Inheritance diagram for umms.core.annotation.Gene:

Collaboration diagram for umms.core.annotation.Gene:

Public Member Functions
	Gene (String chr, String name, Strand orientation, Collection<?extends Annotation > exons, int cdsStart, int cdsEnd)

	Gene (String chr, int start, int end, String name, Strand orientation, int cdsStart, int cdsEnd)

	Gene (Collection<?extends Annotation > exons, String name, Strand orientation, int cdsStart, int cdsEnd)

	Gene (String chr, String name, Strand orientation, Collection<?extends Annotation > exons)

	Gene (Annotation annotation, String name, Strand orientation, Collection<?extends Annotation > exons)

	Gene (Annotation annotation, Collection<?extends Annotation > exons)

	Gene (Annotation annotation, Collection<?extends Annotation > exons, String name, int cdsStart, int cdsEnd)

	Gene (Annotation annotation, Collection<?extends Annotation > exons, String name)

	Gene (Collection<?extends Annotation > exons, String name, Strand orientation)

	Gene (String chr, int start, int end, String name, Strand orientation)

	Gene (String chr, int start, int end, String name)

	Gene (Collection<?extends Annotation > exons, String name)

	Gene (Collection<?extends Annotation > exons)

	Gene (String chr, int start, int end)

	Gene (Alignments align)

	Gene (Annotation annotation)

	Gene (String pslString)

	Gene (String pslString, boolean isPSLFormat)

	Gene (String chr2, int start2, int end, String name2, double bedScore2, String orientation2, String sequence2, String[] extraFields2)

	Gene (String chr2, int start2, int end, String name2, double bedScore2, String orientation2, String sequence2)

	Gene (String chr, int start, int end, String name, double mybedScore, String orientation, int[] exonsStart, int[] exonsEnd)

	Gene (String chr, int start, int end, String name, String orientation, List< Integer > exonsStart, List< Integer > exonsEnd)

	Gene (String chr, int start, int end, String name, String orientation, List< Integer > exonsStart, List< Integer > exonsEnd, int blockStart, int blockEnd)

	Gene (String chr, int start, int end, String name, String orientation, List< Integer > exonsStart, List< Integer > exonsEnd, String[] extraData)

	Gene (String chr2, int start2, int end, String name2, double bedScore2, String orientation2, int[] exonStarts2, int[] exonEnds2, double[] exonScores2, String sequence2)

	Gene (String chr2, int start2, int end, String name2, double bedScore2, String orientation2, int[] exonStarts2, int[] exonEnds2, double[] exonScores2, String sequence2, String[] extraFields2)

	Gene (String chr, int start, int end, String name, double score, String strand, List< Integer > exonsStart, List< Integer > exonsEnd, int blockStart2, int blockEnd2)

	Gene (String chr, int start, int end, String name, String orientation, List< Integer > exonsStart, List< Integer > exonsEnd, int blockStart, int blockEnd, String[] extraData)

	Gene (String chr, int start, int end, String name, double score, String strand, List< Integer > exonsStart, List< Integer > exonsEnd, int blockStart2, int blockEnd2, String[] extraColumns)

	Gene (Gene gene)

void	setSequence (String seq)

void	setSequenceFromChromosome (Sequence chrSequence)

void	setOrientation (String orientation)

void	setSAMString (String sam)

void	setExtraFields (double[] d)

void	setExtraFields (double val, int i)

void	setExtraFields (String[] extraData)

int	getCDSEnd ()

int	getCDSStart ()

void	setCDSRegion (int start, int end)

void	setBedScore (double d)

void	setCountScore (double score)

int	getSize ()

int	getGenomicLength ()

boolean	isNegativeStrand ()

String	getSequence ()

Sequence	getSequence (Sequence chrSequence)

String	getSequence (Sequence chr2, boolean repeatMask, boolean stranded) throws Exception

Sequence	getSequenceObject ()

String	getString ()

String	getSAMString ()

String	getAttribute (String name)

Map	getAttributes ()

String[]	getExtraFields ()

String	getExtraFields (int i)

double	getNormalizedScore ()

double	getRPKM ()

double	getPValue ()

double	getCountScore ()

double[]	getExonsScores ()

int	getTranscriptLength ()

Collection<?extends Annotation >	get5Utr ()

Collection<?extends Annotation >	get3Utr ()

Gene	get3UTRGene ()

Gene	get5UTRGene ()

Annotation	get5UTR ()

Annotation	get3UTR ()

boolean	hasCDS ()

Iterator< Integer >	getAllPositions ()

Collection< GeneWindow >	getWindows (int windowSize)

Collection< GeneWindow >	getWindows (int windowSize, int stepSize, int start)

Gene	getStartCodon ()

Annotation	get5UtrIncludingIntrons ()

String	getChrNum ()

Alignments	get3UtrIncludingIntrons ()

int	getNumExons ()

Alignments[]	getExons ()

Set<?extends Annotation >	getExonSet ()

Collection<?extends Annotation >	getSortedAndUniqueExons ()

IntervalTree< Annotation >	getExonTree ()

Annotation	getFirstExon ()

Annotation	getLastExon ()

Annotation	getOrientedLastExon ()

Annotation	get5PrimeExon ()

Annotation	get3PrimeExon (int size)

Annotation	get3PrimeExon ()

Gene	getIntrons ()

Annotation	getLastIntron ()

Annotation	getFirstIntron ()

Alignments[]	getIntronsBlocks ()

Collection<?extends Annotation >	getIntronSet ()

Gene	getIntronTranscript ()

boolean	isCodingGene ()

Gene	getCDS ()

Alignments	getCDSRegion ()

Annotation	getAlignment ()

Alignments	getPromoter (int fudgeFactor)

Alignments	getPromoter (int upstream, int downstream)

double	getNumberPositions (int rate)

int	getGappedSize ()

double	getBedScore ()

int	get3PrimeGenomicDistance (LightweightGenomicAnnotation annot)

Gene	getOverlap (Gene second)

Gene	getOverlap (Collection< Gene > others)

ArrayList< Integer >	getSpliceJunctionCoordinates () throws Exception

IntervalTree< Integer >	getSpliceJunctionCoordinatesTree () throws Exception

String	toString ()

String	toRefSeq ()

String	toUCSC ()

String	toBED ()

String	toBED (int r, int g, int b)

String	toBED (boolean useExtraFields)

String	toBED (boolean useExtraFields, int r, int g, int b)

String	toBEDwithBedScore ()

String	toGTF (String source)

String	toGTF (String source, String geneName, String transcriptName)

String	toCufflinksGTF (String source, String geneName, String transcriptName, String nonParsedAttrs)

String	toSAM ()

String	toSAM (String originalSAMLine)

String	toSAM (String originalSAMLine, boolean flip)

void	setCDS (Annotation cdsRegion)

int	absoluteToRelativePosition (int referenceCoordinate)

boolean	isInExon (int snp)

Collection< Gene >	findAllORFs (boolean trim3UTRs)

TreeSet < BasicLightweightAnnotation >	findAllStartCodons ()

Collection< Gene >	findAllORFs (Sequence chrSeq, boolean trim3UTRs)

void	addSequence (Sequence seq)

void	addSuffixToName (String refName)

void	addAttribute (String name, String val)

void	addExtraField (String value)

void	expandUtrs (Integer utr1, Integer utr2)

boolean	geneSpanContains (Gene gene)

boolean	containsAttribute (String key)

boolean	isFullyCompatible (Gene iso)

boolean	overlapsExon (Annotation gen)

boolean	overlapsExon (LightweightGenomicAnnotation exon)

boolean	overlaps (Gene other)

int	distanceToNearestNonOverlapper (Collection< Annotation > others)

boolean	overlaps (Gene other, boolean ignoreOrientation)

boolean	overlaps (Gene other, double minPctOverlap)

boolean	overlapsStranded (Gene other, double minPctOverlap)

boolean	overlapsGene (Collection< Gene > others)

boolean	overlapsGene (Gene gen)

boolean	overlapsGeneInAnyOrientation (Gene otherGene)

boolean	overlaps2 (LightweightGenomicAnnotation next)

boolean	almostEqual (Gene other, int exonFudgeFactor)

boolean	almostSameStructure (Gene other, int intronFudgeFactor)

boolean	almostContains (Gene other, int exonFudgeFactor)

int	hashCode ()

int	compareTo (Annotation other)

Gene	copy ()

GeneWindow	trimGene (int relativeStart, int relativeEnd)

void	setCDSStart (int start)

void	setCDSEnd (int end)

Gene	findLongestORF ()

int	numOverlappingExons (Gene iso)

int	numOfCompatibleIntrons (Gene g)

GeneWindow	trimAbsolute (int alignmentStart, int alignmentEnd)

double	percentOverlapping (Gene gene2)

Double	percentGenomeOverlapping (Gene gene2)

int	transcriptToGenomicPosition (int transcriptPosition)

int	getMidpointGenomicCoords ()

Gene	transcriptToGenomicPosition (int startPosOnTranscript, int endPosOnTranscript)

int	genomicToTranscriptPosition (int genomicPosition)

int	genomicToGenomicPositionWithOffset (int genomicPosition, int offset)

Gene	takeUnion (Gene other)

double	getPercentCDS ()

double	getPercent3UTR ()

Gene	extendAnnotation (int deltaStart, int deltaEnd)

void	addIsoform (Gene g)

Collection< Gene >	getIsoforms ()

Public Member Functions inherited from umms.core.annotation.BasicAnnotation
	BasicAnnotation ()

	BasicAnnotation (SAMRecord samRecord)

	BasicAnnotation (String ucsc)

	BasicAnnotation (String referenceName, int start, int end, Strand orientation, String name)

	BasicAnnotation (String referenceName, Strand orientation, String name, Collection<?extends Annotation > blocks)

	BasicAnnotation (String referenceName, int start, int end)

	BasicAnnotation (String referenceName, int start, int end, Strand orientation)

	BasicAnnotation (String referenceName, int start, int end, String orientation)

	BasicAnnotation (BasicAnnotation other)

	BasicAnnotation (Annotation other)

	BasicAnnotation (Collection<?extends Annotation > blocks)

	BasicAnnotation (Collection<?extends Annotation > blocks, Strand orientation, String name)

	BasicAnnotation (Collection<?extends Annotation > blocks, String name)

	BasicAnnotation (String referenceName, CompoundInterval blocks, Strand orientation, String name)

	BasicAnnotation (String referenceName, CompoundInterval blocks, Strand orientation)

	BasicAnnotation (String referenceName, CompoundInterval blocks)

Annotation	copy ()

int	getStart ()

int	getEnd ()

int	getMidpoint ()

String	getReferenceName ()

String	getName ()

Strand	getOrientation ()

boolean	isUnoriented ()

List<?extends Annotation >	getBlocks ()

List<?extends Annotation >	getBlocks (boolean oriented)

Annotation[]	getFlankingBlocks (Annotation spliceJunction)

int	numBlocks ()

int	length ()

int	getReferenceCoordinateAtPosition (int positionInAnnotation, boolean ignoreOrientation)

int	getPositionAtReferenceCoordinate (int referenceCoordinate, boolean ignoreOrientation)

double	getScore ()

String	toString ()

void	setStart (int start)

void	setEnd (int end)

void	setOrientation (Strand orientation)

void	setOrientedStart (int orientedStart)

void	setOrientedEnd (int orientedEnd)

void	setReferenceName (String refName)

void	setName (String n)

void	setScore (double s)

void	addBlocks (Annotation block)

void	addBlocks (Collection<?extends Annotation > blocks)

void	shift (int delta)

void	moveToCoordinate (int coordinateInReference)

boolean	overlaps (Annotation other, int buffer, boolean considerOrientation)

boolean	overlaps (List<?extends Annotation > otherBlocks, int buffer)

int	getOverlap (Annotation other)

boolean	contains (Annotation other)

Annotation	union (Annotation other)

Annotation	intersect (Annotation other)

List< Annotation >	disect (Annotation a)

List< Annotation >	disect (List<?extends Annotation > disectors)

Annotation	minus (Annotation other)

Annotation	minus (Collection<?extends Annotation > others)

void	stitchTo (Annotation next)

Annotation	complement ()

Collection<?extends Annotation >	getSpliceConnections ()

Public Member Functions inherited from umms.core.annotation.AbstractAnnotation
int	size ()

int	getSize ()

int	getMidpoint ()

Strand	getStrand ()

boolean	hasOrientation ()

boolean	isNegativeStrand ()

String	getChr ()

int	getOrientedStart ()

int	getOrientedEnd ()

int	getLengthOnReference ()

int	getReferenceCoordinateAtPosition (int positionInAnnotation)

int	getPositionAtReferenceCoordinate (int referenceCoordinate)

void	setOrientation (char orientation)

void	expand (int deltaStart, int deltaEnd)

Annotation	trim (int deltaStart, int deltaEnd)

boolean	fullyContains (Annotation other)

boolean	overlaps (Annotation other)

boolean	overlaps (Annotation other, int buffer)

boolean	overlapsStranded (Annotation other)

boolean	overlaps (Annotation other, boolean considerOrientation)

boolean	overlaps (Collection<?extends Annotation > others)

boolean	overlaps (Collection<?extends Annotation > others, int buffer)

String	toUCSC ()

String	toBED ()

final String	getFullInfoString ()

String	toBED (int r, int g, int b)

String	toShortBED ()

String	toBEDGraph ()

int	getDistanceTo (Annotation other)

String	toCigar ()

List< Annotation >	intersect (List<?extends Annotation > others)

int	compareTo (Annotation other)

int	compareToAnnotation (Annotation b)

int	compareToAnnotation (Annotation b, boolean useOrientation)

boolean	equals (Annotation a)

boolean	equals (Annotation a, boolean useOrientation)

int	getSAMStart ()

int	getSAMEnd ()

Static Public Member Functions
static Collection< int[]>	findAllORFs (String sequence)

static boolean	isStopCodon (String currentCodon)

static Collection< Gene >	getOverlappers (Collection< Gene > genes, String chr, int start, int end, Strand strand, boolean ignoreOrientation)

static int[]	findLongestORF (String sequence)

Static Public Member Functions inherited from umms.core.annotation.BasicAnnotation
static Annotation	createFromUCSC (String ucsc)

static BasicAnnotation	fromFullInfoString (String fullInfoString)

static void	main (String[] args) throws IOException

Static Public Member Functions inherited from umms.core.annotation.AbstractAnnotation
static Strand	getStrand (String orientation)

static Strand	getStrand (char orientation)

Static Public Attributes
static final Pattern	START_CODON_PATRN = Pattern.compile("ATG", Pattern.CASE_INSENSITIVE)

static final String[]	STOP_CODONS = {"TAG", "TAA", "TGA"}

Static Public Attributes inherited from umms.core.annotation.AbstractAnnotation
static final int	MAX_DISTANCE = 1000000000

Protected Member Functions
void	initFromGene (Gene gene)

boolean	almostContainsRefSeq (Gene other, int exonFudgeFactor)

Additional Inherited Members
Protected Attributes inherited from umms.core.annotation.BasicAnnotation
CompoundInterval	blocks = new CompoundInterval()

Constructor & Destructor Documentation

umms.core.annotation.Gene.Gene	(	String	chr,
		String	name,
		Strand	orientation,
		Collection<?extends Annotation >	exons,
		int	cdsStart,
		int	cdsEnd
	)

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umms.core.annotation.Gene.Gene	(	String	chr,
		int	start,
		int	end,
		String	name,
		Strand	orientation,
		int	cdsStart,
		int	cdsEnd
	)

umms.core.annotation.Gene.Gene	(	Collection<?extends Annotation >	exons,
		String	name,
		Strand	orientation,
		int	cdsStart,
		int	cdsEnd
	)

umms.core.annotation.Gene.Gene	(	String	chr,
		String	name,
		Strand	orientation,
		Collection<?extends Annotation >	exons
	)

umms.core.annotation.Gene.Gene	(	Annotation	annotation,
		String	name,
		Strand	orientation,
		Collection<?extends Annotation >	exons
	)

umms.core.annotation.Gene.Gene	(	Annotation	annotation,
		Collection<?extends Annotation >	exons
	)

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umms.core.annotation.Gene.Gene	(	Annotation	annotation,
		Collection<?extends Annotation >	exons,
		String	name,
		int	cdsStart,
		int	cdsEnd
	)

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umms.core.annotation.Gene.Gene	(	Annotation	annotation,
		Collection<?extends Annotation >	exons,
		String	name
	)

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umms.core.annotation.Gene.Gene	(	Collection<?extends Annotation >	exons,
		String	name,
		Strand	orientation
	)

umms.core.annotation.Gene.Gene	(	String	chr,
		int	start,
		int	end,
		String	name,
		Strand	orientation
	)

umms.core.annotation.Gene.Gene	(	String	chr,
		int	start,
		int	end,
		String	name
	)

umms.core.annotation.Gene.Gene	(	Collection<?extends Annotation >	exons,
		String	name
	)

umms.core.annotation.Gene.Gene ( Collection<?extends Annotation > exons )

umms.core.annotation.Gene.Gene	(	String	chr,
		int	start,
		int	end
	)

umms.core.annotation.Gene.Gene ( Alignments align )

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umms.core.annotation.Gene.Gene ( Annotation annotation )

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umms.core.annotation.Gene.Gene ( String pslString )

umms.core.annotation.Gene.Gene	(	String	pslString,
		boolean	isPSLFormat
	)

umms.core.annotation.Gene.Gene	(	String	chr2,
		int	start2,
		int	end,
		String	name2,
		double	bedScore2,
		String	orientation2,
		String	sequence2,
		String[]	extraFields2
	)

umms.core.annotation.Gene.Gene	(	String	chr2,
		int	start2,
		int	end,
		String	name2,
		double	bedScore2,
		String	orientation2,
		String	sequence2
	)

umms.core.annotation.Gene.Gene	(	String	chr,
		int	start,
		int	end,
		String	name,
		double	mybedScore,
		String	orientation,
		int[]	exonsStart,
		int[]	exonsEnd
	)

umms.core.annotation.Gene.Gene	(	String	chr,
		int	start,
		int	end,
		String	name,
		String	orientation,
		List< Integer >	exonsStart,
		List< Integer >	exonsEnd
	)

umms.core.annotation.Gene.Gene	(	String	chr,
		int	start,
		int	end,
		String	name,
		String	orientation,
		List< Integer >	exonsStart,
		List< Integer >	exonsEnd,
		int	blockStart,
		int	blockEnd
	)

umms.core.annotation.Gene.Gene	(	String	chr,
		int	start,
		int	end,
		String	name,
		String	orientation,
		List< Integer >	exonsStart,
		List< Integer >	exonsEnd,
		String[]	extraData
	)

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umms.core.annotation.Gene.Gene	(	String	chr2,
		int	start2,
		int	end,
		String	name2,
		double	bedScore2,
		String	orientation2,
		int[]	exonStarts2,
		int[]	exonEnds2,
		double[]	exonScores2,
		String	sequence2
	)

umms.core.annotation.Gene.Gene	(	String	chr2,
		int	start2,
		int	end,
		String	name2,
		double	bedScore2,
		String	orientation2,
		int[]	exonStarts2,
		int[]	exonEnds2,
		double[]	exonScores2,
		String	sequence2,
		String[]	extraFields2
	)

umms.core.annotation.Gene.Gene	(	String	chr,
		int	start,
		int	end,
		String	name,
		double	score,
		String	strand,
		List< Integer >	exonsStart,
		List< Integer >	exonsEnd,
		int	blockStart2,
		int	blockEnd2
	)

umms.core.annotation.Gene.Gene	(	String	chr,
		int	start,
		int	end,
		String	name,
		String	orientation,
		List< Integer >	exonsStart,
		List< Integer >	exonsEnd,
		int	blockStart,
		int	blockEnd,
		String[]	extraData
	)

umms.core.annotation.Gene.Gene	(	String	chr,
		int	start,
		int	end,
		String	name,
		double	score,
		String	strand,
		List< Integer >	exonsStart,
		List< Integer >	exonsEnd,
		int	blockStart2,
		int	blockEnd2,
		String[]	extraColumns
	)

umms.core.annotation.Gene.Gene ( Gene gene )

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Member Function Documentation

int umms.core.annotation.Gene.absoluteToRelativePosition ( int referenceCoordinate )

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void umms.core.annotation.Gene.addAttribute	(	String	name,
		String	val
	)

void umms.core.annotation.Gene.addExtraField ( String value )

void umms.core.annotation.Gene.addIsoform ( Gene g )

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void umms.core.annotation.Gene.addSequence ( Sequence seq )

void umms.core.annotation.Gene.addSuffixToName ( String refName )

boolean umms.core.annotation.Gene.almostContains	(	Gene	other,
		int	exonFudgeFactor
	)

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boolean umms.core.annotation.Gene.almostContainsRefSeq	(	Gene	other,
		int	exonFudgeFactor
	)

protected

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boolean umms.core.annotation.Gene.almostEqual	(	Gene	other,
		int	exonFudgeFactor
	)

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boolean umms.core.annotation.Gene.almostSameStructure	(	Gene	other,
		int	intronFudgeFactor
	)

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int umms.core.annotation.Gene.compareTo ( Annotation other )

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boolean umms.core.annotation.Gene.containsAttribute ( String key )

Gene umms.core.annotation.Gene.copy ( )

Returns: A deep clone of this Annotation object

Implements umms.core.annotation.Annotation.

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int umms.core.annotation.Gene.distanceToNearestNonOverlapper ( Collection< Annotation > others )

Get inner distance between this gene and its nearest neighbor in a collection Ignore genes that overlap this gene in any orientation Looks at entire gene span, not just exons

Parameters

others Other genes to check

Returns: Min distance to a non-overlapper in the collection, or -1 if no other genes on same chromosome

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void umms.core.annotation.Gene.expandUtrs	(	Integer	utr1,
		Integer	utr2
	)

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Gene umms.core.annotation.Gene.extendAnnotation	(	int	deltaStart,
		int	deltaEnd
	)

Get new gene extended in either direction

Parameters

deltaStart	Distance to extend at begin position
deltaEnd	Distance to extend at end position

Returns: New extended gene

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Collection<Gene> umms.core.annotation.Gene.findAllORFs ( boolean trim3UTRs )

Get all ORFs as gene objects

Parameters

trim3UTRs whether to trim 3'UTRs to end at the beginning of next ORF

Returns: the collection of ORFs

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static Collection<int[]> umms.core.annotation.Gene.findAllORFs ( String sequence )

static

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Collection<Gene> umms.core.annotation.Gene.findAllORFs	(	Sequence	chrSeq,
		boolean	trim3UTRs
	)

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TreeSet<BasicLightweightAnnotation> umms.core.annotation.Gene.findAllStartCodons ( )

Find start codons

Returns: collection of all start codon genomic coordinates

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Gene umms.core.annotation.Gene.findLongestORF ( )

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static int [] umms.core.annotation.Gene.findLongestORF ( String sequence )

static

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boolean umms.core.annotation.Gene.geneSpanContains ( Gene gene )

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int umms.core.annotation.Gene.genomicToGenomicPositionWithOffset	(	int	genomicPosition,
		int	offset
	)

Get the genomic coordinate of the given position plus offset along the transcript

Parameters

genomicPosition	Genomic position
offset	Offset (positive gives result in 3' direction; negative gives result in 5' direction)

Returns: The genomic position at the given transcript distance from the given position

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int umms.core.annotation.Gene.genomicToTranscriptPosition ( int genomicPosition )

Maps genomic coordinates to cDNA coordinates

Parameters

genomicPosition within transcript

Returns: 0-based position within oriented start of transcript

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Annotation umms.core.annotation.Gene.get3PrimeExon ( int size )

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Annotation umms.core.annotation.Gene.get3PrimeExon ( )

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int umms.core.annotation.Gene.get3PrimeGenomicDistance ( LightweightGenomicAnnotation annot )

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Collection<? extends Annotation> umms.core.annotation.Gene.get3Utr ( )

Get the set of exons comprising the 3' UTR

Returns: the set of exons comprising the 3' UTR as a collection of Alignments objects

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Annotation umms.core.annotation.Gene.get3UTR ( )

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Gene umms.core.annotation.Gene.get3UTRGene ( )

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Alignments umms.core.annotation.Gene.get3UtrIncludingIntrons ( )

Get the region of the gene span that lies 3' of the stop codon, including introns but not the stop codon itself

Returns: the region of the gene span that lies 3' of the stop codon as an Alignments object

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Annotation umms.core.annotation.Gene.get5PrimeExon ( )

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Collection<? extends Annotation> umms.core.annotation.Gene.get5Utr ( )

Get the set of exons comprising the 5' UTR

Returns: the set of exons comprising the 5' UTR as a collection of Alignments objects

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Annotation umms.core.annotation.Gene.get5UTR ( )

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Gene umms.core.annotation.Gene.get5UTRGene ( )

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Annotation umms.core.annotation.Gene.get5UtrIncludingIntrons ( )

Get the region of the gene span that lies 5' of start codon, including introns and the start codon itself

Returns: the region of the gene span that lies 5' of start codon as an Alignments object

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Annotation umms.core.annotation.Gene.getAlignment ( )

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Iterator<Integer> umms.core.annotation.Gene.getAllPositions ( )

Get an iterator over all reference positions making up the gene

Returns: Iterator over all positions in the gene

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String umms.core.annotation.Gene.getAttribute ( String name )

Parameters

name

Returns: attribute value or 0 if the attribute is not defined.

Map umms.core.annotation.Gene.getAttributes ( )

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double umms.core.annotation.Gene.getBedScore ( )

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Gene umms.core.annotation.Gene.getCDS ( )

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int umms.core.annotation.Gene.getCDSEnd ( )

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Alignments umms.core.annotation.Gene.getCDSRegion ( )

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int umms.core.annotation.Gene.getCDSStart ( )

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String umms.core.annotation.Gene.getChrNum ( )

Return the chromosome number without the chr

Returns: the chromosome number without the chr

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double umms.core.annotation.Gene.getCountScore ( )

Alignments [] umms.core.annotation.Gene.getExons ( )

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Set<? extends Annotation> umms.core.annotation.Gene.getExonSet ( )

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double [] umms.core.annotation.Gene.getExonsScores ( )

IntervalTree<Annotation> umms.core.annotation.Gene.getExonTree ( )

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String [] umms.core.annotation.Gene.getExtraFields ( )

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String umms.core.annotation.Gene.getExtraFields ( int i )

Annotation umms.core.annotation.Gene.getFirstExon ( )

Returns: first exon in coordinate order

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Annotation umms.core.annotation.Gene.getFirstIntron ( )

Returns the first intron of this gene

Returns

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int umms.core.annotation.Gene.getGappedSize ( )

int umms.core.annotation.Gene.getGenomicLength ( )

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Gene umms.core.annotation.Gene.getIntrons ( )

Get introns

Returns: Gene object whose blocks are the introns, or null if no introns

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Alignments [] umms.core.annotation.Gene.getIntronsBlocks ( )

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Collection<? extends Annotation> umms.core.annotation.Gene.getIntronSet ( )

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Gene umms.core.annotation.Gene.getIntronTranscript ( )

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Collection<Gene> umms.core.annotation.Gene.getIsoforms ( )

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Annotation umms.core.annotation.Gene.getLastExon ( )

Returns: last exon in coordinate order

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Annotation umms.core.annotation.Gene.getLastIntron ( )

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int umms.core.annotation.Gene.getMidpointGenomicCoords ( )

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double umms.core.annotation.Gene.getNormalizedScore ( )

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double umms.core.annotation.Gene.getNumberPositions ( int rate )

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int umms.core.annotation.Gene.getNumExons ( )

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Annotation umms.core.annotation.Gene.getOrientedLastExon ( )

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Gene umms.core.annotation.Gene.getOverlap ( Gene second )

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Gene umms.core.annotation.Gene.getOverlap ( Collection< Gene > others )

Get all overlaps between this gene and any gene in the collection

Parameters

others The collection of genes to check for overlap

Returns: A RefSeqGene object whose "exons" consist of overlapping intervals between this gene and the collection

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static Collection<Gene> umms.core.annotation.Gene.getOverlappers	(	Collection< Gene >	genes,
		String	chr,
		int	start,
		int	end,
		Strand	strand,
		boolean	ignoreOrientation
	)

static

Get all genes overlapping a window

Parameters

genes	The genes
chr	Window chr
start	Window start
end	Window end

Returns: All genes overlapping the window, not necessarily fully contained

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double umms.core.annotation.Gene.getPercent3UTR ( )

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double umms.core.annotation.Gene.getPercentCDS ( )

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Alignments umms.core.annotation.Gene.getPromoter ( int fudgeFactor )

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Alignments umms.core.annotation.Gene.getPromoter	(	int	upstream,
		int	downstream
	)

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double umms.core.annotation.Gene.getPValue ( )

double umms.core.annotation.Gene.getRPKM ( )

String umms.core.annotation.Gene.getSAMString ( )

String umms.core.annotation.Gene.getSequence ( )

Sequence umms.core.annotation.Gene.getSequence ( Sequence chrSequence )

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String umms.core.annotation.Gene.getSequence	(	Sequence	chr2,
		boolean	repeatMask,
		boolean	stranded
	)		throws Exception

Sequence umms.core.annotation.Gene.getSequenceObject ( )

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int umms.core.annotation.Gene.getSize ( )

Returns: same as size();

Implements umms.core.annotation.Annotation.

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Collection<? extends Annotation> umms.core.annotation.Gene.getSortedAndUniqueExons ( )

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ArrayList<Integer> umms.core.annotation.Gene.getSpliceJunctionCoordinates ( ) throws Exception

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IntervalTree<Integer> umms.core.annotation.Gene.getSpliceJunctionCoordinatesTree ( ) throws Exception

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Gene umms.core.annotation.Gene.getStartCodon ( )

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String umms.core.annotation.Gene.getString ( )

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int umms.core.annotation.Gene.getTranscriptLength ( )

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Collection<GeneWindow> umms.core.annotation.Gene.getWindows ( int windowSize )

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Collection<GeneWindow> umms.core.annotation.Gene.getWindows	(	int	windowSize,
		int	stepSize,
		int	start
	)

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boolean umms.core.annotation.Gene.hasCDS ( )

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int umms.core.annotation.Gene.hashCode ( )

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void umms.core.annotation.Gene.initFromGene ( Gene gene )

protected

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boolean umms.core.annotation.Gene.isCodingGene ( )

Whether the gene is coding or noncoding

Returns: True if the cds exists and has size at least 3

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boolean umms.core.annotation.Gene.isFullyCompatible ( Gene iso )

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boolean umms.core.annotation.Gene.isInExon ( int snp )

boolean umms.core.annotation.Gene.isNegativeStrand ( )

Implements umms.core.annotation.Annotation.

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static boolean umms.core.annotation.Gene.isStopCodon ( String currentCodon )

static

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int umms.core.annotation.Gene.numOfCompatibleIntrons ( Gene g )

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int umms.core.annotation.Gene.numOverlappingExons ( Gene iso )

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boolean umms.core.annotation.Gene.overlaps ( Gene other )

Whether an exon of this gene overlaps an exon of other gene and the two genes have the same orientation

Parameters

other Other gene

Returns: Whether genes have same orientation and at least one overlapping exon

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boolean umms.core.annotation.Gene.overlaps	(	Gene	other,
		boolean	ignoreOrientation
	)

Whether an exon of this gene overlaps an exon of other gene

Parameters

other	Other gene
ignoreOrientation	Ignore orientation. If set to false, orientations must be equal or at least one orientation must be unknown.

Returns: Whether genes overlap at the exon level

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boolean umms.core.annotation.Gene.overlaps	(	Gene	other,
		double	minPctOverlap
	)

Returns true if this and the other gene overlap but at least minPctOverlap

Parameters

other	The other gene with which overlap is checked
minPctOverlap	minimum percent of overlap

Returns

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boolean umms.core.annotation.Gene.overlaps2 ( LightweightGenomicAnnotation next )

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boolean umms.core.annotation.Gene.overlapsExon ( Annotation gen )

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boolean umms.core.annotation.Gene.overlapsExon ( LightweightGenomicAnnotation exon )

boolean umms.core.annotation.Gene.overlapsGene ( Collection< Gene > others )

Whether this gene overlaps any gene in the collection at the exon level

Parameters

others The genes to check for overlap

Returns: True iff this gene overlaps at least one gene in the collection at the exon level

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boolean umms.core.annotation.Gene.overlapsGene ( Gene gen )

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boolean umms.core.annotation.Gene.overlapsGeneInAnyOrientation ( Gene otherGene )

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boolean umms.core.annotation.Gene.overlapsStranded	(	Gene	other,
		double	minPctOverlap
	)

Returns true if this and the other gene overlap but at least minPctOverlap

Parameters

other	The other gene with which overlap is checked
minPctOverlap	minimum percent of overlap

Returns

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Double umms.core.annotation.Gene.percentGenomeOverlapping ( Gene gene2 )

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double umms.core.annotation.Gene.percentOverlapping ( Gene gene2 )

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void umms.core.annotation.Gene.setBedScore ( double d )

void umms.core.annotation.Gene.setCDS ( Annotation cdsRegion )

void umms.core.annotation.Gene.setCDSEnd ( int end )

void umms.core.annotation.Gene.setCDSRegion	(	int	start,
		int	end
	)

Set coding region coordinates (includes start codon but not stop codon)

Parameters

start	start position
end	end position

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void umms.core.annotation.Gene.setCDSStart ( int start )

void umms.core.annotation.Gene.setCountScore ( double score )

void umms.core.annotation.Gene.setExtraFields ( double[] d )

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void umms.core.annotation.Gene.setExtraFields	(	double	val,
		int	i
	)

void umms.core.annotation.Gene.setExtraFields ( String[] extraData )

void umms.core.annotation.Gene.setOrientation ( String orientation )

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void umms.core.annotation.Gene.setSAMString ( String sam )

void umms.core.annotation.Gene.setSequence ( String seq )

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void umms.core.annotation.Gene.setSequenceFromChromosome ( Sequence chrSequence )

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Gene umms.core.annotation.Gene.takeUnion ( Gene other )

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String umms.core.annotation.Gene.toBED ( )

Implements umms.core.annotation.Annotation.

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String umms.core.annotation.Gene.toBED	(	int	r,
		int	g,
		int	b
	)

Implements umms.core.annotation.Annotation.

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String umms.core.annotation.Gene.toBED ( boolean useExtraFields )

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String umms.core.annotation.Gene.toBED	(	boolean	useExtraFields,
		int	r,
		int	g,
		int	b
	)

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String umms.core.annotation.Gene.toBEDwithBedScore ( )

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String umms.core.annotation.Gene.toCufflinksGTF	(	String	source,
		String	geneName,
		String	transcriptName,
		String	nonParsedAttrs
	)

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String umms.core.annotation.Gene.toGTF ( String source )

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String umms.core.annotation.Gene.toGTF	(	String	source,
		String	geneName,
		String	transcriptName
	)

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String umms.core.annotation.Gene.toRefSeq ( )

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String umms.core.annotation.Gene.toSAM ( )

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String umms.core.annotation.Gene.toSAM ( String originalSAMLine )

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String umms.core.annotation.Gene.toSAM	(	String	originalSAMLine,
		boolean	flip
	)

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String umms.core.annotation.Gene.toString ( )

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String umms.core.annotation.Gene.toUCSC ( )

Returns: chrX:start-end

Implements umms.core.annotation.Annotation.

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int umms.core.annotation.Gene.transcriptToGenomicPosition ( int transcriptPosition )

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Gene umms.core.annotation.Gene.transcriptToGenomicPosition	(	int	startPosOnTranscript,
		int	endPosOnTranscript
	)

Convert an interval in transcriptome space to genome space

Parameters

startPosOnTranscript	Start position in transcriptome space
endPosOnTranscript	End position in transcriptome space

Returns: The interval (possibly spliced) in genome space

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GeneWindow umms.core.annotation.Gene.trimAbsolute	(	int	alignmentStart,
		int	alignmentEnd
	)

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GeneWindow umms.core.annotation.Gene.trimGene	(	int	relativeStart,
		int	relativeEnd
	)

Trims the gene in relative space Returns a GeneWindow with pointer to the original

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Member Data Documentation

final Pattern umms.core.annotation.Gene.START_CODON_PATRN = Pattern.compile("ATG", Pattern.CASE_INSENSITIVE)

static

final String [] umms.core.annotation.Gene.STOP_CODONS = {"TAG", "TAA", "TGA"}

static

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

java/umms/core/annotation/Gene.java

Public Member Functions

Static Public Member Functions

Static Public Attributes

Protected Member Functions

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation