X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=660c651d4cab518002b306b5442c59b5a5e92e3e;hb=a5ab6cce3a64d41c3f91ba49f5e4d9536a2b0018;hp=310266e9a4c214eeb90cd42133c8e8b74dc73ae4;hpb=06ce849ffedc7ab10a3c54cda96b9a7dec58c136;p=jalview.git

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 310266e..660c651 100644
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -43,11 +43,10 @@ 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;
 import jalview.schemes.PIDColourScheme;
-import jalview.schemes.ResidueColourScheme;
 import jalview.util.GroupUrlLink;
 import jalview.util.GroupUrlLink.UrlStringTooLongException;
 import jalview.util.MessageManager;
@@ -413,7 +412,6 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
 
         add(menuItem);
       }
-
     }
 
     SequenceGroup sg = ap.av.getSelectionGroup();
@@ -425,7 +423,9 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
       groupName.setText(MessageManager
               .getString("label.edit_name_and_description_current_group"));
 
-      ColourMenuHelper.setColourSelected(colourMenu, sg.cs);
+      ColourMenuHelper.setColourSelected(colourMenu, sg.getColourScheme());
+
+      conservationMenuItem.setEnabled(!sg.isNucleotide());
 
       if (sg.cs != null)
       {
@@ -1177,12 +1177,7 @@ 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);
@@ -1260,7 +1255,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        abovePIDColour_actionPerformed();
+        abovePIDColour_actionPerformed(abovePIDColour.isSelected());
       }
     });
 
@@ -1282,7 +1277,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        conservationMenuItem_actionPerformed();
+        conservationMenuItem_actionPerformed(conservationMenuItem
+                .isSelected());
       }
     });
 
@@ -1527,10 +1523,12 @@ 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)
@@ -1538,14 +1536,14 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
       return;
     }
 
-    boolean selected = abovePIDColour.isSelected();
     if (selected)
     {
       sg.cs.setConsensus(AAFrequency.calculate(
               sg.getSequences(ap.av.getHiddenRepSequences()),
               sg.getStartRes(), sg.getEndRes() + 1));
 
-      int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
+      int threshold = SliderPanel.setPIDSliderSource(ap,
+              sg.getGroupColourScheme(), getGroup()
               .getName());
 
       sg.cs.setThreshold(threshold, ap.av.isIgnoreGapsConsensus());
@@ -1581,7 +1579,7 @@ 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)
@@ -1589,7 +1587,6 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
       return;
     }
 
-    boolean selected = conservationMenuItem.isSelected();
     if (selected)
     {
       // JBPNote: Conservation name shouldn't be i18n translated
@@ -1599,10 +1596,10 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
 
       c.calculate();
       c.verdict(false, ap.av.getConsPercGaps());
-
       sg.cs.setConservation(c);
 
-      SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
+      SliderPanel.setConservationSlider(ap, sg.getGroupColourScheme(),
+              sg.getName());
       SliderPanel.showConservationSlider();
     }
     else
@@ -1616,24 +1613,6 @@ 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.cs = acg;
-
-    refresh();
-  }
-
   /**
    * DOCUMENT ME!
    * 
@@ -1997,32 +1976,26 @@ 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)
   {
     SequenceGroup sg = getGroup();
-    if (ResidueColourScheme.USER_DEFINED.equals(colourSchemeName))
-    {
-      /*
-       * open a panel to load or configure a user-defined colour scheme
-       */
-      new UserDefinedColours(ap, sg);
-    }
-    else
+    /*
+     * switch to the chosen colour scheme (or null for None)
+     */
+    ColourSchemeI colourScheme = ColourSchemes.getInstance()
+            .getColourScheme(colourSchemeName, sg,
+                    ap.av.getHiddenRepSequences());
+    sg.setColourScheme(colourScheme);
+    if (colourScheme instanceof Blosum62ColourScheme
+            || colourScheme instanceof PIDColourScheme)
     {
-      /*
-       * switch to the chosen colour scheme (or null for None)
-       */
-      sg.cs = ColourSchemes.getInstance().getColourScheme(colourSchemeName,
-              sg, ap.av.getHiddenRepSequences());
-      if (sg.cs instanceof Blosum62ColourScheme
-              || sg.cs instanceof PIDColourScheme)
-      {
-        sg.cs.setConsensus(AAFrequency.calculate(
-                sg.getSequences(ap.av.getHiddenRepSequences()),
-                sg.getStartRes(), sg.getEndRes() + 1));
-      }
+      sg.cs.setConsensus(AAFrequency.calculate(
+              sg.getSequences(ap.av.getHiddenRepSequences()),
+              sg.getStartRes(), sg.getEndRes() + 1));
     }
 
     refresh();