JAL-2383 restore PID colour threshold from project; enable/disable

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

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index e36204c..3a99f9e 100644 (file)
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -110,8 +110,6 @@ public class PopupMenu extends JPopupMenu
 
   protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
 
-  protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();
-
   protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
 
   protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
@@ -124,8 +122,14 @@ public class PopupMenu extends JPopupMenu
 
   JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
 
+  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();
@@ -258,7 +262,7 @@ public class PopupMenu extends JPopupMenu
     {
       JMenuItem item = new JMenuItem(ff);
 
-      item.addActionListener(new java.awt.event.ActionListener()
+      item.addActionListener(new ActionListener()
       {
         @Override
         public void actionPerformed(ActionEvent e)
@@ -342,7 +346,7 @@ public class PopupMenu extends JPopupMenu
               menuItem.setText(MessageManager.formatMessage(
                       "label.2d_rna_structure_line",
                       new Object[] { aa.label }));
-              menuItem.addActionListener(new java.awt.event.ActionListener()
+              menuItem.addActionListener(new ActionListener()
               {
                 @Override
                 public void actionPerformed(ActionEvent e)
@@ -370,7 +374,7 @@ public class PopupMenu extends JPopupMenu
               menuItem.setText(MessageManager.formatMessage(
                       "label.2d_rna_sequence_name",
                       new Object[] { seq.getName() }));
-              menuItem.addActionListener(new java.awt.event.ActionListener()
+              menuItem.addActionListener(new ActionListener()
               {
                 @Override
                 public void actionPerformed(ActionEvent e)
@@ -391,7 +395,7 @@ public class PopupMenu extends JPopupMenu
 
       menuItem = new JMenuItem(
               MessageManager.getString("action.hide_sequences"));
-      menuItem.addActionListener(new java.awt.event.ActionListener()
+      menuItem.addActionListener(new ActionListener()
       {
         @Override
         public void actionPerformed(ActionEvent e)
@@ -407,7 +411,7 @@ public class PopupMenu extends JPopupMenu
         menuItem = new JMenuItem(MessageManager.formatMessage(
                 "label.represent_group_with",
                 new Object[] { seq.getName() }));
-        menuItem.addActionListener(new java.awt.event.ActionListener()
+        menuItem.addActionListener(new ActionListener()
         {
           @Override
           public void actionPerformed(ActionEvent e)
@@ -538,13 +542,15 @@ public class PopupMenu extends JPopupMenu
       {
         if (sg.cs.conservationApplied())
         {
-        conservationMenuItem.setSelected(true);
+          conservationMenuItem.setSelected(true);
         }
         if (sg.cs.getThreshold() > 0)
         {
           abovePIDColour.setSelected(true);
         }
       }
+      modifyConservation.setEnabled(conservationMenuItem.isSelected());
+      modifyPID.setEnabled(abovePIDColour.isSelected());
       displayNonconserved.setSelected(sg.getShowNonconserved());
       showText.setSelected(sg.getDisplayText());
       showColourText.setSelected(sg.getColourText());
@@ -668,8 +674,6 @@ public class PopupMenu extends JPopupMenu
 
   }
 
-
-
   /**
    * Add annotation types to 'Show annotations' and/or 'Hide annotations' menus.
    * "All" is added first, followed by a separator. Then add any annotation
@@ -785,7 +789,7 @@ public class PopupMenu extends JPopupMenu
     label = label.substring(1, label.length() - 1); // a, b, c
     final JMenuItem item = new JMenuItem(label);
     item.setToolTipText(calcId);
-    item.addActionListener(new java.awt.event.ActionListener()
+    item.addActionListener(new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
@@ -967,7 +971,7 @@ public class PopupMenu extends JPopupMenu
     JMenuItem item = new JMenuItem(label);
     item.setToolTipText(MessageManager.formatMessage(
             "label.open_url_param", new Object[] { url }));
-    item.addActionListener(new java.awt.event.ActionListener()
+    item.addActionListener(new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
@@ -1044,7 +1048,7 @@ public class PopupMenu extends JPopupMenu
   {
     groupMenu.setText(MessageManager.getString("label.selection"));
     groupName.setText(MessageManager.getString("label.name"));
-    groupName.addActionListener(new java.awt.event.ActionListener()
+    groupName.addActionListener(new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
@@ -1055,7 +1059,7 @@ public class PopupMenu extends JPopupMenu
     sequenceMenu.setText(MessageManager.getString("label.sequence"));
     sequenceName.setText(MessageManager
             .getString("label.edit_name_description"));
-    sequenceName.addActionListener(new java.awt.event.ActionListener()
+    sequenceName.addActionListener(new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
@@ -1065,7 +1069,7 @@ public class PopupMenu extends JPopupMenu
     });
     chooseAnnotations.setText(MessageManager
             .getString("action.choose_annotations"));
-    chooseAnnotations.addActionListener(new java.awt.event.ActionListener()
+    chooseAnnotations.addActionListener(new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
@@ -1075,7 +1079,7 @@ public class PopupMenu extends JPopupMenu
     });
     sequenceDetails.setText(MessageManager
             .getString("label.sequence_details"));
-    sequenceDetails.addActionListener(new java.awt.event.ActionListener()
+    sequenceDetails.addActionListener(new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
@@ -1085,19 +1089,18 @@ public class PopupMenu extends JPopupMenu
     });
     sequenceSelDetails.setText(MessageManager
             .getString("label.sequence_details"));
-    sequenceSelDetails
-            .addActionListener(new java.awt.event.ActionListener()
-            {
-              @Override
-              public void actionPerformed(ActionEvent e)
-              {
-                sequenceSelectionDetails_actionPerformed();
-              }
-            });
+    sequenceSelDetails.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        sequenceSelectionDetails_actionPerformed();
+      }
+    });
     PIDColour.setFocusPainted(false);
     unGroupMenuItem
             .setText(MessageManager.getString("action.remove_group"));
-    unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
+    unGroupMenuItem.addActionListener(new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
@@ -1107,18 +1110,17 @@ public class PopupMenu extends JPopupMenu
     });
     createGroupMenuItem.setText(MessageManager
             .getString("action.create_group"));
-    createGroupMenuItem
-            .addActionListener(new java.awt.event.ActionListener()
-            {
-              @Override
-              public void actionPerformed(ActionEvent e)
-              {
-                createGroupMenuItem_actionPerformed();
-              }
-            });
+    createGroupMenuItem.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        createGroupMenuItem_actionPerformed();
+      }
+    });
 
     outline.setText(MessageManager.getString("action.border_colour"));
-    outline.addActionListener(new java.awt.event.ActionListener()
+    outline.addActionListener(new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
@@ -1385,7 +1387,9 @@ public class PopupMenu extends JPopupMenu
 
     colourMenu.addSeparator();
     colourMenu.add(abovePIDColour);
+    colourMenu.add(modifyPID);
     colourMenu.add(conservationMenuItem);
+    colourMenu.add(modifyConservation);
     editMenu.add(copy);
     editMenu.add(cut);
     editMenu.add(editSequence);
@@ -1404,7 +1408,7 @@ public class PopupMenu extends JPopupMenu
     jMenu1.add(outline);
     jMenu1.add(displayNonconserved);
     noColourmenuItem.setText(MessageManager.getString("label.none"));
-    noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
+    noColourmenuItem.addActionListener(new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
@@ -1415,7 +1419,7 @@ public class PopupMenu extends JPopupMenu
 
     clustalColour.setText(MessageManager
             .getString("label.clustalx_colours"));
-    clustalColour.addActionListener(new java.awt.event.ActionListener()
+    clustalColour.addActionListener(new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
@@ -1424,7 +1428,7 @@ public class PopupMenu extends JPopupMenu
       }
     });
     zappoColour.setText(MessageManager.getString("label.zappo"));
-    zappoColour.addActionListener(new java.awt.event.ActionListener()
+    zappoColour.addActionListener(new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
@@ -1433,7 +1437,7 @@ public class PopupMenu extends JPopupMenu
       }
     });
     taylorColour.setText(MessageManager.getString("label.taylor"));
-    taylorColour.addActionListener(new java.awt.event.ActionListener()
+    taylorColour.addActionListener(new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
@@ -1443,17 +1447,16 @@ public class PopupMenu extends JPopupMenu
     });
     hydrophobicityColour.setText(MessageManager
             .getString("label.hydrophobicity"));
-    hydrophobicityColour
-            .addActionListener(new java.awt.event.ActionListener()
-            {
-              @Override
-              public void actionPerformed(ActionEvent e)
-              {
-                hydrophobicityColour_actionPerformed();
-              }
-            });
+    hydrophobicityColour.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        hydrophobicityColour_actionPerformed();
+      }
+    });
     helixColour.setText(MessageManager.getString("label.helix_propensity"));
-    helixColour.addActionListener(new java.awt.event.ActionListener()
+    helixColour.addActionListener(new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
@@ -1463,7 +1466,7 @@ public class PopupMenu extends JPopupMenu
     });
     strandColour.setText(MessageManager
             .getString("label.strand_propensity"));
-    strandColour.addActionListener(new java.awt.event.ActionListener()
+    strandColour.addActionListener(new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
@@ -1472,7 +1475,7 @@ public class PopupMenu extends JPopupMenu
       }
     });
     turnColour.setText(MessageManager.getString("label.turn_propensity"));
-    turnColour.addActionListener(new java.awt.event.ActionListener()
+    turnColour.addActionListener(new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
@@ -1481,7 +1484,7 @@ public class PopupMenu extends JPopupMenu
       }
     });
     buriedColour.setText(MessageManager.getString("label.buried_index"));
-    buriedColour.addActionListener(new java.awt.event.ActionListener()
+    buriedColour.addActionListener(new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
@@ -1489,19 +1492,9 @@ public class PopupMenu extends JPopupMenu
         buriedColour_actionPerformed();
       }
     });
-    abovePIDColour.setText(MessageManager
-            .getString("label.above_identity_percentage"));
-    abovePIDColour.addActionListener(new java.awt.event.ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        abovePIDColour_actionPerformed();
-      }
-    });
     userDefinedColour.setText(MessageManager
             .getString("action.user_defined"));
-    userDefinedColour.addActionListener(new java.awt.event.ActionListener()
+    userDefinedColour.addActionListener(new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
@@ -1511,7 +1504,7 @@ public class PopupMenu extends JPopupMenu
     });
     PIDColour
             .setText(MessageManager.getString("label.percentage_identity"));
-    PIDColour.addActionListener(new java.awt.event.ActionListener()
+    PIDColour.addActionListener(new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
@@ -1520,7 +1513,7 @@ public class PopupMenu extends JPopupMenu
       }
     });
     BLOSUM62Colour.setText(MessageManager.getString("label.blosum62"));
-    BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
+    BLOSUM62Colour.addActionListener(new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
@@ -1530,33 +1523,87 @@ public class PopupMenu extends JPopupMenu
     });
     purinePyrimidineColour.setText(MessageManager
             .getString("label.purine_pyrimidine"));
-    purinePyrimidineColour
-            .addActionListener(new java.awt.event.ActionListener()
-            {
-              @Override
-              public void actionPerformed(ActionEvent e)
-              {
-                purinePyrimidineColour_actionPerformed();
-              }
-            });
+    purinePyrimidineColour.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        purinePyrimidineColour_actionPerformed();
+      }
+    });
 
     /*
-     * covariationColour.addActionListener(new java.awt.event.ActionListener() {
+     * covariationColour.addActionListener(new ActionListener() {
      * public void actionPerformed(ActionEvent e) {
      * covariationColour_actionPerformed(); } });
      */
+    abovePIDColour.setText(MessageManager
+            .getString("label.above_identity_percentage"));
+    abovePIDColour.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        abovePIDColour_actionPerformed();
+      }
+    });
+
+    modifyPID.setText(MessageManager
+            .getString("label.modify_identity_threshold"));
+    modifyPID.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        modifyPID_actionPerformed();
+      }
+    });
 
     conservationMenuItem.setText(MessageManager
             .getString("label.conservation"));
-    conservationMenuItem
-            .addActionListener(new java.awt.event.ActionListener()
-            {
-              @Override
-              public void actionPerformed(ActionEvent e)
-              {
-                conservationMenuItem_actionPerformed();
-              }
-            });
+    conservationMenuItem.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        conservationMenuItem_actionPerformed();
+      }
+    });
+
+    modifyConservation.setText(MessageManager
+            .getString("label.modify_conservation_threshold"));
+    modifyConservation.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        modifyConservation_actionPerformed();
+      }
+    });
+  }
+
+  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();
+    }
   }
 
   /**
@@ -1863,7 +1910,8 @@ public class PopupMenu extends JPopupMenu
       return;
     }
 
-    if (abovePIDColour.isSelected())
+    boolean selected = abovePIDColour.isSelected();
+    if (selected)
     {
       sg.cs.setConsensus(AAFrequency.calculate(
               sg.getSequences(ap.av.getHiddenRepSequences()),
@@ -1880,7 +1928,9 @@ public class PopupMenu extends JPopupMenu
     // remove PIDColouring
     {
       sg.cs.setThreshold(0, ap.av.isIgnoreGapsConsensus());
+      SliderPanel.hidePIDSlider();
     }
+    modifyPID.setEnabled(selected);
 
     refresh();
   }
@@ -1982,7 +2032,8 @@ public class PopupMenu extends JPopupMenu
       return;
     }
 
-    if (conservationMenuItem.isSelected())
+    boolean selected = conservationMenuItem.isSelected();
+    if (selected)
     {
       // JBPNote: Conservation name shouldn't be i18n translated
       Conservation c = new Conservation("Group", sg.getSequences(ap.av
@@ -2001,7 +2052,9 @@ public class PopupMenu extends JPopupMenu
     // remove ConservationColouring
     {
       sg.cs.setConservation(null);
+      SliderPanel.hideConservationSlider();
     }
+    modifyConservation.setEnabled(selected);
 
     refresh();
   }