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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21 import jalview.analysis.*;
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25 import java.util.Vector;
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32 * @version $Revision$
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34 public class ConservationColourScheme extends ResidueColourScheme
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36 /** DOCUMENT ME!! */
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37 public Conservation conserve;
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39 /** DOCUMENT ME!! */
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40 public ColourSchemeI cs;
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42 /** DOCUMENT ME!! */
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43 public int inc = 30;
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46 * Creates a new ConservationColourScheme object.
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48 * @param cons DOCUMENT ME!
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49 * @param oldcs DOCUMENT ME!
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51 public ConservationColourScheme(Conservation cons, ColourSchemeI oldcs)
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61 * @param consensus DOCUMENT ME!
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63 public void setConsensus(Vector consensus)
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65 super.setConsensus(consensus);
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69 cs.setConsensus(consensus);
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76 * @param s DOCUMENT ME!
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77 * @param i DOCUMENT ME!
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79 * @return DOCUMENT ME!
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81 public Color findColour(String s, int i)
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83 Color c = Color.white;
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90 char ch = conserve.getConsSequence().getSequence().charAt(i);
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92 if ((ch == '*') || (ch == '+'))
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94 c = cs.findColour(s, i);
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101 if (!jalview.util.Comparison.isGap(ch))
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103 t = Integer.parseInt(ch + "");
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106 c = cs.findColour(s, i);
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110 c = lighter(c, inc);
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121 * @param c DOCUMENT ME!
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122 * @param inc DOCUMENT ME!
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124 * @return DOCUMENT ME!
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126 public Color lighter(Color c, int inc)
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128 int red = c.getRed();
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129 int blue = c.getBlue();
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130 int green = c.getGreen();
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132 if (red < (255 - inc))
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141 if (blue < (255 - inc))
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150 if (green < (255 - inc))
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152 green = green + inc;
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159 return new Color(red, green, blue);
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