Inheritance diagram for umms.core.feature.GeneWindow:

Collaboration diagram for umms.core.feature.GeneWindow:

Public Member Functions
	GeneWindow (Gene gene)

	GeneWindow (GeneWindow window)

	GeneWindow (Annotation window)

	GeneWindow (Collection<?extends Annotation > exons)

int	getSize ()

void	addSourceAnnotation (Annotation annotation)

Collection<?extends Annotation >	getSourceAnnotations ()

boolean	equals (Object o)

int	compareTo (Annotation g)

Collection< Window >	getWindows (int windowSize, int stepSize)

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

Additional Inherited Members
Static Public Member Functions inherited from umms.core.annotation.Gene
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 inherited from umms.core.annotation.Gene
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 inherited from umms.core.annotation.Gene
void	initFromGene (Gene gene)

boolean	almostContainsRefSeq (Gene other, int exonFudgeFactor)

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