2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
3 * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
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/>.
18 package jalview.schemes;
20 import jalview.analysis.SequenceIdMatcher;
21 import jalview.datamodel.AlignmentAnnotation;
22 import jalview.datamodel.AlignmentI;
23 import jalview.datamodel.AnnotatedCollectionI;
24 import jalview.datamodel.Annotation;
25 import jalview.datamodel.SequenceCollectionI;
26 import jalview.datamodel.SequenceI;
27 import jalview.io.TCoffeeScoreFile;
29 import java.awt.Color;
30 import java.util.ArrayList;
31 import java.util.IdentityHashMap;
33 import java.util.TreeMap;
36 * Defines the color score for T-Coffee MSA
38 * See http://tcoffee.org
41 * @author Paolo Di Tommaso
44 public class TCoffeeColourScheme extends ResidueColourScheme
47 static final Color[] colors =
48 { new Color(102, 102, 255), // #6666FF
49 new Color(0, 255, 0), // #00FF00
50 new Color(102, 255, 0), // #66FF00
51 new Color(204, 255, 0), // #CCFF00
52 new Color(255, 255, 0), // #FFFF00
53 new Color(255, 204, 0), // #FFCC00
54 new Color(255, 153, 0), // #FF9900
55 new Color(255, 102, 0), // #FF6600
56 new Color(255, 51, 0), // #FF3300
57 new Color(255, 34, 0) // #FF2000
60 IdentityHashMap<SequenceI, Color[]> seqMap;
63 * the color scheme needs to look at the alignment to get and cache T-COFFEE
67 * - annotated sequences to be searched
69 public TCoffeeColourScheme(AnnotatedCollectionI alignment)
71 alignmentChanged(alignment, null);
75 public void alignmentChanged(AnnotatedCollectionI alignment,
76 Map<SequenceI, SequenceCollectionI> hiddenReps)
78 // TODO: if sequences have been represented and they have scores, could
79 // compute an average sequence score for the representative
81 // assume only one set of TCOFFEE scores - but could have more than one
83 ArrayList<AlignmentAnnotation> annots = new ArrayList<AlignmentAnnotation>();
84 // Search alignment to get all tcoffee annotation and pick one set of
85 // annotation to use to colour seqs.
86 seqMap = new IdentityHashMap<SequenceI, Color[]>();
88 for (AlignmentAnnotation al : alignment
89 .findAnnotation(TCoffeeScoreFile.TCOFFEE_SCORE))
91 if (al.sequenceRef != null && !al.belowAlignment)
94 if (w < al.annotations.length)
96 w = al.annotations.length;
98 Color[] scores = new Color[al.annotations.length];
100 for (Annotation an : al.annotations)
102 scores[i++] = (an != null) ? an.colour : Color.white;
104 seqMap.put(al.sequenceRef, scores);
107 // TODO: compute average colour for each symbol type in each column - gives
108 // a second order colourscheme for colouring a sequence logo derived from
109 // the alignment (colour reflects quality of alignment for each residue
114 public Color findColour(char c, int j, SequenceI seq)
118 if (seqMap == null || (cols = seqMap.get(seq)) == null)
120 // see above TODO about computing a colour for each residue in each
121 // column: cc = _rcols[i][indexFor[c]];
125 if (j < 0 || j >= cols.length)