Inheritance diagram for umms.core.coordinatesystem.MaskedGenomicSpace:

Collaboration diagram for umms.core.coordinatesystem.MaskedGenomicSpace:

Public Member Functions
	MaskedGenomicSpace (Map< String, Integer > chrSizes, Map< String, Collection< Annotation >> maskedRegions, int distance)

	MaskedGenomicSpace (Map< String, Integer > chrSizes, Map< String, Collection< Annotation >> maskedRegions, int distance, boolean constantWidth)

Collection<?extends Window >	getFragment (String chr, int start, int end)

Collection<?extends Window >	getOverlappingRegion (String chr, int start, int end)

Iterator<?extends Window >	getWindowIterator (int windowSize, String chr, int start, int end, int overlap)

Iterator<?extends Window >	getWindowIterator (String chr, int windowSize, int overlap)

Iterator<?extends Window >	getWindowIterator (int windowSize, int overlap)

Iterator<?extends Window >	getWindowIterator (Annotation window, int windowSize, int overlap)

long	getLength ()

long	getLength (String chr)

Annotation	permuteAnnotation (Annotation a)

Annotation	permuteAnnotation (Annotation a, Annotation bounds)

Collection< String >	getReferenceNames ()

Collection<?extends Annotation >	getReferenceAnnotations ()

Annotation	getReferenceAnnotation (String name)

Iterator< Window >	getWindowIterator (Collection< Gene > baseGenes, int windowSize, int overlap)

Collection<?extends Window >	getFragment (Annotation annotation)

int	getSize (Annotation region)

Collection< String >	getChromosomeNames ()

boolean	hasChromosome (String chr)

Annotation	getEntireChromosome (String chrName)

boolean	isValidWindow (Annotation window)

Constructor & Destructor Documentation

umms.core.coordinatesystem.MaskedGenomicSpace.MaskedGenomicSpace	(	Map< String, Integer >	chrSizes,
		Map< String, Collection< Annotation >>	maskedRegions,
		int	distance
	)

This is meant to represent a coordinate space that excludes masked regions This way we wont count reads in the global stats in these regions Wont use them in estimating parameters or length calculations

Parameters

maskedRegions	a collection of masked region
chrSizes	the lengths of the associated chromosomes

umms.core.coordinatesystem.MaskedGenomicSpace.MaskedGenomicSpace	(	Map< String, Integer >	chrSizes,
		Map< String, Collection< Annotation >>	maskedRegions,
		int	distance,
		boolean	constantWidth
	)

This is meant to represent a coordinate space that excludes masked regions This way we wont count reads in the global stats in these regions Wont use them in estimating parameters or length calculations

Parameters

maskedRegions	a collection of masked region
chrSizes	the lengths of the associated chromosomes
constantWidth	a boolean (true= ensure that windows have the same final length even if represent different genomic space, false= all windows will have same genomic space even if shorter window length because of masked regions)

Member Function Documentation

Collection<String> umms.core.coordinatesystem.MaskedGenomicSpace.getChromosomeNames ( )

Returns: A list of chromosome names contained in the coordinate space

Implements umms.core.coordinatesystem.CoordinateSpace.

Annotation umms.core.coordinatesystem.MaskedGenomicSpace.getEntireChromosome ( String chrName )

Get an annotation spanning an entire chromosome

Parameters

chrName The chromosome name

Returns: Annotation consisting of the entire chromosome

Implements umms.core.coordinatesystem.CoordinateSpace.

Collection<? extends Window> umms.core.coordinatesystem.MaskedGenomicSpace.getFragment	(	String	chr,
		int	start,
		int	end
	)

Will return the continuous fragment

Implements umms.core.coordinatesystem.CoordinateSpace.

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Collection<? extends Window> umms.core.coordinatesystem.MaskedGenomicSpace.getFragment ( Annotation annotation )

Returns a fragment of type Window between start and end on chromosome

Parameters

Annotation

Returns

Implements umms.core.coordinatesystem.CoordinateSpace.

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long umms.core.coordinatesystem.MaskedGenomicSpace.getLength ( )

Always returns the gapped space length

Implements umms.core.coordinatesystem.CoordinateSpace.

long umms.core.coordinatesystem.MaskedGenomicSpace.getLength ( String chr )

Returns the total number of positions in the coordinate space For non-contiguous coordinate spaces, this will return a collapsed count such that overlapping blocks are not double counted

Parameters

only	positions on a given chromosome

Returns: number of positions in space

Implements umms.core.coordinatesystem.CoordinateSpace.

Collection<? extends Window> umms.core.coordinatesystem.MaskedGenomicSpace.getOverlappingRegion	(	String	chr,
		int	start,
		int	end
	)

Will return the overlapping regions in gapped space

Implements umms.core.coordinatesystem.CoordinateSpace.

Annotation umms.core.coordinatesystem.MaskedGenomicSpace.getReferenceAnnotation ( String name )

Parameters

name

Returns: The named reference as an annotation

Implements umms.core.coordinatesystem.CoordinateSpace.

Collection<? extends Annotation> umms.core.coordinatesystem.MaskedGenomicSpace.getReferenceAnnotations ( )

Returns: The reference annotations contained in this coordinate space.

Implements umms.core.coordinatesystem.CoordinateSpace.

Collection<String> umms.core.coordinatesystem.MaskedGenomicSpace.getReferenceNames ( )

Returns: A list of reference names contained in the coordinate space (e.g. chr1, chr2, etc.)

Implements umms.core.coordinatesystem.CoordinateSpace.

int umms.core.coordinatesystem.MaskedGenomicSpace.getSize ( Annotation region )

Get the size of the annotation with respect to the coordinate space

Parameters

region

Returns

Implements umms.core.coordinatesystem.CoordinateSpace.

Iterator<? extends Window> umms.core.coordinatesystem.MaskedGenomicSpace.getWindowIterator	(	int	windowSize,
		String	chr,
		int	start,
		int	end,
		int	overlap
	)

Interprets the windowSize based on how it was initialized

Implements umms.core.coordinatesystem.CoordinateSpace.

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Iterator<? extends Window> umms.core.coordinatesystem.MaskedGenomicSpace.getWindowIterator	(	String	chr,
		int	windowSize,
		int	overlap
	)

Returns: returns an iterator that goes from first window to last window on chromosome chr sequentially

Implements umms.core.coordinatesystem.CoordinateSpace.

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Iterator<? extends Window> umms.core.coordinatesystem.MaskedGenomicSpace.getWindowIterator	(	int	windowSize,
		int	overlap
	)

Returns: returns an iterator that goes from first window to last window in the coordinate space sequentially

Implements umms.core.coordinatesystem.CoordinateSpace.

Iterator<? extends Window> umms.core.coordinatesystem.MaskedGenomicSpace.getWindowIterator	(	Annotation	window,
		int	windowSize,
		int	overlap
	)

Returns: returns an iterator over an annotation sequentially

Implements umms.core.coordinatesystem.CoordinateSpace.

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Iterator<Window> umms.core.coordinatesystem.MaskedGenomicSpace.getWindowIterator	(	Collection< Gene >	baseGenes,
		int	windowSize,
		int	overlap
	)

Get a window iterator over a collection of GeneWindows

Parameters

baseGenes	The regions over which to iterate
windowSize	Window size
overlap	Overlap size

Returns: Iterator over windows on the collection of regions

Implements umms.core.coordinatesystem.CoordinateSpace.

boolean umms.core.coordinatesystem.MaskedGenomicSpace.hasChromosome ( String chr )

Returns true if the coordinate space contains any annotations on the queried chromosome

Parameters

chr

Returns

Implements umms.core.coordinatesystem.CoordinateSpace.

boolean umms.core.coordinatesystem.MaskedGenomicSpace.isValidWindow ( Annotation window )

Check if window in coordinate space and not masked

Parameters

window

Returns

Implements umms.core.coordinatesystem.CoordinateSpace.

Annotation umms.core.coordinatesystem.MaskedGenomicSpace.permuteAnnotation ( Annotation a )

Permutes an annotation to a new location on the same reference in the given coordinate space, preserving the length of the annotation and maintaining a consistent block structure. Does not check whether the given annotation was valid in the coordinate space in the first place.

Parameters

a	Annotation to permute. Will be modified.

Returns: The permuted Annotation

Exceptions

PermutationNotFoundException if an annotation cannot be found

Implements umms.core.coordinatesystem.CoordinateSpace.

Annotation umms.core.coordinatesystem.MaskedGenomicSpace.permuteAnnotation	(	Annotation	a,
		Annotation	bounds
	)

Permutes an annotation to a new location within the given bounds, preserving the length of the annotation and maintaining a consistent block structure. Does not check whether the given annotation was valid in the coordinate space in the first place.

Parameters

a	Annotation to permute. Will be modified.
bounds	Boundaries within which the annotation will be permuted

Returns: The permuted Annotation

Exceptions

PermutationNotFoundException if a permuted location cannot be found

Implements umms.core.coordinatesystem.CoordinateSpace.

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

java/umms/core/coordinatesystem/MaskedGenomicSpace.java

Public Member Functions

Constructor & Destructor Documentation

Member Function Documentation