JAL-2383 fixup from last merge

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

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index b0f8347..897c78c 100644 (file)
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -36,7 +36,8 @@ import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.io.AppletFormatAdapter;
 import jalview.io.DataSourceType;
-import jalview.io.FileFormat;
+import jalview.io.FileFormatI;
+import jalview.io.FileFormats;
 import jalview.io.SequenceAnnotationReport;
 import jalview.schemes.Blosum62ColourScheme;
 import jalview.schemes.BuriedColourScheme;
@@ -110,8 +111,14 @@ 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();
@@ -222,7 +229,7 @@ public class APopupMenu extends java.awt.PopupMenu implements
       e.printStackTrace();
     }
 
-    for (String ff : FileFormat.getWritableFormats(true))
+    for (String ff : FileFormats.getInstance().getWritableFormats(true))
     {
       MenuItem item = new MenuItem(ff);
 
@@ -254,6 +261,8 @@ 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);
@@ -633,6 +642,14 @@ 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();
@@ -834,7 +851,8 @@ public class APopupMenu extends java.awt.PopupMenu implements
     // now returns a full copy of sequence data
     // TODO consider using getSequenceSelection instead here
 
-    FileFormat fileFormat = FileFormat.valueOf(e.getActionCommand());
+    FileFormatI fileFormat = FileFormats.getInstance().forName(
+            e.getActionCommand());
     cap.setText(new AppletFormatAdapter().formatSequences(fileFormat,
             ap.av.getShowJVSuffix(), ap, true));
 
@@ -897,14 +915,14 @@ 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
       {
@@ -920,7 +938,7 @@ 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);
     }
@@ -940,6 +958,8 @@ 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);
@@ -995,8 +1015,10 @@ 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);
@@ -1062,9 +1084,18 @@ 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);
@@ -1195,11 +1226,11 @@ 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()
@@ -1254,9 +1285,10 @@ public class APopupMenu extends java.awt.PopupMenu implements
     else
     // remove ConservationColouring
     {
+      SliderPanel.hideConservationSlider();
       sg.cs.setConservation(null);
     }
-
+    modifyConservation.setEnabled(conservationColour.getState());
     refresh();
   }