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  1. Project Clover database Wed Oct 31 2018 15:13:58 GMT
  2. Package jalview.ws.dbsources

File GeneDbSource.java

 

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Classes

Class Line # Actions
GeneDbSource 34 10 10 20
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1    /*
2    * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3    * Copyright (C) $$Year-Rel$$ The Jalview Authors
4    *
5    * This file is part of Jalview.
6    *
7    * Jalview is free software: you can redistribute it and/or
8    * modify it under the terms of the GNU General Public License
9    * as published by the Free Software Foundation, either version 3
10    * of the License, or (at your option) any later version.
11    *
12    * Jalview is distributed in the hope that it will be useful, but
13    * WITHOUT ANY WARRANTY; without even the implied warranty
14    * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15    * PURPOSE. See the GNU General Public License for more details.
16    *
17    * You should have received a copy of the GNU General Public License
18    * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19    * The Jalview Authors are detailed in the 'AUTHORS' file.
20    */
21    package jalview.ws.dbsources;
22   
23    import jalview.datamodel.AlignmentI;
24    import jalview.datamodel.DBRefSource;
25   
26    import com.stevesoft.pat.Regex;
27   
28    /**
29    * Test class for accessing GeneDB - not yet finished.
30    *
31    * @author JimP
32    *
33    */
 
34    public class GeneDbSource extends EmblXmlSource
35    {
36   
 
37  0 toggle public GeneDbSource()
38    {
39  0 super();
40    }
41   
42    /*
43    * (non-Javadoc)
44    *
45    * @see jalview.ws.DbSourceProxy#getAccessionSeparator()
46    */
 
47  0 toggle @Override
48    public String getAccessionSeparator()
49    {
50    // TODO Auto-generated method stub
51  0 return null;
52    }
53   
54    /*
55    * (non-Javadoc)
56    *
57    * @see jalview.ws.DbSourceProxy#getAccessionValidator()
58    */
 
59  0 toggle @Override
60    public Regex getAccessionValidator()
61    {
62    // TODO Auto-generated method stub
63  0 return null;
64    }
65   
66    /*
67    * (non-Javadoc)
68    *
69    * @see jalview.ws.DbSourceProxy#getDbSource()
70    */
 
71  0 toggle @Override
72    public String getDbSource()
73    {
74  0 return DBRefSource.GENEDB;
75    }
76   
77    /*
78    * (non-Javadoc)
79    *
80    * @see jalview.ws.DbSourceProxy#getDbVersion()
81    */
 
82  0 toggle @Override
83    public String getDbVersion()
84    {
85    // TODO Auto-generated method stub
86  0 return "0";
87    }
88   
89    /*
90    * (non-Javadoc)
91    *
92    * @see jalview.ws.DbSourceProxy#getSequenceRecords(java.lang.String[])
93    */
 
94  0 toggle @Override
95    public AlignmentI getSequenceRecords(String queries) throws Exception
96    {
97    // query of form
98    // http://www.genedb.org/genedb/ArtemisFormHandler?id=&dest=EMBL
99    //
100  0 return getEmblSequenceRecords(DBRefSource.GENEDB, queries);
101    }
102   
103    /*
104    * (non-Javadoc)
105    *
106    * @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)
107    */
 
108  0 toggle @Override
109    public boolean isValidReference(String accession)
110    {
111    // TODO Auto-generated method stub
112  0 return false;
113    }
114   
115    /**
116    * return T.Brucei Mannosyl-Transferase TbPIG-M
117    */
 
118  0 toggle @Override
119    public String getTestQuery()
120    {
121  0 return "Tb927.6.3300";
122    }
123   
 
124  0 toggle @Override
125    public String getDbName()
126    {
127  0 return "GeneDB"; // getDbSource();
128    }
129   
 
130  0 toggle @Override
131    public int getTier()
132    {
133  0 return 0;
134    }
135    }