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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28 public class ConservationColourScheme extends ResidueColourScheme {
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29 public Conservation conserve;
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30 public ColourSchemeI cs;
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31 public int inc = 30;
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33 public ConservationColourScheme(Conservation cons, ColourSchemeI oldcs) {
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39 public void setConsensus(Vector consensus) {
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40 this.consensus = consensus;
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43 cs.setConsensus(consensus);
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47 public Color findColour(String s, int i) {
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48 Color c = Color.white;
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54 char ch = conserve.getConsSequence().getSequence().charAt(i);
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56 if ((ch == '*') || (ch == '+')) {
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57 c = cs.findColour(s, i);
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62 if (!jalview.util.Comparison.isGap(ch)) {
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63 t = Integer.parseInt(ch + "");
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66 c = cs.findColour(s, i);
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69 c = lighter(c, inc);
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77 public Color lighter(Color c, int inc) {
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78 int red = c.getRed();
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79 int blue = c.getBlue();
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80 int green = c.getGreen();
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82 if (red < (255 - inc)) {
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88 if (blue < (255 - inc)) {
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94 if (green < (255 - inc)) {
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95 green = green + inc;
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100 return new Color(red, green, blue);
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