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.analysis.SequenceIdMatcher;
24 import jalview.datamodel.AlignmentAnnotation;
25 import jalview.datamodel.AlignmentI;
26 import jalview.datamodel.AnnotatedCollectionI;
27 import jalview.datamodel.Annotation;
28 import jalview.datamodel.SequenceCollectionI;
29 import jalview.datamodel.SequenceI;
30 import jalview.io.TCoffeeScoreFile;
32 import java.awt.Color;
33 import java.util.ArrayList;
34 import java.util.IdentityHashMap;
36 import java.util.TreeMap;
39 * Defines the color score for T-Coffee MSA
41 * See http://tcoffee.org
44 * @author Paolo Di Tommaso
47 public class TCoffeeColourScheme extends ResidueColourScheme
50 static final Color[] colors =
51 { new Color(102, 102, 255), // #6666FF
52 new Color(0, 255, 0), // #00FF00
53 new Color(102, 255, 0), // #66FF00
54 new Color(204, 255, 0), // #CCFF00
55 new Color(255, 255, 0), // #FFFF00
56 new Color(255, 204, 0), // #FFCC00
57 new Color(255, 153, 0), // #FF9900
58 new Color(255, 102, 0), // #FF6600
59 new Color(255, 51, 0), // #FF3300
60 new Color(255, 34, 0) // #FF2000
63 IdentityHashMap<SequenceI, Color[]> seqMap;
66 * the color scheme needs to look at the alignment to get and cache T-COFFEE
70 * - annotated sequences to be searched
72 public TCoffeeColourScheme(AnnotatedCollectionI alignment)
74 alignmentChanged(alignment, null);
78 public void alignmentChanged(AnnotatedCollectionI alignment,
79 Map<SequenceI, SequenceCollectionI> hiddenReps)
81 // TODO: if sequences have been represented and they have scores, could
82 // compute an average sequence score for the representative
84 // assume only one set of TCOFFEE scores - but could have more than one
86 ArrayList<AlignmentAnnotation> annots = new ArrayList<AlignmentAnnotation>();
87 // Search alignment to get all tcoffee annotation and pick one set of
88 // annotation to use to colour seqs.
89 seqMap = new IdentityHashMap<SequenceI, Color[]>();
90 AnnotatedCollectionI alcontext = alignment instanceof AlignmentI ? alignment
91 : alignment.getContext();
93 for (AlignmentAnnotation al : alcontext
94 .findAnnotation(TCoffeeScoreFile.TCOFFEE_SCORE))
96 if (al.sequenceRef != null && !al.belowAlignment)
99 if (w < al.annotations.length)
101 w = al.annotations.length;
103 Color[] scores = new Color[al.annotations.length];
105 for (Annotation an : al.annotations)
107 scores[i++] = (an != null) ? an.colour : Color.white;
109 seqMap.put(al.sequenceRef, scores);
112 // TODO: compute average colour for each symbol type in each column - gives
113 // a second order colourscheme for colouring a sequence logo derived from
114 // the alignment (colour reflects quality of alignment for each residue
119 public Color findColour(char c, int j, SequenceI seq)
123 if (seqMap == null || (cols = seqMap.get(seq)) == null)
125 // see above TODO about computing a colour for each residue in each
126 // column: cc = _rcols[i][indexFor[c]];
130 if (j < 0 || j >= cols.length)
138 public ColourSchemeI applyTo(AnnotatedCollectionI sg,
139 Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
141 return new TCoffeeColourScheme(sg);