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.api.AlignViewportI;
24 import jalview.datamodel.AnnotatedCollectionI;
26 import java.awt.Color;
29 * A hydrophobicity colour scheme based on
32 * Kyte, J., and Doolittle, R.F., J. Mol. Biol. 1157, 105-132, 1982
35 public class HydrophobicColourScheme extends ScoreColourScheme
37 private static final Color minScoreColour = new Color(0, 0, 255);
39 private static final Color maxScoreColour = new Color(255, 0, 0);
44 public HydrophobicColourScheme()
46 super(JalviewColourScheme.Hydrophobic.toString(),
47 ResidueProperties.aaIndex, ResidueProperties.hyd,
48 minScoreColour, maxScoreColour);
52 public boolean isPeptideSpecific()
58 * Returns a new instance of this colour scheme with which the given data may
62 public ColourSchemeI getInstance(AlignViewportI view,
63 AnnotatedCollectionI coll)
65 return new HydrophobicColourScheme();