X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBViewer.java;h=4c9351bdd3b678e318a206a90d2c096ad0257ac9;hb=3f9c1d052c8fe2e92ae0d7a1c3088ccb82c58ba5;hp=50a4a36cc6a6a1fd510249ae97fda2a5606a8522;hpb=c44b1974aea543db46790f6cb88f5ac0aae10a94;p=jalview.git

diff --git a/src/MCview/PDBViewer.java b/src/MCview/PDBViewer.java
index 50a4a36..4c9351b 100755
--- a/src/MCview/PDBViewer.java
+++ b/src/MCview/PDBViewer.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  *
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
@@ -26,19 +26,22 @@ 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,
                    Sequence seq,
                    SeqCanvas seqcanvas)
   {
-    /*Uncomment this to modify in Jbuilder
     try
     {
       jbInit();
@@ -46,27 +49,51 @@ public class PDBViewer extends JInternalFrame implements Runnable
     catch (Exception ex)
     {
       ex.printStackTrace();
-    }*/
+    }
 
 
+    if (entry==null)
+      return;
     pdb = entry;
     sequence = seq;
+    pdbcanvas = new PDBCanvas(seqcanvas, sequence);
+
+    if(pdb.getFile()!=null)
+    {
+        try{
+          tmpPDBFile = pdb.getFile();
+          PDBfile pdbfile = new PDBfile(tmpPDBFile,
+                                        jalview.io.AppletFormatAdapter.FILE);
+          pdbcanvas.setPDBFile(pdbfile);
+
+        }catch(java.io.IOException ex)
+        {
+          ex.printStackTrace();
+        }
+    }
+    else
+    {
+      Thread worker = new Thread(this);
+      worker.start();
+    }
 
-    Thread worker = new Thread(this);
-    worker.start();
 
-    pdbcanvas = new PDBCanvas(seqcanvas, seq);
 
     setContentPane(pdbcanvas);
     StringBuffer title = new StringBuffer(sequence.getName() + ":" + pdb.getId());
     if(pdb.getProperty()!=null)
     {
-      title.append( " Method: " );
-      title.append(pdb.getProperty().get("method"));
-      title.append( " Chain:" );
-      title.append( pdb.getProperty().get("chains"));
+      if (pdb.getProperty().get("method")!=null)
+      {
+        title.append(" Method: ");
+        title.append(pdb.getProperty().get("method"));
+      }
+      if (pdb.getProperty().get("chains") != null)
+      {
+        title.append(" Chain:");
+        title.append(pdb.getProperty().get("chains"));
+      }
     }
-
      Desktop.addInternalFrame(this,title.toString(),400, 400);
   }
 
@@ -74,25 +101,24 @@ public class PDBViewer extends JInternalFrame implements Runnable
   {
     try
     {
-      EBIFetchClient ebi = new EBIFetchClient();
-      String[] result = ebi.fetchData("pdb:" + pdb.getId(), "default","raw");
-
-      PDBfile pdbfile = new PDBfile(result);
-
-      pdbcanvas.setPDBFile(pdbfile);
-
-      try
-      {
-        jbInit();
-      }
-      catch (Exception ex)
-      {
-        ex.printStackTrace();
-      }
+        EBIFetchClient ebi = new EBIFetchClient();
+        String query = "pdb:" + pdb.getId();
+        tmpPDBFile = ebi.fetchDataAsFile(query, "default", "raw").getAbsolutePath();
+        if (tmpPDBFile != null)
+        {
+          PDBfile pdbfile = new PDBfile(tmpPDBFile, jalview.io.AppletFormatAdapter.FILE);
+          pdbcanvas.setPDBFile(pdbfile);
+        }
+        else
+        {
+          throw new Exception("Empty result for WSDbFetch Query: " + query);
+        }
     }
     catch (Exception ex)
     {
       ex.printStackTrace();
+      showErrorMessage("Failed to retrieve PDB structure.");
+//      this.dispose();
     }
   }
 
@@ -261,11 +287,28 @@ public class PDBViewer extends JInternalFrame implements Runnable
       }
     });
     viewMenu.setText("View");
+    background.setText("Background Colour...");
+    background.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        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);
@@ -279,6 +322,7 @@ public class PDBViewer extends JInternalFrame implements Runnable
     coloursMenu.add(turn);
     coloursMenu.add(buried);
     coloursMenu.add(user);
+    coloursMenu.add(background);
     ButtonGroup bg = new ButtonGroup();
     bg.add(seqButton);
     bg.add(chain);
@@ -373,6 +417,8 @@ public class PDBViewer extends JInternalFrame implements Runnable
   JRadioButtonMenuItem strand = new JRadioButtonMenuItem();
   JRadioButtonMenuItem helix = new JRadioButtonMenuItem();
   JMenu viewMenu = new JMenu();
+  JMenuItem background = new JMenuItem();
+  JMenuItem savePDB = new JMenuItem();
 
   /**
    * DOCUMENT ME!
@@ -490,6 +536,12 @@ public class PDBViewer extends JInternalFrame implements Runnable
   {
     pdbcanvas.setAllchainsVisible(allchains.getState());
   }
+  void showErrorMessage(String error)
+  {
+    JOptionPane.showInternalMessageDialog(Desktop.desktop,
+         error, "PDB Viewer Error", JOptionPane.WARNING_MESSAGE);
+  }
+
 
   public void zappo_actionPerformed(ActionEvent e)
   {
@@ -555,4 +607,54 @@ public class PDBViewer extends JInternalFrame implements Runnable
       pdbcanvas.repaint();
     }
   }
+
+  public void background_actionPerformed(ActionEvent e)
+  {
+      java.awt.Color col = JColorChooser.showDialog(this, "Select Background Colour",
+                pdbcanvas.backgroundColour);
+
+      if(col!=null)
+       {
+         pdbcanvas.backgroundColour = col;
+         pdbcanvas.redrawneeded = true;
+         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();
+        }
+      }
+  }
 }