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;
21 import jalview.datamodel.SequenceI;
23 import java.awt.Color;
31 public class NucleotideColourScheme extends ResidueColourScheme
34 * Creates a new NucleotideColourScheme object.
36 public NucleotideColourScheme()
38 super(ResidueProperties.nucleotideIndex, ResidueProperties.nucleotide,
48 * @return DOCUMENT ME!
51 public Color findColour(char c)
53 // System.out.println("called"); log.debug
54 return colors[ResidueProperties.nucleotideIndex[c]];
65 * @return DOCUMENT ME!
68 public Color findColour(char c, int j, SequenceI seq)
71 if ((threshold == 0) || aboveThreshold(c, j))
75 currentColour = colors[ResidueProperties.nucleotideIndex[c]];
76 } catch (Exception ex)
86 if (conservationColouring)
88 currentColour = applyConservation(currentColour, j);