2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
3 * Copyright (C) 2014 The Jalview Authors
5 * This file is part of Jalview.
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 of the License, or (at your option) any later version.
11 * Jalview is distributed in the hope that it will be useful, but
12 * WITHOUT ANY WARRANTY; without even the implied warranty
13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
14 * PURPOSE. See the GNU General Public License for more details.
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
17 * The Jalview Authors are detailed in the 'AUTHORS' file.
19 package jalview.schemes;
21 // //////////////////////////////////////////
22 // This does nothing at all at the moment!!!!!!!!!!
24 // ///////////////////////////////////////
25 public class Consensus
33 public Consensus(String mask, double threshold)
39 this.threshold = threshold;
42 public void setMask(String s)
44 this.mask = setNums(s);
46 // for (int i=0; i < mask.length; i++) {
47 // System.out.println(mask[i] + " " + ResidueProperties.aa[mask[i]]);
52 * @deprecated Use {@link #isConserved(int[][],int,int,boolean)} instead
54 public boolean isConserved(int[][] cons2, int col, int size)
56 return isConserved(cons2, col, size, true);
59 public boolean isConserved(int[][] cons2, int col, int size,
65 size -= cons2[col][cons2[col].length - 1];
67 for (int i = 0; i < mask.length; i++)
69 tot += cons2[col][mask[i]];
72 if ((double) tot > ((threshold * size) / 100))
74 // System.out.println("True conserved "+tot+" from "+threshold+" out of
75 // "+size+" : "+maskstr);
82 int[] setNums(String s)
84 int[] out = new int[s.length()];
87 while (i < s.length())
89 out[i] = ResidueProperties.aaIndex[s.charAt(i)];