Merge branch 'Jalview-JS/develop_j2s_v3_2_9_j11' into Jalview-JS/develop

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

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index 46bd4fd..311f1e7 100644 (file)
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -20,6 +20,25 @@
  */
 package jalview.appletgui;
 
+import java.awt.CheckboxMenuItem;
+import java.awt.Frame;
+import java.awt.Menu;
+import java.awt.MenuItem;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.SortedMap;
+import java.util.TreeMap;
+import java.util.Vector;
+
 import jalview.analysis.AAFrequency;
 import jalview.analysis.AlignmentAnnotationUtils;
 import jalview.analysis.AlignmentUtils;
@@ -57,25 +76,6 @@ import jalview.schemes.ZappoColourScheme;
 import jalview.util.MessageManager;
 import jalview.util.UrlLink;
 
-import java.awt.CheckboxMenuItem;
-import java.awt.Frame;
-import java.awt.Menu;
-import java.awt.MenuItem;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.awt.event.ItemEvent;
-import java.awt.event.ItemListener;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collection;
-import java.util.Collections;
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.SortedMap;
-import java.util.TreeMap;
-import java.util.Vector;
-
 public class APopupMenu extends java.awt.PopupMenu
         implements ActionListener, ItemListener
 {
@@ -773,8 +773,7 @@ public class APopupMenu extends java.awt.PopupMenu
 
           ap.alignFrame.addHistoryItem(editCommand);
 
-          ap.av.firePropertyChange("alignment", null,
-                  ap.av.getAlignment().getSequences());
+          ap.av.notifyAlignment();
         }
       }
     }
@@ -811,8 +810,7 @@ public class APopupMenu extends java.awt.PopupMenu
 
         ap.alignFrame.addHistoryItem(caseCommand);
 
-        ap.av.firePropertyChange("alignment", null,
-                ap.av.getAlignment().getSequences());
+        ap.av.notifyAlignment();
 
       }
     }
@@ -900,11 +898,8 @@ public class APopupMenu extends java.awt.PopupMenu
       contents.append(MessageManager
               .formatMessage("label.annotation_for_displayid", new Object[]
               { seq.getDisplayId(true) }));
-      new SequenceAnnotationReport(null).createSequenceAnnotationReport(
-              contents, seq, true, true,
-              (ap.seqPanel.seqCanvas.fr != null)
-                      ? ap.seqPanel.seqCanvas.fr.getMinMax()
-                      : null);
+      new SequenceAnnotationReport(false).createSequenceAnnotationReport(
+              contents, seq, true, true, ap.seqPanel.seqCanvas.fr);
       contents.append("</p>");
     }
     Frame frame = new Frame();
@@ -948,7 +943,7 @@ public class APopupMenu extends java.awt.PopupMenu
       }
       else
       {
-        new MCview.AppletPDBViewer(entry, new SequenceI[] { seq }, null, ap,
+        new mc_view.AppletPDBViewer(entry, new SequenceI[] { seq }, null, ap,
                 DataSourceType.URL);
       }