Associate pdb files

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 6fbd0ee..018c1c2 100755 (executable)
--- 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();\r
   JMenuItem toggle = new JMenuItem();\r
   JMenu outputMenu = new JMenu();\r
+  JMenu pdbMenu = new JMenu();\r
+  JMenuItem pdbFromFile = new JMenuItem();\r
+  JMenuItem enterPDB = new JMenuItem();\r
+  JMenuItem discoverPDB = new JMenuItem();\r
 \r
   /**\r
      * Creates a new PopupMenu object.\r
@@ -145,6 +149,7 @@ public class PopupMenu extends JPopupMenu
           {\r
             java.util.Enumeration e = seq.getDatasetSequence().getPDBId().\r
                 elements();\r
+\r
             while (e.hasMoreElements())\r
             {\r
               final PDBEntry pdb = (PDBEntry) e.nextElement();\r
@@ -312,6 +317,7 @@ public class PopupMenu extends JPopupMenu
         if (seq == null)\r
         {\r
             sequenceMenu.setVisible(false);\r
+            pdbMenu.setVisible(false);\r
         }\r
 \r
         if(links != null && links.size()>0)\r
@@ -476,10 +482,37 @@ public class PopupMenu extends JPopupMenu
       }\r
     });\r
     outputMenu.setText("Output to Textbox...");\r
+    pdbMenu.setText("Associate Structure with Sequence");\r
+    pdbFromFile.setText("From File");\r
+    pdbFromFile.addActionListener(new ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        pdbFromFile_actionPerformed(e);\r
+      }\r
+    });\r
+    enterPDB.setText("Enter PDB Id");\r
+    enterPDB.addActionListener(new ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        enterPDB_actionPerformed(e);\r
+      }\r
+    });\r
+    discoverPDB.setText("Discover PDB ids");\r
+    discoverPDB.addActionListener(new ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        discoverPDB_actionPerformed(e);\r
+      }\r
+    });\r
     add(groupMenu);\r
-        add(sequenceMenu);\r
+\r
     this.add(editMenu);\r
     this.add(outputMenu);\r
+    add(sequenceMenu);\r
+    this.add(pdbMenu);\r
     groupMenu.add(groupName);\r
         groupMenu.addSeparator();\r
         groupMenu.add(unGroupMenuItem);\r
@@ -534,6 +567,9 @@ public class PopupMenu extends JPopupMenu
     editMenu.add(upperCase);\r
     editMenu.add(lowerCase);\r
     editMenu.add(toggle);\r
+    pdbMenu.add(pdbFromFile);\r
+    pdbMenu.add(enterPDB);\r
+    pdbMenu.add(discoverPDB);\r
     noColourmenuItem.setText("None");\r
         noColourmenuItem.addActionListener(new java.awt.event.ActionListener()\r
             {\r
@@ -1191,4 +1227,85 @@ public class PopupMenu extends JPopupMenu
         ap.av.getSelectionAsNewSequence(),\r
         omitHidden));\r
   }\r
+\r
+\r
+  public void pdbFromFile_actionPerformed(ActionEvent e)\r
+  {\r
+     jalview.io.JalviewFileChooser chooser\r
+         = new jalview.io.JalviewFileChooser(jalview.bin.Cache.\r
+         getProperty(\r
+             "LAST_DIRECTORY"));\r
+     chooser.setFileView(new jalview.io.JalviewFileView());\r
+     chooser.setDialogTitle("Select a PDB file");\r
+     chooser.setToolTipText("Load a PDB file");\r
+\r
+     int value = chooser.showOpenDialog(null);\r
+\r
+     if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)\r
+     {\r
+       PDBEntry entry = new PDBEntry();\r
+       String choice = chooser.getSelectedFile().getPath();\r
+       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);\r
+       try\r
+       {\r
+         MCview.PDBfile pdbfile = new MCview.PDBfile(choice,\r
+                                       jalview.io.AppletFormatAdapter.FILE);\r
+\r
+         if (pdbfile.id == null)\r
+         {\r
+           String reply = JOptionPane.showInternalInputDialog(\r
+               Desktop.desktop,\r
+               "Couldn't find a PDB id in the file supplied."\r
+               + "Please enter an Id to identify this structure.",\r
+               "No PDB Id in File", JOptionPane.QUESTION_MESSAGE);\r
+           if (reply == null)\r
+             return;\r
+\r
+           entry.setId(reply);\r
+         }\r
+         else\r
+           entry.setId(pdbfile.id);\r
+       }\r
+       catch (java.io.IOException ex)\r
+       {\r
+         ex.printStackTrace();\r
+       }\r
+\r
+       entry.setFile(choice);\r
+       sequence.getDatasetSequence().addPDBId(entry);\r
+     }\r
+\r
+  }\r
+\r
+  public void enterPDB_actionPerformed(ActionEvent e)\r
+  {\r
+    int size = (ap.av.getSelectionGroup() == null ? 0 :\r
+                ap.av.getSelectionGroup().getSize(false));\r
+\r
+    if (size == 0 || size > 1)\r
+    {\r
+      JOptionPane.showInternalMessageDialog(\r
+          Desktop.desktop,\r
+          "Select a single sequence to specify a PDB id for first",\r
+          "Select Single Selected", JOptionPane.WARNING_MESSAGE);\r
+      return;\r
+    }\r
+\r
+    String id = JOptionPane.showInternalInputDialog(Desktop.desktop,\r
+        "Enter PDB Id", "Enter PDB Id", JOptionPane.QUESTION_MESSAGE);\r
+\r
+    if (id != null && id.length() > 0)\r
+    {\r
+      PDBEntry entry = new PDBEntry();\r
+      entry.setId(id);\r
+      ap.av.getSelectionGroup().getSequenceAt(0).getDatasetSequence()\r
+          .addPDBId(entry);\r
+    }\r
+  }\r
+\r
+  public void discoverPDB_actionPerformed(ActionEvent e)\r
+  {\r
+    new jalview.io.DBRefFetcher(\r
+             ap.av.getAlignment(), ap.alignFrame).fetchDBRefs(false);\r
+  }\r
 }\r