method will return the total number of bases that are covered by alignments in the collection If discontinuous region, it will only count blocks The maximum possible value is defined by region.getTranscriptSize();

Parameters

region	The region to determine overlap
fullyContained	Whether to count only fully contained reads

Returns

int umms.core.annotation.AnnotationCollection< T extends Annotation >.getBasesCovered ( Annotation region )

This method will return the total number of bases that are covered by alignments in the collection If discontinuous region, it will only count blocks. The maximum possible value is defined by region.getTranscriptSize(); Annotations counted here do not need to be fully contained in the region.

Parameters

region The region to determine overlap

Returns

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

Returns: The coordinate space currently used by the AnnotationCollection

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

This method will return the number of reads overlapping a given region

Parameters

region	The reference region to count overlapping elements
fullyContained	whether to only count overlapping elements if they are fully contained within the reference region

Returns: returns a double to allow implementing methods to utilize a weight object

Exceptions

IOException

double umms.core.annotation.AnnotationCollection< T extends Annotation >.getCount ( Annotation region )

This method will return the number of reads overlapping a given region (not necessarily fully contained)

Parameters

region The reference region to count overlapping elements

Returns: returns a double to allow implementing methods to utilize a weight object

Exceptions

IOException

double umms.core.annotation.AnnotationCollection< T extends Annotation >.getCount ( AnnotationList<?extends Annotation > set )

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

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

Compute the reads fully contained in region that are NOT overlapping excluded

Parameters

region
excluded

Returns: Count contained in region that do not overlap the excluded region

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

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

Returns: Global count, possibly weighted. Might be different from size if only counting reads that map, etc.

CloseableIterator<T> umms.core.annotation.AnnotationCollection< T extends Annotation >.getOverlappingAnnotations ( Annotation region )

This method will return a collection of the annotations that overlap a given region (not necessarily fully contained)

Parameters

region The region to overlap

Returns

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

This method will return a collection of the annotations that overlap a given region

Parameters

region	The region to determine overlap
fullyContained	Whether to count only fully contained reads

Returns

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

Shuffle the locations of annotations within the given region and return an iterator over the permuted annotations. Permuted annotations will not be necessarily sorted. NOTE: This will alter the annotations in the reader, so re-reading or reloading might be necessary.

Parameters

region reads reads fully contained in this region will be shuffled

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

double umms.core.annotation.AnnotationCollection< T extends Annotation >.getTotalCoverage ( Annotation region )

Returns the total base-level coverage for the given region.

Parameters

region

Returns

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

Returns: A closeable iterator through all annotations that pass the filters.

WindowScoreIterator<CountScore> umms.core.annotation.AnnotationCollection< T extends Annotation >.scan	(	int	windowSize,
		int	overlap
	)

public<W extends WindowScore> WindowScoreIterator<W> umms.core.annotation.AnnotationCollection< T extends Annotation >.scan	(	int	windowSize,
		int	overlap,
		WindowProcessor< W >	processor
	)

public<W extends WindowScore> WindowScoreIterator<W> umms.core.annotation.AnnotationCollection< T extends Annotation >.scan	(	Annotation	region,
		int	windowSize,
		int	overlap,
		WindowProcessor< W >	processor
	)

WindowScoreIterator<CountScore> umms.core.annotation.AnnotationCollection< T extends Annotation >.scan	(	Annotation	region,
		int	windowSize,
		int	overlap
	)

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

Returns: Total number of annotations. Considers filters.

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

java/umms/core/annotation/AnnotationCollection.java

Public Member Functions

Detailed Description

Member Function Documentation