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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20 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,
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35 this.scores = scores;
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41 public Color findColour(String s,int j)
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46 if (!aboveThreshold(s,j))
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50 float red = (float)(scores[((Integer)ResidueProperties.aaHash.get(s)).intValue()]
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51 - (float)min)/(float)(max - min);
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58 char c = s.charAt(0);
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60 if(jalview.util.Comparison.isGap((c)))
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63 // This isn';t great - pool of colours in here?
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64 return makeColour(red);
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66 public Color makeColour(float c) {
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67 return new Color(c,(float)0.0,(float)1.0-c);
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