Merge branch 'develop' into bug/JAL-2431splitFrameNewView

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

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index e186145..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);
@@ -1261,7 +1256,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        abovePIDColour_actionPerformed();
+        abovePIDColour_actionPerformed(abovePIDColour.isSelected());
       }
     });
 
@@ -1283,7 +1278,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        conservationMenuItem_actionPerformed();
+        conservationMenuItem_actionPerformed(conservationMenuItem
+                .isSelected());
       }
     });
 
@@ -1528,10 +1524,12 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
   /**
    * DOCUMENT ME!
    * 
+   * @param selected
+   * 
    * @param e
    *          DOCUMENT ME!
    */
-  protected void abovePIDColour_actionPerformed()
+  public void abovePIDColour_actionPerformed(boolean selected)
   {
     SequenceGroup sg = getGroup();
     if (sg.cs == null)
@@ -1539,7 +1537,6 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
       return;
     }
 
-    boolean selected = abovePIDColour.isSelected();
     if (selected)
     {
       sg.cs.setConsensus(AAFrequency.calculate(
@@ -1583,7 +1580,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
    * @param e
    *          DOCUMENT ME!
    */
-  protected void conservationMenuItem_actionPerformed()
+  public void conservationMenuItem_actionPerformed(boolean selected)
   {
     SequenceGroup sg = getGroup();
     if (sg.cs == null)
@@ -1591,7 +1588,6 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
       return;
     }
 
-    boolean selected = conservationMenuItem.isSelected();
     if (selected)
     {
       // JBPNote: Conservation name shouldn't be i18n translated
@@ -1618,24 +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!
    * 
@@ -1999,6 +1977,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
   /**
    * Action on user selecting an item from the colour menu (that does not have
    * its bespoke action handler)
+   * 
+   * @return
    */
   @Override
   public void changeColour_actionPerformed(String colourSchemeName)