org.utgenome.gwt.utgb.server
Class BrowserServiceImpl

java.lang.Object
  javax.servlet.GenericServlet
      javax.servlet.http.HttpServlet
          com.google.gwt.user.server.rpc.AbstractRemoteServiceServlet
              com.google.gwt.user.server.rpc.RemoteServiceServlet
                  org.utgenome.gwt.utgb.server.BrowserServiceImpl

All Implemented Interfaces:

com.google.gwt.user.client.rpc.RemoteService, com.google.gwt.user.server.rpc.SerializationPolicyProvider, Serializable, javax.servlet.Servlet, javax.servlet.ServletConfig, BrowserService

public class BrowserServiceImpl
extends com.google.gwt.user.server.rpc.RemoteServiceServlet
implements BrowserService

{"species":{"type":0, "target":"human"}, "genome":{"type":0}, "chromosome":{"type":0}}

Author:

leo

See Also:

Serialized Form

Field Summary

Fields inherited from class com.google.gwt.user.server.rpc.AbstractRemoteServiceServlet

perThreadRequest, perThreadResponse

Constructor Summary

BrowserServiceImpl()

Method Summary

TrackView	createTrackView(String silk)
List<String>	getChildDBGroups(String parentDBGroup)
ChrRange	getChrRegion(String species, String revision)
List<CompactWIGData>	getCompactWigDataList(String path, int windowWidth, ChrLoc location, GraphWindow window)
String	getCurrentView()
String	getDatabaseCatalog(String jdbcAddress)
String	getDataModelParameter(String amoebaQuery)
List<DatabaseEntry>	getDBEntry(String dbGroup)
List<String>	getDBNames(String dbGroup)
List<Gene>	getGeneList(String serviceURI)
String	getHTTPContent(String url)
List<Interval>	getLocusList(String dbGroup, String dbName, ChrLoc location)
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 numEntriesPerPage, int page)
int	numHitsOfTracks(String prefix)
List<SAMRead>	querySAMReadList(String bamFileName, String indexFileName, String refSeqFileName, String rname, int start, int end)
void	saveView(String viewXML)

Methods inherited from class com.google.gwt.user.server.rpc.RemoteServiceServlet

checkPermutationStrongName, doGetSerializationPolicy, getSerializationPolicy, onAfterResponseSerialized, onBeforeRequestDeserialized, processCall, processPost, shouldCompressResponse

Methods inherited from class com.google.gwt.user.server.rpc.AbstractRemoteServiceServlet

doPost, doUnexpectedFailure, getPermutationStrongName, getThreadLocalRequest, getThreadLocalResponse, onAfterRequestDeserialized, readContent

Methods inherited from class javax.servlet.http.HttpServlet

doDelete, doGet, doHead, doOptions, doPut, doTrace, getLastModified, service, service

Methods inherited from class javax.servlet.GenericServlet

destroy, getInitParameter, getInitParameterNames, getServletConfig, getServletContext, getServletInfo, getServletName, init, init, log, log

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

BrowserServiceImpl

public BrowserServiceImpl()
                   throws org.xerial.db.DBException

Throws:

org.xerial.db.DBException

Method Detail

createTrackView

public TrackView createTrackView(String silk)
                          throws UTGBClientException

Specified by:

createTrackView in interface BrowserService

Throws:

UTGBClientException

getTrackView

public TrackView getTrackView(String viewName)
                       throws UTGBClientException

Specified by:

getTrackView in interface BrowserService

Throws:

UTGBClientException

getDataModelParameter

public String getDataModelParameter(String amoebaQuery)

getHTTPContent

public String getHTTPContent(String url)

Specified by:

getHTTPContent in interface BrowserService

getDatabaseCatalog

public String getDatabaseCatalog(String jdbcAddress)

Specified by:

getDatabaseCatalog in interface BrowserService

getTableData

public String getTableData(String jdbcAddress,
                           String tableName)

Specified by:

getTableData in interface BrowserService

getTrackList

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

Specified by:

getTrackList in interface BrowserService

getTrackList

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

Specified by:

getTrackList in interface BrowserService

numHitsOfTracks

public int numHitsOfTracks(String prefix)

Specified by:

numHitsOfTracks in interface BrowserService

keywordSearch

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

Specified by:

keywordSearch in interface BrowserService

Throws:

UTGBClientException

saveView

public void saveView(String viewXML)

getCurrentView

public String getCurrentView()

getGeneList

public List<Gene> getGeneList(String serviceURI)

getChrRegion

public ChrRange getChrRegion(String species,
                             String revision)

Specified by:

getChrRegion in interface BrowserService

getLocusList

public List<Interval> getLocusList(String dbGroup,
                                   String dbName,
                                   ChrLoc location)

getChildDBGroups

public List<String> getChildDBGroups(String parentDBGroup)

Specified by:

getChildDBGroups in interface BrowserService

getDBNames

public List<String> getDBNames(String dbGroup)

Specified by:

getDBNames in interface BrowserService

getDBEntry

public List<DatabaseEntry> getDBEntry(String dbGroup)

Specified by:

getDBEntry in interface BrowserService

getWigDataList

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

Specified by:

getWigDataList in interface BrowserService

getCompactWigDataList

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

Specified by:

getCompactWigDataList in interface BrowserService

getSAMReadList

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

Specified by:

getSAMReadList in interface BrowserService

querySAMReadList

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

Specified by:

querySAMReadList in interface BrowserService

getRefSeq

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

Specified by:

getRefSeq in interface BrowserService

getOnGenomeData

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

Description copied from interface: BrowserService

Get read data from the specified DB and location

Specified by:

getOnGenomeData in interface BrowserService

Parameters:

db - database to search

range - (chr, start, end)

Returns: