X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=1c7be464b88154657ea2c65f1fb8c33ec8061cc7;hb=03496bf88fc1bec3ce628ac79ce69440ce244007;hp=175adeaef9f78a89741cc0e205de229df98c556a;hpb=d305e02d8b425bb501141ad32142aeb8572adc57;p=jalview.git

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 175adea..1c7be46 100644
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -22,8 +22,6 @@ package jalview.gui;
 
 import jalview.analysis.AAFrequency;
 import jalview.analysis.AlignmentAnnotationUtils;
-import jalview.analysis.AnnotationSorter;
-import jalview.analysis.AnnotationSorter.SortOrder;
 import jalview.analysis.Conservation;
 import jalview.commands.ChangeCaseCommand;
 import jalview.commands.EditCommand;
@@ -1901,11 +1899,6 @@ public class PopupMenu extends JPopupMenu
         copyAnn.visible = true;
       }
     }
-    // TODO: save annotation sort order on AlignViewport
-    // do sorting from AlignmentPanel.updateAnnotation()
-    new AnnotationSorter(this.ap.getAlignment()).sort(this.ap
-            .getAlignment().getAlignmentAnnotation(),
-            SortOrder.SEQUENCE_AND_TYPE);
     refresh();
   }
 
@@ -2573,7 +2566,8 @@ public class PopupMenu extends JPopupMenu
       String choice = chooser.getSelectedFile().getPath();
       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
       new AssociatePdbFileWithSeq().associatePdbWithSeq(choice,
-              jalview.io.AppletFormatAdapter.FILE, sequence, true);
+              jalview.io.AppletFormatAdapter.FILE, sequence, true,
+              Desktop.instance);
     }
 
   }