X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fschemes%2FTCoffeeColourScheme.java;h=db85cc842445951459e9a5166ec5e63a6f6694f1;hb=155a17a423e980849fd4dc5f857da1a72b0010b9;hp=47aebd1eb832a44cb1d3ffd6a4144d3656536ca7;hpb=516ce4f35f75fe4775f3299742b2f453ae7d21fe;p=jalview.git
diff --git a/src/jalview/schemes/TCoffeeColourScheme.java b/src/jalview/schemes/TCoffeeColourScheme.java
index 47aebd1..db85cc8 100644
--- a/src/jalview/schemes/TCoffeeColourScheme.java
+++ b/src/jalview/schemes/TCoffeeColourScheme.java
@@ -1,89 +1,181 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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 .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.schemes;
-import jalview.analysis.SequenceIdMatcher;
+import jalview.api.AlignViewportI;
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.List;
+import java.util.Map;
/**
- * Defines the color score for T-Coffee MSA
+ * Defines the color score for T-Coffee MSA
*
* See http://tcoffee.org
*
*
* @author Paolo Di Tommaso
- *
+ *
*/
-public class TCoffeeColourScheme extends ResidueColourScheme {
+public class TCoffeeColourScheme extends ResidueColourScheme
+{
+ IdentityHashMap seqMap;
+
+ /**
+ * Default constructor (required for Class.newInstance())
+ */
+ public TCoffeeColourScheme()
+ {
+
+ }
+
+ /**
+ * 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);
+ }
+
+ /**
+ * Finds the TCoffeeScore annotation (if any) for each sequence and notes the
+ * annotation colour for each column position. The colours are fixed for
+ * scores 0-9 and are set when annotation is parsed.
+ *
+ * @see TCoffeeScoreFile#annotateAlignment(AlignmentI, boolean)
+ */
+ @Override
+ public void alignmentChanged(AnnotatedCollectionI alignment,
+ Map 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.
+ List annots = new ArrayList<>();
+ // Search alignment to get all tcoffee annotation and pick one set of
+ // annotation to use to colour seqs.
+ seqMap = new IdentityHashMap<>();
+ AnnotatedCollectionI alcontext = alignment instanceof AlignmentI
+ ? alignment
+ : alignment.getContext();
+ if (alcontext == null)
+ {
+ return;
+ }
+ 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)
+ {
+ if (seqMap == null)
+ {
+ return Color.WHITE;
+ }
+ Color[] cols = seqMap.get(seq);
+ if (cols == 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];
+ }
- 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
- };
+ @Override
+ public ColourSchemeI getInstance(AlignViewportI view,
+ AnnotatedCollectionI sg)
+ {
+ return new TCoffeeColourScheme(sg);
+ }
+ /**
+ * Answers true if the data has TCoffee score annotation
+ */
+ @Override
+ public boolean isApplicableTo(AnnotatedCollectionI ac)
+ {
+ AnnotatedCollectionI alcontext = ac instanceof AlignmentI ? ac
+ : ac.getContext();
+ if (alcontext == null)
+ {
+ return false;
+ }
+ Iterable anns = alcontext
+ .findAnnotation(TCoffeeScoreFile.TCOFFEE_SCORE);
+ return anns.iterator().hasNext();
+ }
- IdentityHashMap 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 annots = new ArrayList();
- // Search alignment to get all tcoffee annotation and pick one set of annotation to use to colour seqs.
- seqMap = new IdentityHashMap();
- int w=0;
- for (AlignmentAnnotation al:alignment.findAnnotation(TCoffeeScoreFile.TCOFFEE_SCORE))
- {
- if (al.sequenceRef!=null && !al.belowAlignment)
- {
- annots.add(al);
- if (w= cols.length ) {
- return Color.white;
- }
- return cols[j];
- }
+ @Override
+ public boolean isSimple()
+ {
+ return false;
+ }
}