/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
*/
package jalview.schemes;
-import jalview.analysis.SequenceIdMatcher;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AnnotatedCollectionI;
import java.util.ArrayList;
import java.util.IdentityHashMap;
import java.util.Map;
-import java.util.TreeMap;
/**
* Defines the color score for T-Coffee MSA
public class TCoffeeColourScheme extends ResidueColourScheme
{
- static final Color[] colors =
- { new Color(102, 102, 255), // #6666FF
+ 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
// 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();
+ AnnotatedCollectionI alcontext = alignment instanceof AlignmentI ? alignment
+ : alignment.getContext();
int w = 0;
for (AlignmentAnnotation al : alcontext
.findAnnotation(TCoffeeScoreFile.TCOFFEE_SCORE))
}
return cols[j];
}
-
+
@Override
public ColourSchemeI applyTo(AnnotatedCollectionI sg,
Map<SequenceI, SequenceCollectionI> hiddenRepSequences)