2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
3 * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
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/>.
18 package jalview.schemes;
23 * Class is based off of NucleotideColourScheme
25 * @author Lauren Michelle Lui
27 public class PurinePyrimidineColourScheme extends ResidueColourScheme
30 * Creates a new PurinePyrimidineColourScheme object.
32 public PurinePyrimidineColourScheme()
34 super(ResidueProperties.purinepyrimidineIndex,
35 ResidueProperties.purinepyrimidine, 0);
39 * Finds the corresponding color for the type of character inputed
42 * Character in sequence
44 * @return Color from purinepyrimidineIndex in
45 * jalview.schemes.ResidueProperties
47 public Color findColour(char c)
49 return colors[ResidueProperties.purinepyrimidineIndex[c]];
53 * Returns color based on conservation
56 * Character in sequence
60 * @return Color in RGB
62 public Color findColour(char c, int j)
65 if ((threshold == 0) || aboveThreshold(c, j))
69 currentColour = colors[ResidueProperties.purinepyrimidineIndex[c]];
70 } catch (Exception ex)
80 if (conservationColouring)
82 currentColour = applyConservation(currentColour, j);