Merge branch 'develop' into update_212_Dec_merge_with_21125_chamges

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

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 2fd5180..3c32180 100644 (file)
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -20,6 +20,8 @@
  */
 package jalview.gui;
 
+import java.util.Locale;
+
 import java.awt.BorderLayout;
 import java.awt.Color;
 import java.awt.event.ActionEvent;
@@ -54,7 +56,7 @@ import jalview.analysis.AlignmentAnnotationUtils;
 import jalview.analysis.AlignmentUtils;
 import jalview.analysis.Conservation;
 import jalview.api.AlignViewportI;
-import jalview.bin.Cache;
+import jalview.bin.Console;
 import jalview.commands.ChangeCaseCommand;
 import jalview.commands.EditCommand;
 import jalview.commands.EditCommand.Action;
@@ -91,7 +93,6 @@ 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.
@@ -233,13 +234,13 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
         urlLink = new UrlLink(link);
       } catch (Exception foo)
       {
-        Cache.log.error("Exception for URLLink '" + link + "'", foo);
+        Console.error("Exception for URLLink '" + link + "'", foo);
         continue;
       }
 
       if (!urlLink.isValid())
       {
-        Cache.log.error(urlLink.getInvalidMessage());
+        Console.error(urlLink.getInvalidMessage());
         continue;
       }
 
@@ -306,7 +307,7 @@ 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);
@@ -579,7 +580,6 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
         });
         add(menuItem);
       }
-
       menuItem = new JMenuItem(
               MessageManager.getString("action.hide_sequences"));
       menuItem.addActionListener(new ActionListener()
@@ -703,6 +703,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
       {
         buildGroupURLMenu(sg, groupLinks);
       }
+      // TODO REMOVE FOR 2.12 ?
       // Add a 'show all structures' for the current selection
       Hashtable<String, PDBEntry> pdbe = new Hashtable<>();
       Hashtable<String, PDBEntry> reppdb = new Hashtable<>();
@@ -873,10 +874,14 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
       /*
        * show local rather than linked feature coordinates
        */
-      int[] beginRange = mf.getMappedPositions(start, start);
-      start = beginRange[0];
-      int[] endRange = mf.getMappedPositions(end, end);
-      end = endRange[endRange.length - 1];
+      int[] localRange = mf.getMappedPositions(start, end);
+      if (localRange == null)
+      {
+        // e.g. variant extending to stop codon so not mappable
+        return;
+      }
+      start = localRange[0];
+      end = localRange[localRange.length - 1];
     }
     StringBuilder desc = new StringBuilder();
     desc.append(sf.getType()).append(" ").append(String.valueOf(start));
@@ -1161,7 +1166,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
         for (int d = 0; d < nd; d++)
         {
           DBRefEntry e = dbr.get(d);
-          String src = e.getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase();
+          String src = e.getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase(Locale.ROOT);
           Object[] sarray = commonDbrefs.get(src);
           if (sarray == null)
           {
@@ -1195,19 +1200,19 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
         urlLink = new GroupUrlLink(link);
       } catch (Exception foo)
       {
-        Cache.log.error("Exception for GroupURLLink '" + link + "'", foo);
+        Console.error("Exception for GroupURLLink '" + link + "'", foo);
         continue;
       }
       if (!urlLink.isValid())
       {
-        Cache.log.error(urlLink.getInvalidMessage());
+        Console.error(urlLink.getInvalidMessage());
         continue;
       }
       final String label = urlLink.getLabel();
       boolean usingNames = false;
       // Now see which parts of the group apply for this URL
       String ltarget = urlLink.getTarget(); // jalview.util.DBRefUtils.getCanonicalName(urlLink.getTarget());
-      Object[] idset = commonDbrefs.get(ltarget.toUpperCase());
+      Object[] idset = commonDbrefs.get(ltarget.toUpperCase(Locale.ROOT));
       String[] seqstr, ids; // input to makeUrl
       if (idset != null)
       {
@@ -1843,7 +1848,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
       contents.append("<p><h2>" + MessageManager.formatMessage(
               "label.create_sequence_details_report_annotation_for",
               new Object[]
-              { seq.getDisplayId(true) }) + "</h2></p><p>");
+              { seq.getDisplayId(true) }) + "</h2></p>\n<p>");
       new SequenceAnnotationReport(false).createSequenceAnnotationReport(
               contents, seq, true, true, ap.getSeqPanel().seqCanvas.fr);
       contents.append("</p>");
@@ -2076,8 +2081,7 @@ 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();
               }
             });
   }
@@ -2119,7 +2123,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
         refresh();
       }
     };
-    JalviewColourChooser.showColourChooser(Desktop.getDesktop(),
+    JalviewColourChooser.showColourChooser(Desktop.getDesktopPane(),
             title, Color.BLUE, listener);
   }
 
@@ -2208,9 +2212,8 @@ 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());
 
     }
   }
@@ -2317,8 +2320,7 @@ 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();
                 }
               });
     }