2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
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;
22 import java.util.Hashtable;
24 import jalview.datamodel.AlignmentAnnotation;
27 * Became RNAHelicesColour.java. Placeholder for true covariation color scheme
29 * @author Lauren Michelle Lui
32 public class CovariationColourScheme extends ResidueColourScheme
34 public Hashtable helixcolorhash = new Hashtable();
36 public Hashtable positionsToHelix = new Hashtable();
40 public AlignmentAnnotation annotation;
43 * Creates a new CovariationColourScheme object.
45 public CovariationColourScheme(AlignmentAnnotation annotation)
47 this.annotation = annotation;
49 for (int x = 0; x < this.annotation._rnasecstr.length; x++)
51 // System.out.println(this.annotation._rnasecstr[x] + " Begin" +
52 // this.annotation._rnasecstr[x].getBegin());
53 // System.out.println(this.annotation._rnasecstr[x].getFeatureGroup());
54 // pairs.put(this.annotation._rnasecstr[x].getBegin(),
55 // this.annotation._rnasecstr[x].getEnd());
57 positionsToHelix.put(this.annotation._rnasecstr[x].getBegin(),
58 this.annotation._rnasecstr[x].getFeatureGroup());
59 positionsToHelix.put(this.annotation._rnasecstr[x].getEnd(),
60 this.annotation._rnasecstr[x].getFeatureGroup());
62 if (Integer.parseInt(this.annotation._rnasecstr[x].getFeatureGroup()) > numHelix)
64 numHelix = Integer.parseInt(this.annotation._rnasecstr[x]
70 for (int j = 0; j <= numHelix; j++)
72 helixcolorhash.put(Integer.toString(j),
73 jalview.util.ColorUtils.generateRandomColor(Color.white));
84 * @return DOCUMENT ME!
86 public Color findColour(char c)
88 // System.out.println("called"); log.debug
89 // Generate a random pastel color
91 return ResidueProperties.purinepyrimidine[ResidueProperties.purinepyrimidineIndex[c]];// jalview.util.ColorUtils.generateRandomColor(Color.white);
102 * @return DOCUMENT ME!
104 public Color findColour(char c, int j)
106 Color currentColour = Color.white;
107 String currentHelix = null;
108 // System.out.println(c + " " + j);
109 currentHelix = (String) positionsToHelix.get(j);
110 // System.out.println(positionsToHelix.get(j));
112 if (currentHelix != null)
114 currentColour = (Color) helixcolorhash.get(currentHelix);
117 // System.out.println(c + " " + j + " helix " + currentHelix + " " +
119 return currentColour;