umms.core.coordinatesystem.TranscriptomeSpace Class Reference

Inheritance diagram for umms.core.coordinatesystem.TranscriptomeSpace:

Collaboration diagram for umms.core.coordinatesystem.TranscriptomeSpace:

Classes
class	GeneTree

Public Member Functions
	TranscriptomeSpace (Map< String, Collection< Gene >> chrToGenesMap)
	TranscriptomeSpace (File bamFile, String genomeSeq)
	TranscriptomeSpace (File bamFile, Map< String, Collection< Gene >> chrToGenesMap, String genomeSeq)
Collection<?extends Window >	getFragment (String chr, int start, int end)
Collection<?extends Window >	getFragment (Annotation annotation)
Collection<?extends Window >	getOverlappingRegion (String chr, int start, int end)
Iterator< Window >	getWindowIterator (Collection< Gene > baseGenes, int windowSize, int overlap)
Iterator< Window >	getWindowIterator (int windowSize, String chr, int start, int end, int overlap)
Iterator<?extends Window >	getWindowIterator (Annotation window, int windowSize, int overlap)
Iterator< Window >	getWindowIterator (String chr, int windowSize, int overlap)
Iterator< Window >	getWindowIterator (int windowSize, int overlap)
TreeMap< Integer, Double >	getPositionCountMap (Gene region, AlignmentModel data) throws IOException
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)
Annotation	getEntireChromosome (String chrName)
int	getSize (Annotation region)
boolean	hasChromosome (String chr)
Annotation	moveAnnotation (Annotation read, int relativeStart, Annotation gene)
Collection< String >	getChromosomeNames ()
boolean	isValidWindow (Annotation a)

Static Public Member Functions
static TranscriptomeSpace	getTranscriptomeSpace (String bedFile) throws IOException

Static Public Attributes
static final int	PERMUTATION_ATTEMPTS = 10

Constructor & Destructor Documentation

umms.core.coordinatesystem.TranscriptomeSpace.TranscriptomeSpace

(

Map< String, Collection< Gene >>

chrToGenesMap

)

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umms.core.coordinatesystem.TranscriptomeSpace.TranscriptomeSpace	(	File	bamFile,
		String	genomeSeq
	)

Builds a transcriptome space from a bam file directly This will collapse all reads into an assembly of transcripts

Parameters

bamFile	Alignment file
genomeSeq	A fasta file with the reference sequence

umms.core.coordinatesystem.TranscriptomeSpace.TranscriptomeSpace	(	File	bamFile,
		Map< String, Collection< Gene >>	chrToGenesMap,
		String	genomeSeq
	)

Builds a transcriptome space from a bam file plus a known annotation file

Parameters

bamFile	The reads to build the assembly from
chrToGenesMap	The known transcriptome to use

Member Function Documentation

Collection<String> umms.core.coordinatesystem.TranscriptomeSpace.getChromosomeNames

(

)

Returns

A list of chromosome names contained in the coordinate space

Implements umms.core.coordinatesystem.CoordinateSpace.

Annotation umms.core.coordinatesystem.TranscriptomeSpace.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.TranscriptomeSpace.getFragment	(	String	chr,
		int	start,
		int	end
	)

Return a fragment between start and end on chr

Implements umms.core.coordinatesystem.CoordinateSpace.

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Collection<? extends Window> umms.core.coordinatesystem.TranscriptomeSpace.getFragment

(

Annotation

annotation

)

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

Parameters

Annotation

Returns

Implements umms.core.coordinatesystem.CoordinateSpace.

long umms.core.coordinatesystem.TranscriptomeSpace.getLength

(

)

This will sum up the blocks ignoring the overlaps

Implements umms.core.coordinatesystem.CoordinateSpace.

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

Returns an interval tree over the specified transcriptome region

Implements umms.core.coordinatesystem.CoordinateSpace.

TreeMap<Integer,Double> umms.core.coordinatesystem.TranscriptomeSpace.getPositionCountMap	(	Gene	region,
		AlignmentModel	data
	)		throws IOException

Get map of position to of position level counts in mature transcript

Parameters

region	The region
data	Alignment data

Returns

Map of position to count

Exceptions

IOException

Annotation umms.core.coordinatesystem.TranscriptomeSpace.getReferenceAnnotation

(

String

name

)

Parameters

name

Returns

The named reference as an annotation

Implements umms.core.coordinatesystem.CoordinateSpace.

Collection<? extends Annotation> umms.core.coordinatesystem.TranscriptomeSpace.getReferenceAnnotations

(

)

Returns

The reference annotations contained in this coordinate space.

Implements umms.core.coordinatesystem.CoordinateSpace.

Collection<String> umms.core.coordinatesystem.TranscriptomeSpace.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.TranscriptomeSpace.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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static TranscriptomeSpace umms.core.coordinatesystem.TranscriptomeSpace.getTranscriptomeSpace ( String  bedFile ) throws IOException

static

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

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

Implements umms.core.coordinatesystem.CoordinateSpace.

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

Returns

returns an iterator over an annotation sequentially

Implements umms.core.coordinatesystem.CoordinateSpace.

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

Get a window iterator from start to finish on chromosome

Implements umms.core.coordinatesystem.CoordinateSpace.

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

boolean umms.core.coordinatesystem.TranscriptomeSpace.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.TranscriptomeSpace.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.TranscriptomeSpace.moveAnnotation	(	Annotation	read,
		int	relativeStart,
		Annotation	gene
	)

Moves the annotation to a new start location using the coordinate space to decide on gaps

Parameters

read	the read to be moved
newStartLocation	the start location of the annotation (relative to the annotation start)
gene	the original transcript moving over

Returns

A new annotation object in the start location reflecting the move

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Annotation umms.core.coordinatesystem.TranscriptomeSpace.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.TranscriptomeSpace.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.

Member Data Documentation

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

static

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

• java/umms/core/coordinatesystem/TranscriptomeSpace.java