JAL-1499 patch from Mungo Carstairs

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

diff --git a/src/jalview/io/FormatAdapter.java b/src/jalview/io/FormatAdapter.java
old mode 100755 (executable)
new mode 100644 (file)
index 13dbb95..c57ef8d
--- a/src/jalview/io/FormatAdapter.java
+++ b/src/jalview/io/FormatAdapter.java
@@ -20,7 +20,13 @@
  */
 package jalview.io;
 
-import jalview.datamodel.*;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
 
 /**
  * Additional formatting methods used by the application in a number of places.
@@ -125,6 +131,12 @@ public class FormatAdapter extends AppletFormatAdapter
         afile.addJVSuffix(jalview.bin.Cache.getDefault("PFAM_JVSUFFIX",
                 true));
       }
+      else if (format.equalsIgnoreCase("MEGA"))
+      {
+        afile = new MegaFile();
+        afile.addJVSuffix(jalview.bin.Cache.getDefault("MEGA_JVSUFFIX",
+                true));
+      }
       /*
        * amsa is not supported by this function - it requires an alignment
        * rather than a sequence vector else if (format.equalsIgnoreCase("AMSA"))
@@ -199,7 +211,8 @@ public class FormatAdapter extends AppletFormatAdapter
     {
       // TODO consider using AlignmentView to prune to visible region
       // TODO prune sequence annotation and groups to visible region
-      // TODO: JAL-1486 - set start and end for output correctly. basically, AlignmentView.getVisibleContigs does this.
+      // TODO: JAL-1486 - set start and end for output correctly. basically,
+      // AlignmentView.getVisibleContigs does this.
       Alignment alv = new Alignment(replaceStrings(
               alignment.getSequencesArray(), omitHidden));
       AlignmentAnnotation[] ala = alignment.getAlignmentAnnotation();