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

Packages that use ChrLoc

org.utgenome.core.cui	CUI commands.
org.utgenome.format.bed
org.utgenome.format.fasta	FASTA utilities
org.utgenome.format.sam
org.utgenome.format.wig
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.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.

Uses of ChrLoc in org.utgenome.core.cui

Methods in org.utgenome.core.cui that return ChrLoc

static ChrLoc

RegionQueryExpr.parse(String expr)

Methods in org.utgenome.core.cui with parameters of type ChrLoc

BufferedImage	ScreenShot.createReadAlignmentImage(ChrLoc loc, String dbPath)
String	ScreenShot.replaceVariable(String path, ChrLoc loc)

Uses of ChrLoc in org.utgenome.format.bed

Methods in org.utgenome.format.bed with parameters of type ChrLoc

static List<GenomeRange>

BEDDatabase.overlapQuery(File bedPath, ChrLoc location)

Uses of ChrLoc in org.utgenome.format.fasta

Methods in org.utgenome.format.fasta with parameters of type ChrLoc

static ReferenceSequence	FASTADatabase.querySequence(File fastaFile, ChrLoc location)
static void	FASTADatabase.querySequence(File dbFile, ChrLoc location, org.xerial.db.sql.BeanResultHandler<FASTADatabase.NSeq> handler)
static void	FASTADatabase.querySequence(org.xerial.db.sql.sqlite.SQLiteAccess db, ChrLoc location, org.xerial.db.sql.BeanResultHandler<FASTADatabase.NSeq> handler)

Uses of ChrLoc in org.utgenome.format.sam

Methods in org.utgenome.format.sam with parameters of type ChrLoc

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

Uses of ChrLoc in org.utgenome.format.wig

Methods in org.utgenome.format.wig with parameters of type ChrLoc

static CompactWIGData	WIGDatabaseReader.convertResolution(WigGraphData w, ChrLoc location, int windowWidth)
static List<CompactWIGData>	WIGDatabaseReader.getCompactWigDataList(File path, int pixelWidth, ChrLoc location, GraphWindow windowFunc)
static List<CompactWIGData>	WIGDatabaseReader.getRoughCompactWigDataList(File path, int pixelWidth, ChrLoc location, GraphWindow windowFunc)
static List<WigGraphData>	WIGDatabaseReader.getWigDataList(File fileName, int windowWidth, ChrLoc location, GraphWindow windowFunc)
static CompactWIGData	WIGDatabaseReader.prepareCompactWigData(WigGraphData w, ChrLoc location)

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

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

List<CompactWIGData>	BrowserService.getCompactWigDataList(String fileName, int windowWidth, ChrLoc location, GraphWindow window)
void	BrowserServiceAsync.getCompactWigDataList(String fileName, int windowWidth, ChrLoc location, GraphWindow window, com.google.gwt.user.client.rpc.AsyncCallback<List<CompactWIGData>> callback)
List<GenomeRange>	BrowserService.getOnGenomeData(GenomeDB db, ChrLoc range, ReadQueryConfig config) Get read data from the specified DB and location
void	BrowserServiceAsync.getOnGenomeData(GenomeDB db, ChrLoc range, ReadQueryConfig config, com.google.gwt.user.client.rpc.AsyncCallback<List<GenomeRange>> callback)
List<WigGraphData>	BrowserService.getWigDataList(String fileName, int windowWidth, ChrLoc location)
void	BrowserServiceAsync.getWigDataList(String fileName, int windowWidth, ChrLoc location, com.google.gwt.user.client.rpc.AsyncCallback<List<WigGraphData>> callback)

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

Fields in org.utgenome.gwt.utgb.client.bio declared as ChrLoc

ChrLoc

GenomeRangeDataSet.location

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

ArrayList<ChrLoc>

ChrRange.ranges

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

ChrLoc

ChrLoc.getLocForPositiveStrand()

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

ReadCoverage

CompactWIGData.toReadCoverage(ChrLoc loc)

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

Methods in org.utgenome.gwt.utgb.server with parameters of type ChrLoc

List<CompactWIGData>	BrowserServiceImpl.getCompactWigDataList(String path, int windowWidth, ChrLoc location, GraphWindow window)
List<Interval>	BrowserServiceImpl.getLocusList(String dbGroup, String dbName, ChrLoc location)
List<GenomeRange>	BrowserServiceImpl.getOnGenomeData(GenomeDB db, ChrLoc range, ReadQueryConfig config)
List<WigGraphData>	BrowserServiceImpl.getWigDataList(String fileName, int windowWidth, ChrLoc location)

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

Methods in org.utgenome.gwt.utgb.server.app with parameters of type ChrLoc

static List<GenomeRange>	ReadView.overlapQuery(File baseDir, GenomeDB db, ChrLoc loc, ReadQueryConfig config)
static List<GenomeRange>	ReadView.overlapQuery(GenomeDB db, ChrLoc loc, ReadQueryConfig config)
static DASResult	DASViewer.queryDAS(String baseURL, String dasType, ChrLoc chrLoc)