broad.pda.gene.GeneWithIsoforms Class Reference

Inheritance diagram for broad.pda.gene.GeneWithIsoforms:

Collaboration diagram for broad.pda.gene.GeneWithIsoforms:

Public Member Functions
	GeneWithIsoforms (Collection<?extends LightweightGenomicAnnotation > exons)
	GeneWithIsoforms (LightweightGenomicAnnotation align)
	GeneWithIsoforms (String pslString)
	GeneWithIsoforms (String chrString, int start, int end)
	GeneWithIsoforms (String chr, int start, int end, String name, Strand orientation, Collection< Annotation > exons)
	GeneWithIsoforms (String chr, int start, int end, String name, String orientation, List< Integer > exonsStart, List< Integer > exonsEnd)
	GeneWithIsoforms (String chr, int start, int end, String name, String orientation, List< Integer > exonsStart, List< Integer > exonsEnd, int blockStart, int blockEnd)
	GeneWithIsoforms (String chr, int start, int end, String name, String orientation, List< Integer > exonsStart, List< Integer > exonsEnd, int blockStart, int blockEnd, String[] extraData)
	GeneWithIsoforms (String chr, int start, int end, String name, String orientation, List< Integer > exonsStart, List< Integer > exonsEnd, String[] extraData)
	GeneWithIsoforms (Gene gene)
boolean	IsExactOverlappingIsoform (Gene gene)
boolean	AddIsoform (Gene gene)
boolean	AddIsoform (Gene gene, boolean updateMainIsoform)
boolean	addContainedIsoform (Gene isoform)
boolean	AddAllIsoforms (GeneWithIsoforms overlapper)
boolean	AddAllIsoforms (GeneWithIsoforms overlapper, boolean updateMainIsoform)
boolean	AddAllIsoNotIncludedforms (GeneWithIsoforms other)
Collection< Gene >	getAllIsoforms ()
Collection< Gene >	getAllIsoforms (boolean includeContainingIsoform)
void	setBedScore (double scr)
void	setExtraFields (double[] scores)
void	updateScrToBedScore (double score)
List< Annotation >	getScoredExons ()
boolean	overlapsByGenomicRegion (IntervalTree< GeneWithIsoforms > otherTree, boolean considerOrientation)
void	dedup ()
Gene	findCompatibleGenes (IntervalTree< GeneWithIsoforms > overlapTree, int[] numIntrons)
void	expandUtrs (Integer utr1, Integer utr2)
void	addSuffixToName (String refName)
boolean	overlapsExon (LightweightGenomicAnnotation exon)
boolean	overlapsExon (Gene gene)
boolean	overlaps (Gene other)
Gene	getMerged ()
void	cleanIsoforms ()
Collection< Annotation >	getAllIsoformExonSet ()
Collection< Annotation >	getAllIsoformIntronSet ()
Gene	constituentIsoform ()
Gene	constituentIntrons ()
void	colapse (int exonFudgeFactor)
boolean	almostContains (Gene other, int exonFudgeFactor)
boolean	almostContains (GeneWithIsoforms other, int exonFudgeFactor)
boolean	hasOverlapping3PUTR (GeneWithIsoforms other)
boolean	hasOverlapping5PUTR (GeneWithIsoforms other)
String	allIsoformsToBED ()
void	standardizeOreintation ()
String	toString (String name)
Integer	getNumberOfIsoforms ()
Collection<?extends Gene >	selectRandIsoSubset (Integer maxIsoPerLoci)

Constructor & Destructor Documentation

broad.pda.gene.GeneWithIsoforms.GeneWithIsoforms

(

Collection<?extends LightweightGenomicAnnotation >

exons

)

broad.pda.gene.GeneWithIsoforms.GeneWithIsoforms

(

LightweightGenomicAnnotation

align

)

broad.pda.gene.GeneWithIsoforms.GeneWithIsoforms

(

String

pslString

)

broad.pda.gene.GeneWithIsoforms.GeneWithIsoforms	(	String	chrString,
		int	start,
		int	end
	)

broad.pda.gene.GeneWithIsoforms.GeneWithIsoforms	(	String	chr,
		int	start,
		int	end,
		String	name,
		Strand	orientation,
		Collection< Annotation >	exons
	)

broad.pda.gene.GeneWithIsoforms.GeneWithIsoforms	(	String	chr,
		int	start,
		int	end,
		String	name,
		String	orientation,
		List< Integer >	exonsStart,
		List< Integer >	exonsEnd
	)

broad.pda.gene.GeneWithIsoforms.GeneWithIsoforms	(	String	chr,
		int	start,
		int	end,
		String	name,
		String	orientation,
		List< Integer >	exonsStart,
		List< Integer >	exonsEnd,
		int	blockStart,
		int	blockEnd
	)

broad.pda.gene.GeneWithIsoforms.GeneWithIsoforms	(	String	chr,
		int	start,
		int	end,
		String	name,
		String	orientation,
		List< Integer >	exonsStart,
		List< Integer >	exonsEnd,
		int	blockStart,
		int	blockEnd,
		String[]	extraData
	)

broad.pda.gene.GeneWithIsoforms.GeneWithIsoforms	(	String	chr,
		int	start,
		int	end,
		String	name,
		String	orientation,
		List< Integer >	exonsStart,
		List< Integer >	exonsEnd,
		String[]	extraData
	)

broad.pda.gene.GeneWithIsoforms.GeneWithIsoforms

(

Gene

gene

)

Member Function Documentation

boolean broad.pda.gene.GeneWithIsoforms.AddAllIsoforms

(

GeneWithIsoforms

overlapper

)

boolean broad.pda.gene.GeneWithIsoforms.AddAllIsoforms	(	GeneWithIsoforms	overlapper,
		boolean	updateMainIsoform
	)

boolean broad.pda.gene.GeneWithIsoforms.AddAllIsoNotIncludedforms

(

GeneWithIsoforms

other

)

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boolean broad.pda.gene.GeneWithIsoforms.addContainedIsoform

(

Gene

isoform

)

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boolean broad.pda.gene.GeneWithIsoforms.AddIsoform

(

Gene

gene

)

boolean broad.pda.gene.GeneWithIsoforms.AddIsoform	(	Gene	gene,
		boolean	updateMainIsoform
	)

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void broad.pda.gene.GeneWithIsoforms.addSuffixToName

(

String

refName

)

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String broad.pda.gene.GeneWithIsoforms.allIsoformsToBED

(

)

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boolean broad.pda.gene.GeneWithIsoforms.almostContains	(	Gene	other,
		int	exonFudgeFactor
	)

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boolean broad.pda.gene.GeneWithIsoforms.almostContains	(	GeneWithIsoforms	other,
		int	exonFudgeFactor
	)

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void broad.pda.gene.GeneWithIsoforms.cleanIsoforms

(

)

void broad.pda.gene.GeneWithIsoforms.colapse

(

int

exonFudgeFactor

)

Gene broad.pda.gene.GeneWithIsoforms.constituentIntrons

(

)

Constructs an artificial gene where the constituent introns (regions that are intronic in all isoforms) are the exons of the gene.

Returns

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Gene broad.pda.gene.GeneWithIsoforms.constituentIsoform

(

)

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void broad.pda.gene.GeneWithIsoforms.dedup

(

)

void broad.pda.gene.GeneWithIsoforms.expandUtrs	(	Integer	utr1,
		Integer	utr2
	)

Gene broad.pda.gene.GeneWithIsoforms.findCompatibleGenes	(	IntervalTree< GeneWithIsoforms >	overlapTree,
		int[]	numIntrons
	)

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Collection<Annotation> broad.pda.gene.GeneWithIsoforms.getAllIsoformExonSet

(

)

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Collection<Annotation> broad.pda.gene.GeneWithIsoforms.getAllIsoformIntronSet

(

)

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Collection<Gene> broad.pda.gene.GeneWithIsoforms.getAllIsoforms

(

)

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Collection<Gene> broad.pda.gene.GeneWithIsoforms.getAllIsoforms

(

boolean

includeContainingIsoform

)

In cases were the containg gene is artificial, like when building gene loci and adding all isoforms contain in the loci. The containing gene is not desired. This methods allows the caller to exclude the containing isoform from the list.

Parameters

includeContainingIsoform

- boolean flag indicating whether or not to include the containing isoform

Returns

Collection<RefSeqGene> of all the isoforms for this gene

Gene broad.pda.gene.GeneWithIsoforms.getMerged

(

)

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Integer broad.pda.gene.GeneWithIsoforms.getNumberOfIsoforms

(

)

List<Annotation> broad.pda.gene.GeneWithIsoforms.getScoredExons

(

)

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boolean broad.pda.gene.GeneWithIsoforms.hasOverlapping3PUTR

(

GeneWithIsoforms

other

)

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boolean broad.pda.gene.GeneWithIsoforms.hasOverlapping5PUTR

(

GeneWithIsoforms

other

)

boolean broad.pda.gene.GeneWithIsoforms.IsExactOverlappingIsoform

(

Gene

gene

)

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boolean broad.pda.gene.GeneWithIsoforms.overlaps

(

Gene

other

)

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boolean broad.pda.gene.GeneWithIsoforms.overlapsByGenomicRegion	(	IntervalTree< GeneWithIsoforms >	otherTree,
		boolean	considerOrientation
	)

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boolean broad.pda.gene.GeneWithIsoforms.overlapsExon

(

LightweightGenomicAnnotation

exon

)

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boolean broad.pda.gene.GeneWithIsoforms.overlapsExon

(

Gene

gene

)

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Collection<? extends Gene> broad.pda.gene.GeneWithIsoforms.selectRandIsoSubset

(

Integer

maxIsoPerLoci

)

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void broad.pda.gene.GeneWithIsoforms.setBedScore

(

double

scr

)

void broad.pda.gene.GeneWithIsoforms.setExtraFields

(

double[]

scores

)

Commented out by skadri on 04/02/12 Replaces extra fields for all children of a gene.

void broad.pda.gene.GeneWithIsoforms.standardizeOreintation

(

)

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String broad.pda.gene.GeneWithIsoforms.toString

(

String

name

)

void broad.pda.gene.GeneWithIsoforms.updateScrToBedScore

(

double

score

)

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

• java/broad/pda/gene/GeneWithIsoforms.java