Merge branch 'features/JAL-2360colourSchemeApplicability' into features/JAL-2371colle...

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

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index ac2fbc2..37cd8b3 100644 (file)
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -45,6 +45,7 @@ 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;
@@ -87,8 +88,12 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
 
   protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();
 
+  protected JMenuItem modifyPID = new JMenuItem();
+
   protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
 
+  protected JMenuItem modifyConservation = new JMenuItem();
+
   AlignmentPanel ap;
 
   JMenu sequenceMenu = new JMenu();
@@ -421,7 +426,7 @@ 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());
 
       if (sg.cs != null)
       {
@@ -434,6 +439,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
           abovePIDColour.setSelected(true);
         }
       }
+      modifyConservation.setEnabled(conservationMenuItem.isSelected());
+      modifyPID.setEnabled(abovePIDColour.isSelected());
       displayNonconserved.setSelected(sg.getShowNonconserved());
       showText.setSelected(sg.getDisplayText());
       showColourText.setSelected(sg.getColourText());
@@ -557,8 +564,6 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
 
   }
 
-
-
   /**
    * Add annotation types to 'Show annotations' and/or 'Hide annotations' menus.
    * "All" is added first, followed by a separator. Then add any annotation
@@ -982,6 +987,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
         sequenceSelectionDetails_actionPerformed();
       }
     });
+
     unGroupMenuItem
             .setText(MessageManager.getString("action.remove_group"));
     unGroupMenuItem.addActionListener(new ActionListener()
@@ -1231,7 +1237,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
     jMenu1.add(outline);
     jMenu1.add(displayNonconserved);
   }
-
+  
   /**
    * Constructs the entries for the colour menu
    */
@@ -1247,6 +1253,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
         textColour_actionPerformed();
       }
     });
+
     abovePIDColour.setText(MessageManager
             .getString("label.above_identity_threshold"));
     abovePIDColour.addActionListener(new ActionListener()
@@ -1254,7 +1261,18 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        abovePIDColour_actionPerformed();
+        abovePIDColour_actionPerformed(abovePIDColour.isSelected());
+      }
+    });
+
+    modifyPID.setText(MessageManager
+            .getString("label.modify_identity_threshold"));
+    modifyPID.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        modifyPID_actionPerformed();
       }
     });
 
@@ -1265,7 +1283,19 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        conservationMenuItem_actionPerformed();
+        conservationMenuItem_actionPerformed(conservationMenuItem
+                .isSelected());
+      }
+    });
+
+    modifyConservation.setText(MessageManager
+            .getString("label.modify_conservation_threshold"));
+    modifyConservation.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        modifyConservation_actionPerformed();
       }
     });
   }
@@ -1292,7 +1322,33 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
 
     colourMenu.addSeparator();
     colourMenu.add(conservationMenuItem);
+    colourMenu.add(modifyConservation);
     colourMenu.add(abovePIDColour);
+    colourMenu.add(modifyPID);
+  }
+
+  protected void modifyConservation_actionPerformed()
+  {
+    SequenceGroup sg = getGroup();
+    if (sg.cs != null)
+    {
+      SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
+      SliderPanel.showConservationSlider();
+    }
+  }
+
+  protected void modifyPID_actionPerformed()
+  {
+    SequenceGroup sg = getGroup();
+    if (sg.cs != null)
+    {
+      // int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
+      // .getName());
+      // sg.cs.setThreshold(threshold, ap.av.isIgnoreGapsConsensus());
+      SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
+              .getName());
+      SliderPanel.showPIDSlider();
+    }
   }
 
   /**
@@ -1473,10 +1529,12 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
   /**
    * DOCUMENT ME!
    * 
+   * @param selected
+   * 
    * @param e
    *          DOCUMENT ME!
    */
-  protected void abovePIDColour_actionPerformed()
+  protected void abovePIDColour_actionPerformed(boolean selected)
   {
     SequenceGroup sg = getGroup();
     if (sg.cs == null)
@@ -1484,13 +1542,14 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
       return;
     }
 
-    if (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());
@@ -1501,7 +1560,9 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
     // remove PIDColouring
     {
       sg.cs.setThreshold(0, ap.av.isIgnoreGapsConsensus());
+      SliderPanel.hidePIDSlider();
     }
+    modifyPID.setEnabled(selected);
 
     refresh();
   }
@@ -1524,7 +1585,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
    * @param e
    *          DOCUMENT ME!
    */
-  protected void conservationMenuItem_actionPerformed()
+  protected void conservationMenuItem_actionPerformed(boolean selected)
   {
     SequenceGroup sg = getGroup();
     if (sg.cs == null)
@@ -1532,7 +1593,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
       return;
     }
 
-    if (conservationMenuItem.isSelected())
+    if (selected)
     {
       // JBPNote: Conservation name shouldn't be i18n translated
       Conservation c = new Conservation("Group", sg.getSequences(ap.av
@@ -1541,17 +1602,19 @@ 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
     // remove ConservationColouring
     {
       sg.cs.setConservation(null);
+      SliderPanel.hideConservationSlider();
     }
+    modifyConservation.setEnabled(selected);
 
     refresh();
   }
@@ -1569,7 +1632,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
             AnnotationColourGradient.NO_THRESHOLD);
 
     acg.setPredefinedColours(true);
-    sg.cs = acg;
+    sg.setColourScheme(acg);
 
     refresh();
   }
@@ -1937,6 +2000,8 @@ 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)
@@ -1954,10 +2019,11 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
       /*
        * 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)
+      ColourSchemeI colourScheme = ColourSchemes.getInstance().getColourScheme(
+              colourSchemeName, sg, ap.av.getHiddenRepSequences());
+      sg.setColourScheme(colourScheme);
+      if (colourScheme instanceof Blosum62ColourScheme
+              || colourScheme instanceof PIDColourScheme)
       {
         sg.cs.setConsensus(AAFrequency.calculate(
                 sg.getSequences(ap.av.getHiddenRepSequences()),