org.utgenome.gwt.utgb.client
Interface BrowserService

All Superinterfaces:

com.google.gwt.user.client.rpc.RemoteService

All Known Implementing Classes:

BrowserServiceImpl

@RemoteServiceRelativePath(value="service")
public interface BrowserService
extends com.google.gwt.user.client.rpc.RemoteService

Method Summary

TrackView	createTrackView(String silk)
List<String>	getChildDBGroups(String parentDBGroup)
ChrRange	getChrRegion(String species, String revision)
List<CompactWIGData>	getCompactWigDataList(String fileName, int windowWidth, ChrLoc location, GraphWindow window)
String	getDatabaseCatalog(String jdbcAddress)
List<DatabaseEntry>	getDBEntry(String dbGroup)
List<String>	getDBNames(String dbGroup)
String	getHTTPContent(String url)
List<GenomeRange>	getOnGenomeData(GenomeDB db, ChrLoc range, ReadQueryConfig config) Get read data from the specified DB and location
String	getRefSeq(String refSeqFileName, String rname, int start, int end)
List<SAMRead>	getSAMReadList(String readFileName, String refSeqFileName)
String	getTableData(String jdbcAddress, String tableName)
List<TrackBean>	getTrackList(int entriesPerPage, int page)
List<TrackBean>	getTrackList(String prefix, int entriesPerPage, int page)
TrackView	getTrackView(String viewName)
List<WigGraphData>	getWigDataList(String fileName, int windowWidth, ChrLoc location)
KeywordSearchResult	keywordSearch(String species, String revision, String keyword, int entriesPerPage, int page)
int	numHitsOfTracks(String prefix)
List<SAMRead>	querySAMReadList(String bamFileName, String indexFileName, String refSeqFileName, String rname, int start, int end)

Method Detail

createTrackView

TrackView createTrackView(String silk)
                          throws UTGBClientException

Throws:

UTGBClientException

getTrackView

TrackView getTrackView(String viewName)
                       throws UTGBClientException

Throws:

UTGBClientException

getHTTPContent

String getHTTPContent(String url)

getDatabaseCatalog

String getDatabaseCatalog(String jdbcAddress)

getTableData

String getTableData(String jdbcAddress,
                    String tableName)

getTrackList

List<TrackBean> getTrackList(int entriesPerPage,
                             int page)

numHitsOfTracks

int numHitsOfTracks(String prefix)

getTrackList

List<TrackBean> getTrackList(String prefix,
                             int entriesPerPage,
                             int page)

keywordSearch

KeywordSearchResult keywordSearch(String species,
                                  String revision,
                                  String keyword,
                                  int entriesPerPage,
                                  int page)
                                  throws UTGBClientException

Throws:

UTGBClientException

getChrRegion

ChrRange getChrRegion(String species,
                      String revision)

getChildDBGroups

List<String> getChildDBGroups(String parentDBGroup)

getDBNames

List<String> getDBNames(String dbGroup)

getDBEntry

List<DatabaseEntry> getDBEntry(String dbGroup)

getWigDataList

List<WigGraphData> getWigDataList(String fileName,
                                  int windowWidth,
                                  ChrLoc location)

getCompactWigDataList

List<CompactWIGData> getCompactWigDataList(String fileName,
                                           int windowWidth,
                                           ChrLoc location,
                                           GraphWindow window)

getSAMReadList

List<SAMRead> getSAMReadList(String readFileName,
                             String refSeqFileName)

querySAMReadList

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

getRefSeq

String getRefSeq(String refSeqFileName,
                 String rname,
                 int start,
                 int end)

getOnGenomeData

List<GenomeRange> getOnGenomeData(GenomeDB db,
                                  ChrLoc range,
                                  ReadQueryConfig config)

Get read data from the specified DB and location

Parameters:

db - database to search

range - (chr, start, end)

userAgent - browser information

Returns: