Public Member Functions
	Locus (GeneWithIsoforms g)

void	addIsoform (GeneWithIsoforms iso, String set)

GeneWithIsoforms	getReferenceTranscript ()

HashMap< String, Integer >	getNumIsoformsPerSet ()

HashMap< String, Double >	getMaxScorePerSet ()

HashMap< String, Integer >	getIsComaptibleWithRefPerSet ()

HashMap< String, Integer >	getIsPartiallyComaptibleWithRefPerSet ()

int	getIsComaptibleBetweenSubsets (ArrayList< String > set1Lst, ArrayList< String > set2Lst, boolean isFully)

int	getIsComaptibleBetweenAny2Sets (ArrayList< String > setLst, boolean isFully)

int	getIsComaptibleBetweenSubsets (ArrayList< String > set1Lst, ArrayList< String > set2Lst, BEDFileParser uniqIsoBed)

int	getIsComaptibleBetweenAny2Sets (ArrayList< String > set3Lst, BEDFileParser uniqIsoBed)

Gene	getExonUnion ()

double[]	getDistanceTo3primeNeighbor (BEDFileParser geneSet) throws IOException

double[]	getDistanceTo5primeNeighbor (BEDFileParser geneSet) throws IOException

double[]	distanceToOppositeStrand5primeNeighbor (BEDFileParser geneSet) throws IOException

double	getMaxScoreAcrossAllIso ()

void	updateIsoformsNameWithLocusName ()

Collection< Gene >	getSetIsoforms (String setName)

Collection< Gene >	getAllIsoforms (String excludeSet)

Collection< Gene >	getComaptibleBetweenAny2Sets (ArrayList< String > setLst, boolean isFully)

Collection< Gene >	getUnqComaptibleBetweenAny2Sets (ArrayList< String > setLst, Collection<?extends Gene > unqIsoSet, boolean isFully)

Collection< Gene >	getUnqComaptibleBetweenSubsets (ArrayList< String > set1Lst, ArrayList< String > set2Lst, Collection< Gene > unqIsoSet, boolean isFully)

Collection< Gene >	getComaptibleIsoforms (Gene g, boolean isFully)

Gene	getLongestIntornChainIso (String refSet)

Gene	getMerged ()

List< Gene >	getAllMerged ()

int	numOfOverlapSets (ArrayList< String > setLst)

double	getMaxPctCovered ()

double	getMaxExonsCovered ()

double	getMaxPctGenomeCovered ()

HashMap< Gene, ArrayList < Double > >	pctOverlapWithRef ()

int	isTerminiCoverageBias ()

Collection<?extends Gene >	getAllIsoforms ()

Integer	getNumberOfIsoforms ()

Collection<?extends Gene >	selectRandIsoSubset (Integer maxIsoPerLoci)

Static Public Member Functions
static Collection< Gene >	SelectLongestIntronChainCandidate (Collection< Gene > betweenSubsetsIsoSet)

static boolean	isFullyComaptible (Gene iso1, Gene iso2, boolean stringent)

Constructor & Destructor Documentation

broad.pda.annotation.Locus.Locus ( GeneWithIsoforms g )

Member Function Documentation

void broad.pda.annotation.Locus.addIsoform	(	GeneWithIsoforms	iso,
		String	set
	)

double [] broad.pda.annotation.Locus.distanceToOppositeStrand5primeNeighbor ( BEDFileParser geneSet ) throws IOException

Collection<Gene> broad.pda.annotation.Locus.getAllIsoforms ( String excludeSet )

Collection<? extends Gene> broad.pda.annotation.Locus.getAllIsoforms ( )

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List<Gene> broad.pda.annotation.Locus.getAllMerged ( )

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Collection<Gene> broad.pda.annotation.Locus.getComaptibleBetweenAny2Sets	(	ArrayList< String >	setLst,
		boolean	isFully
	)

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Collection<Gene> broad.pda.annotation.Locus.getComaptibleIsoforms	(	Gene	g,
		boolean	isFully
	)

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double [] broad.pda.annotation.Locus.getDistanceTo3primeNeighbor ( BEDFileParser geneSet ) throws IOException

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double [] broad.pda.annotation.Locus.getDistanceTo5primeNeighbor ( BEDFileParser geneSet ) throws IOException

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Gene broad.pda.annotation.Locus.getExonUnion ( )

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int broad.pda.annotation.Locus.getIsComaptibleBetweenAny2Sets	(	ArrayList< String >	setLst,
		boolean	isFully
	)

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int broad.pda.annotation.Locus.getIsComaptibleBetweenAny2Sets	(	ArrayList< String >	set3Lst,
		BEDFileParser	uniqIsoBed
	)

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int broad.pda.annotation.Locus.getIsComaptibleBetweenSubsets	(	ArrayList< String >	set1Lst,
		ArrayList< String >	set2Lst,
		boolean	isFully
	)

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int broad.pda.annotation.Locus.getIsComaptibleBetweenSubsets	(	ArrayList< String >	set1Lst,
		ArrayList< String >	set2Lst,
		BEDFileParser	uniqIsoBed
	)

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HashMap<String,Integer> broad.pda.annotation.Locus.getIsComaptibleWithRefPerSet ( )

HashMap<String,Integer> broad.pda.annotation.Locus.getIsPartiallyComaptibleWithRefPerSet ( )

Gene broad.pda.annotation.Locus.getLongestIntornChainIso ( String refSet )

double broad.pda.annotation.Locus.getMaxExonsCovered ( )

double broad.pda.annotation.Locus.getMaxPctCovered ( )

double broad.pda.annotation.Locus.getMaxPctGenomeCovered ( )

double broad.pda.annotation.Locus.getMaxScoreAcrossAllIso ( )

HashMap<String,Double> broad.pda.annotation.Locus.getMaxScorePerSet ( )

Gene broad.pda.annotation.Locus.getMerged ( )

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Integer broad.pda.annotation.Locus.getNumberOfIsoforms ( )

HashMap<String,Integer> broad.pda.annotation.Locus.getNumIsoformsPerSet ( )

GeneWithIsoforms broad.pda.annotation.Locus.getReferenceTranscript ( )

Collection<Gene> broad.pda.annotation.Locus.getSetIsoforms ( String setName )

Collection<Gene> broad.pda.annotation.Locus.getUnqComaptibleBetweenAny2Sets	(	ArrayList< String >	setLst,
		Collection<?extends Gene >	unqIsoSet,
		boolean	isFully
	)

Collection<Gene> broad.pda.annotation.Locus.getUnqComaptibleBetweenSubsets	(	ArrayList< String >	set1Lst,
		ArrayList< String >	set2Lst,
		Collection< Gene >	unqIsoSet,
		boolean	isFully
	)

static boolean broad.pda.annotation.Locus.isFullyComaptible	(	Gene	iso1,
		Gene	iso2,
		boolean	stringent
	)

static

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int broad.pda.annotation.Locus.isTerminiCoverageBias ( )

int broad.pda.annotation.Locus.numOfOverlapSets ( ArrayList< String > setLst )

HashMap<Gene, ArrayList<Double> > broad.pda.annotation.Locus.pctOverlapWithRef ( )

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static Collection<Gene> broad.pda.annotation.Locus.SelectLongestIntronChainCandidate ( Collection< Gene > betweenSubsetsIsoSet )

static

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Collection<? extends Gene> broad.pda.annotation.Locus.selectRandIsoSubset ( Integer maxIsoPerLoci )

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void broad.pda.annotation.Locus.updateIsoformsNameWithLocusName ( )

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

java/broad/pda/annotation/Locus.java

Public Member Functions

Static Public Member Functions

Constructor & Destructor Documentation

Member Function Documentation