From 284dc3090d93f4b149b38bb5106d93eb1a4ae7b2 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Thu, 27 Jul 2006 10:29:45 +0000
Subject: [PATCH] Save PDB file to disk

---
 src/MCview/PDBViewer.java |   58 +++++++++++++++++++++++++++++++++++++++++----
 1 file changed, 54 insertions(+), 4 deletions(-)

diff --git a/src/MCview/PDBViewer.java b/src/MCview/PDBViewer.java
index 69a131c..1f1f94d 100755
--- a/src/MCview/PDBViewer.java
+++ b/src/MCview/PDBViewer.java
@@ -26,12 +26,16 @@ import jalview.gui.*;
 import jalview.io.EBIFetchClient;
 import java.awt.event.ActionListener;
 import java.awt.event.ActionEvent;
+import java.io.*;
+import jalview.io.JalviewFileChooser;
+import jalview.io.JalviewFileView;
 
 public class PDBViewer extends JInternalFrame implements Runnable
 {
   PDBEntry pdb;
   Sequence sequence;
   PDBCanvas pdbcanvas;
+  String tmpPDBFile;
 
 
   public PDBViewer(PDBEntry entry,
@@ -57,7 +61,8 @@ public class PDBViewer extends JInternalFrame implements Runnable
     if(pdb.getFile()!=null)
     {
         try{
-          PDBfile pdbfile = new PDBfile(pdb.getFile(),
+          tmpPDBFile = pdb.getFile();
+          PDBfile pdbfile = new PDBfile(tmpPDBFile,
                                         jalview.io.AppletFormatAdapter.FILE);
           pdbcanvas.setPDBFile(pdbfile);
 
@@ -98,10 +103,10 @@ public class PDBViewer extends JInternalFrame implements Runnable
     {
         EBIFetchClient ebi = new EBIFetchClient();
         String query = "pdb:" + pdb.getId();
-        String file = ebi.fetchDataAsFile(query, "default", "raw").getAbsolutePath();
-        if (file != null)
+        tmpPDBFile = ebi.fetchDataAsFile(query, "default", "raw").getAbsolutePath();
+        if (tmpPDBFile != null)
         {
-          PDBfile pdbfile = new PDBfile(file, jalview.io.AppletFormatAdapter.FILE);
+          PDBfile pdbfile = new PDBfile(tmpPDBFile, jalview.io.AppletFormatAdapter.FILE);
           pdbcanvas.setPDBFile(pdbfile);
         }
         else
@@ -290,11 +295,20 @@ public class PDBViewer extends JInternalFrame implements Runnable
         background_actionPerformed(e);
       }
     });
+    savePDB.setText("PDB File");
+    savePDB.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        savePDB_actionPerformed(e);
+      }
+    });
     jMenuBar1.add(fileMenu);
     jMenuBar1.add(coloursMenu);
     jMenuBar1.add(viewMenu);
     fileMenu.add(saveMenu);
     fileMenu.add(mapping);
+    saveMenu.add(savePDB);
     saveMenu.add(png);
     saveMenu.add(eps);
     coloursMenu.add(seqButton);
@@ -404,6 +418,7 @@ public class PDBViewer extends JInternalFrame implements Runnable
   JRadioButtonMenuItem helix = new JRadioButtonMenuItem();
   JMenu viewMenu = new JMenu();
   JMenuItem background = new JMenuItem();
+  JMenuItem savePDB = new JMenuItem();
 
   /**
    * DOCUMENT ME!
@@ -605,4 +620,39 @@ public class PDBViewer extends JInternalFrame implements Runnable
          pdbcanvas.repaint();
        }
   }
+
+  public void savePDB_actionPerformed(ActionEvent e)
+  {
+    JalviewFileChooser chooser = new JalviewFileChooser(
+        jalview.bin.Cache.getProperty(
+            "LAST_DIRECTORY"));
+
+    chooser.setFileView(new JalviewFileView());
+    chooser.setDialogTitle("Save PDB File");
+    chooser.setToolTipText("Save");
+
+    int value = chooser.showSaveDialog(this);
+
+    if (value == JalviewFileChooser.APPROVE_OPTION)
+    {
+        try
+        {
+          BufferedReader in = new BufferedReader(new FileReader(tmpPDBFile));
+          File outFile = chooser.getSelectedFile();
+
+          PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
+          String data;
+          while ( (data = in.readLine()) != null)
+          {
+            if (data.indexOf("<PRE>") == -1 && data.indexOf("</PRE>") == -1)
+              out.println(data);
+          }
+          out.close();
+        }
+        catch (Exception ex)
+        {
+          ex.printStackTrace();
+        }
+      }
+  }
 }
-- 
1.7.10.2