2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ 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
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.schemes;
23 import jalview.analysis.scoremodels.ScoreModels;
24 import jalview.api.AlignViewportI;
25 import jalview.api.analysis.PairwiseScoreModelI;
26 import jalview.datamodel.AnnotatedCollectionI;
27 import jalview.datamodel.SequenceCollectionI;
28 import jalview.datamodel.SequenceI;
29 import jalview.util.Comparison;
31 import java.awt.Color;
34 public class Blosum62ColourScheme extends ResidueColourScheme
36 private static final Color LIGHT_BLUE = new Color(204, 204, 255);
38 private static final Color DARK_BLUE = new Color(154, 154, 255);
40 public Blosum62ColourScheme()
46 * Returns a new instance of this colour scheme with which the given data may
50 public ColourSchemeI getInstance(AlignViewportI view,
51 AnnotatedCollectionI coll,
52 Map<SequenceI, SequenceCollectionI> hrs)
54 return new Blosum62ColourScheme();
58 public Color findColour(char res, int j, SequenceI seq,
59 String consensusResidue, float pid)
61 PairwiseScoreModelI sm = ScoreModels.getInstance().getBlosum62();
64 * compare as upper case; note consensusResidue is
65 * always computed as uppercase
67 if ('a' <= res && res <= 'z')
72 if (Comparison.isGap(res) || consensusResidue == null)
79 if (consensusResidue.indexOf(res) > -1)
87 for (char consensus : consensusResidue.toCharArray())
89 score += sm.getPairwiseScore(consensus, res);
105 public boolean isPeptideSpecific()
111 public String getSchemeName()
113 return JalviewColourScheme.Blosum62.toString();
117 public boolean isSimple()