X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBViewer.java;h=364a46e67ecafe5280e449e640ff43b259ab9d3e;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=082ce6e1f0b9d7cddc0d1a373e441f55896d3305;hpb=8893c2ac9824d4c566ae69c73d34889c5316b058;p=jalview.git

diff --git a/src/MCview/PDBViewer.java b/src/MCview/PDBViewer.java
index 082ce6e..364a46e 100755
--- a/src/MCview/PDBViewer.java
+++ b/src/MCview/PDBViewer.java
@@ -1,349 +1,745 @@
-package MCview;
-
-import javax.swing.*;
-import java.awt.event.*;
-import jalview.datamodel.*;
-import jalview.gui.*;
-import jalview.io.EBIFetchClient;
-import java.awt.event.ActionListener;
-import java.awt.event.ActionEvent;
-
-public class PDBViewer extends JInternalFrame implements Runnable
-{
-  PDBEntry pdb;
-  Sequence sequence;
-  PDBCanvas pdbcanvas;
-
-
-  public PDBViewer(PDBEntry entry,
-                   Sequence seq,
-                   SeqCanvas seqcanvas)
-  {
-
-    pdb = entry;
-    sequence = seq;
-
-    Thread worker = new Thread(this);
-    worker.start();
-
-    try
-    {
-      jbInit();
-    }
-    catch (Exception ex)
-    {
-      ex.printStackTrace();
-    }
-
-    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"));
-    }
-
-     Desktop.addInternalFrame(this,title.toString(),400, 400);
-  }
-
-  public void run()
-  {
-    try
-    {
-      EBIFetchClient ebi = new EBIFetchClient();
-      String[] result = ebi.fetchData("pdb:" + pdb.getId(), "default","raw");
-
-      PDBfile pdbfile = new PDBfile(result);
-
-      pdbcanvas.setPDBFile(pdbfile);
-
-    }
-    catch (Exception ex)
-    {
-      ex.printStackTrace();
-    }
-  }
-
-  private void jbInit()
-      throws Exception
-  {
-    this.addKeyListener(new KeyAdapter()
-        {
-            public void keyPressed(KeyEvent evt)
-            {
-              pdbcanvas.keyPressed(evt);
-            }
-        });
-
-    this.setJMenuBar(jMenuBar1);
-    fileMenu.setText("File");
-    coloursMenu.setText("Colours");
-    saveMenu.setActionCommand("Save Image");
-    saveMenu.setText("Save As");
-    png.setText("PNG");
-    png.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        png_actionPerformed(e);
-      }
-    });
-    eps.setText("EPS");
-    eps.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        eps_actionPerformed(e);
-      }
-    });
-    mapping.setText("View Mapping");
-    mapping.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        mapping_actionPerformed(e);
-      }
-    });
-    wire.setText("Wireframe");
-    wire.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        wire_actionPerformed(e);
-      }
-    });
-    depth.setSelected(true);
-    depth.setText("Depthcue");
-    depth.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        depth_actionPerformed(e);
-      }
-    });
-    zbuffer.setSelected(true);
-    zbuffer.setText("Z Buffering");
-    zbuffer.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        zbuffer_actionPerformed(e);
-      }
-    });
-    charge.setText("Charge & Cysteine");
-    charge.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        charge_actionPerformed(e);
-      }
-    });
-    hydro.setText("Hydrophobicity");
-    hydro.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        hydro_actionPerformed(e);
-      }
-    });
-    chain.setText("By Chain");
-    chain.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        chain_actionPerformed(e);
-      }
-    });
-    seqButton.setSelected(true);
-    seqButton.setText("By Sequence");
-    seqButton.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        seqButton_actionPerformed(e);
-      }
-    });
-    molecule.setText("By Molecule");
-    molecule.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        molecule_actionPerformed(e);
-      }
-    });
-    allchains.setSelected(true);
-    allchains.setText("Show All Chains");
-    allchains.addItemListener(new ItemListener()
-    {
-      public void itemStateChanged(ItemEvent e)
-      {
-        allchains_itemStateChanged(e);
-      }
-    });
-    jMenuBar1.add(fileMenu);
-    jMenuBar1.add(coloursMenu);
-    fileMenu.add(saveMenu);
-    fileMenu.add(mapping);
-    saveMenu.add(png);
-    saveMenu.add(eps);
-    coloursMenu.add(seqButton);
-    coloursMenu.add(chain);
-    coloursMenu.add(hydro);
-    coloursMenu.add(charge);
-    coloursMenu.addSeparator();
-    coloursMenu.add(wire);
-    coloursMenu.add(depth);
-    coloursMenu.add(zbuffer);
-    coloursMenu.add(molecule);
-    coloursMenu.add(allchains);
-    ButtonGroup bg = new ButtonGroup();
-    bg.add(seqButton);
-    bg.add(chain);
-    bg.add(hydro);
-    bg.add(charge);
-  }
-
-  JMenuBar jMenuBar1 = new JMenuBar();
-  JMenu fileMenu = new JMenu();
-  JMenu coloursMenu = new JMenu();
-  JMenu saveMenu = new JMenu();
-  JMenuItem png = new JMenuItem();
-  JMenuItem eps = new JMenuItem();
-  JMenuItem mapping = new JMenuItem();
-  JCheckBoxMenuItem wire = new JCheckBoxMenuItem();
-  JCheckBoxMenuItem depth = new JCheckBoxMenuItem();
-  JCheckBoxMenuItem zbuffer = new JCheckBoxMenuItem();
-  JRadioButtonMenuItem charge = new JRadioButtonMenuItem();
-  JRadioButtonMenuItem hydro = new JRadioButtonMenuItem();
-  JRadioButtonMenuItem chain = new JRadioButtonMenuItem();
-  JRadioButtonMenuItem seqButton = new JRadioButtonMenuItem();
-  JCheckBoxMenuItem molecule = new JCheckBoxMenuItem();
-  JCheckBoxMenuItem allchains = new JCheckBoxMenuItem();
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
-   */
-  public void eps_actionPerformed(ActionEvent e)
-  {
-    makePDBImage(jalview.util.ImageMaker.EPS);
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
-   */
-  public void png_actionPerformed(ActionEvent e)
-  {
-     makePDBImage(jalview.util.ImageMaker.PNG);
-  }
-
-  void makePDBImage(int type)
-  {
-    int width = pdbcanvas.getWidth();
-    int height = pdbcanvas.getHeight();
-
-    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)
-    {
-      pdbcanvas.drawAll(im.getGraphics(), width, height);
-      im.writeImage();
-    }
-  }
-  public void charge_actionPerformed(ActionEvent e)
-  {
-    clearButtonGroup();
-    pdbcanvas.pdb.setChargeColours();
-    pdbcanvas.redrawneeded=true;
-    pdbcanvas.repaint();
-  }
-
-  public void hydro_actionPerformed(ActionEvent e)
-  {
-    clearButtonGroup();
-    pdbcanvas.pdb.setHydrophobicityColours();
-    pdbcanvas.redrawneeded=true;
-    pdbcanvas.repaint();
-  }
-
-  public void chain_actionPerformed(ActionEvent e)
-  {
-    clearButtonGroup();
-    pdbcanvas.pdb.setChainColours();
-    pdbcanvas.redrawneeded=true;
-    pdbcanvas.repaint();
-  }
-
-  public void zbuffer_actionPerformed(ActionEvent e)
-  {
-    pdbcanvas.zbuffer = ! pdbcanvas.zbuffer;
-    pdbcanvas.redrawneeded=true;
-    pdbcanvas.repaint();
-  }
-
-  public void molecule_actionPerformed(ActionEvent e)
-  {
-    pdbcanvas.bymolecule = ! pdbcanvas.bymolecule;
-    pdbcanvas.redrawneeded=true;
-    pdbcanvas.repaint();
-  }
-
-  public void depth_actionPerformed(ActionEvent e)
-  {
-  pdbcanvas.depthcue = ! pdbcanvas.depthcue;
-  pdbcanvas.redrawneeded=true;
-    pdbcanvas.repaint();
-  }
-
-  public void wire_actionPerformed(ActionEvent e)
-  {
-    pdbcanvas.wire = ! pdbcanvas.wire;
-    pdbcanvas.redrawneeded=true;
-    pdbcanvas.repaint();
-  }
-
-  public void seqButton_actionPerformed(ActionEvent e)
-  {
-    clearButtonGroup();
-    pdbcanvas.bysequence = seqButton.isSelected();
-    pdbcanvas.updateSeqColours();
-  }
-
-  void clearButtonGroup()
-  {
-   pdbcanvas.bysequence = false;
-   pdbcanvas.bymolecule = false;
-  }
-
-  public void mapping_actionPerformed(ActionEvent e)
-  {
-    jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();
-    Desktop.addInternalFrame(cap, "PDB - Sequence Mapping", 550, 600);
-    cap.setText(pdbcanvas.mappingDetails.toString());
-  }
-
-  public void allchains_itemStateChanged(ItemEvent e)
-  {
-    pdbcanvas.setAllchainsVisible(allchains.getState());
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package MCview;
+
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignmentPanel;
+import jalview.gui.Desktop;
+import jalview.gui.OOMWarning;
+import jalview.gui.UserDefinedColours;
+import jalview.io.JalviewFileChooser;
+import jalview.io.JalviewFileView;
+import jalview.schemes.BuriedColourScheme;
+import jalview.schemes.HelixColourScheme;
+import jalview.schemes.HydrophobicColourScheme;
+import jalview.schemes.StrandColourScheme;
+import jalview.schemes.TaylorColourScheme;
+import jalview.schemes.TurnColourScheme;
+import jalview.schemes.UserColourScheme;
+import jalview.schemes.ZappoColourScheme;
+import jalview.util.MessageManager;
+import jalview.ws.ebi.EBIFetchClient;
+
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.awt.event.KeyAdapter;
+import java.awt.event.KeyEvent;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileOutputStream;
+import java.io.FileReader;
+import java.io.PrintWriter;
+
+import javax.swing.ButtonGroup;
+import javax.swing.JCheckBoxMenuItem;
+import javax.swing.JColorChooser;
+import javax.swing.JInternalFrame;
+import javax.swing.JMenu;
+import javax.swing.JMenuBar;
+import javax.swing.JMenuItem;
+import javax.swing.JOptionPane;
+import javax.swing.JRadioButtonMenuItem;
+import javax.swing.SwingUtilities;
+
+public class PDBViewer extends JInternalFrame implements Runnable
+{
+
+  /**
+   * 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)
+  {
+    this.pdbentry = pdbentry;
+    this.seq = seq;
+    this.chains = chains;
+    this.ap = ap;
+    this.protocol = protocol;
+
+    try
+    {
+      jbInit();
+    } catch (Exception ex)
+    {
+      ex.printStackTrace();
+    }
+
+    StringBuffer title = new StringBuffer(seq[0].getName() + ":"
+            + pdbentry.getFile());
+
+    pdbcanvas = new PDBCanvas();
+
+    setContentPane(pdbcanvas);
+
+    if (pdbentry.getFile() != null)
+    {
+      try
+      {
+        tmpPDBFile = pdbentry.getFile();
+        PDBfile pdbfile = new PDBfile(false, false, false, tmpPDBFile,
+                jalview.io.AppletFormatAdapter.FILE);
+
+        pdbcanvas.init(pdbentry, seq, chains, ap, protocol);
+
+      } catch (java.io.IOException ex)
+      {
+        ex.printStackTrace();
+      }
+    }
+    else
+    {
+      Thread worker = new Thread(this);
+      worker.start();
+    }
+
+    if (pdbentry.getProperty() != null)
+    {
+      if (pdbentry.getProperty().get("method") != null)
+      {
+        title.append(" Method: ");
+        title.append(pdbentry.getProperty().get("method"));
+      }
+      if (pdbentry.getProperty().get("chains") != null)
+      {
+        title.append(" Chain:");
+        title.append(pdbentry.getProperty().get("chains"));
+      }
+    }
+    Desktop.addInternalFrame(this, title.toString(), 400, 400);
+  }
+
+  public void run()
+  {
+    try
+    {
+      EBIFetchClient ebi = new EBIFetchClient();
+      String query = "pdb:" + pdbentry.getId();
+      pdbentry.setFile(ebi.fetchDataAsFile(query, "default", "raw")
+              .getAbsolutePath());
+
+      if (pdbentry.getFile() != null)
+      {
+        pdbcanvas.init(pdbentry, seq, chains, ap, protocol);
+      }
+    } catch (Exception ex)
+    {
+      pdbcanvas.errorMessage = "Error retrieving file: " + pdbentry.getId();
+      ex.printStackTrace();
+    }
+  }
+
+  private void jbInit() throws Exception
+  {
+    this.addKeyListener(new KeyAdapter()
+    {
+      public void keyPressed(KeyEvent evt)
+      {
+        pdbcanvas.keyPressed(evt);
+      }
+    });
+
+    this.setJMenuBar(jMenuBar1);
+    fileMenu.setText(MessageManager.getString("action.file"));
+    coloursMenu.setText(MessageManager.getString("label.colours"));
+    saveMenu.setActionCommand(MessageManager.getString("action.save_image"));
+    saveMenu.setText(MessageManager.getString("action.save_as"));
+    png.setText("PNG");
+    png.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        png_actionPerformed(e);
+      }
+    });
+    eps.setText("EPS");
+    eps.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        eps_actionPerformed(e);
+      }
+    });
+    mapping.setText(MessageManager.getString("label.view_mapping"));
+    mapping.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        mapping_actionPerformed(e);
+      }
+    });
+    wire.setText(MessageManager.getString("label.wireframe"));
+    wire.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        wire_actionPerformed(e);
+      }
+    });
+    depth.setSelected(true);
+    depth.setText(MessageManager.getString("label.depthcue"));
+    depth.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        depth_actionPerformed(e);
+      }
+    });
+    zbuffer.setSelected(true);
+    zbuffer.setText(MessageManager.getString("label.z_buffering"));
+    zbuffer.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        zbuffer_actionPerformed(e);
+      }
+    });
+    charge.setText(MessageManager.getString("label.charge_cysteine"));
+    charge.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        charge_actionPerformed(e);
+      }
+    });
+    chain.setText(MessageManager.getString("action.by_chain"));
+    chain.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        chain_actionPerformed(e);
+      }
+    });
+    seqButton.setSelected(true);
+    seqButton.setText(MessageManager.getString("action.by_sequence"));
+    seqButton.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        seqButton_actionPerformed(e);
+      }
+    });
+    allchains.setSelected(true);
+    allchains.setText(MessageManager.getString("label.show_all_chains"));
+    allchains.addItemListener(new ItemListener()
+    {
+      public void itemStateChanged(ItemEvent e)
+      {
+        allchains_itemStateChanged(e);
+      }
+    });
+    zappo.setText(MessageManager.getString("label.zappo"));
+    zappo.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        zappo_actionPerformed(e);
+      }
+    });
+    taylor.setText(MessageManager.getString("label.taylor"));
+    taylor.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        taylor_actionPerformed(e);
+      }
+    });
+    hydro.setText(MessageManager.getString("label.hydrophobicity"));
+    hydro.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        hydro_actionPerformed(e);
+      }
+    });
+    helix.setText(MessageManager.getString("label.helix_propensity"));
+    helix.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        helix_actionPerformed(e);
+      }
+    });
+    strand.setText(MessageManager.getString("label.strand_propensity"));
+    strand.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        strand_actionPerformed(e);
+      }
+    });
+    turn.setText(MessageManager.getString("label.turn_propensity"));
+    turn.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        turn_actionPerformed(e);
+      }
+    });
+    buried.setText(MessageManager.getString("label.buried_index"));
+    buried.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        buried_actionPerformed(e);
+      }
+    });
+    user.setText(MessageManager.getString("action.user_defined"));
+    user.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        user_actionPerformed(e);
+      }
+    });
+    viewMenu.setText(MessageManager.getString("action.view"));
+    background
+            .setText(MessageManager.getString("action.background_colour"));
+    background.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        background_actionPerformed(e);
+      }
+    });
+    savePDB.setText(MessageManager.getString("label.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);
+    coloursMenu.add(chain);
+    coloursMenu.add(charge);
+    coloursMenu.add(zappo);
+    coloursMenu.add(taylor);
+    coloursMenu.add(hydro);
+    coloursMenu.add(helix);
+    coloursMenu.add(strand);
+    coloursMenu.add(turn);
+    coloursMenu.add(buried);
+    coloursMenu.add(user);
+    coloursMenu.add(background);
+    ButtonGroup bg = new ButtonGroup();
+    bg.add(seqButton);
+    bg.add(chain);
+    bg.add(charge);
+    bg.add(zappo);
+    bg.add(taylor);
+    bg.add(hydro);
+    bg.add(helix);
+    bg.add(strand);
+    bg.add(turn);
+    bg.add(buried);
+    bg.add(user);
+
+    if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
+    {
+      java.util.Enumeration userColours = jalview.gui.UserDefinedColours
+              .getUserColourSchemes().keys();
+
+      while (userColours.hasMoreElements())
+      {
+        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))
+            {
+              radioItem.removeActionListener(radioItem.getActionListeners()[0]);
+
+              int option = JOptionPane.showInternalConfirmDialog(
+                      jalview.gui.Desktop.desktop,
+                      MessageManager
+                              .getString("label.remove_from_default_list"),
+                      MessageManager
+                              .getString("label.remove_user_defined_colour"),
+                      JOptionPane.YES_NO_OPTION);
+              if (option == JOptionPane.YES_OPTION)
+              {
+                jalview.gui.UserDefinedColours
+                        .removeColourFromDefaults(radioItem.getText());
+                coloursMenu.remove(radioItem);
+              }
+              else
+              {
+                radioItem.addActionListener(new ActionListener()
+                {
+                  public void actionPerformed(ActionEvent evt)
+                  {
+                    user_actionPerformed(evt);
+                  }
+                });
+              }
+            }
+          }
+        });
+        radioItem.addActionListener(new ActionListener()
+        {
+          public void actionPerformed(ActionEvent evt)
+          {
+            user_actionPerformed(evt);
+          }
+        });
+        coloursMenu.add(radioItem);
+        bg.add(radioItem);
+      }
+    }
+
+    viewMenu.add(wire);
+    viewMenu.add(depth);
+    viewMenu.add(zbuffer);
+    viewMenu.add(allchains);
+  }
+
+  JMenuBar jMenuBar1 = new JMenuBar();
+
+  JMenu fileMenu = new JMenu();
+
+  JMenu coloursMenu = new JMenu();
+
+  JMenu saveMenu = new JMenu();
+
+  JMenuItem png = new JMenuItem();
+
+  JMenuItem eps = new JMenuItem();
+
+  JMenuItem mapping = new JMenuItem();
+
+  JCheckBoxMenuItem wire = new JCheckBoxMenuItem();
+
+  JCheckBoxMenuItem depth = new JCheckBoxMenuItem();
+
+  JCheckBoxMenuItem zbuffer = new JCheckBoxMenuItem();
+
+  JCheckBoxMenuItem allchains = new JCheckBoxMenuItem();
+
+  JRadioButtonMenuItem charge = new JRadioButtonMenuItem();
+
+  JRadioButtonMenuItem chain = new JRadioButtonMenuItem();
+
+  JRadioButtonMenuItem seqButton = new JRadioButtonMenuItem();
+
+  JRadioButtonMenuItem hydro = new JRadioButtonMenuItem();
+
+  JRadioButtonMenuItem taylor = 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!
+   * 
+   * @param e
+   *          DOCUMENT ME!
+   */
+  public void eps_actionPerformed(ActionEvent e)
+  {
+    makePDBImage(jalview.util.ImageMaker.TYPE.EPS);
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param e
+   *          DOCUMENT ME!
+   */
+  public void png_actionPerformed(ActionEvent e)
+  {
+    makePDBImage(jalview.util.ImageMaker.TYPE.PNG);
+  }
+
+  void makePDBImage(jalview.util.ImageMaker.TYPE type)
+  {
+    int width = pdbcanvas.getWidth();
+    int height = pdbcanvas.getHeight();
+
+    jalview.util.ImageMaker im;
+
+    if (type == jalview.util.ImageMaker.TYPE.PNG)
+    {
+      im = new jalview.util.ImageMaker(this,
+              jalview.util.ImageMaker.TYPE.PNG, "Make PNG image from view",
+              width, height, null, null);
+    }
+    else if (type == jalview.util.ImageMaker.TYPE.EPS)
+    {
+      im = new jalview.util.ImageMaker(this,
+              jalview.util.ImageMaker.TYPE.EPS, "Make EPS file from view",
+              width, height, null, this.getTitle());
+    }
+    else
+    {
+
+      im = new jalview.util.ImageMaker(this,
+              jalview.util.ImageMaker.TYPE.SVG, "Make SVG file from PCA",
+              width, height, null, this.getTitle());
+    }
+
+    if (im.getGraphics() != null)
+    {
+      pdbcanvas.drawAll(im.getGraphics(), width, height);
+      im.writeImage();
+    }
+  }
+
+  public void charge_actionPerformed(ActionEvent e)
+  {
+    pdbcanvas.bysequence = false;
+    pdbcanvas.pdb.setChargeColours();
+    pdbcanvas.redrawneeded = true;
+    pdbcanvas.repaint();
+  }
+
+  public void hydro_actionPerformed(ActionEvent e)
+  {
+    pdbcanvas.bysequence = false;
+    pdbcanvas.pdb.setColours(new HydrophobicColourScheme());
+    pdbcanvas.redrawneeded = true;
+    pdbcanvas.repaint();
+  }
+
+  public void chain_actionPerformed(ActionEvent e)
+  {
+    pdbcanvas.bysequence = false;
+    pdbcanvas.pdb.setChainColours();
+    pdbcanvas.redrawneeded = true;
+    pdbcanvas.repaint();
+  }
+
+  public void zbuffer_actionPerformed(ActionEvent e)
+  {
+    pdbcanvas.zbuffer = !pdbcanvas.zbuffer;
+    pdbcanvas.redrawneeded = true;
+    pdbcanvas.repaint();
+  }
+
+  public void molecule_actionPerformed(ActionEvent e)
+  {
+    pdbcanvas.bymolecule = !pdbcanvas.bymolecule;
+    pdbcanvas.redrawneeded = true;
+    pdbcanvas.repaint();
+  }
+
+  public void depth_actionPerformed(ActionEvent e)
+  {
+    pdbcanvas.depthcue = !pdbcanvas.depthcue;
+    pdbcanvas.redrawneeded = true;
+    pdbcanvas.repaint();
+  }
+
+  public void wire_actionPerformed(ActionEvent e)
+  {
+    pdbcanvas.wire = !pdbcanvas.wire;
+    pdbcanvas.redrawneeded = true;
+    pdbcanvas.repaint();
+  }
+
+  public void seqButton_actionPerformed(ActionEvent e)
+  {
+    pdbcanvas.bysequence = true;
+    pdbcanvas.updateSeqColours();
+  }
+
+  public void mapping_actionPerformed(ActionEvent e)
+  {
+    jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();
+    try
+    {
+      cap.setText(pdbcanvas.mappingDetails.toString());
+      Desktop.addInternalFrame(cap,
+              MessageManager.getString("label.pdb_sequence_mapping"), 550,
+              600);
+    } catch (OutOfMemoryError oom)
+    {
+      new OOMWarning("Opening sequence to structure mapping report", oom);
+      cap.dispose();
+    }
+  }
+
+  public void allchains_itemStateChanged(ItemEvent e)
+  {
+    pdbcanvas.setAllchainsVisible(allchains.getState());
+  }
+
+  public void zappo_actionPerformed(ActionEvent e)
+  {
+    pdbcanvas.bysequence = false;
+    pdbcanvas.pdb.setColours(new ZappoColourScheme());
+    pdbcanvas.redrawneeded = true;
+    pdbcanvas.repaint();
+  }
+
+  public void taylor_actionPerformed(ActionEvent e)
+  {
+    pdbcanvas.bysequence = false;
+    pdbcanvas.pdb.setColours(new TaylorColourScheme());
+    pdbcanvas.redrawneeded = true;
+    pdbcanvas.repaint();
+  }
+
+  public void helix_actionPerformed(ActionEvent e)
+  {
+    pdbcanvas.bysequence = false;
+    pdbcanvas.pdb.setColours(new HelixColourScheme());
+    pdbcanvas.redrawneeded = true;
+    pdbcanvas.repaint();
+  }
+
+  public void strand_actionPerformed(ActionEvent e)
+  {
+    pdbcanvas.bysequence = false;
+    pdbcanvas.pdb.setColours(new StrandColourScheme());
+    pdbcanvas.redrawneeded = true;
+    pdbcanvas.repaint();
+  }
+
+  public void turn_actionPerformed(ActionEvent e)
+  {
+    pdbcanvas.bysequence = false;
+    pdbcanvas.pdb.setColours(new TurnColourScheme());
+    pdbcanvas.redrawneeded = true;
+    pdbcanvas.repaint();
+  }
+
+  public void buried_actionPerformed(ActionEvent e)
+  {
+    pdbcanvas.bysequence = false;
+    pdbcanvas.pdb.setColours(new BuriedColourScheme());
+    pdbcanvas.redrawneeded = true;
+    pdbcanvas.repaint();
+  }
+
+  public void user_actionPerformed(ActionEvent e)
+  {
+    if (e.getActionCommand().equals(
+            MessageManager.getString("action.user_defined")))
+    {
+      // new UserDefinedColours(pdbcanvas, null);
+    }
+    else
+    {
+      UserColourScheme udc = (UserColourScheme) UserDefinedColours
+              .getUserColourSchemes().get(e.getActionCommand());
+
+      pdbcanvas.pdb.setColours(udc);
+      pdbcanvas.redrawneeded = true;
+      pdbcanvas.repaint();
+    }
+  }
+
+  public void background_actionPerformed(ActionEvent e)
+  {
+    java.awt.Color col = JColorChooser.showDialog(this,
+            MessageManager.getString("label.select_backgroud_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(MessageManager.getString("label.save_pdb_file"));
+    chooser.setToolTipText(MessageManager.getString("action.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();
+        in.close();
+      } catch (Exception ex)
+      {
+        ex.printStackTrace();
+      }
+    }
+  }
+}