Clover icon

Coverage Report

  1. Project Clover database Thu Aug 13 2020 12:04:21 BST
  2. Package jalview.ws.dbsources

File Xfam.java

 

Coverage histogram

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

Code metrics

6
15
5
1
114
57
8
0.53
3
5
1.6

Classes

Class Line # Actions
Xfam 37 15 8
0.2307692323.1%
 

Contributing tests

This file is covered by 101 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.bin.Cache;
24    import jalview.datamodel.AlignmentI;
25    import jalview.datamodel.DBRefEntry;
26    import jalview.io.DataSourceType;
27    import jalview.io.FileFormat;
28    import jalview.io.FormatAdapter;
29    import jalview.ws.seqfetcher.DbSourceProxyImpl;
30   
31    /**
32    * Acts as a superclass for the Rfam and Pfam classes
33    *
34    * @author Lauren Michelle Lui
35    *
36    */
 
37    public abstract class Xfam extends DbSourceProxyImpl
38    {
 
39  32 toggle public Xfam()
40    {
41  32 super();
42    }
43   
44    /**
45    * the base URL for this Xfam-like service
46    *
47    * @return
48    */
49    protected abstract String getURLPrefix();
50   
51    @Override
52    public abstract String getDbVersion();
53   
54    abstract String getXfamSource();
55   
 
56  0 toggle @Override
57    public AlignmentI getSequenceRecords(String queries) throws Exception
58    {
59    // TODO: this is not a perfect implementation. We need to be able to add
60    // individual references to each sequence in each family alignment that's
61    // retrieved.
62  0 startQuery();
63    // TODO: trap HTTP 404 exceptions and return null
64  0 String xfamUrl = getURL(queries);
65   
66  0 if (Cache.log != null)
67    {
68  0 Cache.log.debug("XFAM URL for retrieval is: " + xfamUrl);
69    }
70   
71  0 AlignmentI rcds = new FormatAdapter().readFile(xfamUrl,
72    DataSourceType.URL, FileFormat.Stockholm);
73   
74  0 for (int s = 0, sNum = rcds.getHeight(); s < sNum; s++)
75    {
76  0 rcds.getSequenceAt(s).addDBRef(new DBRefEntry(getXfamSource(),
77    // getDbSource(),
78    getDbVersion(), queries.trim().toUpperCase()));
79  0 if (!getDbSource().equals(getXfamSource()))
80    { // add the specific ref too
81  0 rcds.getSequenceAt(s).addDBRef(new DBRefEntry(getDbSource(),
82    getDbVersion(), queries.trim().toUpperCase()));
83    }
84    }
85  0 stopQuery();
86  0 return rcds;
87    }
88   
 
89  8 toggle String getURL(String queries)
90    {
91  8 return getURLPrefix() + "/family/" + queries.trim().toUpperCase()
92    + getURLSuffix();
93    }
94   
95    /**
96    * Pfam and Rfam provide alignments
97    */
 
98  5241 toggle @Override
99    public boolean isAlignmentSource()
100    {
101  5241 return true;
102    }
103   
104    /**
105    * default suffix to append the retrieval URL for this source.
106    *
107    * @return "" for most Xfam sources
108    */
 
109  0 toggle public String getURLSuffix()
110    {
111  0 return "";
112    }
113   
114    }
  • Report generated by OpenClover v 4.4.1 on Thu Aug 13 2020 12:06:48 BST using coverage data from Thu Aug 13 2020 12:06:40 BST.
  • OpenClover is free and open-source software.