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Coverage Report

  1. Project Clover database Mon Nov 18 2024 09:38:20 GMT
  2. Package jalview.analysis

File CodonComparator.java

 

Coverage histogram

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

Code metrics

14
16
1
1
111
40
15
0.94
16
1
15

Classes

Class Line # Actions
CodonComparator 35 16 15
1.0100%
 

Contributing tests

This file is covered by 12 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.analysis;
22   
23    import jalview.datamodel.AlignedCodon;
24   
25    import java.util.Comparator;
26   
27    /**
28    * Implements rules for comparing two aligned codons, i.e. determining whether
29    * they should occupy the same position in a translated protein alignment, or
30    * one or the other should 'follow' (by preceded by a gap).
31    *
32    * @author gmcarstairs
33    *
34    */
 
35    public final class CodonComparator implements Comparator<AlignedCodon>
36    {
37   
 
38  3526 toggle @Override
39    public int compare(AlignedCodon ac1, AlignedCodon ac2)
40    {
41  3526 if (ac1 == null || ac2 == null || ac1.equals(ac2))
42    {
43  1755 return 0;
44    }
45   
46    /**
47    * <pre>
48    * Case 1: if one starts before the other, and doesn't end after it, then it
49    * precedes. We ignore the middle base position here.
50    * A--GT
51    * -CT-G
52    * </pre>
53    */
54  1771 if (ac1.pos1 < ac2.pos1 && ac1.pos3 <= ac2.pos3)
55    {
56  235 return -1;
57    }
58  1536 if (ac2.pos1 < ac1.pos1 && ac2.pos3 <= ac1.pos3)
59    {
60  1485 return 1;
61    }
62   
63    /**
64    * <pre>
65    * Case 2: if one ends after the other, and doesn't start before it, then it
66    * follows. We ignore the middle base position here.
67    * -TG-A
68    * G-TC
69    * </pre>
70    */
71  51 if (ac1.pos3 > ac2.pos3 && ac1.pos1 >= ac2.pos1)
72    {
73  15 return 1;
74    }
75  36 if (ac2.pos3 > ac1.pos3 && ac2.pos1 >= ac1.pos1)
76    {
77  12 return -1;
78    }
79   
80    /*
81    * Case 3: if start and end match, compare middle base positions.
82    */
83  24 if (ac1.pos1 == ac2.pos1 && ac1.pos3 == ac2.pos3)
84    {
85  6 return Integer.compare(ac1.pos2, ac2.pos2);
86    }
87   
88    /*
89    * That just leaves the 'enclosing' case - one codon starts after but ends
90    * before the other. If the middle bases don't match, use their comparison
91    * (majority vote).
92    */
93  18 int compareMiddles = Integer.compare(ac1.pos2, ac2.pos2);
94  18 if (compareMiddles != 0)
95    {
96  12 return compareMiddles;
97    }
98   
99    /**
100    * <pre>
101    * Finally just leaves overlap with matching middle base, e.g.
102    * -A-A-A
103    * G--GG
104    * In this case the choice is arbitrary whether to compare based on
105    * first or last base position. We pick the first. Note this preserves
106    * symmetricality of the comparison.
107    * </pre>
108    */
109  6 return Integer.compare(ac1.pos1, ac2.pos1);
110    }
111    }