Inheritance diagram for umms.core.coordinatesystem.GenomicSpace:

Collaboration diagram for umms.core.coordinatesystem.GenomicSpace:

Public Member Functions
	GenomicSpace (Map< String, Integer > chromosomeSizes)

	GenomicSpace (String chromosomeSizes)

	GenomicSpace (String chromosomeSizes, String maskedRegionFile)

	GenomicSpace (Map< String, Integer > chromosomeSizes, String maskedRegionFile)

	GenomicSpace (String chromosomeSizes, String maskedRegionFile, double pctMaskedAllowed)

void	setPercentMaskedAllowed (double pct)

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

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

Iterator< Window >	getWindowIterator (int windowSize, String chr, int start, int end, int overlap, boolean backward)

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

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

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

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

boolean	isValidWindow (Annotation window)

boolean	containsDataFor (String chromosome)

long	getLength ()

long	getLength (String chr)

long	getUnmaskedLength (String chr)

Annotation	permuteAnnotation (Annotation a)

boolean	hasChromosome (String chr)

Annotation	permuteAnnotation (Annotation a, Annotation bounds)

final Collection< String >	getReferenceNames ()

final Collection<?extends Annotation >	getReferenceAnnotations ()

Annotation	getEntireChromosome (String chrName)

Annotation	getReferenceAnnotation (String name)

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

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

Collection<?extends Window >	getFragment (Annotation annotation)

int	getSize (Annotation region)

Collection< String >	getChromosomeNames ()

Static Public Member Functions
static void	setSeed (long seed)

Static Public Attributes
static final int	PERMUTATION_ATTEMPTS = 10

Detailed Description

Author: engreitz Class representing a genome with defined linear chromosomes. Masking behavior can be controlled through setting masked regions and percent masked allowed parameters, which will filter out windows that overlap masked regions.

Constructor & Destructor Documentation

umms.core.coordinatesystem.GenomicSpace.GenomicSpace ( Map< String, Integer > chromosomeSizes )

Parameters

chromosomeSizes

umms.core.coordinatesystem.GenomicSpace.GenomicSpace ( String chromosomeSizes )

Chromosome name and accompanying sizes

Parameters

chromosomeSizes

umms.core.coordinatesystem.GenomicSpace.GenomicSpace	(	String	chromosomeSizes,
		String	maskedRegionFile
	)

umms.core.coordinatesystem.GenomicSpace.GenomicSpace	(	Map< String, Integer >	chromosomeSizes,
		String	maskedRegionFile
	)

umms.core.coordinatesystem.GenomicSpace.GenomicSpace	(	String	chromosomeSizes,
		String	maskedRegionFile,
		double	pctMaskedAllowed
	)

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Member Function Documentation

boolean umms.core.coordinatesystem.GenomicSpace.containsDataFor ( String chromosome )

Returns true if this coordinate space contains data for the specified chromosome

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

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

Implements umms.core.coordinatesystem.CoordinateSpace.

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Annotation umms.core.coordinatesystem.GenomicSpace.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.

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

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

Parameters

Implements umms.core.coordinatesystem.CoordinateSpace.

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Collection<? extends Window> umms.core.coordinatesystem.GenomicSpace.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.GenomicSpace.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

Implements umms.core.coordinatesystem.CoordinateSpace.

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long umms.core.coordinatesystem.GenomicSpace.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.GenomicSpace.getOverlappingRegion	(	String	chr,
		int	start,
		int	end
	)

Returns an interval tree over the genomic region

Implements umms.core.coordinatesystem.CoordinateSpace.

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

Parameters

name

Returns: The named reference as an annotation

Implements umms.core.coordinatesystem.CoordinateSpace.

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

Returns: The reference annotations contained in this coordinate space.

Implements umms.core.coordinatesystem.CoordinateSpace.

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final Collection<String> umms.core.coordinatesystem.GenomicSpace.getReferenceNames ( )

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

Implements umms.core.coordinatesystem.CoordinateSpace.

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

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

Parameters

region

Returns

Implements umms.core.coordinatesystem.CoordinateSpace.

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long umms.core.coordinatesystem.GenomicSpace.getUnmaskedLength ( String chr )

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

Returns an iterator on chromosome chr starting at start, ending at end, of size, windowSize with overlap between consecutive windows

Implements umms.core.coordinatesystem.CoordinateSpace.

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Iterator<Window> umms.core.coordinatesystem.GenomicSpace.getWindowIterator	(	int	windowSize,
		String	chr,
		int	start,
		int	end,
		int	overlap,
		boolean	backward
	)

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

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

Get a window iterator from start to finish on chromosome chr

Implements umms.core.coordinatesystem.CoordinateSpace.

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Iterator<Window> umms.core.coordinatesystem.GenomicSpace.getWindowIterator	(	int	windowSize,
		int	overlap
	)

Get a window iterator from start to finish in the entire space

Implements umms.core.coordinatesystem.CoordinateSpace.

Iterator<Window> umms.core.coordinatesystem.GenomicSpace.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.GenomicSpace.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.GenomicSpace.isValidWindow ( Annotation window )

Check if window in coordinate space and not masked

Parameters

window

Returns

Implements umms.core.coordinatesystem.CoordinateSpace.

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Annotation umms.core.coordinatesystem.GenomicSpace.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.

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Annotation umms.core.coordinatesystem.GenomicSpace.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.

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void umms.core.coordinatesystem.GenomicSpace.setPercentMaskedAllowed ( double pct )

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static void umms.core.coordinatesystem.GenomicSpace.setSeed ( long seed )

static

Set the seed for the random generator (used for permuting regions).

Member Data Documentation

final int umms.core.coordinatesystem.GenomicSpace.PERMUTATION_ATTEMPTS = 10

static

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

java/umms/core/coordinatesystem/GenomicSpace.java

Public Member Functions

Static Public Member Functions

Static Public Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation