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jalviewX

  1. Project Clover database Wed Oct 31 2018 15:13:58 GMT
  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
115
57
8
0.53
3
5
1.6

Classes

Class Line # Actions
Xfam 37 15 8 20
0.2307692323.1%
 

Contributing tests

This file is covered by 83 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   
 
40  26 toggle public Xfam()
41    {
42  26 super();
43    }
44   
45    /**
46    * the base URL for this Xfam-like service
47    *
48    * @return
49    */
50    protected abstract String getURLPrefix();
51   
52    @Override
53    public abstract String getDbVersion();
54   
55    abstract String getXfamSource();
56   
 
57  0 toggle @Override
58    public AlignmentI getSequenceRecords(String queries) throws Exception
59    {
60    // TODO: this is not a perfect implementation. We need to be able to add
61    // individual references to each sequence in each family alignment that's
62    // retrieved.
63  0 startQuery();
64    // TODO: trap HTTP 404 exceptions and return null
65  0 String xfamUrl = getURL(queries);
66   
67  0 if (Cache.log != null)
68    {
69  0 Cache.log.debug("XFAM URL for retrieval is: " + xfamUrl);
70    }
71   
72  0 AlignmentI rcds = new FormatAdapter().readFile(xfamUrl,
73    DataSourceType.URL, FileFormat.Stockholm);
74   
75  0 for (int s = 0, sNum = rcds.getHeight(); s < sNum; s++)
76    {
77  0 rcds.getSequenceAt(s).addDBRef(new DBRefEntry(getXfamSource(),
78    // getDbSource(),
79    getDbVersion(), queries.trim().toUpperCase()));
80  0 if (!getDbSource().equals(getXfamSource()))
81    { // add the specific ref too
82  0 rcds.getSequenceAt(s).addDBRef(new DBRefEntry(getDbSource(),
83    getDbVersion(), queries.trim().toUpperCase()));
84    }
85    }
86  0 stopQuery();
87  0 return rcds;
88    }
89   
 
90  8 toggle String getURL(String queries)
91    {
92  8 return getURLPrefix() + "/family/" + queries.trim().toUpperCase()
93    + getURLSuffix();
94    }
95   
96    /**
97    * Pfam and Rfam provide alignments
98    */
 
99  3306 toggle @Override
100    public boolean isAlignmentSource()
101    {
102  3306 return true;
103    }
104   
105    /**
106    * default suffix to append the retrieval URL for this source.
107    *
108    * @return "" for most Xfam sources
109    */
 
110  0 toggle public String getURLSuffix()
111    {
112  0 return "";
113    }
114   
115    }
  • 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.