JAL-629 implementation of --tempfac options

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

diff --git a/src/jalview/io/FormatAdapter.java b/src/jalview/io/FormatAdapter.java
index 735619f..0ca2b50 100755 (executable)
--- a/src/jalview/io/FormatAdapter.java
+++ b/src/jalview/io/FormatAdapter.java
@@ -20,6 +20,8 @@
  */
 package jalview.io;
 
+import java.io.File;
+import java.io.IOException;
 import java.util.Locale;
 
 import jalview.api.AlignExportSettingsI;
@@ -27,6 +29,7 @@ import jalview.api.AlignmentViewPanel;
 import jalview.bin.Cache;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentAnnotation.TFType;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.Sequence;
@@ -34,9 +37,6 @@ import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.util.Comparison;
 
-import java.io.File;
-import java.io.IOException;
-
 /**
  * Additional formatting methods used by the application in a number of places.
  * 
@@ -228,6 +228,16 @@ public class FormatAdapter extends AppletFormatAdapter
   }
 
   @Override
+  public AlignmentI readFile(File selectedFile, String file,
+          DataSourceType sourceType, FileFormatI fileFormat,
+          AlignmentAnnotation.TFType tempfacType) throws IOException
+  {
+    AlignmentI al = super.readFile(selectedFile, file, sourceType,
+            fileFormat, tempfacType);
+    return al;
+  }
+
+  @Override
   public AlignmentI readFile(String file, DataSourceType sourceType,
           FileFormatI fileFormat) throws IOException
   {