2 * Jalview - A Sequence Alignment Editor and Viewer
3 * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
5 * This program is free software; you can redistribute it and/or
6 * modify it under the terms of the GNU General Public License
7 * as published by the Free Software Foundation; either version 2
8 * of the License, or (at your option) any later version.
10 * This program is distributed in the hope that it will be useful,
11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
13 * GNU General Public License for more details.
15 * You should have received a copy of the GNU General Public License
16 * along with this program; if not, write to the Free Software
17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
19 package jalview.schemes;
24 public class Blosum62ColourScheme
25 extends ResidueColourScheme
27 public Blosum62ColourScheme()
32 public Color findColour(String s, int j)
34 char res = s.charAt(0);
35 if ('a' <= res && res <= 'z' )
38 s = String.valueOf( res -= ('a' - 'A') );
42 if ( j>=consensus.length || (threshold != 0 && !aboveThreshold(s, j) ))
47 if (!jalview.util.Comparison.isGap( res ))
49 String max = (String) consensus[j].get("maxResidue");
51 if (max.indexOf(s) > -1)
53 currentColour = new Color(154, 154, 255);
63 c += ResidueProperties.getBLOSUM62(max.substring(max_aa,
70 currentColour = new Color(204, 204, 255);
74 currentColour = Color.white;
78 if(conservationColouring)