From b0e1b14e744426d4dbd682805aa8f3f2d5747e53 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Thu, 10 Nov 2005 11:05:24 +0000
Subject: [PATCH] PDB implementation updated

---
 src/jalview/gui/PopupMenu.java |   66 ++++++++++++++--------------------------
 1 file changed, 22 insertions(+), 44 deletions(-)

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 6055230..b9d379c 100755
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -63,7 +63,6 @@ public class PopupMenu extends JPopupMenu
     JMenuItem sequenceName = new JMenuItem();
     Sequence sequence;
     JMenuItem unGroupMenuItem = new JMenuItem();
-    JMenuItem pdbMenuItem = new JMenuItem();
     JMenuItem outline = new JMenuItem();
     JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem();
     JMenu colourMenu = new JMenu();
@@ -77,7 +76,7 @@ public class PopupMenu extends JPopupMenu
      * @param ap DOCUMENT ME!
      * @param seq DOCUMENT ME!
      */
-    public PopupMenu(AlignmentPanel ap, Sequence seq)
+    public PopupMenu(final AlignmentPanel ap, Sequence seq)
     {
         ///////////////////////////////////////////////////////////
         // If this is activated from the sequence panel, the user may want to
@@ -112,9 +111,27 @@ public class PopupMenu extends JPopupMenu
             e.printStackTrace();
         }
 
-        if ((seq == null) || (seq.getPDBId() == null))
+
+        if ((seq != null)
+            && seq.getDatasetSequence().getPDBId() != null)
         {
-            pdbMenuItem.setVisible(false);
+          java.util.Enumeration e = seq.getDatasetSequence().getPDBId().elements();
+          while(e.hasMoreElements())
+          {
+
+            final PDBEntry pdb = (PDBEntry)e.nextElement();
+            JMenuItem pdbMenuItem = new JMenuItem();
+            pdbMenuItem.setText("View PDB entry: "+pdb.getId());
+            pdbMenuItem.addActionListener(new java.awt.event.ActionListener()
+            {
+                public void actionPerformed(ActionEvent e)
+                {
+                  PDBViewer viewer = new PDBViewer(pdb, sequence, ap.seqPanel.seqCanvas);
+                }
+            });
+            sequenceMenu.add(pdbMenuItem);
+          }
+
         }
 
         SequenceGroup sg = ap.av.getSelectionGroup();
@@ -261,14 +278,7 @@ public class PopupMenu extends JPopupMenu
                     unGroupMenuItem_actionPerformed(e);
                 }
             });
-        pdbMenuItem.setText("View PDB structure");
-        pdbMenuItem.addActionListener(new java.awt.event.ActionListener()
-            {
-                public void actionPerformed(ActionEvent e)
-                {
-                    pdbMenuItem_actionPerformed(e);
-                }
-            });
+
         outline.setText("Border colour");
         outline.addActionListener(new java.awt.event.ActionListener()
             {
@@ -325,7 +335,6 @@ public class PopupMenu extends JPopupMenu
         groupMenu.addSeparator();
         groupMenu.add(outline);
         sequenceMenu.add(sequenceName);
-        sequenceMenu.add(pdbMenuItem);
         colourMenu.add(noColourmenuItem);
         colourMenu.add(clustalColour);
         colourMenu.add(BLOSUM62Colour);
@@ -830,37 +839,6 @@ public class PopupMenu extends JPopupMenu
         refresh();
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    void pdbMenuItem_actionPerformed(ActionEvent e)
-    {
-        if (sequence.getPDBId() == null)
-        {
-            return;
-        }
-
-        try
-        {
-            EBIFetchClient ebi = new EBIFetchClient();
-            String[] result = ebi.fetchData("pdb:" + sequence.getPDBId(), null,
-                    null);
-
-            PDBfile pdb = new PDBfile(result);
-
-            rotCanvas rc = new rotCanvas(pdb, sequence, ap.av);
-            JInternalFrame frame = new JInternalFrame();
-            frame.setContentPane(rc);
-            Desktop.addInternalFrame(frame,
-                sequence.getName() + " " + sequence.getPDBId(), 400, 400);
-        }
-        catch (Exception ex)
-        {
-            ex.printStackTrace();
-        }
-    }
 
     /**
      * DOCUMENT ME!
-- 
1.7.10.2