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.AlignmentAnnotation;
24 import jalview.util.ColorUtils;
26 import java.awt.Color;
27 import java.util.Hashtable;
30 * Became RNAHelicesColour.java. Placeholder for true covariation color scheme
32 * @author Lauren Michelle Lui
35 public class CovariationColourScheme extends ResidueColourScheme
37 public Hashtable helixcolorhash = new Hashtable();
39 public Hashtable positionsToHelix = new Hashtable();
43 public AlignmentAnnotation annotation;
46 * Creates a new CovariationColourScheme object.
48 public CovariationColourScheme(AlignmentAnnotation annotation)
50 this.annotation = annotation;
52 for (int x = 0; x < this.annotation._rnasecstr.length; x++)
54 // System.out.println(this.annotation._rnasecstr[x] + " Begin" +
55 // this.annotation._rnasecstr[x].getBegin());
56 // System.out.println(this.annotation._rnasecstr[x].getFeatureGroup());
57 // pairs.put(this.annotation._rnasecstr[x].getBegin(),
58 // this.annotation._rnasecstr[x].getEnd());
60 positionsToHelix.put(this.annotation._rnasecstr[x].getBegin(),
61 this.annotation._rnasecstr[x].getFeatureGroup());
62 positionsToHelix.put(this.annotation._rnasecstr[x].getEnd(),
63 this.annotation._rnasecstr[x].getFeatureGroup());
65 if (Integer.parseInt(this.annotation._rnasecstr[x].getFeatureGroup()) > numHelix)
67 numHelix = Integer.parseInt(this.annotation._rnasecstr[x]
73 for (int j = 0; j <= numHelix; j++)
75 helixcolorhash.put(Integer.toString(j),
76 ColorUtils.generateRandomColor(Color.white));
87 * @return DOCUMENT ME!
89 public Color findColour(char c)
91 // System.out.println("called"); log.debug
92 // Generate a random pastel color
94 return ResidueProperties.purinepyrimidine[ResidueProperties.purinepyrimidineIndex[c]];// jalview.util.ColorUtils.generateRandomColor(Color.white);
105 * @return DOCUMENT ME!
107 public Color findColour(char c, int j)
109 Color currentColour = Color.white;
110 String currentHelix = null;
111 // System.out.println(c + " " + j);
112 currentHelix = (String) positionsToHelix.get(j);
113 // System.out.println(positionsToHelix.get(j));
115 if (currentHelix != null)
117 currentColour = (Color) helixcolorhash.get(currentHelix);
120 // System.out.println(c + " " + j + " helix " + currentHelix + " " +
122 return currentColour;