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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25 import jalview.datamodel.*;
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27 public class PIDColourScheme
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28 extends ResidueColourScheme
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30 public Color[] pidColours;
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31 public float[] thresholds;
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32 SequenceGroup group;
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34 public PIDColourScheme()
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36 this.pidColours = ResidueProperties.pidColours;
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37 this.thresholds = ResidueProperties.pidThresholds;
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40 public Color findColour(String s, int j)
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42 if ( (threshold != 0) && !aboveThreshold(s, j))
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47 Color c = Color.white;
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48 Hashtable hash = (Hashtable) consensus.elementAt(j);
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52 if ( (Integer.parseInt(hash.get("maxCount").toString()) != -1) &&
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55 sc = ( ( (Integer) hash.get(s)).intValue() * 100.0) /
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56 ( (Integer) hash.get(
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57 "size")).intValue();
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59 // MC Should be isGap
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60 if (!jalview.util.Comparison.isGap( (s.charAt(0))))
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62 for (int i = 0; i < thresholds.length; i++)
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64 if (sc > thresholds[i])
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