Inheritance diagram for umms.core.coordinatesystem.CoordinateSpace:

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

Collection<?extends Window >	getFragment (Annotation annotation)

int	getSize (Annotation region)

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< Window >	getWindowIterator (Collection< Gene > baseGenes, 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< String >	getChromosomeNames ()

Collection<?extends Annotation >	getReferenceAnnotations ()

Annotation	getReferenceAnnotation (String name)

boolean	hasChromosome (String chr)

Annotation	getEntireChromosome (String chrName)

boolean	isValidWindow (Annotation window)

Detailed Description

This interface represents the coordinate space in which we analyze the models

Author: skadri; mguttman

Member Function Documentation

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

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

Implemented in umms.core.coordinatesystem.TranscriptomeSpace, umms.core.coordinatesystem.TranscriptInGenomicSpace, umms.core.coordinatesystem.GenomicSpace, and umms.core.coordinatesystem.MaskedGenomicSpace.

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

Get an annotation spanning an entire chromosome

Parameters

chrName The chromosome name

Returns: Annotation consisting of the entire chromosome

Implemented in umms.core.coordinatesystem.TranscriptomeSpace, umms.core.coordinatesystem.MaskedGenomicSpace, umms.core.coordinatesystem.GenomicSpace, and umms.core.coordinatesystem.TranscriptInGenomicSpace.

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

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

Parameters

chr
start
end

Returns

Implemented in umms.core.coordinatesystem.GenomicSpace, umms.core.coordinatesystem.TranscriptInGenomicSpace, umms.core.coordinatesystem.MaskedGenomicSpace, and umms.core.coordinatesystem.TranscriptomeSpace.

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

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

Parameters

Annotation

Returns

Implemented in umms.core.coordinatesystem.MaskedGenomicSpace, umms.core.coordinatesystem.GenomicSpace, umms.core.coordinatesystem.TranscriptInGenomicSpace, and umms.core.coordinatesystem.TranscriptomeSpace.

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

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

Returns: number of positions in space

Implemented in umms.core.coordinatesystem.TranscriptomeSpace, umms.core.coordinatesystem.GenomicSpace, umms.core.coordinatesystem.TranscriptInGenomicSpace, and umms.core.coordinatesystem.MaskedGenomicSpace.

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long umms.core.coordinatesystem.CoordinateSpace.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

Implemented in umms.core.coordinatesystem.TranscriptomeSpace, umms.core.coordinatesystem.GenomicSpace, umms.core.coordinatesystem.TranscriptInGenomicSpace, and umms.core.coordinatesystem.MaskedGenomicSpace.

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

Returns a collection of regions overlapping start and end on chromosome

Parameters

chr
start
end

Returns

Implemented in umms.core.coordinatesystem.MaskedGenomicSpace, umms.core.coordinatesystem.TranscriptomeSpace, umms.core.coordinatesystem.GenomicSpace, and umms.core.coordinatesystem.TranscriptInGenomicSpace.

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

Parameters

name

Returns: The named reference as an annotation

Implemented in umms.core.coordinatesystem.TranscriptomeSpace, umms.core.coordinatesystem.MaskedGenomicSpace, umms.core.coordinatesystem.GenomicSpace, and umms.core.coordinatesystem.TranscriptInGenomicSpace.

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

Returns: The reference annotations contained in this coordinate space.

Implemented in umms.core.coordinatesystem.TranscriptomeSpace, umms.core.coordinatesystem.MaskedGenomicSpace, umms.core.coordinatesystem.GenomicSpace, and umms.core.coordinatesystem.TranscriptInGenomicSpace.

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

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

Implemented in umms.core.coordinatesystem.TranscriptomeSpace, umms.core.coordinatesystem.MaskedGenomicSpace, umms.core.coordinatesystem.GenomicSpace, and umms.core.coordinatesystem.TranscriptInGenomicSpace.

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

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

Parameters

region

Returns

Implemented in umms.core.coordinatesystem.TranscriptomeSpace, umms.core.coordinatesystem.TranscriptInGenomicSpace, umms.core.coordinatesystem.GenomicSpace, and umms.core.coordinatesystem.MaskedGenomicSpace.

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

Iterate over windows within the defined region

Parameters

windowSize
chr
start
end

Returns: returns an iterator that iterates over the region

Implemented in umms.core.coordinatesystem.MaskedGenomicSpace, umms.core.coordinatesystem.TranscriptomeSpace, umms.core.coordinatesystem.GenomicSpace, and umms.core.coordinatesystem.TranscriptInGenomicSpace.

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

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

Implemented in umms.core.coordinatesystem.MaskedGenomicSpace, umms.core.coordinatesystem.TranscriptomeSpace, umms.core.coordinatesystem.GenomicSpace, and umms.core.coordinatesystem.TranscriptInGenomicSpace.

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

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

Implemented in umms.core.coordinatesystem.MaskedGenomicSpace, umms.core.coordinatesystem.TranscriptomeSpace, umms.core.coordinatesystem.GenomicSpace, and umms.core.coordinatesystem.TranscriptInGenomicSpace.

Iterator<Window> umms.core.coordinatesystem.CoordinateSpace.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

Implemented in umms.core.coordinatesystem.MaskedGenomicSpace, umms.core.coordinatesystem.GenomicSpace, umms.core.coordinatesystem.TranscriptInGenomicSpace, and umms.core.coordinatesystem.TranscriptomeSpace.

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

Returns: returns an iterator over an annotation sequentially

Implemented in umms.core.coordinatesystem.MaskedGenomicSpace, umms.core.coordinatesystem.TranscriptomeSpace, umms.core.coordinatesystem.GenomicSpace, and umms.core.coordinatesystem.TranscriptInGenomicSpace.

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

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

Parameters

chr

Returns

Implemented in umms.core.coordinatesystem.TranscriptomeSpace, umms.core.coordinatesystem.MaskedGenomicSpace, umms.core.coordinatesystem.GenomicSpace, and umms.core.coordinatesystem.TranscriptInGenomicSpace.

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

Check if window in coordinate space and not masked

Parameters

window

Returns

Implemented in umms.core.coordinatesystem.TranscriptomeSpace, umms.core.coordinatesystem.MaskedGenomicSpace, umms.core.coordinatesystem.GenomicSpace, and umms.core.coordinatesystem.TranscriptInGenomicSpace.

Annotation umms.core.coordinatesystem.CoordinateSpace.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

Implemented in umms.core.coordinatesystem.TranscriptomeSpace, umms.core.coordinatesystem.MaskedGenomicSpace, umms.core.coordinatesystem.GenomicSpace, and umms.core.coordinatesystem.TranscriptInGenomicSpace.

Annotation umms.core.coordinatesystem.CoordinateSpace.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

Implemented in umms.core.coordinatesystem.TranscriptomeSpace, umms.core.coordinatesystem.MaskedGenomicSpace, umms.core.coordinatesystem.GenomicSpace, and umms.core.coordinatesystem.TranscriptInGenomicSpace.

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

java/umms/core/coordinatesystem/CoordinateSpace.java

Public Member Functions

Detailed Description

Member Function Documentation