Merge branch 'feature/JAL-2909bamfiles_features' into features/JAL-2909_bamImport2_11

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

diff --git a/src/jalview/io/FormatAdapter.java b/src/jalview/io/FormatAdapter.java
index 7647a16..bc3a560 100755 (executable)
--- a/src/jalview/io/FormatAdapter.java
+++ b/src/jalview/io/FormatAdapter.java
@@ -212,12 +212,12 @@ public class FormatAdapter extends AppletFormatAdapter
           AlignmentAnnotation na = new AlignmentAnnotation(ala[i]);
           if (selgp != null)
           {
-            hidden.makeVisibleAnnotation(selgp.getStartRes(),
-                    selgp.getEndRes(), na);
+            na.makeVisibleAnnotation(selgp.getStartRes(), selgp.getEndRes(),
+                    hidden);
           }
           else
           {
-            hidden.makeVisibleAnnotation(na);
+            na.makeVisibleAnnotation(hidden);
           }
           alv.addAnnotation(na);
         }
@@ -266,5 +266,4 @@ public class FormatAdapter extends AppletFormatAdapter
             source.getDataSourceType());
     return readFromFile(fp, format);
   }
-
 }