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1   /*--------------------------------------------------------------------------
2    *  Copyright 2007 utgenome.org
3    *
4    *  Licensed under the Apache License, Version 2.0 (the "License");
5    *  you may not use this file except in compliance with the License.
6    *  You may obtain a copy of the License at
7    *
8    *     http://www.apache.org/licenses/LICENSE-2.0
9    *
10   *  Unless required by applicable law or agreed to in writing, software
11   *  distributed under the License is distributed on an "AS IS" BASIS,
12   *  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
13   *  See the License for the specific language governing permissions and
14   *  limitations under the License.
15   *--------------------------------------------------------------------------*/
16  //--------------------------------------
17  // GenomeBrowser Project
18  //
19  // BrowserService.java
20  // Since: Apr 20, 2007
21  //
22  // $URL$ 
23  // $Author$
24  //--------------------------------------
25  package org.utgenome.gwt.utgb.client;
26  
27  import java.util.List;
28  
29  import org.utgenome.gwt.utgb.client.bean.DatabaseEntry;
30  import org.utgenome.gwt.utgb.client.bio.ChrLoc;
31  import org.utgenome.gwt.utgb.client.bio.ChrRange;
32  import org.utgenome.gwt.utgb.client.bio.CompactWIGData;
33  import org.utgenome.gwt.utgb.client.bio.GenomeDB;
34  import org.utgenome.gwt.utgb.client.bio.KeywordSearchResult;
35  import org.utgenome.gwt.utgb.client.bio.OnGenome;
36  import org.utgenome.gwt.utgb.client.bio.ReadQueryConfig;
37  import org.utgenome.gwt.utgb.client.bio.SAMRead;
38  import org.utgenome.gwt.utgb.client.bio.WigGraphData;
39  import org.utgenome.gwt.utgb.client.track.bean.TrackBean;
40  import org.utgenome.gwt.utgb.client.view.TrackView;
41  
42  import com.google.gwt.user.client.rpc.RemoteService;
43  import com.google.gwt.user.client.rpc.RemoteServiceRelativePath;
44  
45  @RemoteServiceRelativePath("service")
46  public interface BrowserService extends RemoteService {
47  
48  	public TrackView createTrackView(String silk) throws UTGBClientException;
49  
50  	public TrackView getTrackView(String viewName) throws UTGBClientException;
51  
52  	public String getHTTPContent(String url);
53  
54  	public String getDatabaseCatalog(String jdbcAddress);
55  
56  	public String getTableData(String jdbcAddress, String tableName);
57  
58  	public List<TrackBean> getTrackList(int entriesPerPage, int page);
59  
60  	public int numHitsOfTracks(String prefix);
61  
62  	/**
63  	 */
64  	public List<TrackBean> getTrackList(String prefix, int entriesPerPage, int page);
65  
66  	public KeywordSearchResult keywordSearch(String species, String revision, String keyword, int entriesPerPage, int page) throws UTGBClientException;
67  
68  	public ChrRange getChrRegion(String species, String revision);
69  
70  	public List<String> getChildDBGroups(String parentDBGroup);
71  
72  	public List<String> getDBNames(String dbGroup);
73  
74  	public List<DatabaseEntry> getDBEntry(String dbGroup);
75  
76  	public List<WigGraphData> getWigDataList(String fileName, int windowWidth, ChrLoc location);
77  
78  	public List<CompactWIGData> getCompactWigDataList(String fileName, int windowWidth, ChrLoc location);
79  
80  	public List<SAMRead> getSAMReadList(String readFileName, String refSeqFileName);
81  
82  	public List<SAMRead> querySAMReadList(String bamFileName, String indexFileName, String refSeqFileName, String rname, int start, int end);
83  
84  	public String getRefSeq(String refSeqFileName, String rname, int start, int end);
85  
86  	/**
87  	 * Get read data from the specified DB and location
88  	 * 
89  	 * @param db
90  	 *            database to search
91  	 * @param range
92  	 *            (chr, start, end)
93  	 * @param userAgent
94  	 *            browser information
95  	 * @return
96  	 */
97  	public List<OnGenome> getOnGenomeData(GenomeDB db, ChrLoc range, ReadQueryConfig config);
98  
99  }