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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21 import jalview.gui.*;
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22 import jalview.datamodel.*;
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23 import jalview.analysis.*;
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25 public class ConservationColourScheme extends ResidueColourScheme {
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26 public Conservation conserve;
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27 boolean byResidue = true;
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28 public ColourSchemeI cs;
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29 public int inc = 30;
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30 int colourThreshold = 7;
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32 public ConservationColourScheme(Conservation cons, ColourSchemeI oldcs)
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41 public Color findColour(String s, int i, java.util.Vector whatever)
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44 if (colourThreshold > 0 && conserve.getConsSequence() != null)
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46 if (conserve.getConsSequence().getSequence().charAt(i)=='*'
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47 || conserve.getConsSequence().getSequence().charAt(i)=='+')
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50 c = findColour(s, i);
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61 if (!jalview.util.Comparison.isGap(conserve.getConsSequence().
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62 getSequence().charAt(i)))
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63 t = Integer.parseInt(conserve.getConsSequence().getSequence().
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64 substring(i, i + 1));
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66 c = findColour(s, i);
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71 c = lighter(c, inc);
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82 public Color findColour(String s, int j) {
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84 return cs.findColour( s, j, null);
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91 public Color lighter(Color c, int inc) {
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92 int red = c.getRed();
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93 int blue = c.getBlue();
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94 int green = c.getGreen();
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96 if (red < 255-inc) { red = red +inc;} else {red = 255;}
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97 if (blue < 255-inc) { blue = blue +inc;} else {blue = 255;}
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98 if (green < 255-inc) { green = green +inc;} else {green = 255;}
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100 return new Color(red,green,blue);
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