2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
3 * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
11 * Jalview is distributed in the hope that it will be useful, but
12 * WITHOUT ANY WARRANTY; without even the implied warranty
13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
14 * PURPOSE. See the GNU General Public License for more details.
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
18 package jalview.schemes;
20 import jalview.analysis.AAFrequency;
22 import java.awt.Color;
23 import jalview.datamodel.SequenceI;
25 public class Blosum62ColourScheme extends ResidueColourScheme
27 public Blosum62ColourScheme()
33 public Color findColour(char res, int j, SequenceI seq)
35 if ('a' <= res && res <= 'z')
41 if (consensus == null || j >= consensus.length || consensus[j] == null
42 || (threshold != 0 && !aboveThreshold(res, j)))
49 if (!jalview.util.Comparison.isGap(res))
51 String max = (String) consensus[j].get(AAFrequency.MAXRESIDUE);
53 if (max.indexOf(res) > -1)
55 currentColour = new Color(154, 154, 255);
65 c += ResidueProperties.getBLOSUM62(max.charAt(max_aa), res);
66 } while (++max_aa < n);
70 currentColour = new Color(204, 204, 255);
74 currentColour = Color.white;
78 if (conservationColouring)
80 currentColour = applyConservation(currentColour, j);