Updated with latest from mchmmer branch

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

diff --git a/src/jalview/io/FormatAdapter.java b/src/jalview/io/FormatAdapter.java
index 3027ab1..6d3c18a 100755 (executable)
--- a/src/jalview/io/FormatAdapter.java
+++ b/src/jalview/io/FormatAdapter.java
@@ -161,7 +161,8 @@ public class FormatAdapter extends AppletFormatAdapter
 
   public boolean getCacheSuffixDefault(FileFormatI format)
   {
-    return Cache.getDefault(format.getName() + "_JVSUFFIX", true);
+    return Cache.getDefault(format.getName().toUpperCase() + "_JVSUFFIX",
+            true);
   }
 
   public String formatSequences(FileFormatI format, AlignmentI alignment,
@@ -211,12 +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);
         }