Uses of Class
org.utgenome.gwt.utgb.client.bio.Interval

Packages that use Interval

org.utgenome.format.bed
org.utgenome.gwt.utgb.client.bio	Biological data objects for Google Web Toolkit RPC (Remote Procedure Call).
org.utgenome.gwt.utgb.client.canvas	Browser-side graphic drawing libraries using HTML canvas (or VML in IE).
org.utgenome.gwt.utgb.server	UTGB's server-side libraries for supporting web request handling, managing database connections, initialization of UTGB web applications, etc.
org.utgenome.gwt.utgb.server.app	Contains sample codes of web actions.
org.utgenome.util.repeat

Uses of Interval in org.utgenome.format.bed

Subclasses of Interval in org.utgenome.format.bed

class

BEDEntry Representing each gene line of BED format

Uses of Interval in org.utgenome.gwt.utgb.client.bio

Subclasses of Interval in org.utgenome.gwt.utgb.client.bio

class	BEDGene Representing each gene line of BED format
class	BlastResult Read with cigar and sequence information
class	BSSRead BSS read data object
class	CDS Coding Sequence (CDS)
class	ChrInterval Interval in a chromosome
static class	DASResult.DASFeature
class	Exon Exon
class	Gap Gap of paired-end, mate-pair reads
class	Gene Gene with Exon and CDS regions
class	Read An interval with starnd information
class	ReadCoverage Read coverage histogram
class	ReadList ReadList is a list of read objects, and used to draw a sequence of blocks on genome.
class	ReferenceSequence reference genome sequence to which genome reads are aligned
class	SAMRead Genome Read data
class	SAMReadLight Light weight SAMRead
class	SAMReadPair Mate pair (paired end) of SAMReads
class	SAMReadPairFragment Paired-end reads without the other mate data

Methods in org.utgenome.gwt.utgb.client.bio that return Interval

Interval	Read.downstreamRegion(int length)
Interval	Interval.intersect(Interval other) Return the intersected interval with the other
Interval	Read.upstreamRegion(int length)

Methods in org.utgenome.gwt.utgb.client.bio with parameters of type Interval

int	Interval.compareTo(Interval other)
boolean	Interval.contains(Interval other)
boolean	Interval.follows(Interval other)
Interval	Interval.intersect(Interval other) Return the intersected interval with the other
boolean	Interval.intersectsWith(Interval other)
boolean	Interval.precedes(Interval other)
void	GenomeRangeVisitorBase.visitInterval(Interval interval)
void	GenomeRangeVisitor.visitInterval(Interval interval)
void	InfoSilkGenerator.visitInterval(Interval interval)

Constructors in org.utgenome.gwt.utgb.client.bio with parameters of type Interval

ChrInterval(String chr, Interval interval)

Interval(Interval other)

Uses of Interval in org.utgenome.gwt.utgb.client.canvas

Methods in org.utgenome.gwt.utgb.client.canvas with parameters of type Interval

void	GWTGenomeCanvas.draw(Interval gene, int yPosition)
com.google.gwt.widgetideas.graphics.client.Color	GWTGenomeCanvas.getCDSColor(Interval g)
com.google.gwt.widgetideas.graphics.client.Color	GWTGenomeCanvas.getCDSColor(Interval g, float alpha)
com.google.gwt.widgetideas.graphics.client.Color	GWTGenomeCanvas.getGeneColor(Interval l)
com.google.gwt.widgetideas.graphics.client.Color	GWTGenomeCanvas.getGeneColor(Interval l, float alpha)
void	IntervalLayout.IntervalRetriever.visitInterval(Interval interval)

Uses of Interval in org.utgenome.gwt.utgb.server

Methods in org.utgenome.gwt.utgb.server that return types with arguments of type Interval

List<Interval>

BrowserServiceImpl.getLocusList(String dbGroup, String dbName, ChrLoc location)

Uses of Interval in org.utgenome.gwt.utgb.server.app

Subclasses of Interval in org.utgenome.gwt.utgb.server.app

static class	BSSReadView.BSSAlignment
static class	ChromosomeMap.ReadLocus
static class	MethylViewer.MethlEntry

Uses of Interval in org.utgenome.util.repeat

Subclasses of Interval in org.utgenome.util.repeat

static class	RepeatChainFinder.FlippedInterval2D
static class	RepeatChainFinder.Interval2D 2D interval

Methods in org.utgenome.util.repeat that return Interval

Interval	RepeatChainFinder.Interval2D.endPoint()
Interval	RepeatChainFinder.Interval2D.startPoint()