/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
+ * 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.
+ * 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/>.
+ * 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 java.awt.Color;
import java.util.ArrayList;
import java.util.IdentityHashMap;
+import java.util.List;
import java.util.Map;
-import java.util.TreeMap;
/**
* Defines the color score for T-Coffee MSA
*/
public class TCoffeeColourScheme extends ResidueColourScheme
{
+ IdentityHashMap<SequenceI, Color[]> seqMap;
- 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
- };
+ /**
+ * Default constructor (required for Class.newInstance())
+ */
+ public TCoffeeColourScheme()
+ {
- IdentityHashMap<SequenceI, Color[]> seqMap;
+ }
/**
* the color scheme needs to look at the alignment to get and cache T-COFFEE
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<SequenceI, SequenceCollectionI> hiddenReps)
// assume only one set of TCOFFEE scores - but could have more than one
// potentially.
- ArrayList<AlignmentAnnotation> annots = new ArrayList<AlignmentAnnotation>();
+ List<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();
+ if (alcontext == null)
+ {
+ return;
+ }
int w = 0;
- for (AlignmentAnnotation al : alignment
+ for (AlignmentAnnotation al : alcontext
.findAnnotation(TCoffeeScoreFile.TCOFFEE_SCORE))
{
if (al.sequenceRef != null && !al.belowAlignment)
@Override
public Color findColour(char c, int j, SequenceI seq)
{
- Color[] cols;
-
- if (seqMap == null || (cols = seqMap.get(seq)) == null)
+ 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 cols[j];
}
+
+ @Override
+ public ColourSchemeI getInstance(AnnotatedCollectionI sg,
+ Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
+ {
+ 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<AlignmentAnnotation> anns = alcontext
+ .findAnnotation(TCoffeeScoreFile.TCOFFEE_SCORE);
+ return anns.iterator().hasNext();
+ }
+
+ @Override
+ public String getSchemeName()
+ {
+ return JalviewColourScheme.TCoffee.toString();
+ }
+
+ @Override
+ public boolean isSimple()
+ {
+ return false;
+ }
}