X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFormatAdapter.java;h=31751f5c8fd34a5d39236f9aa50b5a9983902897;hb=48a66195bf4aee8b2c479d3bbbf4c1fb8b824f5a;hp=7647a16aa8f53cf3ad24d77b98b443a7b9bff085;hpb=720039fe28c2222e9a6872f93454e7ea1a86839a;p=jalview.git

diff --git a/src/jalview/io/FormatAdapter.java b/src/jalview/io/FormatAdapter.java
index 7647a16..31751f5 100755
--- a/src/jalview/io/FormatAdapter.java
+++ b/src/jalview/io/FormatAdapter.java
@@ -20,7 +20,9 @@
  */
 package jalview.io;
 
-import jalview.api.AlignExportSettingI;
+import java.util.Locale;
+
+import jalview.api.AlignExportSettingsI;
 import jalview.api.AlignmentViewPanel;
 import jalview.bin.Cache;
 import jalview.datamodel.Alignment;
@@ -32,6 +34,7 @@ import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.util.Comparison;
 
+import java.io.File;
 import java.io.IOException;
 
 /**
@@ -55,7 +58,7 @@ public class FormatAdapter extends AppletFormatAdapter
   }
 
   public FormatAdapter(AlignmentViewPanel alignPanel,
-          AlignExportSettingI settings)
+          AlignExportSettingsI settings)
   {
     super(alignPanel, settings);
   }
@@ -161,7 +164,7 @@ public class FormatAdapter extends AppletFormatAdapter
 
   public boolean getCacheSuffixDefault(FileFormatI format)
   {
-    return Cache.getDefault(format.getName().toUpperCase() + "_JVSUFFIX",
+    return Cache.getDefault(format.getName().toUpperCase(Locale.ROOT) + "_JVSUFFIX",
             true);
   }
 
@@ -212,12 +215,12 @@ 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);
         }
@@ -235,6 +238,13 @@ public class FormatAdapter extends AppletFormatAdapter
     return al;
   }
 
+  public AlignmentI readFile(File file, DataSourceType sourceType,
+          FileFormatI fileFormat) throws IOException
+  {
+    AlignmentI al = super.readFile(file, null, sourceType, fileFormat);
+    return al;
+  }
+
   @Override
   public AlignmentI readFromFile(FileParse source, FileFormatI format)
           throws IOException