Revert "JAL-3032 net.sf.j2s.core_3.2.1 upgrade"

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

diff --git a/src/jalview/io/FormatAdapter.java b/src/jalview/io/FormatAdapter.java
index 6a28b1d..2264a6a 100755 (executable)
--- a/src/jalview/io/FormatAdapter.java
+++ b/src/jalview/io/FormatAdapter.java
@@ -32,6 +32,7 @@ import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.util.Comparison;
 
+import java.io.File;
 import java.io.IOException;
 
 /**
@@ -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() + "_JVSUFFIX",
+            true);
   }
 
   public String formatSequences(FileFormatI format, AlignmentI alignment,
@@ -234,6 +236,13 @@ 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