Merge commit 'alpha/update_2_12_for_2_11_2_series_merge^2' into HEAD

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

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 6b32efa..49542db 100644 (file)
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -66,11 +66,13 @@ import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.MappedFeatures;
 import jalview.datamodel.PDBEntry;
+import jalview.datamodel.ResidueCount;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.gui.ColourMenuHelper.ColourChangeListener;
 import jalview.gui.JalviewColourChooser.ColourChooserListener;
+import jalview.io.CountReader;
 import jalview.io.FileFormatI;
 import jalview.io.FileFormats;
 import jalview.io.FormatAdapter;
@@ -89,6 +91,9 @@ import jalview.util.StringUtils;
 import jalview.util.UrlLink;
 import jalview.viewmodel.seqfeatures.FeatureRendererModel;
 
+import java.io.IOException;
+import java.net.MalformedURLException;
+
 /**
  * The popup menu that is displayed on right-click on a sequence id, or in the
  * sequence alignment.
@@ -303,7 +308,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
       jalview.util.BrowserLauncher.openURL(url);
     } catch (Exception ex)
     {
-      JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+      JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
               MessageManager.getString("label.web_browser_not_found_unix"),
               MessageManager.getString("label.web_browser_not_found"),
               JvOptionPane.WARNING_MESSAGE);
@@ -547,6 +552,36 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
         }
       }
 
+      if (seq.hasHMMProfile())
+      {
+        menuItem = new JMenuItem(MessageManager
+                .getString("action.add_background_frequencies"));
+        menuItem.addActionListener(new ActionListener()
+        {
+          @Override
+          public void actionPerformed(ActionEvent e)
+          {
+            try
+            {
+              ResidueCount counts = CountReader.getBackgroundFrequencies(ap,
+                      seq);
+              if (counts != null)
+              {
+                seq.getHMM().setBackgroundFrequencies(counts);
+                ap.alignFrame.buildColourMenu();
+              }
+            } catch (MalformedURLException e1)
+            {
+              e1.printStackTrace();
+            } catch (IOException e1)
+            {
+              e1.printStackTrace();
+            }
+          }
+        });
+        add(menuItem);
+      }
+
       menuItem = new JMenuItem(
               MessageManager.getString("action.hide_sequences"));
       menuItem.addActionListener(new ActionListener()
@@ -671,7 +706,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
         buildGroupURLMenu(sg, groupLinks);
       }
       // Add a 'show all structures' for the current selection
-      Hashtable<String, PDBEntry> pdbe = new Hashtable<>(), reppdb = new Hashtable<>();
+      Hashtable<String, PDBEntry> pdbe = new Hashtable<>();
+      Hashtable<String, PDBEntry> reppdb = new Hashtable<>();
 
       SequenceI sqass = null;
       for (SequenceI sq : alignPanel.av.getSequenceSelection())
@@ -1701,7 +1737,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
       menuItem.setEnabled(true);
       for (String calcId : tipEntries.keySet())
       {
-        tooltip.append("<br/>" + calcId + "/" + tipEntries.get(calcId));
+        tooltip.append("<br>" + calcId + "/" + tipEntries.get(calcId));
       }
       String tooltipText = JvSwingUtils.wrapTooltip(true,
               tooltip.toString());
@@ -2042,8 +2078,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
                   ap.paintAlignment(false, false);
                 }
                 sequence.setDescription(dialog.getDescription());
-                ap.av.firePropertyChange("alignment", null,
-                        ap.av.getAlignment().getSequences());
+                ap.av.notifyAlignment();
               }
             });
   }
@@ -2085,7 +2120,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
         refresh();
       }
     };
-    JalviewColourChooser.showColourChooser(Desktop.getDesktop(),
+    JalviewColourChooser.showColourChooser(Desktop.getDesktopPane(),
             title, Color.BLUE, listener);
   }
 
@@ -2174,9 +2209,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
               startEnd, caseChange);
 
       ap.alignFrame.addHistoryItem(caseCommand);
+      ap.av.notifyAlignment();
 
-      ap.av.firePropertyChange("alignment", null,
-              ap.av.getAlignment().getSequences());
 
     }
   }
@@ -2283,8 +2317,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
                           sg.getStartRes(), sg.getEndRes() + 1,
                           ap.av.getAlignment());
                   ap.alignFrame.addHistoryItem(editCommand);
-                  ap.av.firePropertyChange("alignment", null,
-                          ap.av.getAlignment().getSequences());
+                  ap.av.notifyAlignment();
                 }
               });
     }