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 Blosum62ColourScheme
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25 extends ResidueColourScheme
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27 public Blosum62ColourScheme()
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32 public Color findColour(String s, int j)
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34 if ( (threshold != 0) && !aboveThreshold(s, j))
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40 if (!jalview.util.Comparison.isGap( (s.charAt(0))))
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42 String max = (String) consensus[j].get("maxResidue");
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44 if (max.indexOf(s) > -1)
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46 return new Color(154, 154, 255);
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52 int n = max.length();
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56 c += ResidueProperties.getBLOSUM62(max.substring(max_aa,
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59 while (++max_aa < n);
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63 return new Color(204, 204, 255);
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