2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
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;
24 * Class is based off of NucleotideColourScheme
26 * @author Lauren Michelle Lui
28 public class PurinePyrimidineColourScheme extends ResidueColourScheme
31 * Creates a new PurinePyrimidineColourScheme object.
33 public PurinePyrimidineColourScheme()
35 super(ResidueProperties.purinepyrimidineIndex,
36 ResidueProperties.purinepyrimidine, 0);
40 * Finds the corresponding color for the type of character inputed
43 * Character in sequence
45 * @return Color from purinepyrimidineIndex in
46 * jalview.schemes.ResidueProperties
48 public Color findColour(char c)
50 return colors[ResidueProperties.purinepyrimidineIndex[c]];
54 * Returns color based on conservation
57 * Character in sequence
61 * @return Color in RGB
63 public Color findColour(char c, int j)
66 if ((threshold == 0) || aboveThreshold(c, j))
70 currentColour = colors[ResidueProperties.purinepyrimidineIndex[c]];
71 } catch (Exception ex)
81 if (conservationColouring)
83 currentColour = applyConservation(currentColour, j);