Uses of Interface
org.utgenome.gwt.utgb.client.bio.OnGenome

Packages that use OnGenome

org.utgenome.format.bed
org.utgenome.format.sam
org.utgenome.graphics	Graphics drawing classes
org.utgenome.gwt.utgb.client	UTGB Browser interface & track implementations.
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.client.track
org.utgenome.gwt.utgb.client.track.lib	Standard track library for UTGB browser.
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
org.utgenome.util.repeat

Uses of OnGenome in org.utgenome.format.bed

Classes in org.utgenome.format.bed that implement OnGenome

class

BEDEntry Representing each gene line of BED format

Fields in org.utgenome.format.bed with type parameters of type OnGenome

List<OnGenome>

BEDDatabase.BEDRangeQuery.geneList

Methods in org.utgenome.format.bed that return types with arguments of type OnGenome

static List<OnGenome>

BEDDatabase.overlapQuery(File bedPath, ChrLoc location)

Constructor parameters in org.utgenome.format.bed with type arguments of type OnGenome

BEDDatabase.BEDRangeQuery(List<OnGenome> geneList, String coordinate, int start, int end)

Uses of OnGenome in org.utgenome.format.sam

Classes in org.utgenome.format.sam with type parameters of type OnGenome

class	ReadSweeper<T extends OnGenome> Sweeping SAM reads in their start order
static interface	ReadSweeper.ReadSetHandler<T extends OnGenome>

Methods in org.utgenome.format.sam that return OnGenome

OnGenome

Sam2WigConverter.SAMRecordCursor.next()

Methods in org.utgenome.format.sam that return types with arguments of type OnGenome

static List<OnGenome>	SAMReader.depthCoverage(ChrLoc loc, int pixelWidth, List<net.sf.samtools.SAMRecord> loadedReadSet, net.sf.samtools.util.CloseableIterator<net.sf.samtools.SAMRecord> cursor)
static List<OnGenome>	SAMReader.depthCoverage(File bamFile, ChrLoc loc, int pixelWidth, ReadQueryConfig config)
static List<OnGenome>	SAMReader.depthCoverageInWIG(File wigFile, ChrLoc loc, int pixelWidth, ReadQueryConfig config)
static List<OnGenome>	SAMReader.overlapQuery(File bamFile, ChrLoc loc, int pixelWidth, ReadQueryConfig config) Retrieved SAMReads (or SAMReadPair) overlapped with the specified interval

Uses of OnGenome in org.utgenome.graphics

Methods in org.utgenome.graphics with type parameters of type OnGenome

<E extends OnGenome> void

GeneCanvas.draw(List<E> geneList)

Methods in org.utgenome.graphics that return OnGenome

OnGenome

GeneCanvas.LocusLayout.getLocus()

Methods in org.utgenome.graphics with parameters of type OnGenome

void	GeneCanvas.draw(OnGenome locus, int yOffset)
void	ReadCanvas.drawLabel(OnGenome region, int yOffset)
void	ReadCanvas.drawRegion(OnGenome region, int y)
Color	GeneCanvas.getCDSColor(OnGenome g)
Color	ReadCanvas.DrawStyle.getClippedReadColor(OnGenome g)
Color	GeneCanvas.getExonColor(OnGenome g)
String	GeneCanvas.getExonColorText(OnGenome g)
Color	GeneCanvas.getGeneColor(OnGenome g)
Color	GeneCanvas.getGeneColor(OnGenome g, float offset)
Color	GeneCanvas.getIntronColor(OnGenome g)
Color	ReadCanvas.DrawStyle.getReadColor(OnGenome g)

Method parameters in org.utgenome.graphics with type arguments of type OnGenome

void	ReadCanvas.draw(List<OnGenome> dataSet)

Constructors in org.utgenome.graphics with parameters of type OnGenome

GeneCanvas.LocusLayout(OnGenome gene, int yOffset)

Uses of OnGenome in org.utgenome.gwt.utgb.client

Methods in org.utgenome.gwt.utgb.client that return types with arguments of type OnGenome

List<OnGenome>

BrowserService.getOnGenomeData(GenomeDB db, ChrLoc range, ReadQueryConfig config) Get read data from the specified DB and location

Method parameters in org.utgenome.gwt.utgb.client with type arguments of type OnGenome

void	BrowserServiceAsync.getOnGenomeData(GenomeDB db, ChrLoc range, ReadQueryConfig config, com.google.gwt.user.client.rpc.AsyncCallback<List<OnGenome>> callback)

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

Subinterfaces of OnGenome in org.utgenome.gwt.utgb.client.bio

interface

GraphData A common interface for graph data

Classes in org.utgenome.gwt.utgb.client.bio that implement OnGenome

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	CompactWIGData
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	Interval An interval in a genome sequence.
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

Fields in org.utgenome.gwt.utgb.client.bio with type parameters of type OnGenome

List<OnGenome>	OnGenomeDataSet.block
List<OnGenome>	OnGenomeDataSet.read

Methods in org.utgenome.gwt.utgb.client.bio that return types with arguments of type OnGenome

List<OnGenome>

ReadList.getRead()

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

void	ReadList.addRead(OnGenome read)
void	OnGenomeDataVisitorBase.visitDefault(OnGenome g)
void	OnGenomeDataVisitor.visitDefault(OnGenome g)

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

Classes in org.utgenome.gwt.utgb.client.canvas with type parameters of type OnGenome

class

IntervalTree<T extends OnGenome> Interval layout

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

<T extends OnGenome> int	IntervalLayout.createLocalLayout(int geneHeight) Creates an X-Y layout of the given intervals, then return the max depth of the intervals
<T extends OnGenome> void	GWTGenomeCanvas.drawBlock(ReadCoverage block)
<T extends OnGenome> int	IntervalLayout.reset(List<T> intervalList, int geneHeight) Creates an X-Y layout of the given intervals

Methods in org.utgenome.gwt.utgb.client.canvas that return OnGenome

OnGenome	IntervalLayout.LocusLayout.getLocus()
OnGenome	IntervalLayout.overlappedInterval(int x, int y, int xBorder, int geneHeight) compute the overlapped intervals for the mouse over event

Methods in org.utgenome.gwt.utgb.client.canvas that return types with arguments of type OnGenome

List<OnGenome>

IntervalLayout.activeReads()

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

void	GWTGenomeCanvas.displayInfo(int clientX, int clientY, OnGenome g)
static int	IntervalLayout.estimiateLabelWidth(OnGenome l, int geneHeight)
T	IntervalTree.findOverlap(OnGenome target)
com.google.gwt.widgetideas.graphics.client.Color	ReadDisplayStyle.getClippedReadColor(OnGenome g)
com.google.gwt.widgetideas.graphics.client.Color	ReadDisplayStyle.getReadColor(OnGenome g)
com.google.gwt.widgetideas.graphics.client.Color	ReadDisplayStyle.getReadColor(OnGenome g, float alpha)
void	LocusClickHandler.onClick(int clientX, int clientY, OnGenome locus)
List<T>	IntervalTree.overlapQuery(OnGenome target)
void	IntervalTree.overlapQuery(OnGenome target, PrioritySearchTree.ResultHandler<T> handler)

Method parameters in org.utgenome.gwt.utgb.client.canvas with type arguments of type OnGenome

void	GWTGenomeCanvas.resetData(List<OnGenome> readSet)

Constructors in org.utgenome.gwt.utgb.client.canvas with parameters of type OnGenome

IntervalLayout.LocusLayout(OnGenome locus, int yOffset)

IntervalLayout.LocusLayout(OnGenome locus, int yOffset, int height)

Uses of OnGenome in org.utgenome.gwt.utgb.client.track

Methods in org.utgenome.gwt.utgb.client.track with parameters of type OnGenome

boolean

TrackWindow.overlapWith(OnGenome g)

Uses of OnGenome in org.utgenome.gwt.utgb.client.track.lib

Methods in org.utgenome.gwt.utgb.client.track.lib with parameters of type OnGenome

String

ReadTrack.resolveURL(String urlTemplate, OnGenome locus)

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

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

List<OnGenome>

BrowserServiceImpl.getOnGenomeData(GenomeDB db, ChrLoc range, ReadQueryConfig config)

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

Classes in org.utgenome.gwt.utgb.server.app that implement OnGenome

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

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

static List<OnGenome>	ReadView.overlapQuery(File baseDir, GenomeDB db, ChrLoc loc, ReadQueryConfig config)
static List<OnGenome>	ReadView.overlapQuery(GenomeDB db, ChrLoc loc, ReadQueryConfig config)

Method parameters in org.utgenome.gwt.utgb.server.app with type arguments of type OnGenome

static ReadCoverage

ReadView.computeCoverage(List<OnGenome> readList, int start, int end, int pixelWidth)

Uses of OnGenome in org.utgenome.util

Method parameters in org.utgenome.util with type arguments of type OnGenome

static void	ReadDepth.compute(String chr, Iterator<OnGenome> cursor, ReadDepth.DepthOutput out) Compute the read depth of the input read set.
protected void	ReadDepth.computeDepth(String chr, Iterator<OnGenome> cursor)

Uses of OnGenome in org.utgenome.util.repeat

Classes in org.utgenome.util.repeat that implement OnGenome

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