update author list in license for (JAL-826)

[jalview.git] / src / jalview / io / AlignFile.java

diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java
index 3f43582..a4fb830 100755 (executable)
--- a/src/jalview/io/AlignFile.java
+++ b/src/jalview/io/AlignFile.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -127,7 +127,17 @@ public abstract class AlignFile extends FileParse
     addProperties(al);
     for (int i = 0; i < annotations.size(); i++)
     {
-      al.addAnnotation((AlignmentAnnotation) annotations.elementAt(i));
+      // detect if annotations.elementAt(i) rna secondary structure
+      // if so then do:
+      /*
+       * SequenceFeature[] pairArray =
+       * Rna.GetBasePairsFromAlignmentAnnotation(annotations.elementAt(i));
+       * Rna.HelixMap(pairArray);
+       */
+      AlignmentAnnotation an = (AlignmentAnnotation) annotations
+              .elementAt(i);
+      an.validateRangeAndDisplay();
+      al.addAnnotation(an);
     }
 
   }