X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FTCoffeeColourScheme.java;h=48c52f1c2c6a664d6727cd10a574c1f3e29cdf20;hb=31a33833640b743a506f7801388b17f96e915ef3;hp=38d1200f9e68304b5fe12b0bcedc035da2de1696;hpb=50eb1f492f5c64b56594ee49be8183fab8a2f73b;p=jalview.git
diff --git a/src/jalview/schemes/TCoffeeColourScheme.java b/src/jalview/schemes/TCoffeeColourScheme.java
index 38d1200..48c52f1 100644
--- a/src/jalview/schemes/TCoffeeColourScheme.java
+++ b/src/jalview/schemes/TCoffeeColourScheme.java
@@ -1,19 +1,21 @@
/*
- * 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 .
+ * 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;
@@ -85,8 +87,10 @@ public class TCoffeeColourScheme extends ResidueColourScheme
// 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();
int w = 0;
- for (AlignmentAnnotation al : alignment
+ for (AlignmentAnnotation al : alcontext
.findAnnotation(TCoffeeScoreFile.TCOFFEE_SCORE))
{
if (al.sequenceRef != null && !al.belowAlignment)
@@ -129,7 +133,7 @@ public class TCoffeeColourScheme extends ResidueColourScheme
}
return cols[j];
}
-
+
@Override
public ColourSchemeI applyTo(AnnotatedCollectionI sg,
Map hiddenRepSequences)