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

[jalview.git] / src / jalview / appletgui / APopupMenu.java

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index 4eaa18a..018b227 100644 (file)
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -42,7 +42,8 @@ import jalview.io.SequenceAnnotationReport;
 import jalview.schemes.Blosum62ColourScheme;
 import jalview.schemes.BuriedColourScheme;
 import jalview.schemes.ClustalxColourScheme;
-import jalview.schemes.ColourSchemeI;
+import jalview.schemes.CollectionColourScheme;
+import jalview.schemes.CollectionColourSchemeI;
 import jalview.schemes.HelixColourScheme;
 import jalview.schemes.HydrophobicColourScheme;
 import jalview.schemes.JalviewColourScheme;
@@ -111,8 +112,14 @@ public class APopupMenu extends java.awt.PopupMenu implements
 
   protected CheckboxMenuItem abovePIDColour = new CheckboxMenuItem();
 
+  MenuItem modifyPID = new MenuItem();
+
   protected CheckboxMenuItem conservationColour = new CheckboxMenuItem();
 
+  MenuItem modifyConservation = new MenuItem();
+
+  MenuItem noColourmenuItem = new MenuItem();
+
   final AlignmentPanel ap;
 
   MenuItem unGroupMenuItem = new MenuItem();
@@ -255,6 +262,8 @@ public class APopupMenu extends java.awt.PopupMenu implements
         {
           abovePIDColour.setState(sg.cs.getThreshold() > 0);
           conservationColour.setState(sg.cs.conservationApplied());
+          modifyPID.setEnabled(abovePIDColour.getState());
+          modifyConservation.setEnabled(conservationColour.getState());
         }
       }
       setSelectedColour(sg.cs);
@@ -321,20 +330,21 @@ public class APopupMenu extends java.awt.PopupMenu implements
    * 
    * @param cs
    */
-  protected void setSelectedColour(ColourSchemeI cs)
+  protected void setSelectedColour(CollectionColourSchemeI cs)
   {
-    if (cs == null)
+    if (cs == null || cs.getColourScheme() == null)
     {
       noColour.setState(true);
     }
     else
     {
+      String name = cs.getColourScheme().getSchemeName();
       for (int i = 0; i < colourMenu.getItemCount(); i++)
       {
         MenuItem item = colourMenu.getItem(i);
         if (item instanceof CheckboxMenuItem)
         {
-          if (cs.getSchemeName().equals(item.getName()))
+          if (name.equals(item.getName()))
           {
             ((CheckboxMenuItem) item).setState(true);
           }
@@ -557,7 +567,7 @@ public class APopupMenu extends java.awt.PopupMenu implements
     {
       BLOSUM62Colour_actionPerformed();
     }
-    else if (source == PIDColour)
+    else if (evt.getSource() == PIDColour)
     {
       PIDColour_actionPerformed();
     }
@@ -634,6 +644,14 @@ public class APopupMenu extends java.awt.PopupMenu implements
     {
       userDefinedColour_actionPerformed();
     }
+    else if (source == modifyConservation)
+    {
+      conservationMenuItem_itemStateChanged();
+    }
+    else if (source == modifyPID)
+    {
+      abovePIDColour_itemStateChanged();
+    }
     else if (source == unGroupMenuItem)
     {
       unGroupMenuItem_actionPerformed();
@@ -899,14 +917,14 @@ public class APopupMenu extends java.awt.PopupMenu implements
   void addPDB()
   {
     Vector<PDBEntry> pdbs = seq.getAllPDBEntries();
-    if (pdbs != null&& !pdbs.isEmpty())
+    if (pdbs != null && !pdbs.isEmpty())
     {
       PDBEntry entry = pdbs.firstElement();
 
       if (ap.av.applet.jmolAvailable)
       {
-        new jalview.appletgui.AppletJmol(entry, new SequenceI[] { seq },
-                null, ap, DataSourceType.URL);
+        new AppletJmol(entry, new SequenceI[] { seq }, null, ap,
+                DataSourceType.URL);
       }
       else
       {
@@ -922,7 +940,7 @@ public class APopupMenu extends java.awt.PopupMenu implements
       cap.setPDBImport(seq);
       Frame frame = new Frame();
       frame.add(cap);
-      jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
+      JalviewLite.addFrame(frame, MessageManager.formatMessage(
               "label.paste_pdb_file_for_sequence",
               new Object[] { seq.getName() }), 400, 300);
     }
@@ -942,6 +960,8 @@ public class APopupMenu extends java.awt.PopupMenu implements
             .getString("action.create_group"));
     createGroupMenuItem.addActionListener(this);
 
+    modifyPID.setEnabled(abovePIDColour.getState());
+    modifyConservation.setEnabled(conservationColour.getState());
     colourMenu.setLabel(MessageManager.getString("label.group_colour"));
     showBoxes.setLabel(MessageManager.getString("action.boxes"));
     showBoxes.setState(true);
@@ -997,8 +1017,10 @@ public class APopupMenu extends java.awt.PopupMenu implements
     colourMenu.add(purinePyrimidineColour);
     colourMenu.add(userDefinedColour);
     colourMenu.addSeparator();
-    colourMenu.add(abovePIDColour);
     colourMenu.add(conservationColour);
+    colourMenu.add(modifyConservation);
+    colourMenu.add(abovePIDColour);
+    colourMenu.add(modifyPID);
 
     noColour.setLabel(MessageManager.getString("label.none"));
     noColour.addItemListener(this);
@@ -1064,9 +1086,18 @@ public class APopupMenu extends java.awt.PopupMenu implements
     abovePIDColour.setLabel(MessageManager
             .getString("label.above_identity_threshold"));
     abovePIDColour.addItemListener(this);
+    modifyPID.setLabel(MessageManager
+            .getString("label.modify_identity_threshold"));
+    modifyPID.addActionListener(this);
     conservationColour.setLabel(MessageManager
-            .getString("label.conservation"));
+            .getString("action.by_conservation"));
     conservationColour.addItemListener(this);
+    modifyConservation.setLabel(MessageManager
+            .getString("label.modify_conservation_threshold"));
+    modifyConservation.addActionListener(this);
+
+    PIDColour.addActionListener(this);
+    BLOSUM62Colour.addActionListener(this);
 
     editMenu.add(copy);
     copy.addActionListener(this);
@@ -1116,61 +1147,63 @@ public class APopupMenu extends java.awt.PopupMenu implements
   protected void clustalColour_actionPerformed()
   {
     SequenceGroup sg = getGroup();
-    sg.cs = new ClustalxColourScheme(sg, ap.av.getHiddenRepSequences());
+    sg.cs = new CollectionColourScheme(new ClustalxColourScheme(sg,
+            ap.av.getHiddenRepSequences()));
     refresh();
   }
 
   protected void zappoColour_actionPerformed()
   {
-    getGroup().cs = new ZappoColourScheme();
+    getGroup().cs = new CollectionColourScheme(new ZappoColourScheme());
     refresh();
   }
 
   protected void taylorColour_actionPerformed()
   {
-    getGroup().cs = new TaylorColourScheme();
+    getGroup().cs = new CollectionColourScheme(new TaylorColourScheme());
     refresh();
   }
 
   protected void hydrophobicityColour_actionPerformed()
   {
-    getGroup().cs = new HydrophobicColourScheme();
+    getGroup().cs = new CollectionColourScheme(new HydrophobicColourScheme());
     refresh();
   }
 
   protected void helixColour_actionPerformed()
   {
-    getGroup().cs = new HelixColourScheme();
+    getGroup().cs = new CollectionColourScheme(new HelixColourScheme());
     refresh();
   }
 
   protected void strandColour_actionPerformed()
   {
-    getGroup().cs = new StrandColourScheme();
+    getGroup().cs = new CollectionColourScheme(new StrandColourScheme());
     refresh();
   }
 
   protected void turnColour_actionPerformed()
   {
-    getGroup().cs = new TurnColourScheme();
+    getGroup().cs = new CollectionColourScheme(new TurnColourScheme());
     refresh();
   }
 
   protected void buriedColour_actionPerformed()
   {
-    getGroup().cs = new BuriedColourScheme();
+    getGroup().cs = new CollectionColourScheme(new BuriedColourScheme());
     refresh();
   }
 
   public void nucleotideMenuItem_actionPerformed()
   {
-    getGroup().cs = new NucleotideColourScheme();
+    getGroup().cs = new CollectionColourScheme(new NucleotideColourScheme());
     refresh();
   }
 
   public void purinePyrimidineColour_actionPerformed()
   {
-    getGroup().cs = new PurinePyrimidineColourScheme();
+    getGroup().cs = new CollectionColourScheme(
+            new PurinePyrimidineColourScheme());
     refresh();
   }
 
@@ -1197,11 +1230,11 @@ public class APopupMenu extends java.awt.PopupMenu implements
     else
     // remove PIDColouring
     {
+      SliderPanel.hidePIDSlider();
       sg.cs.setThreshold(0, ap.av.isIgnoreGapsConsensus());
     }
-
+    modifyPID.setEnabled(abovePIDColour.getState());
     refresh();
-
   }
 
   protected void userDefinedColour_actionPerformed()
@@ -1212,7 +1245,7 @@ public class APopupMenu extends java.awt.PopupMenu implements
   protected void PIDColour_actionPerformed()
   {
     SequenceGroup sg = getGroup();
-    sg.cs = new PIDColourScheme();
+    sg.cs = new CollectionColourScheme(new PIDColourScheme());
     sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av
             .getHiddenRepSequences()), 0, ap.av.getAlignment().getWidth()));
     refresh();
@@ -1222,7 +1255,7 @@ public class APopupMenu extends java.awt.PopupMenu implements
   {
     SequenceGroup sg = getGroup();
 
-    sg.cs = new Blosum62ColourScheme();
+    sg.cs = new CollectionColourScheme(new Blosum62ColourScheme());
 
     sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av
             .getHiddenRepSequences()), 0, ap.av.getAlignment().getWidth()));
@@ -1246,19 +1279,22 @@ public class APopupMenu extends java.awt.PopupMenu implements
 
     if (conservationColour.getState())
     {
-      sg.cs.setConservation(Conservation.calculateConservation("Group", sg
+      Conservation conservation = Conservation.calculateConservation(
+              "Group", sg
               .getSequences(ap.av.getHiddenRepSequences()), 0, ap.av
               .getAlignment().getWidth(), false, ap.av.getConsPercGaps(),
-              false));
+              false);
+      sg.getGroupColourScheme().setConservation(conservation);
       SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
       SliderPanel.showConservationSlider();
     }
     else
     // remove ConservationColouring
     {
+      SliderPanel.hideConservationSlider();
       sg.cs.setConservation(null);
     }
-
+    modifyConservation.setEnabled(conservationColour.getState());
     refresh();
   }