Collaboration diagram for broad.pda.gene.GeneTools:

Static Public Member Functions
static void	main (String[] args) throws Exception

static Map< String, IntervalTree< Gene > >	merge (Map< String, Collection< Gene >> originalMap)

static IntervalTree< Gene >	merge (Collection< Gene > original)

static String	orientationForGene (Gene g, Sequence cSeq)

static String	orientationFromSpliceSites (Annotation introns, Sequence seq, boolean onlyCanonical)

static String	orientationFromSpliceSites (Annotation introns, Sequence chrSeq)

static Map< String, IntervalTree< Gene > >	overlap (Map< String, IntervalTree< Gene >> set1, Map< String, IntervalTree< Gene >>set2, Boolean byExon)

static Map< String, IntervalTree< Gene > >	mergeSets (Map< String, IntervalTree< Gene >> set1, Map< String, IntervalTree< Gene >> set2)

static Gene	selectHighScoringIsoform (Gene transcript, BEDFileParser set)

static BEDFileParser	mergeByGtfGeneId (String inFile, String outFile, String outFormat, String src, boolean writeMode) throws Exception

static BEDFileParser	intersectGeneSets (Collection< Gene > set1, Collection< Gene > set2, boolean takeComplement)

Member Function Documentation

static BEDFileParser broad.pda.gene.GeneTools.intersectGeneSets	(	Collection< Gene >	set1,
		Collection< Gene >	set2,
		boolean	takeComplement
	)

static

static void broad.pda.gene.GeneTools.main ( String[] args ) throws Exception

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static Map<String, IntervalTree<Gene> > broad.pda.gene.GeneTools.merge ( Map< String, Collection< Gene >> originalMap )

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static IntervalTree<Gene> broad.pda.gene.GeneTools.merge ( Collection< Gene > original )

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static BEDFileParser broad.pda.gene.GeneTools.mergeByGtfGeneId	(	String	inFile,
		String	outFile,
		String	outFormat,
		String	src,
		boolean	writeMode
	)		throws Exception

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static Map<String, IntervalTree<Gene> > broad.pda.gene.GeneTools.mergeSets	(	Map< String, IntervalTree< Gene >>	set1,
		Map< String, IntervalTree< Gene >>	set2
	)

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static String broad.pda.gene.GeneTools.orientationForGene	(	Gene	g,
		Sequence	cSeq
	)

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static String broad.pda.gene.GeneTools.orientationFromSpliceSites	(	Annotation	introns,
		Sequence	seq,
		boolean	onlyCanonical
	)

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static String broad.pda.gene.GeneTools.orientationFromSpliceSites	(	Annotation	introns,
		Sequence	chrSeq
	)

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static Map<String, IntervalTree<Gene> > broad.pda.gene.GeneTools.overlap	(	Map< String, IntervalTree< Gene >>	set1,
		Map< String, IntervalTree< Gene >>	set2,
		Boolean	byExon
	)

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static Gene broad.pda.gene.GeneTools.selectHighScoringIsoform	(	Gene	transcript,
		BEDFileParser	set
	)

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

Static Public Member Functions