showUnconserved view and group setting

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 1feffa5..33ac298 100755 (executable)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -600,7 +600,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     annotationPanelMenuItem.setState(av.showAnnotation);
     viewBoxesMenuItem.setSelected(av.showBoxes);
     viewTextMenuItem.setSelected(av.showText);
-
+    showUnconservedMenuItem.setSelected(av.showUnconserved);
     setColourSelected(ColourSchemeProperty.getColourName(av
             .getGlobalColourScheme()));
 
@@ -3764,7 +3764,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       showProducts.removeAll();
       final boolean dna = viewport.getAlignment().isNucleotide();
       final Alignment ds = dataset;
-      String[] ptypes = CrossRef.findSequenceXrefTypes(dna, selection,
+      String[] ptypes = (selection==null || selection.length==0) ? null
+              : CrossRef.findSequenceXrefTypes(dna, selection,
               dataset);
       // Object[] prods =
       // CrossRef.buildXProductsList(viewport.getAlignment().isNucleotide(),
@@ -4332,6 +4333,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     showSeqFeatures.setSelected(true);
     viewport.setShowSequenceFeatures(true);
   }
+  /* (non-Javadoc)
+   * @see jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.awt.event.ActionEvent)
+   */
+  protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
+  {
+    viewport.setShowUnconserved(showUnconservedMenuItem.getState());
+    alignPanel.paintAlignment(true);
+  }
 }
 
 class PrintThread extends Thread