X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FCommands.java;h=001e32ea1d977864479c3985017ba372261d4a3d;hb=71fc2ec36ecf51f66225d9b98eb475ae657bef05;hp=b42f08e6db95ec65461eb7739a1850b372be7eaf;hpb=3303ad135025ac8b36ebb95f52d113a7b7df5444;p=jalview.git

diff --git a/src/jalview/bin/Commands.java b/src/jalview/bin/Commands.java
index b42f08e..001e32e 100644
--- a/src/jalview/bin/Commands.java
+++ b/src/jalview/bin/Commands.java
@@ -77,6 +77,7 @@ public class Commands
     {
       for (String id : argParser.linkedIds())
       {
+        ArgValuesMap avm = argParser.linkedArgs(id);
         Commands cmds = new Commands();
         if (id == null)
         {
@@ -90,6 +91,17 @@ public class Commands
         }
         cmds.processImages(id);
         argsWereParsed &= cmds.wereParsed();
+
+        // close ap
+        if (avm.getBoolean(Arg.CLOSE))
+        {
+          AlignFrame af = cmds.afMap.get(id);
+          if (af != null)
+          {
+            af.closeMenuItem_actionPerformed(true);
+          }
+        }
+
       }
 
     }