2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
3 * Copyright (C) 2014 The Jalview Authors
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/>.
17 * The Jalview Authors are detailed in the 'AUTHORS' file.
19 package jalview.schemes;
21 import jalview.analysis.AAFrequency;
23 import java.awt.Color;
26 import jalview.datamodel.AnnotatedCollectionI;
27 import jalview.datamodel.SequenceCollectionI;
28 import jalview.datamodel.SequenceI;
30 public class Blosum62ColourScheme extends ResidueColourScheme
32 public Blosum62ColourScheme()
38 public Color findColour(char res, int j, SequenceI seq)
40 if ('a' <= res && res <= 'z')
46 if (consensus == null || j >= consensus.length || consensus[j] == null
47 || (threshold != 0 && !aboveThreshold(res, j)))
54 if (!jalview.util.Comparison.isGap(res))
56 String max = (String) consensus[j].get(AAFrequency.MAXRESIDUE);
58 if (max.indexOf(res) > -1)
60 currentColour = new Color(154, 154, 255);
70 c += ResidueProperties.getBLOSUM62(max.charAt(max_aa), res);
71 } while (++max_aa < n);
75 currentColour = new Color(204, 204, 255);
79 currentColour = Color.white;
83 if (conservationColouring)
85 currentColour = applyConservation(currentColour, j);
96 public ColourSchemeI applyTo(AnnotatedCollectionI sg,
97 Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
99 ColourSchemeI newcs = super.applyTo(sg, hiddenRepSequences);