merge

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

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index fee47e5..7491aa1 100644 (file)
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -176,12 +176,6 @@ public class PopupMenu extends JPopupMenu
 
   JMenu pdbMenu = new JMenu();
 
-  JMenuItem pdbFromFile = new JMenuItem();
-
-  JMenuItem enterPDB = new JMenuItem();
-
-  JMenuItem discoverPDB = new JMenuItem();
-
   JMenu outputMenu = new JMenu();
 
   JMenu seqShowAnnotationsMenu = new JMenu();
@@ -642,7 +636,7 @@ public class PopupMenu extends JPopupMenu
 
           // collect matching db-refs
           DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(
-                  seq.getDBRef(), new String[] { urlLink.getTarget() });
+                  seq.getDBRefs(), new String[] { urlLink.getTarget() });
           // collect id string too
           String id = seq.getName();
           String descr = seq.getDescription();
@@ -896,7 +890,7 @@ public class PopupMenu extends JPopupMenu
       {
         sqi = sqi.getDatasetSequence();
       }
-      DBRefEntry[] dbr = sqi.getDBRef();
+      DBRefEntry[] dbr = sqi.getDBRefs();
       if (dbr != null && dbr.length > 0)
       {
         for (int d = 0; d < dbr.length; d++)
@@ -1284,36 +1278,6 @@ public class PopupMenu extends JPopupMenu
         changeCase(e);
       }
     });
-    pdbMenu.setText(MessageManager
-            .getString("label.associate_structure_with_sequence"));
-    pdbFromFile.setText(MessageManager.getString("label.from_file"));
-    pdbFromFile.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        pdbFromFile_actionPerformed();
-      }
-    });
-
-    enterPDB.setText(MessageManager.getString("label.enter_pdb_id"));
-    enterPDB.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        enterPDB_actionPerformed();
-      }
-    });
-    discoverPDB.setText(MessageManager.getString("label.discover_pdb_ids"));
-    discoverPDB.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        discoverPDB_actionPerformed();
-      }
-    });
     outputMenu.setText(MessageManager.getString("label.out_to_textbox")
             + "...");
     seqShowAnnotationsMenu.setText(MessageManager
@@ -1483,13 +1447,10 @@ public class PopupMenu extends JPopupMenu
     editMenu.add(upperCase);
     editMenu.add(lowerCase);
     editMenu.add(toggle);
-    pdbMenu.add(pdbFromFile);
     // JBPNote: These shouldn't be added here - should appear in a generic
     // 'apply web service to this sequence menu'
     // pdbMenu.add(RNAFold);
     // pdbMenu.add(ContraFold);
-    pdbMenu.add(enterPDB);
-    pdbMenu.add(discoverPDB);
     jMenu1.add(groupName);
     jMenu1.add(colourMenu);
     jMenu1.add(showBoxes);
@@ -2451,9 +2412,13 @@ public class PopupMenu extends JPopupMenu
       @Override
       public void run()
       {
+        boolean isNuclueotide = ap.alignFrame.getViewport().getAlignment()
+                .isNucleotide();
 
-        new jalview.ws.DBRefFetcher(sequences, ap.alignFrame)
+        new jalview.ws.DBRefFetcher(sequences, ap.alignFrame, null,
+                ap.alignFrame.featureSettings, isNuclueotide)
                 .fetchDBRefs(false);
+
       }
 
     });