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Consensus | 27 | 20 | 9 |
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.schemes; | |
22 | ||
23 | // ////////////////////////////////////////// | |
24 | // This does nothing at all at the moment!!!!!!!!!! | |
25 | // AW 15th Dec 2004 | |
26 | // /////////////////////////////////////// | |
27 | public class Consensus | |
28 | { | |
29 | int[] mask; | |
30 | ||
31 | double threshold; | |
32 | ||
33 | String maskstr; | |
34 | ||
35 | 527 | public Consensus(String mask, double threshold) |
36 | { | |
37 | // this.id = id; | |
38 | // this.mask = mask; | |
39 | 527 | this.maskstr = mask; |
40 | 527 | setMask(mask); |
41 | 527 | this.threshold = threshold; |
42 | } | |
43 | ||
44 | 527 | public void setMask(String s) |
45 | { | |
46 | 527 | this.mask = setNums(s); |
47 | ||
48 | // for (int i=0; i < mask.length; i++) { | |
49 | // jalview.bin.Console.outPrintln(mask[i] + " " + | |
50 | // ResidueProperties.aa[mask[i]]); | |
51 | // } | |
52 | } | |
53 | ||
54 | /** | |
55 | * @deprecated Use {@link #isConserved(int[][],int,int,boolean)} instead | |
56 | */ | |
57 | 0 | @Deprecated |
58 | public boolean isConserved(int[][] cons2, int col, int size) | |
59 | { | |
60 | 0 | jalview.bin.Console.outPrintln("DEPRECATED!!!!"); |
61 | 0 | return isConserved(cons2, col, size, true); |
62 | } | |
63 | ||
64 | 154 | public boolean isConserved(int[][] cons2, int col, int size, |
65 | boolean includeGaps) | |
66 | { | |
67 | 154 | int tot = 0; |
68 | 154 | if (!includeGaps) |
69 | { | |
70 | 15 | size -= cons2[col][cons2[col].length - 1]; |
71 | } | |
72 | 478 | for (int i = 0; i < mask.length; i++) |
73 | { | |
74 | 324 | tot += cons2[col][mask[i]]; |
75 | } | |
76 | ||
77 | 154 | if (tot > ((threshold * size) / 100)) |
78 | { | |
79 | // jalview.bin.Console.outPrintln("True conserved "+tot+" from | |
80 | // "+threshold+" out of | |
81 | // "+size+" : "+maskstr); | |
82 | 23 | return true; |
83 | } | |
84 | ||
85 | 131 | return false; |
86 | } | |
87 | ||
88 | 527 | int[] setNums(String s) |
89 | { | |
90 | 527 | int[] out = new int[s.length()]; |
91 | 527 | int i = 0; |
92 | ||
93 | 1462 | while (i < s.length()) |
94 | { | |
95 | 935 | out[i] = ResidueProperties.aaIndex[s.charAt(i)]; |
96 | 935 | i++; |
97 | } | |
98 | ||
99 | 527 | return out; |
100 | } | |
101 | } |