headless warning messages, prototype group annotation and annotation update method

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index d5a98fe..131e79e 100755 (executable)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -622,6 +622,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     viewBoxesMenuItem.setSelected(av.showBoxes);
     viewTextMenuItem.setSelected(av.showText);
     showUnconservedMenuItem.setSelected(av.showUnconserved);
+    showGroupConsensus.setSelected(av.showGroupConsensus);
+    showGroupConservation.setSelected(av.showGroupConservation);
     setColourSelected(ColourSchemeProperty.getColourName(av
             .getGlobalColourScheme()));
 
@@ -893,12 +895,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     {
       if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true))
       {
-        // JBPNote need to have a raise_gui flag here
-        JOptionPane.showInternalMessageDialog(this, "Cannot save file "
+        warningMessage("Cannot save file "
                 + fileName + " using format " + format,
-                "Alignment output format not supported",
-                JOptionPane.WARNING_MESSAGE);
+                "Alignment output format not supported");
         saveAs_actionPerformed(null);
+        // JBPNote need to have a raise_gui flag here
         return false;
       }
 
@@ -959,6 +960,18 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     return success;
   }
 
+  private void warningMessage(String warning, String title)
+  {
+    if (new jalview.util.Platform().isHeadless())
+    {
+      System.err.println("Warning: "+title+"\nWarning: "+warning);
+      
+    } else {
+      JOptionPane.showInternalMessageDialog(this,warning,title,JOptionPane.WARNING_MESSAGE);
+    }
+    return;
+  }
+
   /**
    * DOCUMENT ME!
    * 
@@ -1913,6 +1926,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     viewport.sequenceColours = null;
     viewport.setSelectionGroup(null);
     PaintRefresher.Refresh(this, viewport.getSequenceSetId());
+    alignPanel.updateAnnotation();
     alignPanel.paintAlignment(true);
   }
 
@@ -4412,6 +4426,25 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     viewport.setShowUnconserved(showUnconservedMenuItem.getState());
     alignPanel.paintAlignment(true);
   }
+
+  /* (non-Javadoc)
+   * @see jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event.ActionEvent)
+   */
+  protected void showGroupConsensus_actionPerformed(ActionEvent e)
+  {
+    viewport.setShowGroupConsensus(showGroupConsensus.getState());
+    alignPanel.updateAnnotation();
+    
+  }
+
+  /* (non-Javadoc)
+   * @see jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt.event.ActionEvent)
+   */
+  protected void showGroupConservation_actionPerformed(ActionEvent e)
+  {
+    viewport.setShowGroupConservation(showGroupConservation.getState());
+    alignPanel.updateAnnotation();
+  }
 }
 
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