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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24 public class ScoreColourScheme extends ResidueColourScheme {
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27 public double[] scores;
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29 public ScoreColourScheme(double[] scores, double min, double max) {
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32 this.scores = scores;
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37 public Color findColour(String s, int j) {
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38 if (threshold > 0) {
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39 if (!aboveThreshold(s, j)) {
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44 float red = (float) (scores[((Integer) ResidueProperties.aaHash.get(s)).intValue()] -
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45 (float) min) / (float) (max - min);
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55 char c = s.charAt(0);
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57 if (jalview.util.Comparison.isGap((c))) {
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61 // This isn';t great - pool of colours in here?
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62 return makeColour(red);
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65 public Color makeColour(float c) {
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66 return new Color(c, (float) 0.0, (float) 1.0 - c);
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