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

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

Public Member Functions
int	getBasesCovered (Annotation region)

double	getTotalCoverage (Annotation region)

double	getAverageCoverage (Annotation region)

double	getCount (Annotation region)

double	getCount (AnnotationList<?extends Annotation > set)

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

CloseableIterator< T >	getOverlappingAnnotations (Annotation region)

Annotation	collapse (Annotation region, boolean fullyContained)

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

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

Protected Member Functions
WindowProcessor< CountScore >	getCountProcessor ()

Detailed Description

Author: engreitz Abstract class for functions common to both AlignmentModel and AnnotationSet. Mostly here for consistency in function between the two classes

Parameters

<T>

Member Function Documentation

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

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

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

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

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

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

WindowProcessor<CountScore> umms.core.annotation.AbstractAnnotationCollection< T extends Annotation >.getCountProcessor ( )

protected

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

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

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

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

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