X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=f9e0d19d262ed88f4e7bfdfba5c8f19c079c5aa4;hb=0705a85fe0a3d391e5aba360340a0c342c898366;hp=137ca1462889764105d36885e9b7eef5659900dc;hpb=95a46891288f4fc63d690cab4f56879678f54fb6;p=jalview.git

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 137ca14..f9e0d19 100755
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -24,7 +24,6 @@ import jalview.analysis.*;
 
 import jalview.datamodel.*;
 
-import jalview.io.*;
 
 import jalview.schemes.*;
 
@@ -63,7 +62,6 @@ 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 +75,7 @@ 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 +110,27 @@ 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)
+                {
+                  new PDBViewer(pdb, sequence, ap.seqPanel.seqCanvas);
+                }
+            });
+            sequenceMenu.add(pdbMenuItem);
+          }
+
         }
 
         SequenceGroup sg = ap.av.getSelectionGroup();
@@ -206,9 +222,12 @@ public class PopupMenu extends JPopupMenu
             String link = links.elementAt(i).toString();
 
             item = new JMenuItem(link.substring(0, link.indexOf("|")));
+            String id = sequence.getName();
+            if(id.indexOf("|")>-1)
+              id = id.substring(id.lastIndexOf("|")+1);
 
             final String url = link.substring(link.indexOf("|")+1, link.indexOf("$SEQUENCE_ID$"))
-                + sequence.getName() +
+                + id +
                 link.substring(link.indexOf("$SEQUENCE_ID$") + 13);
 
 
@@ -261,14 +280,7 @@ 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 +337,6 @@ 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);
@@ -494,6 +505,9 @@ public class PopupMenu extends JPopupMenu
             superG.setSuperGroupProperties(sg);
           }
         }
+        if (ap.overviewPanel != null)
+          ap.overviewPanel.updateOverviewImage();
+
         ap.seqPanel.repaint();
     }
 
@@ -606,6 +620,8 @@ public class PopupMenu extends JPopupMenu
     protected void abovePIDColour_actionPerformed(ActionEvent e)
     {
         SequenceGroup sg = getGroup();
+        if(sg.cs==null)
+          return;
 
         if (abovePIDColour.isSelected())
         {
@@ -696,6 +712,8 @@ public class PopupMenu extends JPopupMenu
     protected void conservationMenuItem_actionPerformed(ActionEvent e)
     {
         SequenceGroup sg = getGroup();
+        if(sg.cs==null)
+          return;
 
         if (conservationMenuItem.isSelected())
         {
@@ -823,37 +841,6 @@ 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!