Merge branch 'develop' into bug/JAL-2399textColour

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

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index c94d24d..d91fa70 100644 (file)
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -43,7 +43,6 @@ import jalview.io.FileFormatI;
 import jalview.io.FileFormats;
 import jalview.io.FormatAdapter;
 import jalview.io.SequenceAnnotationReport;
-import jalview.schemes.AnnotationColourGradient;
 import jalview.schemes.Blosum62ColourScheme;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemes;
@@ -414,7 +413,6 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
 
         add(menuItem);
       }
-
     }
 
     SequenceGroup sg = ap.av.getSelectionGroup();
@@ -428,6 +426,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
 
       ColourMenuHelper.setColourSelected(colourMenu, sg.getColourScheme());
 
+      conservationMenuItem.setEnabled(!sg.isNucleotide());
+
       if (sg.cs != null)
       {
         if (sg.cs.conservationApplied())
@@ -1178,12 +1178,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
         hideInsertions_actionPerformed(e);
       }
     });
-    /*
-     * annotationMenuItem.setText("By Annotation");
-     * annotationMenuItem.addActionListener(new ActionListener() { public void
-     * actionPerformed(ActionEvent actionEvent) {
-     * annotationMenuItem_actionPerformed(actionEvent); } });
-     */
+
     groupMenu.add(sequenceSelDetails);
     add(groupMenu);
     add(sequenceMenu);
@@ -1619,24 +1614,6 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
     refresh();
   }
 
-  public void annotationMenuItem_actionPerformed(ActionEvent actionEvent)
-  {
-    SequenceGroup sg = getGroup();
-    if (sg == null)
-    {
-      return;
-    }
-
-    AnnotationColourGradient acg = new AnnotationColourGradient(
-            sequence.getAnnotation()[0], null,
-            AnnotationColourGradient.NO_THRESHOLD);
-
-    acg.setPredefinedColours(true);
-    sg.setColourScheme(acg);
-
-    refresh();
-  }
-
   /**
    * DOCUMENT ME!
    *