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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26 public class ResidueColourScheme implements ColourSchemeI {
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29 public Vector consensus;
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31 public ResidueColourScheme(Color[] colors, int threshold) {
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32 this.colors = colors;
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33 this.threshold = threshold;
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36 public ResidueColourScheme() {
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39 public void setConsensus(Vector consensus) {
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40 this.consensus = consensus;
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43 public Color findColour(String aa) {
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44 return colors[((Integer) (ResidueProperties.aaHash.get(aa))).intValue()];
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47 public Color findColour(String s, int j) {
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48 if ((threshold == 0) || aboveThreshold(s, j)) {
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49 return colors[((Integer) (ResidueProperties.aaHash.get(s))).intValue()];
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55 public int getThreshold() {
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59 public void setThreshold(int ct) {
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63 public boolean aboveThreshold(String s, int j) {
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64 Hashtable hash = (Hashtable) consensus.elementAt(j);
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66 if ((((Integer) hash.get("maxCount")).intValue() != -1) &&
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68 //// resCount//////////////////// ///////////////seq count////////////
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69 double sc = (((Integer) hash.get(s)).intValue() * 100.0) / ((Integer) hash.get(
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70 "size")).intValue();
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72 if (sc >= threshold) {
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