jalviewX
File Consensus.java
Coverage histogram
0% of files have more coverage
Classes
| Class | Line # | Actions | ||||
|---|---|---|---|---|---|---|
| Consensus | 27 | 19 | 9 | 2 |
Contributing tests
This file is covered by 7 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.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 | 372 |  public Consensus(String mask, double threshold) |
| 36 | { | |
| 37 | // this.id = id; | |
| 38 | // this.mask = mask; | |
| 39 | 372 | this.maskstr = mask; |
| 40 | 372 | setMask(mask); |
| 41 | 372 | this.threshold = threshold; |
| 42 | } | |
| 43 | ||
| 44 | 372 | public void setMask(String s) |
| 45 | { | |
| 46 | 372 | this.mask = setNums(s); |
| 47 | ||
| 48 | // for (int i=0; i < mask.length; i++) { | |
| 49 | // System.out.println(mask[i] + " " + ResidueProperties.aa[mask[i]]); | |
| 50 | // } | |
| 51 | } | |
| 52 | ||
| 53 | /** | |
| 54 | * @deprecated Use {@link #isConserved(int[][],int,int,boolean)} instead | |
| 55 | */ | |
| 56 | 0 | public boolean isConserved(int[][] cons2, int col, int size) |
| 57 | { | |
| 58 | 0 | return isConserved(cons2, col, size, true); |
| 59 | } | |
| 60 | ||
| 61 | 154 | public boolean isConserved(int[][] cons2, int col, int size, |
| 62 | boolean includeGaps) | |
| 63 | { | |
| 64 | 154 | int tot = 0; |
| 65 | 154 | if (!includeGaps) |
| 66 | { | |
| 67 | 15 | size -= cons2[col][cons2[col].length - 1]; |
| 68 | } | |
| 69 | 478 | for (int i = 0; i < mask.length; i++) |
| 70 | { | |
| 71 | 324 | tot += cons2[col][mask[i]]; |
| 72 | } | |
| 73 | ||
| 74 | 154 | if ((double) tot > ((threshold * size) / 100)) |
| 75 | { | |
| 76 | // System.out.println("True conserved "+tot+" from "+threshold+" out of | |
| 77 | // "+size+" : "+maskstr); | |
| 78 | 23 | return true; |
| 79 | } | |
| 80 | ||
| 81 | 131 | return false; |
| 82 | } | |
| 83 | ||
| 84 | 372 | int[] setNums(String s) |
| 85 | { | |
| 86 | 372 | int[] out = new int[s.length()]; |
| 87 | 372 | int i = 0; |
| 88 | ||
| 89 | 1032 | while (i < s.length()) |
| 90 | { | |
| 91 | 660 | out[i] = ResidueProperties.aaIndex[s.charAt(i)]; |
| 92 | 660 | i++; |
| 93 | } | |
| 94 | ||
| 95 | 372 | return out; |
| 96 | } | |
| 97 | } |