2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
3 * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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 jalview.datamodel.SequenceI;
22 import java.awt.Color;
30 public class NucleotideColourScheme extends ResidueColourScheme
33 * Creates a new NucleotideColourScheme object.
35 public NucleotideColourScheme()
37 super(ResidueProperties.nucleotideIndex, ResidueProperties.nucleotide, 0);
46 * @return DOCUMENT ME!
49 public Color findColour(char c)
51 // System.out.println("called"); log.debug
52 return colors[ResidueProperties.nucleotideIndex[c]];
63 * @return DOCUMENT ME!
66 public Color findColour(char c, int j, SequenceI seq)
69 if ((threshold == 0) || aboveThreshold(c, j))
73 currentColour = colors[ResidueProperties.nucleotideIndex[c]];
74 } catch (Exception ex)
84 if (conservationColouring)
86 currentColour = applyConservation(currentColour, j);