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 java.awt.Color;
26 * Class is based off of NucleotideColourScheme
28 * @author Lauren Michelle Lui
30 public class PurinePyrimidineColourScheme extends ResidueColourScheme
33 * Creates a new PurinePyrimidineColourScheme object.
35 public PurinePyrimidineColourScheme()
37 super(ResidueProperties.purinepyrimidineIndex,
38 ResidueProperties.purinepyrimidine, 0);
42 * Finds the corresponding color for the type of character inputed
45 * Character in sequence
47 * @return Color from purinepyrimidineIndex in
48 * jalview.schemes.ResidueProperties
51 public Color findColour(char c)
53 return colors[ResidueProperties.purinepyrimidineIndex[c]];
57 * Returns color based on conservation
60 * Character in sequence
64 * @return Color in RGB
66 public Color findColour(char c, int j)
69 if ((threshold == 0) || aboveThreshold(c, j))
73 currentColour = colors[ResidueProperties.purinepyrimidineIndex[c]];
74 } catch (Exception ex)
84 if (conservationColouring)
86 currentColour = applyConservation(currentColour, j);
93 public boolean isNucleotideSpecific()
99 public String getSchemeName()
101 return JalviewColourScheme.PurinePyrimidine.toString();