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 jalview.datamodel.AnnotatedCollectionI;
24 import jalview.datamodel.SequenceCollectionI;
25 import jalview.datamodel.SequenceI;
27 import java.awt.Color;
36 public class NucleotideColourScheme extends ResidueColourScheme
39 * Creates a new NucleotideColourScheme object.
41 public NucleotideColourScheme()
43 super(ResidueProperties.nucleotideIndex, ResidueProperties.nucleotide,
53 * @return DOCUMENT ME!
56 public Color findColour(char c)
58 // System.out.println("called"); log.debug
59 return colors[ResidueProperties.nucleotideIndex[c]];
70 * @return DOCUMENT ME!
73 public Color findColour(char c, int j, SequenceI seq)
76 if ((threshold == 0) || aboveThreshold(c, j))
80 currentColour = colors[ResidueProperties.nucleotideIndex[c]];
81 } catch (Exception ex)
91 if (conservationColouring)
93 currentColour = applyConservation(currentColour, j);
100 public boolean isNucleotideSpecific()
106 public String getSchemeName()
108 return JalviewColourScheme.Nucleotide.toString();
112 * Returns a new instance of this colour scheme with which the given data may
116 public ColourSchemeI getInstance(AnnotatedCollectionI coll,
117 Map<SequenceI, SequenceCollectionI> hrs)
119 return new NucleotideColourScheme();