Class |
Line # |
Actions |
|||
---|---|---|---|---|---|
CodonComparator | 35 | 16 | 15 |
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 | 150632 | @Override |
39 | public int compare(AlignedCodon ac1, AlignedCodon ac2) | |
40 | { | |
41 | 150632 | if (ac1 == null || ac2 == null || ac1.equals(ac2)) |
42 | { | |
43 | 12411 | 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 | 138221 | if (ac1.pos1 < ac2.pos1 && ac1.pos3 <= ac2.pos3) |
55 | { | |
56 | 40919 | return -1; |
57 | } | |
58 | 97302 | if (ac2.pos1 < ac1.pos1 && ac2.pos3 <= ac1.pos3) |
59 | { | |
60 | 96911 | 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 | 391 | if (ac1.pos3 > ac2.pos3 && ac1.pos1 >= ac2.pos1) |
72 | { | |
73 | 27 | return 1; |
74 | } | |
75 | 364 | if (ac2.pos3 > ac1.pos3 && ac2.pos1 >= ac1.pos1) |
76 | { | |
77 | 28 | return -1; |
78 | } | |
79 | ||
80 | /* | |
81 | * Case 3: if start and end match, compare middle base positions. | |
82 | */ | |
83 | 336 | 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 | 330 | int compareMiddles = Integer.compare(ac1.pos2, ac2.pos2); |
94 | 330 | if (compareMiddles != 0) |
95 | { | |
96 | 324 | 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 | } |