JAL-3691 toUpperCase(Locale.ROOT) for all standard file format operations

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

diff --git a/src/jalview/io/FormatAdapter.java b/src/jalview/io/FormatAdapter.java
index f09e8a0..4d8794f 100755 (executable)
--- a/src/jalview/io/FormatAdapter.java
+++ b/src/jalview/io/FormatAdapter.java
@@ -33,6 +33,7 @@ import jalview.datamodel.SequenceI;
 import jalview.util.Comparison;
 
 import java.io.IOException;
+import java.util.Locale;
 
 /**
  * Additional formatting methods used by the application in a number of places.
@@ -116,8 +117,8 @@ public class FormatAdapter extends AppletFormatAdapter
           startIndex = startEnd[0];
           endIndex = startEnd[1];
           // get first non-gaped residue start position
-          while (Comparison.isGap(seqs[i]
-                  .getCharAt(startIndex)) && startIndex < endIndex)
+          while (Comparison.isGap(seqs[i].getCharAt(startIndex))
+                  && startIndex < endIndex)
           {
             startIndex++;
           }
@@ -161,7 +162,8 @@ public class FormatAdapter extends AppletFormatAdapter
 
   public boolean getCacheSuffixDefault(FileFormatI format)
   {
-    return Cache.getDefault(format.getName() + "_JVSUFFIX", true);
+    return Cache.getDefault(format.getName().toUpperCase(Locale.ROOT) + "_JVSUFFIX",
+            true);
   }
 
   public String formatSequences(FileFormatI format, AlignmentI alignment,
@@ -211,12 +213,12 @@ 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);
         }