From 5eedbb315e861ef49368574842d8a8788b4231b4 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Tue, 25 Jul 2006 09:37:53 +0000
Subject: [PATCH] Associate pdb files

---
 src/jalview/gui/PopupMenu.java |  119 +++++++++++++++++++++++++++++++++++++++-
 1 file changed, 118 insertions(+), 1 deletion(-)

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 6fbd0ee..018c1c2 100755
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -78,6 +78,10 @@ public class PopupMenu extends JPopupMenu
   JMenuItem lowerCase = new JMenuItem();
   JMenuItem toggle = new JMenuItem();
   JMenu outputMenu = new JMenu();
+  JMenu pdbMenu = new JMenu();
+  JMenuItem pdbFromFile = new JMenuItem();
+  JMenuItem enterPDB = new JMenuItem();
+  JMenuItem discoverPDB = new JMenuItem();
 
   /**
      * Creates a new PopupMenu object.
@@ -145,6 +149,7 @@ public class PopupMenu extends JPopupMenu
           {
             java.util.Enumeration e = seq.getDatasetSequence().getPDBId().
                 elements();
+
             while (e.hasMoreElements())
             {
               final PDBEntry pdb = (PDBEntry) e.nextElement();
@@ -312,6 +317,7 @@ public class PopupMenu extends JPopupMenu
         if (seq == null)
         {
             sequenceMenu.setVisible(false);
+            pdbMenu.setVisible(false);
         }
 
         if(links != null && links.size()>0)
@@ -476,10 +482,37 @@ public class PopupMenu extends JPopupMenu
       }
     });
     outputMenu.setText("Output to Textbox...");
+    pdbMenu.setText("Associate Structure with Sequence");
+    pdbFromFile.setText("From File");
+    pdbFromFile.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        pdbFromFile_actionPerformed(e);
+      }
+    });
+    enterPDB.setText("Enter PDB Id");
+    enterPDB.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        enterPDB_actionPerformed(e);
+      }
+    });
+    discoverPDB.setText("Discover PDB ids");
+    discoverPDB.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        discoverPDB_actionPerformed(e);
+      }
+    });
     add(groupMenu);
-        add(sequenceMenu);
+
     this.add(editMenu);
     this.add(outputMenu);
+    add(sequenceMenu);
+    this.add(pdbMenu);
     groupMenu.add(groupName);
         groupMenu.addSeparator();
         groupMenu.add(unGroupMenuItem);
@@ -534,6 +567,9 @@ public class PopupMenu extends JPopupMenu
     editMenu.add(upperCase);
     editMenu.add(lowerCase);
     editMenu.add(toggle);
+    pdbMenu.add(pdbFromFile);
+    pdbMenu.add(enterPDB);
+    pdbMenu.add(discoverPDB);
     noColourmenuItem.setText("None");
         noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
             {
@@ -1191,4 +1227,85 @@ public class PopupMenu extends JPopupMenu
         ap.av.getSelectionAsNewSequence(),
         omitHidden));
   }
+
+
+  public void pdbFromFile_actionPerformed(ActionEvent e)
+  {
+     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");
+
+     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);
+     }
+
+  }
+
+  public void enterPDB_actionPerformed(ActionEvent e)
+  {
+    int size = (ap.av.getSelectionGroup() == null ? 0 :
+                ap.av.getSelectionGroup().getSize(false));
+
+    if (size == 0 || size > 1)
+    {
+      JOptionPane.showInternalMessageDialog(
+          Desktop.desktop,
+          "Select a single sequence to specify a PDB id for first",
+          "Select Single Selected", JOptionPane.WARNING_MESSAGE);
+      return;
+    }
+
+    String id = JOptionPane.showInternalInputDialog(Desktop.desktop,
+        "Enter PDB Id", "Enter PDB Id", JOptionPane.QUESTION_MESSAGE);
+
+    if (id != null && id.length() > 0)
+    {
+      PDBEntry entry = new PDBEntry();
+      entry.setId(id);
+      ap.av.getSelectionGroup().getSequenceAt(0).getDatasetSequence()
+          .addPDBId(entry);
+    }
+  }
+
+  public void discoverPDB_actionPerformed(ActionEvent e)
+  {
+    new jalview.io.DBRefFetcher(
+             ap.av.getAlignment(), ap.alignFrame).fetchDBRefs(false);
+  }
 }
-- 
1.7.10.2