X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=94b38ed656a678d8d05b3c7d2d6f201d7f959da8;hb=daae26d77ca41f38972dfcada536e95bdfb5c753;hp=e08fce5e9740dea7efb1592b338f001915c4fd36;hpb=948bd3bcbacc509da0cefaae3eedd97300a6ccce;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index e08fce5..94b38ed 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -1828,7 +1828,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   protected void copy_actionPerformed(ActionEvent e)
   {
-    System.gc();
     if (viewport.getSelectionGroup() == null)
     {
       return;
@@ -3261,6 +3260,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                 alignPanel.setOverviewPanel(null);
               };
             });
+    if (getKeyListeners().length > 0)
+    {
+      frame.addKeyListener(getKeyListeners()[0]);
+    }
 
     alignPanel.setOverviewPanel(overview);
   }
@@ -4461,17 +4464,21 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             int assocfiles = 0;
             if (filesmatched.size() > 0)
             {
-              if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
-                      || JvOptionPane.showConfirmDialog(thisaf,
-                              MessageManager.formatMessage(
-                                      "label.automatically_associate_structure_files_with_sequences_same_name",
-                                      new Object[]
-                                      { Integer.valueOf(filesmatched.size())
-                                              .toString() }),
-                              MessageManager.getString(
-                                      "label.automatically_associate_structure_files_by_name"),
-                              JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION)
-
+              boolean autoAssociate = Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false);
+              if (!autoAssociate)
+              {
+                String msg = MessageManager.formatMessage(
+                        "label.automatically_associate_structure_files_with_sequences_same_name",
+                        new Object[]
+                        { Integer.valueOf(filesmatched.size())
+                                .toString() });
+                String ttl = MessageManager.getString(
+                        "label.automatically_associate_structure_files_by_name");
+                int choice = JvOptionPane.showConfirmDialog(thisaf, msg,
+                        ttl, JvOptionPane.YES_NO_OPTION);
+                autoAssociate = choice == JvOptionPane.YES_OPTION;
+              }
+              if (autoAssociate)
               {
                 for (Object[] fm : filesmatched)
                 {
@@ -4497,6 +4504,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                   alignPanel.paintAlignment(true, false);
                 }
               }
+              else
+              {
+                /*
+                 * add declined structures as sequences
+                 */
+                for (Object[] o : filesmatched)
+                {
+                  filesnotmatched.add((String) o[0]);
+                }
+              }
             }
             if (filesnotmatched.size() > 0)
             {
@@ -5288,6 +5305,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   {
     if (avc.createGroup())
     {
+      if (applyAutoAnnotationSettings.isSelected())
+      {
+        alignPanel.updateAnnotation(true, false);
+      }
       alignPanel.alignmentChanged();
     }
   }