2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
3 * Copyright (C) 2011 J Procter, AM Waterhouse, 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;
20 import java.awt.Color;
28 public class NucleotideColourScheme extends ResidueColourScheme
31 * Creates a new NucleotideColourScheme object.
33 public NucleotideColourScheme()
35 super(ResidueProperties.nucleotide, 0);
44 * @return DOCUMENT ME!
47 public Color findColour(char c)
49 // System.out.println("called"); log.debug
50 return colors[ResidueProperties.nucleotideIndex[c]];
61 * @return DOCUMENT ME!
64 public Color findColour(char c, int j, int sequenceIndex)
67 if ((threshold == 0) || aboveThreshold(c, j))
71 currentColour = colors[ResidueProperties.nucleotideIndex[c]];
72 } catch (Exception ex)
82 if (conservationColouring)
84 currentColour = applyConservation(currentColour, j);