1 /* Jalview - a java multiple alignment editor
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2 * Copyright (C) 1998 Michele Clamp
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4 * This program is free software; you can redistribute it and/or
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5 * modify it under the terms of the GNU General Public License
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6 * as published by the Free Software Foundation; either version 2
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7 * of the License, or (at your option) any later version.
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9 * This program is distributed in the hope that it will be useful,
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10 * but WITHOUT ANY WARRANTY; without even the implied warranty of
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11 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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12 * GNU General Public License for more details.
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14 * You should have received a copy of the GNU General Public License
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15 * along with this program; if not, write to the Free Software
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16 * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
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19 package jalview.schemes;
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21 ////////////////////////////////////////////
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22 // This does nothing at all at the moment!!!!!!!!!!
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24 /////////////////////////////////////////
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25 public class Consensus {
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31 public Consensus(String mask, double threshold) {
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33 // this.mask = mask;
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34 this.maskstr = mask;
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36 this.threshold = threshold;
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39 public void setMask(String s) {
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40 this.mask = setNums(s);
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41 // for (int i=0; i < mask.length; i++) {
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42 // System.out.println(mask[i] + " " + ResidueProperties.aa[mask[i]]);
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46 public boolean isConserved(int[][] cons2,int col ,int size) {
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48 for (int i = 0; i < mask.length; i++)
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49 tot += cons2[col][mask[i]];
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51 if ( (double) tot > threshold * size / 100)
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57 int[] setNums(String s)
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59 int [] out = new int[s.length()];
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61 while (i < s.length())
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63 out[i] = ( (Integer) ResidueProperties.aaHash.get(s.substring(i, i + 1))).intValue();
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