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.datamodel.AnnotatedCollectionI;
25 import jalview.datamodel.SequenceCollectionI;
26 import jalview.datamodel.SequenceI;
28 import java.awt.Color;
29 import java.util.Hashtable;
33 * Looks at the information computed from an RNA Stockholm format file on the
34 * secondary structure of the alignment. Extracts the information on the
35 * positions of the helices present and assigns colors.
37 * @author Lauren Michelle Lui
40 public class RNAHelicesColour extends ResidueColourScheme
45 * Maps sequence positions to the RNA helix they belong to. Key: position,
46 * Value: helix TODO: Revise or drop in favour of annotation position numbers
48 public Hashtable<Integer, String> positionsToHelix = new Hashtable<Integer, String>();
51 * Number of helices in the RNA secondary structure
55 public AlignmentAnnotation annotation;
58 * Creates a new RNAHelicesColour object.
60 public RNAHelicesColour(AlignmentAnnotation annotation)
62 super(ResidueProperties.nucleotideIndex);
63 this.annotation = annotation;
67 public RNAHelicesColour(AnnotatedCollectionI alignment)
69 super(ResidueProperties.nucleotideIndex);
70 alignmentChanged(alignment, null);
74 * clones colour settings and annotation row data
76 * @param rnaHelicesColour
78 public RNAHelicesColour(RNAHelicesColour rnaHelicesColour)
80 super(ResidueProperties.nucleotideIndex);
81 annotation = rnaHelicesColour.annotation;
86 public void alignmentChanged(AnnotatedCollectionI alignment,
87 Map<SequenceI, SequenceCollectionI> hiddenReps)
90 // This loop will find the first rna structure annotation by which to colour
92 AlignmentAnnotation[] annotations = alignment.getAlignmentAnnotation();
93 for (int i = 0; i < annotations.length; i++)
96 // is this a sensible way of determining type of annotation?
97 if (annotations[i].visible && annotations[i].isRNA()
98 && annotations[i].isValidStruc())
100 annotation = annotations[i];
109 private long lastrefresh = -1;
111 public void refresh()
114 if (annotation != null
115 && ((annotation._rnasecstr == null || lastrefresh != annotation._rnasecstr
116 .hashCode()) && annotation.isValidStruc()))
118 annotation.getRNAStruc();
119 lastrefresh = annotation._rnasecstr.hashCode();
121 positionsToHelix = new Hashtable<Integer, String>();
123 // Figure out number of helices
124 // Length of rnasecstr is the number of pairs of positions that base pair
125 // with each other in the secondary structure
126 for (int x = 0; x < this.annotation._rnasecstr.length; x++)
130 * System.out.println(this.annotation._rnasecstr[x] + " Begin" +
131 * this.annotation._rnasecstr[x].getBegin());
133 // System.out.println(this.annotation._rnasecstr[x].getFeatureGroup());
135 positionsToHelix.put(this.annotation._rnasecstr[x].getBegin(),
136 this.annotation._rnasecstr[x].getFeatureGroup());
137 positionsToHelix.put(this.annotation._rnasecstr[x].getEnd(),
138 this.annotation._rnasecstr[x].getFeatureGroup());
140 if (Integer.parseInt(this.annotation._rnasecstr[x]
141 .getFeatureGroup()) > numHelix)
143 numHelix = Integer.parseInt(this.annotation._rnasecstr[x]
148 ColourSchemeProperty.initRnaHelicesShading(numHelix);
153 * Returns default color base on purinepyrimidineIndex in
154 * jalview.schemes.ResidueProperties (Allows coloring in sequence logo)
157 * Character in sequence
159 * @return color in RGB
162 public Color findColour(char c)
164 return ResidueProperties.purinepyrimidine[ResidueProperties.purinepyrimidineIndex[c]];
165 // random colors for all positions
166 // jalview.util.ColorUtils.generateRandomColor(Color.white); If you want
170 * Returns color based on helices
173 * Character in sequence
175 * position in sequence - used to locate helix
177 * @return Color in RGB
180 public Color findColour(char c, int j, SequenceI seq)
183 Color currentColour = Color.white;
184 String currentHelix = null;
185 currentHelix = positionsToHelix.get(j);
186 if (currentHelix != null)
188 currentColour = ColourSchemeProperty.rnaHelices[Integer
189 .parseInt(currentHelix)];
191 return currentColour;
195 public ColourSchemeI applyTo(AnnotatedCollectionI sg,
196 Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
198 return new RNAHelicesColour(this);