X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=e36204cfdb0c4f06ddfb72049690a4135259ca5e;hb=95ebbef7b78bf266a8252bd479510be3c80cd234;hp=6f4f3b9c4cdcaade899a8ec09370de3f1f205f92;hpb=7d67fb613ec026dc9a265e351e7fab542e3f1d61;p=jalview.git

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 6f4f3b9..e36204c 100644
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -38,8 +38,8 @@ import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
-import jalview.io.FileFormat;
 import jalview.io.FileFormatI;
+import jalview.io.FileFormats;
 import jalview.io.FormatAdapter;
 import jalview.io.SequenceAnnotationReport;
 import jalview.schemes.AnnotationColourGradient;
@@ -79,7 +79,6 @@ import javax.swing.JCheckBoxMenuItem;
 import javax.swing.JColorChooser;
 import javax.swing.JMenu;
 import javax.swing.JMenuItem;
-import javax.swing.JOptionPane;
 import javax.swing.JPopupMenu;
 import javax.swing.JRadioButtonMenuItem;
 
@@ -249,14 +248,13 @@ public class PopupMenu extends JPopupMenu
     colours.add(strandColour);
     colours.add(turnColour);
     colours.add(buriedColour);
-    colours.add(abovePIDColour);
     colours.add(userDefinedColour);
     colours.add(PIDColour);
     colours.add(BLOSUM62Colour);
     colours.add(purinePyrimidineColour);
     colours.add(RNAInteractionColour);
 
-    for (String ff : FileFormat.getWritableFormats(true))
+    for (String ff : FileFormats.getInstance().getWritableFormats(true))
     {
       JMenuItem item = new JMenuItem(ff);
 
@@ -536,9 +534,16 @@ public class PopupMenu extends JPopupMenu
         noColourmenuItem.setSelected(true);
       }
 
-      if (sg.cs != null && sg.cs.conservationApplied())
+      if (sg.cs != null)
       {
+        if (sg.cs.conservationApplied())
+        {
         conservationMenuItem.setSelected(true);
+        }
+        if (sg.cs.getThreshold() > 0)
+        {
+          abovePIDColour.setSelected(true);
+        }
       }
       displayNonconserved.setSelected(sg.getShowNonconserved());
       showText.setSelected(sg.getDisplayText());
@@ -2089,14 +2094,14 @@ public class PopupMenu extends JPopupMenu
     {
       if (dialog.getName().indexOf(" ") > -1)
       {
-        JOptionPane
+        JvOptionPane
                 .showMessageDialog(
                         ap,
                         MessageManager
                                 .getString("label.spaces_converted_to_backslashes"),
                         MessageManager
                                 .getString("label.no_spaces_allowed_sequence_name"),
-                        JOptionPane.WARNING_MESSAGE);
+                        JvOptionPane.WARNING_MESSAGE);
       }
 
       sequence.setName(dialog.getName().replace(' ', '_'));
@@ -2195,10 +2200,10 @@ public class PopupMenu extends JPopupMenu
       jalview.util.BrowserLauncher.openURL(url);
     } catch (Exception ex)
     {
-      JOptionPane.showInternalMessageDialog(Desktop.desktop,
+      JvOptionPane.showInternalMessageDialog(Desktop.desktop,
               MessageManager.getString("label.web_browser_not_found_unix"),
               MessageManager.getString("label.web_browser_not_found"),
-              JOptionPane.WARNING_MESSAGE);
+              JvOptionPane.WARNING_MESSAGE);
 
       ex.printStackTrace();
     }
@@ -2274,7 +2279,8 @@ public class PopupMenu extends JPopupMenu
     // or we simply trust the user wants
     // wysiwig behaviour
 
-    FileFormatI fileFormat = FileFormat.forName(e.getActionCommand());
+    FileFormatI fileFormat = FileFormats.getInstance().forName(
+            e.getActionCommand());
     cap.setText(new FormatAdapter(ap).formatSequences(fileFormat, ap, true));
   }