Clover icon

Coverage Report

  1. Project Clover database Thu Nov 27 2025 16:51:35 GMT
  2. Package jalview.ws

File SequenceFetcher.java

 

Coverage histogram

../../img/srcFileCovDistChart10.png
0% of files have more coverage

Code metrics

6
20
2
1
101
53
5
0.25
10
2
2.5

Classes

Class Line # Actions
SequenceFetcher 44 20 5
1.0100%
 

Contributing tests

This file is covered by 206 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;
22   
23    import jalview.ext.ensembl.EnsemblGene;
24    import jalview.ws.dbsources.EBIAlfaFold;
25    import jalview.ws.dbsources.EmblCdsSource;
26    import jalview.ws.dbsources.EmblSource;
27    import jalview.ws.dbsources.Pdb;
28    import jalview.ws.dbsources.PfamFull;
29    import jalview.ws.dbsources.PfamSeed;
30    import jalview.ws.dbsources.RfamSeed;
31    import jalview.ws.dbsources.TDBeacons;
32    import jalview.ws.dbsources.Uniprot;
33    import jalview.ws.seqfetcher.ASequenceFetcher;
34    import jalview.ws.seqfetcher.DbSourceProxy;
35   
36    import java.util.ArrayList;
37    import java.util.Collections;
38    import java.util.List;
39   
40    /**
41    * This implements the run-time discovery of sequence database clients.
42    *
43    */
 
44    public class SequenceFetcher extends ASequenceFetcher
45    {
46    /**
47    * Thread safe construction of database proxies TODO: extend to a configurable
48    * database plugin mechanism where classes are instantiated by reflection and
49    * queried for their DbRefSource and version association.
50    *
51    */
 
52  16 toggle public SequenceFetcher()
53    {
54  16 addDBRefSourceImpl(EnsemblGene.class);
55    // addDBRefSourceImpl(EnsemblGenomes.class);
56  16 addDBRefSourceImpl(EmblSource.class);
57  16 addDBRefSourceImpl(EmblCdsSource.class);
58  16 addDBRefSourceImpl(Uniprot.class);
59    // not a sequence source yet
60    // addDBRefSourceImpl(TDBeacons.class);
61  16 addDBRefSourceImpl(Pdb.class);
62  16 addDBRefSourceImpl(PfamFull.class);
63  16 addDBRefSourceImpl(PfamSeed.class);
64  16 addDBRefSourceImpl(RfamSeed.class);
65    // Technically not a database cross reference we fetch directly
66    // Useful for AlphaFold debugging
67    // addDBRefSourceImpl(EBIAlfaFold.class);
68    }
69   
70    /**
71    * return an ordered list of database sources excluding alignment only
72    * databases
73    */
 
74  2619 toggle public String[] getNonAlignmentSources()
75    {
76  2619 String[] srcs = this.getSupportedDb();
77  2619 List<String> src = new ArrayList<>();
78   
79  23571 for (int i = 0; i < srcs.length; i++)
80    {
81  20952 boolean accept = true;
82  20952 for (DbSourceProxy dbs : getSourceProxy(srcs[i]))
83    {
84    // Skip the alignment databases for the moment - they're not useful for
85    // verifying a single sequence against its reference source
86  20952 if (dbs.isAlignmentSource())
87    {
88  7857 accept = false;
89  7857 break;
90    }
91    }
92  20952 if (accept)
93    {
94  13095 src.add(srcs[i]);
95    }
96    }
97   
98  2619 Collections.sort(src, String.CASE_INSENSITIVE_ORDER);
99  2619 return src.toArray(new String[src.size()]);
100    }
101    }
  • Report generated by OpenClover v 4.4.1 on Thu Nov 27 2025 17:01:26 GMT using coverage data from Thu Nov 27 2025 17:01:12 GMT.
  • OpenClover is free and open-source software.