2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
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5 * This program is free software; you can redistribute it and/or
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6 * modify it under the terms of the GNU General Public License
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7 * as published by the Free Software Foundation; either version 2
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8 * of the License, or (at your option) any later version.
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10 * This program is distributed in the hope that it will be useful,
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11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
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12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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13 * GNU General Public License for more details.
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15 * You should have received a copy of the GNU General Public License
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16 * along with this program; if not, write to the Free Software
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17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
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19 package jalview.schemes;
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22 ////////////////////////////////////////////
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23 // This does nothing at all at the moment!!!!!!!!!!
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25 /////////////////////////////////////////
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26 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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42 // for (int i=0; i < mask.length; i++) {
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43 // System.out.println(mask[i] + " " + ResidueProperties.aa[mask[i]]);
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47 public boolean isConserved(int[][] cons2, int col, int size) {
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50 for (int i = 0; i < mask.length; i++)
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51 tot += cons2[col][mask[i]];
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53 if ((double) tot > ((threshold * size) / 100)) {
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60 int[] setNums(String s) {
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61 int[] out = new int[s.length()];
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64 while (i < s.length()) {
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65 out[i] = ((Integer) ResidueProperties.aaHash.get(s.substring(i,
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66 i + 1))).intValue();
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