needed for linkedapplets_ng.html (JAL-859,JAL-469)

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

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
old mode 100755 (executable)
new mode 100644 (file)
index 94d22ef..d44ecdf
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -37,7 +37,7 @@ import jalview.util.UrlLink;
  * DOCUMENT ME!
  * 
  * @author $author$
- * @version $Revision$
+ * @version $Revision: 1.118 $
  */
 public class PopupMenu extends JPopupMenu
 {
@@ -341,7 +341,8 @@ public class PopupMenu extends JPopupMenu
 
     if (sg != null)
     {
-      groupName.setText(sg.getName());
+      groupName.setText("Name: "+sg.getName());
+      groupName.setText("Edit name and description of current group.");
 
       if (sg.cs instanceof ZappoColourScheme)
       {
@@ -1730,47 +1731,16 @@ public class PopupMenu extends JPopupMenu
     jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
     chooser.setFileView(new jalview.io.JalviewFileView());
-    chooser.setDialogTitle("Select a PDB file");
-    chooser.setToolTipText("Load a PDB file");
+    chooser.setDialogTitle("Select a PDB file for "+sequence.getDisplayId(false));
+    chooser.setToolTipText("Load a PDB file and associate it with sequence '"+sequence.getDisplayId(false)+"'");
 
     int value = chooser.showOpenDialog(null);
 
     if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
     {
-      PDBEntry entry = new PDBEntry();
       String choice = chooser.getSelectedFile().getPath();
       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
-      try
-      {
-        MCview.PDBfile pdbfile = new MCview.PDBfile(choice,
-                jalview.io.AppletFormatAdapter.FILE);
-
-        if (pdbfile.id == null)
-        {
-          String reply = JOptionPane
-                  .showInternalInputDialog(
-                          Desktop.desktop,
-                          "Couldn't find a PDB id in the file supplied."
-                                  + "Please enter an Id to identify this structure.",
-                          "No PDB Id in File", JOptionPane.QUESTION_MESSAGE);
-          if (reply == null)
-          {
-            return;
-          }
-
-          entry.setId(reply);
-        }
-        else
-        {
-          entry.setId(pdbfile.id);
-        }
-      } catch (java.io.IOException ex)
-      {
-        ex.printStackTrace();
-      }
-
-      entry.setFile(choice);
-      sequence.getDatasetSequence().addPDBId(entry);
+      new AssociatePdbFileWithSeq().associatePdbWithSeq(choice, jalview.io.AppletFormatAdapter.FILE, sequence, true);
     }
 
   }
@@ -1856,8 +1826,7 @@ public class PopupMenu extends JPopupMenu
 
   public void colourByStructure(String pdbid)
   {
-    Annotation[] anots = jalview.structure.StructureSelectionManager
-            .getStructureSelectionManager().colourSequenceFromStructure(
+    Annotation[] anots = ap.av.getStructureSelectionManager().colourSequenceFromStructure(
                     sequence, pdbid);
 
     AlignmentAnnotation an = new AlignmentAnnotation("Structure",