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

Packages that use SAMRead

org.utgenome.format.sam
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.server	UTGB's server-side libraries for supporting web request handling, managing database connections, initialization of UTGB web applications, etc.

Uses of SAMRead in org.utgenome.format.sam

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

static SAMRead	SAM2SilkReader.convertToSAMRead(net.sf.samtools.SAMRecord record) convert a SAMRecord into a SAMRead, which can be used in GWT code.
SAMRead	SAMReadIterator.next()

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

static Iterator<SAMRead>	SAMReadIterator.getIteratorOnChr(File bamFile, String chr)
static Iterator<SAMRead>	SAMReadIterator.getOverlappingIterator(File bamFile, ChrLoc loc)

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

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

List<SAMRead>	BrowserService.getSAMReadList(String readFileName, String refSeqFileName)
List<SAMRead>	BrowserService.querySAMReadList(String bamFileName, String indexFileName, String refSeqFileName, String rname, int start, int end)

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

void	BrowserServiceAsync.getSAMReadList(String readFileName, String refSeqFileName, com.google.gwt.user.client.rpc.AsyncCallback<List<SAMRead>> callback)
void	BrowserServiceAsync.querySAMReadList(String bamFileName, String indexFileName, String refSeqFileName, String rname, int start, int end, com.google.gwt.user.client.rpc.AsyncCallback<List<SAMRead>> callback)

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

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

boolean	SAMRead.isMate(SAMRead other)
void	GenomeRangeVisitorBase.visitSAMRead(SAMRead r)
void	GenomeRangeVisitor.visitSAMRead(SAMRead r)
void	InfoSilkGenerator.visitSAMRead(SAMRead r)

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

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

void	SAMCanvas.drawLabelPanel(int count, SAMRead read, com.google.gwt.user.client.ui.AbsolutePanel panel, int leftMargin)
void	SAMCanvas.drawSAMCanvas(int count, SAMRead read)
void	SAMCanvas.drawSAMRead(int count, SAMRead read)

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

void	SAMCanvas.drawLabelPanel(List<SAMRead> readList, com.google.gwt.user.client.ui.AbsolutePanel panel, int leftMargin)
void	SAMCanvas.drawSAMRead(List<SAMRead> readList)

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

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

List<SAMRead>	BrowserServiceImpl.getSAMReadList(String readFileName, String refSeqFileName)
List<SAMRead>	BrowserServiceImpl.querySAMReadList(String bamFileName, String indexFileName, String refSeqFileName, String rname, int start, int end)