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:


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