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Coverage Report

  1. Project Clover database Wed Nov 6 2024 14:47:21 GMT
  2. Package jalview.io.gff

File GffHelperFactory.java

 

Coverage histogram

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

Code metrics

12
18
2
1
89
43
11
0.61
9
2
5.5

Classes

Class Line # Actions
GffHelperFactory 26 18 11
1.0100%
 

Contributing tests

This file is covered by 9 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.io.gff;
22   
23    /**
24    * A factory to serve instances of GFF helper classes
25    */
 
26    public class GffHelperFactory
27    {
28   
29    /**
30    * Returns a class to process the GFF line based on inspecting its column
31    * data. This may return a general-purpose GFF2 or GFF3 helper, or a
32    * specialisation for a flavour of GFF generated by a particular tool.
33    *
34    * @param gff
35    * @return
36    */
 
37  39 toggle public static GffHelperI getHelper(String[] gff)
38    {
39  39 if (gff == null || gff.length < 6)
40    {
41  1 return null;
42    }
43   
44  38 GffHelperI result = null;
45  38 if (ExonerateHelper.recognises(gff))
46    {
47  14 result = new ExonerateHelper();
48    }
49  24 else if (InterProScanHelper.recognises(gff))
50    {
51  1 result = new InterProScanHelper();
52    }
53  23 else if (looksLikeGff3(gff))
54    {
55  4 result = new Gff3Helper();
56    }
57    else
58    {
59  19 result = new Gff2Helper();
60    }
61   
62  38 return result;
63    }
64   
65    /**
66    * Heuristic rule: if column 9 seems to have Name=Value entries, assume this
67    * is GFF3. GFF3 uses '=' as name-value separator, GFF2 uses space ' '.
68    *
69    * @param gff
70    * @return
71    */
 
72  23 toggle protected static boolean looksLikeGff3(String[] gff)
73    {
74  23 if (gff.length >= 9)
75    {
76  16 String attributes = gff[8].trim();
77  16 int pos1 = attributes.indexOf(';');
78  16 int pos2 = attributes.indexOf('=');
79  16 if (pos2 != -1 && (pos1 == -1 || pos2 < pos1))
80    {
81    // there is an '=' before the first ';' (if any)
82    // not foolproof as theoretically GFF2 could be like "Name Value=123;"
83  4 return true;
84    }
85    }
86  19 return false;
87    }
88   
89    }