+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.schemes;
-import jalview.analysis.SequenceIdMatcher;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.Annotation;
+import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceI;
import jalview.io.TCoffeeScoreFile;
import java.awt.Color;
import java.util.ArrayList;
import java.util.IdentityHashMap;
-import java.util.TreeMap;
+import java.util.Map;
/**
- * Defines the color score for T-Coffee MSA
+ * Defines the color score for T-Coffee MSA
* <p>
* See http://tcoffee.org
*
*
* @author Paolo Di Tommaso
- *
+ *
*/
-public class TCoffeeColourScheme extends ResidueColourScheme {
+public class TCoffeeColourScheme extends ResidueColourScheme
+{
- static final Color[] colors = {
- new Color( 102, 102, 255 ), // #6666FF
- new Color( 0, 255, 0), // #00FF00
- new Color( 102, 255, 0), // #66FF00
- new Color( 204, 255, 0), // #CCFF00
- new Color( 255, 255, 0), // #FFFF00
- new Color( 255, 204, 0), // #FFCC00
- new Color( 255, 153, 0), // #FF9900
- new Color( 255, 102, 0), // #FF6600
- new Color( 255, 51, 0), // #FF3300
- new Color( 255, 34, 0) // #FF2000
- };
+ static final Color[] colors = { new Color(102, 102, 255), // #6666FF
+ new Color(0, 255, 0), // #00FF00
+ new Color(102, 255, 0), // #66FF00
+ new Color(204, 255, 0), // #CCFF00
+ new Color(255, 255, 0), // #FFFF00
+ new Color(255, 204, 0), // #FFCC00
+ new Color(255, 153, 0), // #FF9900
+ new Color(255, 102, 0), // #FF6600
+ new Color(255, 51, 0), // #FF3300
+ new Color(255, 34, 0) // #FF2000
+ };
+ IdentityHashMap<SequenceI, Color[]> seqMap;
- IdentityHashMap<SequenceI, Color[]> seqMap;
- /**
- * the color scheme needs to look at the alignment to get and cache T-COFFEE scores
- *
- * @param alignment - annotated sequences to be searched
- */
- public TCoffeeColourScheme(AnnotatedCollectionI alignment) {
- alignmentChanged(alignment);
- }
- @Override public void alignmentChanged(AnnotatedCollectionI alignment)
- {
- // assume only one set of TCOFFEE scores - but could have more than one potentially.
- ArrayList<AlignmentAnnotation> annots = new ArrayList<AlignmentAnnotation>();
- // Search alignment to get all tcoffee annotation and pick one set of annotation to use to colour seqs.
- seqMap = new IdentityHashMap<SequenceI, Color[]>();
- int w=0;
- for (AlignmentAnnotation al:alignment.findAnnotation(TCoffeeScoreFile.TCOFFEE_SCORE))
- {
- if (al.sequenceRef!=null && !al.belowAlignment)
- {
- annots.add(al);
- if (w<al.annotations.length)
- {
- w=al.annotations.length;
- }
- Color[] scores=new Color[al.annotations.length];
- int i=0;
- for (Annotation an:al.annotations)
- {
- scores[i++]=(an!=null) ? an.colour : Color.white;
- }
- seqMap.put(al.sequenceRef, scores);
- }
- }
+ /**
+ * the color scheme needs to look at the alignment to get and cache T-COFFEE
+ * scores
+ *
+ * @param alignment
+ * - annotated sequences to be searched
+ */
+ public TCoffeeColourScheme(AnnotatedCollectionI alignment)
+ {
+ alignmentChanged(alignment, null);
+ }
+
+ @Override
+ public void alignmentChanged(AnnotatedCollectionI alignment,
+ Map<SequenceI, SequenceCollectionI> hiddenReps)
+ {
+ // TODO: if sequences have been represented and they have scores, could
+ // compute an average sequence score for the representative
+
+ // assume only one set of TCOFFEE scores - but could have more than one
+ // potentially.
+ ArrayList<AlignmentAnnotation> annots = new ArrayList<AlignmentAnnotation>();
+ // Search alignment to get all tcoffee annotation and pick one set of
+ // annotation to use to colour seqs.
+ seqMap = new IdentityHashMap<SequenceI, Color[]>();
+ AnnotatedCollectionI alcontext = alignment instanceof AlignmentI ? alignment
+ : alignment.getContext();
+ int w = 0;
+ for (AlignmentAnnotation al : alcontext
+ .findAnnotation(TCoffeeScoreFile.TCOFFEE_SCORE))
+ {
+ if (al.sequenceRef != null && !al.belowAlignment)
+ {
+ annots.add(al);
+ if (w < al.annotations.length)
+ {
+ w = al.annotations.length;
+ }
+ Color[] scores = new Color[al.annotations.length];
+ int i = 0;
+ for (Annotation an : al.annotations)
+ {
+ scores[i++] = (an != null) ? an.colour : Color.white;
+ }
+ seqMap.put(al.sequenceRef, scores);
+ }
+ }
// TODO: compute average colour for each symbol type in each column - gives
// a second order colourscheme for colouring a sequence logo derived from
// the alignment (colour reflects quality of alignment for each residue
// class)
- }
- @Override
- public Color findColour(char c, int j, SequenceI seq) {
- Color[] cols;
+ }
+
+ @Override
+ public Color findColour(char c, int j, SequenceI seq)
+ {
+ Color[] cols;
+
+ if (seqMap == null || (cols = seqMap.get(seq)) == null)
+ {
+ // see above TODO about computing a colour for each residue in each
+ // column: cc = _rcols[i][indexFor[c]];
+ return Color.white;
+ }
+
+ if (j < 0 || j >= cols.length)
+ {
+ return Color.white;
+ }
+ return cols[j];
+ }
- if( seqMap==null || (cols=seqMap.get(seq))==null) {
-// see above TODO about computing a colour for each residue in each column: cc = _rcols[i][indexFor[c]];
- return Color.white;
- }
-
- if( j < 0 || j>= cols.length ) {
- return Color.white;
- }
- return cols[j];
- }
+ @Override
+ public ColourSchemeI applyTo(AnnotatedCollectionI sg,
+ Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
+ {
+ return new TCoffeeColourScheme(sg);
+ }
}
git://source.jalview.org / jalview.git / blobdiff