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jalviewX

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

File EmblCdsSource.java

 

Coverage histogram

../../../img/srcFileCovDistChart3.png
47% of files have more coverage

Code metrics

4
12
10
1
101
61
13
1.08
1.2
10
1.3

Classes

Class Line # Actions
EmblCdsSource 28 12 13 20
0.2307692323.1%
 

Contributing tests

This file is covered by 80 tests. .

Source view

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    public class EmblCdsSource extends EmblXmlSource
29    {
30   
 
31  6 toggle public EmblCdsSource()
32    {
33  6 super();
34    }
35   
 
36  0 toggle @Override
37    public String getAccessionSeparator()
38    {
39  0 return null;
40    }
41   
 
42  0 toggle @Override
43    public Regex getAccessionValidator()
44    {
45  0 return new Regex("^[A-Z]+[0-9]+");
46    }
47   
 
48  2216 toggle @Override
49    public String getDbSource()
50    {
51  2216 return DBRefSource.EMBLCDS;
52    }
53   
 
54  0 toggle @Override
55    public String getDbVersion()
56    {
57  0 return "0"; // TODO : this is dynamically set for a returned record - not
58    // tied to proxy
59    }
60   
 
61  0 toggle @Override
62    public AlignmentI getSequenceRecords(String queries) throws Exception
63    {
64  0 if (queries.indexOf(".") > -1)
65    {
66  0 queries = queries.substring(0, queries.indexOf("."));
67    }
68  0 return getEmblSequenceRecords(DBRefSource.EMBLCDS, queries);
69    }
70   
 
71  0 toggle @Override
72    public boolean isValidReference(String accession)
73    {
74    // most embl CDS refs look like ..
75    // TODO: improve EMBLCDS regex
76  0 return (accession == null || accession.length() < 2) ? false
77    : getAccessionValidator().search(accession);
78    }
79   
80    /**
81    * cDNA for LDHA_CHICK swissprot sequence
82    */
 
83  0 toggle @Override
84    public String getTestQuery()
85    {
86  0 return "CAA37824";
87    }
88   
 
89  2210 toggle @Override
90    public String getDbName()
91    {
92  2210 return "EMBL (CDS)";
93    }
94   
 
95  0 toggle @Override
96    public int getTier()
97    {
98  0 return 0;
99    }
100   
101    }
  • Report generated by OpenClover v 4.2.1 on Wed Oct 31 2018 15:15:54 GMT using coverage data from Wed Oct 31 2018 15:15:47 GMT.
  • Clover free edition.