X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FTCoffeeColourScheme.java;h=48c52f1c2c6a664d6727cd10a574c1f3e29cdf20;hb=e0c1dde5b241a8ac5b8c960f1f55f0940da55788;hp=6eb48c24f0f5420fe300f112f69c26c1dfad4325;hpb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;p=jalview.git

diff --git a/src/jalview/schemes/TCoffeeColourScheme.java b/src/jalview/schemes/TCoffeeColourScheme.java
index 6eb48c2..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 <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;
@@ -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<SequenceI, Color[]>();
+    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)
@@ -129,4 +133,11 @@ public class TCoffeeColourScheme extends ResidueColourScheme
     }
     return cols[j];
   }
+
+  @Override
+  public ColourSchemeI applyTo(AnnotatedCollectionI sg,
+          Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
+  {
+    return new TCoffeeColourScheme(sg);
+  }
 }