JAL-2629 add non-functional HMMER menu

[jalview.git] / src / jalview / gui / AlignFrame.java

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 9e4f37b..b14423c 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -383,6 +383,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       }
     });
     buildColourMenu();
+    buildHMMERMenu();
 
     if (Desktop.desktop != null)
     {
@@ -489,6 +490,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   }
 
+  private void buildHMMERMenu()
+  {
+    hmmerMenu.removeAll();
+
+    hmmerMenu.add(autoAlignSeqs);
+    hmmerMenu.addSeparator();
+
+    hmmerMenu.add(hmmAlign);
+    hmmerMenu.add(hmmBuild);
+    hmmerMenu.add(hmmSearch);
+    
+  }
+
   /**
    * Change the filename and format for the alignment, and enable the 'reload'
    * button functionality.
@@ -4680,6 +4694,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             newAlignment.append(getViewport().getAlignment());
             getViewport().setAlignment(newAlignment);
             isAnnotation = true;
+            alignPanel.repaint();
 
           }
           else if (FileFormat.Jnet.equals(format))