Merge branch 'releases/Release_2_11_3_Branch'

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

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 6903034..8875288 100644 (file)
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -20,8 +20,6 @@
  */
 package jalview.gui;
 
-import java.util.Locale;
-
 import java.awt.BorderLayout;
 import java.awt.Color;
 import java.awt.event.ActionEvent;
@@ -34,6 +32,7 @@ import java.util.Collections;
 import java.util.Hashtable;
 import java.util.LinkedHashMap;
 import java.util.List;
+import java.util.Locale;
 import java.util.Map;
 import java.util.Objects;
 import java.util.SortedMap;
@@ -907,6 +906,7 @@ 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);
@@ -1735,10 +1735,8 @@ 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);
+    AlignmentUtils.addReferenceAnnotations(candidates, alignment, null);
     refresh();
   }
 
@@ -1836,6 +1834,7 @@ 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
@@ -1987,15 +1986,10 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
             MessageManager.getString("label.group_description"));
     dialog.showDialog(ap.alignFrame,
             MessageManager.getString("label.edit_group_name_description"),
-            new Runnable()
-            {
-              @Override
-              public void run()
-              {
-                sg.setName(dialog.getName());
-                sg.setDescription(dialog.getDescription());
-                refresh();
-              }
+            () -> {
+              sg.setName(dialog.getName());
+              sg.setDescription(dialog.getDescription());
+              refresh();
             });
   }
 
@@ -2027,30 +2021,30 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
             sequence.getDescription(),
             MessageManager.getString("label.sequence_name"),
             MessageManager.getString("label.sequence_description"));
-    dialog.showDialog(ap.alignFrame, MessageManager.getString(
-            "label.edit_sequence_name_description"), new Runnable()
-            {
-              @Override
-              public void run()
+    dialog.showDialog(ap.alignFrame, MessageManager
+            .getString("label.edit_sequence_name_description"), () -> {
+              if (dialog.getName() != null)
               {
-                if (dialog.getName() != null)
+                if (dialog.getName().indexOf(" ") > -1)
                 {
-                  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);
-                  }
-                  sequence.setName(dialog.getName().replace(' ', '_'));
-                  ap.paintAlignment(false, false);
+                  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.setDescription(dialog.getDescription());
-                ap.av.firePropertyChange("alignment", null,
-                        ap.av.getAlignment().getSequences());
+                sequence.setName(dialog.getName().replace(' ', '_'));
+                ap.paintAlignment(false, false);
               }
+              sequence.setDescription(dialog.getDescription());
+              ap.av.firePropertyChange("alignment", null,
+                      ap.av.getAlignment().getSequences());
             });
   }
 
@@ -2196,7 +2190,8 @@ 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
 
@@ -2272,25 +2267,19 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
               seq.getSequenceAsString(sg.getStartRes(), sg.getEndRes() + 1),
               null, MessageManager.getString("label.edit_sequence"), null);
       dialog.showDialog(ap.alignFrame,
-              MessageManager.getString("label.edit_sequence"),
-              new Runnable()
-              {
-                @Override
-                public void run()
-                {
-                  EditCommand editCommand = new EditCommand(
-                          MessageManager.getString("label.edit_sequences"),
-                          Action.REPLACE,
-                          dialog.getName().replace(' ',
-                                  ap.av.getGapCharacter()),
-                          sg.getSequencesAsArray(
-                                  ap.av.getHiddenRepSequences()),
-                          sg.getStartRes(), sg.getEndRes() + 1,
-                          ap.av.getAlignment());
-                  ap.alignFrame.addHistoryItem(editCommand);
-                  ap.av.firePropertyChange("alignment", null,
-                          ap.av.getAlignment().getSequences());
-                }
+              MessageManager.getString("label.edit_sequence"), () -> {
+                EditCommand editCommand = new EditCommand(
+                        MessageManager.getString("label.edit_sequences"),
+                        Action.REPLACE,
+                        dialog.getName().replace(' ',
+                                ap.av.getGapCharacter()),
+                        sg.getSequencesAsArray(
+                                ap.av.getHiddenRepSequences()),
+                        sg.getStartRes(), sg.getEndRes() + 1,
+                        ap.av.getAlignment());
+                ap.alignFrame.addHistoryItem(editCommand);
+                ap.av.firePropertyChange("alignment", null,
+                        ap.av.getAlignment().getSequences());
               });
     }
   }