X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=ca0fb7f24f62570bd016e6cec11d24495f441c91;hb=refs%2Fheads%2Fspike%2FJAL-4047%2FJAL-4048_columns_in_sequenceID;hp=47da7fc4f0d4ff470358d743ef40acdc4aa232f3;hpb=a79849ceb618568ed1b0ed2b400e1cf8e6d1ea81;p=jalview.git

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 47da7fc..ca0fb7f 100644
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -741,6 +741,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
     JMenu dis_cols = new JMenu(
             MessageManager.getString("action.displayed_columns"));
     final IdColumns id_cols = ap.av.getIdColumns();
+    id_cols.updateTypeList();
     for (final IdColumn col : id_cols.getIdColumns())
     {
       JMenuItem col_entry = new JCheckBoxMenuItem(col.getLabel(),
@@ -936,6 +937,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
     if (Platform.isJS())
     {
       details = new JInternalFrame();
+      details.setFrameIcon(null);
       JPanel panel = new JPanel(new BorderLayout());
       panel.setOpaque(true);
       panel.setBackground(Color.white);
@@ -1764,10 +1766,9 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
   protected void addReferenceAnnotations_actionPerformed(
           Map<SequenceI, List<AlignmentAnnotation>> candidates)
   {
-    final SequenceGroup selectionGroup = this.ap.av.getSelectionGroup();
     final AlignmentI alignment = this.ap.getAlignment();
     AlignmentUtils.addReferenceAnnotations(candidates, alignment,
-            selectionGroup);
+            null);
     refresh();
   }
 
@@ -1865,6 +1866,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
       pane.setBackground(Color.WHITE);
       pane.add(textLabel, BorderLayout.NORTH);
       frame = new JInternalFrame();
+      frame.setFrameIcon(null);
       frame.getContentPane().add(new JScrollPane(pane));
     }
     else
@@ -2020,7 +2022,6 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
               sg.setName(dialog.getName());
               sg.setDescription(dialog.getDescription());
               refresh();
-              return null;
             });
   }
 
@@ -2058,12 +2059,17 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
               {
                 if (dialog.getName().indexOf(" ") > -1)
                 {
-                  JvOptionPane.showMessageDialog(ap,
-                          MessageManager.getString(
-                                  "label.spaces_converted_to_underscores"),
-                          MessageManager.getString(
-                                  "label.no_spaces_allowed_sequence_name"),
-                          JvOptionPane.WARNING_MESSAGE);
+                  String ok = MessageManager.getString("action.ok");
+                  String cancel = MessageManager.getString("action.cancel");
+                  String message = MessageManager.getString(
+                          "label.spaces_converted_to_underscores");
+                  String title = MessageManager.getString(
+                          "label.no_spaces_allowed_sequence_name");
+                  Object[] options = new Object[] { ok, cancel };
+
+                  JvOptionPane.frameDialog(message, title,
+                          JvOptionPane.WARNING_MESSAGE, null, null, null,
+                          false);
                 }
                 sequence.setName(dialog.getName().replace(' ', '_'));
                 ap.paintAlignment(false, false);
@@ -2071,7 +2077,6 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
               sequence.setDescription(dialog.getDescription());
               ap.av.firePropertyChange("alignment", null,
                       ap.av.getAlignment().getSequences());
-              return null;
             });
   }
 
@@ -2217,7 +2222,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
 
     String[] omitHidden = null;
 
-    System.out.println("PROMPT USER HERE"); // TODO: decide if a prompt happens
+    jalview.bin.Console.outPrintln("PROMPT USER HERE"); // TODO: decide if a prompt happens
     // or we simply trust the user wants
     // wysiwig behaviour
 
@@ -2306,7 +2311,6 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
                 ap.alignFrame.addHistoryItem(editCommand);
                 ap.av.firePropertyChange("alignment", null,
                         ap.av.getAlignment().getSequences());
-                return null;
               });
     }
   }