1 /* Jalview - a java multiple alignment editor
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2 * Copyright (C) 1998 Michele Clamp
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4 * This program is free software; you can redistribute it and/or
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5 * modify it under the terms of the GNU General Public License
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6 * as published by the Free Software Foundation; either version 2
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7 * of the License, or (at your option) any later version.
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9 * This program is distributed in the hope that it will be useful,
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10 * but WITHOUT ANY WARRANTY; without even the implied warranty of
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11 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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12 * GNU General Public License for more details.
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14 * You should have received a copy of the GNU General Public License
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15 * along with this program; if not, write to the Free Software
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16 * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
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19 package jalview.schemes;
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24 import jalview.gui.*;
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25 import jalview.datamodel.*;
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27 public class Blosum62ColourScheme extends ResidueColourScheme
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30 // need to keep an eye on the changing visible consensus sequence
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33 public Blosum62ColourScheme(AlignViewport av)
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39 public Color findColour(String s, int j, Vector aa)
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44 hash = (Hashtable)aa.elementAt(j);
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48 if (!jalview.util.Comparison.isGap((s.charAt(0))))
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50 String max = (String)hash.get("maxResidue");
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52 if (max.indexOf(s)>-1)
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53 return new Color(154, 154, 255);
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60 c+=ResidueProperties.getBLOSUM62(max.substring(max_aa, max_aa+1), s);
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61 } while (++max_aa<n);
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64 return new Color(204, 204, 255);
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74 public boolean canThreshold()
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