X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBViewer.java;h=35e02b8e4d9e79cbb6deda646eb7b96fc639f2c0;hb=29f633ca27df2db2790b81b1ca346d6692d4936c;hp=f0b37dfbfcc97028b52f96ffac2a20e00e8a93cf;hpb=2a22b216be40ead9c5a44c0d5e94ce90ccd92d03;p=jalview.git

diff --git a/src/MCview/PDBViewer.java b/src/MCview/PDBViewer.java
index f0b37df..35e02b8 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) 2007 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
@@ -18,27 +18,48 @@
  */
 package MCview;
 
-import javax.swing.*;
+import java.io.*;
+
 import java.awt.event.*;
+import javax.swing.*;
+
 import jalview.datamodel.*;
-import jalview.schemes.*;
 import jalview.gui.*;
-import jalview.io.EBIFetchClient;
-import java.awt.event.ActionListener;
-import java.awt.event.ActionEvent;
+import jalview.io.*;
+import jalview.schemes.*;
+import jalview.ws.EBIFetchClient;
+
+import java.awt.BorderLayout;
 
-public class PDBViewer extends JInternalFrame implements Runnable
+public class PDBViewer
+    extends JInternalFrame implements Runnable
 {
-  PDBEntry pdb;
-  Sequence sequence;
+
+  /**
+   * The associated sequence in an alignment
+   */
   PDBCanvas pdbcanvas;
 
+  PDBEntry pdbentry;
+  SequenceI[]seq;
+  String[]chains;
+  AlignmentPanel ap;
+  String protocol;
+  String tmpPDBFile;
+
+  public PDBViewer(PDBEntry pdbentry,
+                   SequenceI[] seq,
+                   String[] chains,
+                   AlignmentPanel ap,
+                   String protocol)
 
-  public PDBViewer(PDBEntry entry,
-                   Sequence seq,
-                   SeqCanvas seqcanvas)
   {
-    /*Uncomment this to modify in Jbuilder
+    this.pdbentry = pdbentry;
+    this.seq = seq;
+    this.chains = chains;
+    this.ap = ap;
+    this.protocol = protocol;
+
     try
     {
       jbInit();
@@ -46,34 +67,55 @@ public class PDBViewer extends JInternalFrame implements Runnable
     catch (Exception ex)
     {
       ex.printStackTrace();
-    }*/
+    }
 
-    if (entry==null)
-      return;
-    pdb = entry;
-    sequence = seq;
 
-    Thread worker = new Thread(this);
-    worker.start();
+    StringBuffer title = new StringBuffer(seq[0].getName()
+                                          + ":"
+                                          + pdbentry.getFile());
 
-    pdbcanvas = new PDBCanvas(seqcanvas, seq);
+    pdbcanvas = new PDBCanvas();
 
     setContentPane(pdbcanvas);
-    StringBuffer title = new StringBuffer(sequence.getName() + ":" + pdb.getId());
-    if(pdb.getProperty()!=null)
+
+    if (pdbentry.getFile() != null)
+    {
+      try
+      {
+        tmpPDBFile = pdbentry.getFile();
+        PDBfile pdbfile = new PDBfile(tmpPDBFile,
+                                      jalview.io.AppletFormatAdapter.FILE);
+
+        pdbcanvas.init(pdbentry, seq, chains, ap, protocol);
+
+      }
+      catch (java.io.IOException ex)
+      {
+        ex.printStackTrace();
+      }
+    }
+    else
     {
-      if (pdb.getProperty().get("method")!=null)
+      Thread worker = new Thread(this);
+      worker.start();
+    }
+
+
+
+    if (pdbentry.getProperty() != null)
+    {
+      if (pdbentry.getProperty().get("method") != null)
       {
         title.append(" Method: ");
-        title.append(pdb.getProperty().get("method"));
+        title.append(pdbentry.getProperty().get("method"));
       }
-      if (pdb.getProperty().get("chains") != null)
+      if (pdbentry.getProperty().get("chains") != null)
       {
         title.append(" Chain:");
-        title.append(pdb.getProperty().get("chains"));
+        title.append(pdbentry.getProperty().get("chains"));
       }
     }
-     Desktop.addInternalFrame(this,title.toString(),400, 400);
+    Desktop.addInternalFrame(this, title.toString(), 400, 400);
   }
 
   public void run()
@@ -81,29 +123,17 @@ public class PDBViewer extends JInternalFrame implements Runnable
     try
     {
       EBIFetchClient ebi = new EBIFetchClient();
-      String query = "pdb:" + pdb.getId();
-      String[] result = ebi.fetchData(query, "default","raw");
-      if (result!=null) {
-        PDBfile pdbfile = new PDBfile(result);
-        pdbcanvas.setPDBFile(pdbfile);
-      } else {
-        throw new Exception("Empty result for WSDbFetch Query: "+query);
-      }
+      String query = "pdb:" + pdbentry.getId();
+      pdbentry.setFile(ebi.fetchDataAsFile(query, "default", "raw")
+                       .getAbsolutePath());
 
-      try
-      {
-        jbInit();
-      }
-      catch (Exception ex)
-      {
-        ex.printStackTrace();
-      }
+      if(pdbentry.getFile()!=null)
+        pdbcanvas.init(pdbentry, seq, chains, ap, protocol);
     }
     catch (Exception ex)
     {
+      pdbcanvas.errorMessage = "Error retrieving file: "+pdbentry.getId();
       ex.printStackTrace();
-      showErrorMessage("Failed to retrieve PDB structure.");
-//      this.dispose();
     }
   }
 
@@ -111,12 +141,12 @@ public class PDBViewer extends JInternalFrame implements Runnable
       throws Exception
   {
     this.addKeyListener(new KeyAdapter()
-        {
-            public void keyPressed(KeyEvent evt)
-            {
-              pdbcanvas.keyPressed(evt);
-            }
-        });
+    {
+      public void keyPressed(KeyEvent evt)
+      {
+        pdbcanvas.keyPressed(evt);
+      }
+    });
 
     this.setJMenuBar(jMenuBar1);
     fileMenu.setText("File");
@@ -272,11 +302,28 @@ 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);
@@ -290,6 +337,7 @@ 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);
@@ -303,45 +351,49 @@ public class PDBViewer extends JInternalFrame implements Runnable
     bg.add(buried);
     bg.add(user);
 
-
-    if(jalview.gui.UserDefinedColours.getUserColourSchemes()!=null)
+    if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
     {
       java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
           getUserColourSchemes().keys();
 
       while (userColours.hasMoreElements())
       {
-        final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours.
+        final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
+            userColours.
             nextElement().toString());
         radioItem.setName("USER_DEFINED");
         radioItem.addMouseListener(new MouseAdapter()
+        {
+          public void mousePressed(MouseEvent evt)
+          {
+            if (evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))
             {
-              public void mousePressed(MouseEvent evt)
+              radioItem.removeActionListener(radioItem.getActionListeners()[0]);
+
+              int option = JOptionPane.showInternalConfirmDialog(jalview.gui.
+                  Desktop.desktop,
+                  "Remove from default list?",
+                  "Remove user defined colour",
+                  JOptionPane.YES_NO_OPTION);
+              if (option == JOptionPane.YES_OPTION)
+              {
+                jalview.gui.UserDefinedColours.removeColourFromDefaults(
+                    radioItem.getText());
+                coloursMenu.remove(radioItem);
+              }
+              else
               {
-                if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))
+                radioItem.addActionListener(new ActionListener()
                 {
-                  radioItem.removeActionListener(radioItem.getActionListeners()[0]);
-
-                  int option = JOptionPane.showInternalConfirmDialog(jalview.gui.Desktop.desktop,
-                      "Remove from default list?",
-                      "Remove user defined colour",
-                      JOptionPane.YES_NO_OPTION);
-                  if(option == JOptionPane.YES_OPTION)
+                  public void actionPerformed(ActionEvent evt)
                   {
-                    jalview.gui.UserDefinedColours.removeColourFromDefaults(radioItem.getText());
-                    coloursMenu.remove(radioItem);
+                    user_actionPerformed(evt);
                   }
-                  else
-                    radioItem.addActionListener(new ActionListener()
-                    {
-                      public void actionPerformed(ActionEvent evt)
-                      {
-                        user_actionPerformed(evt);
-                      }
-                    });
-                }
+                });
               }
-            });
+            }
+          }
+        });
         radioItem.addActionListener(new ActionListener()
         {
           public void actionPerformed(ActionEvent evt)
@@ -377,13 +429,15 @@ public class PDBViewer extends JInternalFrame implements Runnable
   JRadioButtonMenuItem seqButton = new JRadioButtonMenuItem();
   JRadioButtonMenuItem hydro = new JRadioButtonMenuItem();
   JRadioButtonMenuItem taylor = new JRadioButtonMenuItem();
-  JRadioButtonMenuItem zappo = new  JRadioButtonMenuItem();
+  JRadioButtonMenuItem zappo = new JRadioButtonMenuItem();
   JRadioButtonMenuItem user = new JRadioButtonMenuItem();
   JRadioButtonMenuItem buried = new JRadioButtonMenuItem();
   JRadioButtonMenuItem turn = new JRadioButtonMenuItem();
   JRadioButtonMenuItem strand = new JRadioButtonMenuItem();
   JRadioButtonMenuItem helix = new JRadioButtonMenuItem();
   JMenu viewMenu = new JMenu();
+  JMenuItem background = new JMenuItem();
+  JMenuItem savePDB = new JMenuItem();
 
   /**
    * DOCUMENT ME!
@@ -402,7 +456,7 @@ public class PDBViewer extends JInternalFrame implements Runnable
    */
   public void png_actionPerformed(ActionEvent e)
   {
-     makePDBImage(jalview.util.ImageMaker.PNG);
+    makePDBImage(jalview.util.ImageMaker.PNG);
   }
 
   void makePDBImage(int type)
@@ -413,17 +467,21 @@ public class PDBViewer extends JInternalFrame implements Runnable
     jalview.util.ImageMaker im;
 
     if (type == jalview.util.ImageMaker.PNG)
+    {
       im = new jalview.util.ImageMaker(this,
                                        jalview.util.ImageMaker.PNG,
                                        "Make PNG image from view",
                                        width, height,
                                        null, null);
+    }
     else
+    {
       im = new jalview.util.ImageMaker(this,
                                        jalview.util.ImageMaker.EPS,
                                        "Make EPS file from view",
                                        width, height,
                                        null, this.getTitle());
+    }
 
     if (im.getGraphics() != null)
     {
@@ -431,11 +489,12 @@ public class PDBViewer extends JInternalFrame implements Runnable
       im.writeImage();
     }
   }
+
   public void charge_actionPerformed(ActionEvent e)
   {
     pdbcanvas.bysequence = false;
     pdbcanvas.pdb.setChargeColours();
-    pdbcanvas.redrawneeded=true;
+    pdbcanvas.redrawneeded = true;
     pdbcanvas.repaint();
   }
 
@@ -443,7 +502,7 @@ public class PDBViewer extends JInternalFrame implements Runnable
   {
     pdbcanvas.bysequence = false;
     pdbcanvas.pdb.setColours(new HydrophobicColourScheme());
-    pdbcanvas.redrawneeded=true;
+    pdbcanvas.redrawneeded = true;
     pdbcanvas.repaint();
   }
 
@@ -451,35 +510,35 @@ public class PDBViewer extends JInternalFrame implements Runnable
   {
     pdbcanvas.bysequence = false;
     pdbcanvas.pdb.setChainColours();
-    pdbcanvas.redrawneeded=true;
+    pdbcanvas.redrawneeded = true;
     pdbcanvas.repaint();
   }
 
   public void zbuffer_actionPerformed(ActionEvent e)
   {
-    pdbcanvas.zbuffer = ! pdbcanvas.zbuffer;
-    pdbcanvas.redrawneeded=true;
+    pdbcanvas.zbuffer = !pdbcanvas.zbuffer;
+    pdbcanvas.redrawneeded = true;
     pdbcanvas.repaint();
   }
 
   public void molecule_actionPerformed(ActionEvent e)
   {
-    pdbcanvas.bymolecule = ! pdbcanvas.bymolecule;
-    pdbcanvas.redrawneeded=true;
+    pdbcanvas.bymolecule = !pdbcanvas.bymolecule;
+    pdbcanvas.redrawneeded = true;
     pdbcanvas.repaint();
   }
 
   public void depth_actionPerformed(ActionEvent e)
   {
-  pdbcanvas.depthcue = ! pdbcanvas.depthcue;
-  pdbcanvas.redrawneeded=true;
+    pdbcanvas.depthcue = !pdbcanvas.depthcue;
+    pdbcanvas.redrawneeded = true;
     pdbcanvas.repaint();
   }
 
   public void wire_actionPerformed(ActionEvent e)
   {
-    pdbcanvas.wire = ! pdbcanvas.wire;
-    pdbcanvas.redrawneeded=true;
+    pdbcanvas.wire = !pdbcanvas.wire;
+    pdbcanvas.redrawneeded = true;
     pdbcanvas.repaint();
   }
 
@@ -489,7 +548,6 @@ public class PDBViewer extends JInternalFrame implements Runnable
     pdbcanvas.updateSeqColours();
   }
 
-
   public void mapping_actionPerformed(ActionEvent e)
   {
     jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();
@@ -501,18 +559,13 @@ 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)
   {
     pdbcanvas.bysequence = false;
     pdbcanvas.pdb.setColours(new ZappoColourScheme());
-    pdbcanvas.redrawneeded=true;
+    pdbcanvas.redrawneeded = true;
     pdbcanvas.repaint();
   }
 
@@ -520,7 +573,7 @@ public class PDBViewer extends JInternalFrame implements Runnable
   {
     pdbcanvas.bysequence = false;
     pdbcanvas.pdb.setColours(new TaylorColourScheme());
-    pdbcanvas.redrawneeded=true;
+    pdbcanvas.redrawneeded = true;
     pdbcanvas.repaint();
   }
 
@@ -528,7 +581,7 @@ public class PDBViewer extends JInternalFrame implements Runnable
   {
     pdbcanvas.bysequence = false;
     pdbcanvas.pdb.setColours(new HelixColourScheme());
-    pdbcanvas.redrawneeded=true;
+    pdbcanvas.redrawneeded = true;
     pdbcanvas.repaint();
   }
 
@@ -536,7 +589,7 @@ public class PDBViewer extends JInternalFrame implements Runnable
   {
     pdbcanvas.bysequence = false;
     pdbcanvas.pdb.setColours(new StrandColourScheme());
-    pdbcanvas.redrawneeded=true;
+    pdbcanvas.redrawneeded = true;
     pdbcanvas.repaint();
   }
 
@@ -544,7 +597,7 @@ public class PDBViewer extends JInternalFrame implements Runnable
   {
     pdbcanvas.bysequence = false;
     pdbcanvas.pdb.setColours(new TurnColourScheme());
-    pdbcanvas.redrawneeded=true;
+    pdbcanvas.redrawneeded = true;
     pdbcanvas.repaint();
   }
 
@@ -552,7 +605,7 @@ public class PDBViewer extends JInternalFrame implements Runnable
   {
     pdbcanvas.bysequence = false;
     pdbcanvas.pdb.setColours(new BuriedColourScheme());
-    pdbcanvas.redrawneeded=true;
+    pdbcanvas.redrawneeded = true;
     pdbcanvas.repaint();
   }
 
@@ -560,7 +613,7 @@ public class PDBViewer extends JInternalFrame implements Runnable
   {
     if (e.getActionCommand().equals("User Defined..."))
     {
-      new UserDefinedColours(pdbcanvas, null);
+     // new UserDefinedColours(pdbcanvas, null);
     }
     else
     {
@@ -568,8 +621,61 @@ public class PDBViewer extends JInternalFrame implements Runnable
           getUserColourSchemes().get(e.getActionCommand());
 
       pdbcanvas.pdb.setColours(udc);
-      pdbcanvas.redrawneeded=true;
+      pdbcanvas.redrawneeded = true;
       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();
+      }
+    }
+  }
 }