X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppJmol.java;h=0cc04f7dd029d31d668468c5bf648208b35e1975;hb=6486a5333807ca300db4a28a6bf9899f5dddf5a6;hp=7945fa7d7fe5e954b60f3823b394000e023d3020;hpb=ea990f32cf34a867377d25f7fc05bfbfb15f6fb3;p=jalview.git

diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java
index 7945fa7..0cc04f7 100644
--- a/src/jalview/gui/AppJmol.java
+++ b/src/jalview/gui/AppJmol.java
@@ -26,6 +26,7 @@ import java.awt.event.*;
 import java.io.*;
 
 import jalview.jbgui.GStructureViewer;
+import jalview.api.SequenceStructureBinding;
 import jalview.bin.Cache;
 import jalview.datamodel.*;
 import jalview.gui.*;
@@ -39,64 +40,90 @@ import org.jmol.api.*;
 import org.jmol.adapter.smarter.SmarterJmolAdapter;
 import org.jmol.popup.*;
 import org.jmol.viewer.JmolConstants;
+import org.openscience.jmol.app.jmolpanel.AppConsole;
 
-public class AppJmol extends GStructureViewer implements StructureListener,
-        JmolStatusListener, Runnable
+public class AppJmol extends GStructureViewer implements Runnable,
+        SequenceStructureBinding
 
 {
-  JmolViewer viewer;
-
-  JmolPopup jmolpopup;
-
-  ScriptWindow scriptWindow;
-
-  PDBEntry pdbentry;
-
-  SequenceI[] sequence;
-
-  String[] chains;
-
-  StructureSelectionManager ssm;
+  AppJmolBinding jmb;
 
+  JPanel scriptWindow;
+  
   JSplitPane splitPane;
 
   RenderPanel renderPanel;
 
   AlignmentPanel ap;
 
-  String fileLoadingError;
-
-  boolean colourBySequence = true;
-
-  boolean loadingFromArchive = false;
-
   Vector atomsPicked = new Vector();
 
+  private boolean addingStructures = false;
+
+  /**
+   * 
+   * @param file
+   * @param id
+   * @param seq
+   * @param ap
+   * @param loadStatus
+   * @param bounds
+   * @deprecated defaults to AppJmol(String[] files, ... , viewid);
+   */
   public AppJmol(String file, String id, SequenceI[] seq,
           AlignmentPanel ap, String loadStatus, Rectangle bounds)
   {
     this(file, id, seq, ap, loadStatus, bounds, null);
   }
 
+  /**
+   * @deprecated
+   */
   public AppJmol(String file, String id, SequenceI[] seq,
           AlignmentPanel ap, String loadStatus, Rectangle bounds,
           String viewid)
   {
-    loadingFromArchive = true;
-    pdbentry = new PDBEntry();
-    pdbentry.setFile(file);
-    pdbentry.setId(id);
-    this.sequence = seq;
+    this(new String[]
+    { file }, new String[]
+    { id }, new SequenceI[][]
+    { seq }, ap, loadStatus, bounds, viewid);
+  }
+
+  /**
+   * 
+   * @param files
+   * @param ids
+   * @param seqs
+   * @param ap
+   * @param loadStatus
+   * @param bounds
+   * @param viewid
+   */
+  public AppJmol(String[] files, String[] ids, SequenceI[][] seqs,
+          AlignmentPanel ap, String loadStatus, Rectangle bounds,
+          String viewid)
+  {
+    PDBEntry[] pdbentrys = new PDBEntry[files.length];
+    for (int i = 0; i < pdbentrys.length; i++)
+    {
+      PDBEntry pdbentry = new PDBEntry();
+      pdbentry.setFile(files[i]);
+      pdbentry.setId(ids[i]);
+      pdbentrys[i] = pdbentry;
+    }
+    // / TODO: check if protocol is needed to be set, and if chains are
+    // autodiscovered.
+    jmb = new AppJmolBinding(this, pdbentrys, seqs, null, null);
+
+    jmb.setLoadingFromArchive(true);
     this.ap = ap;
     this.setBounds(bounds);
-    colourBySequence = false;
+    jmb.setColourBySequence(false);
     seqColour.setSelected(false);
     viewId = viewid;
     // jalview.gui.Desktop.addInternalFrame(this, "Loading File",
     // bounds.width,bounds.height);
 
-    initJmol(loadStatus);
-
     this.addInternalFrameListener(new InternalFrameAdapter()
     {
       public void internalFrameClosing(InternalFrameEvent internalFrameEvent)
@@ -104,26 +131,16 @@ public class AppJmol extends GStructureViewer implements StructureListener,
         closeViewer();
       }
     });
-  }
-
-  public synchronized void addSequence(SequenceI[] seq)
-  {
-    Vector v = new Vector();
-    for (int i = 0; i < sequence.length; i++)
-      v.addElement(sequence[i]);
+    initJmol(loadStatus); // pdbentry, seq, JBPCHECK!
 
-    for (int i = 0; i < seq.length; i++)
-      if (!v.contains(seq[i]))
-        v.addElement(seq[i]);
-
-    SequenceI[] tmp = new SequenceI[v.size()];
-    v.copyInto(tmp);
-    sequence = tmp;
   }
 
+  IProgressIndicator progressBar = null;
+
   public AppJmol(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
           AlignmentPanel ap)
   {
+    progressBar = ap.alignFrame;
     // ////////////////////////////////
     // Is the pdb file already loaded?
     String alreadyMapped = StructureSelectionManager
@@ -132,14 +149,11 @@ public class AppJmol extends GStructureViewer implements StructureListener,
 
     if (alreadyMapped != null)
     {
-      int option = JOptionPane
-              .showInternalConfirmDialog(
-                      Desktop.desktop,
-                      pdbentry.getId()
-                              + " is already displayed."
-                              + "\nDo you want to map sequences to the visible structure?",
-                      "Map Sequences to Visible Window: "
-                              + pdbentry.getId(), JOptionPane.YES_NO_OPTION);
+      int option = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
+              pdbentry.getId() + " is already displayed."
+                      + "\nDo you want to re-use this viewer ?",
+              "Map Sequences to Visible Window: " + pdbentry.getId(),
+              JOptionPane.YES_NO_OPTION);
 
       if (option == JOptionPane.YES_OPTION)
       {
@@ -161,10 +175,15 @@ public class AppJmol extends GStructureViewer implements StructureListener,
           if (frames[i] instanceof AppJmol)
           {
             AppJmol topJmol = ((AppJmol) frames[i]);
-            if (topJmol.pdbentry.getFile().equals(alreadyMapped))
+            // JBPNOTE: this looks like a binding routine, rather than a gui
+            // routine
+            for (int pe = 0; pe < topJmol.jmb.pdbentry.length; pe++)
             {
-              topJmol.addSequence(seq);
-              break;
+              if (topJmol.jmb.pdbentry[pe].getFile().equals(alreadyMapped))
+              {
+                topJmol.jmb.addSequence(pe, seq);
+                break;
+              }
             }
           }
         }
@@ -173,14 +192,35 @@ public class AppJmol extends GStructureViewer implements StructureListener,
       }
     }
     // /////////////////////////////////
+    // Check if there are other Jmol views involving this alignment
+    // and prompt user about adding this molecule to one of them
+    Vector existingViews = getJmolsFor(ap);
+    if (existingViews.size() > 0)
+    {
+      Enumeration jm = existingViews.elements();
+      while (jm.hasMoreElements())
+      {
+        AppJmol topJmol = (AppJmol) jm.nextElement();
+        // TODO: highlight topJmol in view somehow
+        int option = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
+                "Do you want to add " + pdbentry.getId()
+                        + " to the view called\n'" + topJmol.getTitle()
+                        + "'\n", "Align to existing structure view",
+                JOptionPane.YES_NO_OPTION);
+        if (option == JOptionPane.YES_OPTION)
+        {
+          topJmol.addStructure(pdbentry, seq, chains, true, ap.alignFrame);
+          return;
+        }
+      }
+    }
+    // /////////////////////////////////
 
+    jmb = new AppJmolBinding(this, new PDBEntry[]
+    { pdbentry }, new SequenceI[][]
+    { seq }, null, null);
     this.ap = ap;
-    this.pdbentry = pdbentry;
-    this.sequence = seq;
-    this.setSize(400, 400);
-    // jalview.gui.Desktop.addInternalFrame(this, "Jmol
-    // View"+(pdbentry.getId()!=null ? "for "+pdbentry.getId()
-    // : ""), 400, 400);
+    setSize(400, 400); // probably should be a configurable/dynamic default here
 
     if (pdbentry.getFile() != null)
     {
@@ -188,7 +228,8 @@ public class AppJmol extends GStructureViewer implements StructureListener,
     }
     else
     {
-      Thread worker = new Thread(this);
+      addingStructures = false;
+      worker = new Thread(this);
       worker.start();
     }
 
@@ -199,49 +240,120 @@ public class AppJmol extends GStructureViewer implements StructureListener,
         closeViewer();
       }
     });
+
   }
 
-  void initJmol(String command)
+  /**
+   * pdb retrieval thread.
+   */
+  private Thread worker = null;
+
+  /**
+   * add a new structure (with associated sequences and chains) to this viewer,
+   * retrieving it if necessary first.
+   * 
+   * @param pdbentry
+   * @param seq
+   * @param chains
+   * @param alignFrame 
+   * @param align
+   *          if true, new structure(s) will be align using associated alignment
+   */
+  private void addStructure(final PDBEntry pdbentry, final SequenceI[] seq,
+          final String[] chains, final boolean b, final IProgressIndicator alignFrame)
   {
-    renderPanel = new RenderPanel();
+    if (pdbentry.getFile() == null)
+    {
+      if (worker != null && worker.isAlive())
+      {
+        // a retrieval is in progress, wait around and add ourselves to the
+        // queue.
+        new Thread(new Runnable()
+        {
+          public void run()
+          {
+            while (worker != null && worker.isAlive() && _started)
+            {
+              try
+              {
+                Thread.sleep(100 + ((int) Math.random() * 100));
 
-    this.getContentPane().add(renderPanel, java.awt.BorderLayout.CENTER);
+              } catch (Exception e)
+              {
+              }
+
+            }
+            // and call ourselves again.
+            addStructure(pdbentry, seq, chains, b, alignFrame);
+          }
+        }).start();
+        return;
+      }
+    }
+    // otherwise, start adding the structure.
+    jmb.addSequenceAndChain(new PDBEntry[]
+    { pdbentry }, new SequenceI[][]
+    { seq }, new String[][]
+    { chains });
+    addingStructures = true;
+    _started = false;
+    alignAddedStructures = b;
+    progressBar = alignFrame; // visual indication happens on caller frame. 
+    (worker = new Thread(this)).start();
+    return;
+  }
 
-    StringBuffer title = new StringBuffer(sequence[0].getName() + ":"
-            + pdbentry.getId());
+  private Vector getJmolsFor(AlignmentPanel ap2)
+  {
+    Vector otherJmols = new Vector();
+    // Now this AppJmol is mapped to new sequences. We must add them to
+    // the exisiting array
+    JInternalFrame[] frames = Desktop.instance.getAllFrames();
 
-    if (pdbentry.getProperty() != null)
+    for (int i = 0; i < frames.length; i++)
     {
-      if (pdbentry.getProperty().get("method") != null)
-      {
-        title.append(" Method: ");
-        title.append(pdbentry.getProperty().get("method"));
-      }
-      if (pdbentry.getProperty().get("chains") != null)
+      if (frames[i] instanceof AppJmol)
       {
-        title.append(" Chain:");
-        title.append(pdbentry.getProperty().get("chains"));
+        AppJmol topJmol = ((AppJmol) frames[i]);
+        if (topJmol.ap == ap2)
+        {
+          otherJmols.addElement(topJmol);
+        }
       }
     }
+    return otherJmols;
+  }
 
-    this.setTitle(title.toString());
-    jalview.gui.Desktop.addInternalFrame(this, title.toString(),
+  void initJmol(String command)
+  {
+    jmb.setFinishedInit(false);
+    renderPanel = new RenderPanel();
+    // TODO: consider waiting until the structure/view is fully loaded before
+    // displaying
+    this.getContentPane().add(renderPanel, java.awt.BorderLayout.CENTER);
+    jalview.gui.Desktop.addInternalFrame(this, jmb.getViewerTitle(),
             getBounds().width, getBounds().height);
-    // * OK, but safer to assign htmlName, URL bases, comandOptions, and
-    // statusListener now.
-
-    viewer = org.jmol.api.JmolViewer.allocateViewer(renderPanel,
-            new SmarterJmolAdapter(), "", null, null, "", this);
-
-    jmolpopup = JmolPopup.newJmolPopup(viewer, true, "Jmol", true);
-
-    viewer.evalStringQuiet(command);
+    if (scriptWindow == null)
+    {
+      BorderLayout bl = new BorderLayout();
+      bl.setHgap(0);
+      bl.setVgap(0);
+      scriptWindow = new JPanel(bl);
+    };
+    
+    jmb.allocateViewer(renderPanel, true, "", null, null, "", scriptWindow, null);
+    jmb.newJmolPopup(true, "Jmol", true);
+    jmb.evalStateCommand(command);
+    jmb.setFinishedInit(true);
   }
 
   void setChainMenuItems(Vector chains)
   {
     chainMenu.removeAll();
-
+    if (chains == null)
+    {
+      return;
+    }
     JMenuItem menuItem = new JMenuItem("All");
     menuItem.addActionListener(new ActionListener()
     {
@@ -278,78 +390,208 @@ public class AppJmol extends GStructureViewer implements StructureListener,
 
   boolean allChainsSelected = false;
 
+  private boolean alignAddedStructures = false;
+
   void centerViewer()
   {
-    StringBuffer cmd = new StringBuffer();
+    Vector toshow = new Vector();
+    String lbl;
+    int mlength, p, mnum;
     for (int i = 0; i < chainMenu.getItemCount(); i++)
     {
       if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem)
       {
         JCheckBoxMenuItem item = (JCheckBoxMenuItem) chainMenu.getItem(i);
         if (item.isSelected())
-          cmd.append(":" + item.getText() + " or ");
+        {
+          toshow.addElement(item.getText());
+        }
       }
     }
-
-    if (cmd.length() > 0)
-      cmd.setLength(cmd.length() - 4);
-
-    viewer.evalStringQuiet("select *;restrict " + cmd + ";cartoon;center "
-            + cmd);
+    jmb.centerViewer(toshow);
   }
 
   void closeViewer()
   {
-    viewer.setModeMouse(org.jmol.viewer.JmolConstants.MOUSE_NONE);
-    viewer.evalStringQuiet("zap");
-    viewer.setJmolStatusListener(null);
-    viewer = null;
-
-    // We'll need to find out what other
-    // listeners need to be shut down in Jmol
-    StructureSelectionManager.getStructureSelectionManager()
-            .removeStructureViewerListener(this, pdbentry.getFile());
+    jmb.closeViewer();
+    // TODO: check for memory leaks where instance isn't finalised because jmb
+    // holds a reference to the window
+    jmb = null;
   }
 
+  /**
+   * state flag for PDB retrieval thread
+   */
+  private boolean _started = false;
+
   public void run()
   {
+    _started = true;
+    String pdbid = "";
+    // todo - record which pdbids were successfuly imported.
+    StringBuffer errormsgs = new StringBuffer(), files = new StringBuffer();
     try
     {
+      String[] curfiles = jmb.getPdbFile(); // files currently in viewer
       // TODO: replace with reference fetching/transfer code (validate PDBentry
       // as a DBRef?)
       jalview.ws.dbsources.Pdb pdbclient = new jalview.ws.dbsources.Pdb();
-      AlignmentI pdbseq;
-      if ((pdbseq = pdbclient.getSequenceRecords(pdbentry.getId())) != null)
-      {
-        // just transfer the file name from the first seuqence's first PDBEntry
-        pdbentry.setFile(((PDBEntry) pdbseq.getSequenceAt(0).getPDBId()
-                .elementAt(0)).getFile());
-        initJmol("load " + pdbentry.getFile());
-      }
-      else
+      for (int pi = 0; pi < jmb.pdbentry.length; pi++)
       {
-        JOptionPane
-                .showInternalMessageDialog(
-                        Desktop.desktop,
-                        pdbentry.getId()
-                                + " could not be retrieved. Please try downloading the file manually.",
-                        "Couldn't load file", JOptionPane.ERROR_MESSAGE);
-
+        String file = jmb.pdbentry[pi].getFile();
+        if (file == null)
+        {
+          // retrieve the pdb and store it locally
+          AlignmentI pdbseq = null;
+          pdbid = jmb.pdbentry[pi].getId();
+          long hdl=pdbid.hashCode()-System.currentTimeMillis();
+          if (progressBar != null)
+          {
+            progressBar.setProgressBar("Fetching PDB " + pdbid,
+                    hdl);
+          }
+          try
+          {
+            pdbseq = pdbclient.getSequenceRecords(pdbid = jmb.pdbentry[pi]
+                    .getId());
+          } catch (OutOfMemoryError oomerror)
+          {
+            new OOMWarning("Retrieving PDB id " + pdbid, oomerror);
+          } catch (Exception ex)
+          {
+            ex.printStackTrace();
+            errormsgs.append("'" + pdbid + "'");
+          }
+          if (progressBar != null)
+          {
+            progressBar.setProgressBar("Finished.", hdl);
+          }
+          if (pdbseq != null)
+          {
+            // just transfer the file name from the first sequence's first
+            // PDBEntry
+            jmb.pdbentry[pi].setFile(file = ((PDBEntry) pdbseq
+                    .getSequenceAt(0).getPDBId().elementAt(0)).getFile());
+            files.append(" \"" + file + "\"");
+          }
+          else
+          {
+            errormsgs.append("'" + pdbid + "' ");
+          }
+        }
+        else
+        {
+          if (curfiles != null && curfiles.length > 0)
+          {
+            addingStructures = true; // already files loaded.
+            for (int c = 0; c < curfiles.length; c++)
+            {
+              if (curfiles[c].equals(file))
+              {
+                file = null;
+                break;
+              }
+            }
+          }
+          if (file != null)
+          {
+            files.append(" \"" + file + "\"");
+          }
+        }
       }
     } catch (OutOfMemoryError oomerror)
     {
-      new OOMWarning("Retrieving PDB id " + pdbentry.getId() + " from MSD",
-              oomerror);
+      new OOMWarning("Retrieving PDB files: " + pdbid, oomerror);
     } catch (Exception ex)
     {
       ex.printStackTrace();
+      errormsgs.append("When retrieving pdbfiles : current was: '" + pdbid
+              + "'");
+    }
+    if (errormsgs.length() > 0)
+    {
+
+      JOptionPane.showInternalMessageDialog(Desktop.desktop,
+              "The following pdb entries could not be retrieved from the PDB:\n"
+                      + errormsgs.toString()
+                      + "\nPlease try downloading them manually.",
+              "Couldn't load file", JOptionPane.ERROR_MESSAGE);
+
     }
+    if (files.length() > 0)
+    {
+      if (!addingStructures)
+      {
+
+        try
+        {
+          initJmol("load FILES " + files.toString());
+        } catch (OutOfMemoryError oomerror)
+        {
+          new OOMWarning("When trying to open the Jmol viewer!", oomerror);
+          Cache.log.debug("File locations are " + files);
+        } catch (Exception ex)
+        {
+          Cache.log.error("Couldn't open Jmol viewer!", ex);
+        }
+      }
+      else
+      {
+        StringBuffer cmd = new StringBuffer();
+        cmd.append("loadingJalviewdata=true\nload APPEND ");
+        cmd.append(files.toString());
+        cmd.append("\nloadingJalviewdata=null");
+        final String command = cmd.toString();
+        cmd = null;
+        try
+        {
+          jmb.evalStateCommand(command);
+        } catch (OutOfMemoryError oomerror)
+        {
+          new OOMWarning(
+                  "When trying to add structures to the Jmol viewer!",
+                  oomerror);
+          Cache.log.debug("File locations are " + files);
+        } catch (Exception ex)
+        {
+          Cache.log.error("Couldn't add files to Jmol viewer!", ex);
+        }
+          long lastnotify=jmb.getLoadNotifiesHandled();
+          // need to wait around until script has finished
+          while (lastnotify>=jmb.getLoadNotifiesHandled()); 
+          {
+            try
+            {
+              Thread.sleep(35);
+            } catch (Exception e)
+            {
+            }
+          }
+          // refresh the sequence colours for the new structure(s)
+          jmb.updateColours(ap);
+          // do superposition if asked to
+          if (alignAddedStructures)
+          {
+            javax.swing.SwingUtilities.invokeLater(new Runnable()
+          {
+            public void run()
+            {
+              jmb.superposeStructures(ap.av.getAlignment(), -1, null);
+            }
+          });
+          alignAddedStructures = false;
+        }
+        addingStructures = false;
+      }
+    }
+    _started = false;
+    worker = null;
   }
 
   public void pdbFile_actionPerformed(ActionEvent actionEvent)
   {
-    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
-            .getProperty("LAST_DIRECTORY"));
+    JalviewFileChooser chooser = new JalviewFileChooser(
+            jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
 
     chooser.setFileView(new JalviewFileView());
     chooser.setDialogTitle("Save PDB File");
@@ -361,8 +603,9 @@ public class AppJmol extends GStructureViewer implements StructureListener,
     {
       try
       {
-        BufferedReader in = new BufferedReader(new FileReader(pdbentry
-                .getFile()));
+        // TODO: cope with multiple PDB files in view
+        BufferedReader in = new BufferedReader(new FileReader(
+                jmb.getPdbFile()[0]));
         File outFile = chooser.getSelectedFile();
 
         PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
@@ -385,10 +628,25 @@ public class AppJmol extends GStructureViewer implements StructureListener,
   public void viewMapping_actionPerformed(ActionEvent actionEvent)
   {
     jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();
+    try
+    {
+      for (int pdbe = 0; pdbe < jmb.pdbentry.length; pdbe++)
+      {
+        cap.appendText(StructureSelectionManager
+                .getStructureSelectionManager().printMapping(
+                        jmb.pdbentry[pdbe].getFile()));
+        cap.appendText("\n");
+      }
+    } catch (OutOfMemoryError e)
+    {
+      new OOMWarning(
+              "composing sequence-structure alignments for display in text box.",
+              e);
+      cap.dispose();
+      return;
+    }
     jalview.gui.Desktop.addInternalFrame(cap, "PDB - Sequence Mapping",
             550, 600);
-    cap.setText(StructureSelectionManager.getStructureSelectionManager()
-            .printMapping(pdbentry.getFile()));
   }
 
   /**
@@ -428,107 +686,83 @@ public class AppJmol extends GStructureViewer implements StructureListener,
     else
     {
       im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.EPS,
-              "Make EPS file from view", width, height, null, this
-                      .getTitle());
+              "Make EPS file from view", width, height, null,
+              this.getTitle());
     }
 
     if (im.getGraphics() != null)
     {
       Rectangle rect = new Rectangle(width, height);
-      viewer.renderScreenImage(im.getGraphics(), rect.getSize(), rect);
+      jmb.viewer.renderScreenImage(im.getGraphics(), rect.getSize(), rect);
       im.writeImage();
     }
   }
 
   public void seqColour_actionPerformed(ActionEvent actionEvent)
   {
-    lastCommand = null;
-    colourBySequence = seqColour.isSelected();
-    colourBySequence(ap.alignFrame.alignPanel);
+    jmb.setColourBySequence(seqColour.isSelected());
+    // Set the colour using the current view for the associated alignframe
+    jmb.colourBySequence(ap.alignFrame.viewport.showSequenceFeatures,
+            ap.alignFrame.viewport.alignment);
   }
 
   public void chainColour_actionPerformed(ActionEvent actionEvent)
   {
-    colourBySequence = false;
-    seqColour.setSelected(false);
-    viewer.evalStringQuiet("select *;color chain");
+    chainColour.setSelected(true);
+    jmb.colourByChain();
   }
 
   public void chargeColour_actionPerformed(ActionEvent actionEvent)
   {
-    colourBySequence = false;
-    seqColour.setSelected(false);
-    viewer.evalStringQuiet("select *;color white;select ASP,GLU;color red;"
-            + "select LYS,ARG;color blue;select CYS;color yellow");
+    chargeColour.setSelected(true);
+    jmb.colourByCharge();
   }
 
   public void zappoColour_actionPerformed(ActionEvent actionEvent)
   {
-    setJalviewColourScheme(new ZappoColourScheme());
+    zappoColour.setSelected(true);
+    jmb.setJalviewColourScheme(new ZappoColourScheme());
   }
 
   public void taylorColour_actionPerformed(ActionEvent actionEvent)
   {
-    setJalviewColourScheme(new TaylorColourScheme());
+    taylorColour.setSelected(true);
+    jmb.setJalviewColourScheme(new TaylorColourScheme());
   }
 
   public void hydroColour_actionPerformed(ActionEvent actionEvent)
   {
-    setJalviewColourScheme(new HydrophobicColourScheme());
+    hydroColour.setSelected(true);
+    jmb.setJalviewColourScheme(new HydrophobicColourScheme());
   }
 
   public void helixColour_actionPerformed(ActionEvent actionEvent)
   {
-    setJalviewColourScheme(new HelixColourScheme());
+    helixColour.setSelected(true);
+    jmb.setJalviewColourScheme(new HelixColourScheme());
   }
 
   public void strandColour_actionPerformed(ActionEvent actionEvent)
   {
-    setJalviewColourScheme(new StrandColourScheme());
+    strandColour.setSelected(true);
+    jmb.setJalviewColourScheme(new StrandColourScheme());
   }
 
   public void turnColour_actionPerformed(ActionEvent actionEvent)
   {
-    setJalviewColourScheme(new TurnColourScheme());
+    turnColour.setSelected(true);
+    jmb.setJalviewColourScheme(new TurnColourScheme());
   }
 
   public void buriedColour_actionPerformed(ActionEvent actionEvent)
   {
-    setJalviewColourScheme(new BuriedColourScheme());
-  }
-
-  public void setJalviewColourScheme(ColourSchemeI cs)
-  {
-    colourBySequence = false;
-    seqColour.setSelected(false);
-
-    if (cs == null)
-      return;
-
-    String res;
-    int index;
-    Color col;
-
-    Enumeration en = ResidueProperties.aa3Hash.keys();
-    StringBuffer command = new StringBuffer("select *;color white;");
-    while (en.hasMoreElements())
-    {
-      res = en.nextElement().toString();
-      index = ((Integer) ResidueProperties.aa3Hash.get(res)).intValue();
-      if (index > 20)
-        continue;
-
-      col = cs.findColour(ResidueProperties.aa[index].charAt(0));
-
-      command.append("select " + res + ";color[" + col.getRed() + ","
-              + col.getGreen() + "," + col.getBlue() + "];");
-    }
-
-    viewer.evalStringQuiet(command.toString());
+    buriedColour.setSelected(true);
+    jmb.setJalviewColourScheme(new BuriedColourScheme());
   }
 
   public void userColour_actionPerformed(ActionEvent actionEvent)
   {
+    userColour.setSelected(true);
     new UserDefinedColours(this, null);
   }
 
@@ -536,11 +770,9 @@ public class AppJmol extends GStructureViewer implements StructureListener,
   {
     java.awt.Color col = JColorChooser.showDialog(this,
             "Select Background Colour", null);
-
     if (col != null)
     {
-      viewer.evalStringQuiet("background [" + col.getRed() + ","
-              + col.getGreen() + "," + col.getBlue() + "];");
+      jmb.setBackgroundColour(col);
     }
   }
 
@@ -554,370 +786,8 @@ public class AppJmol extends GStructureViewer implements StructureListener,
     {
     }
   }
-
-  // ////////////////////////////////
-  // /StructureListener
-  public String getPdbFile()
-  {
-    return pdbentry.getFile();
-  }
-
-  Pattern pattern = Pattern
-          .compile("\\[(.*)\\]([0-9]+)(:[a-zA-Z]*)?\\.([a-zA-Z]+)(/[0-9]*)?");
-
-  String lastMessage;
-
-  public void mouseOverStructure(int atomIndex, String strInfo)
-  {
-    Matcher matcher = pattern.matcher(strInfo);
-    matcher.find();
-    matcher.group(1);
-    int pdbResNum = Integer.parseInt(matcher.group(2));
-    String chainId = matcher.group(3);
-
-    if (chainId != null)
-      chainId = chainId.substring(1, chainId.length());
-    else
-    {
-      chainId = " ";
-    }
-
-    if (lastMessage == null || !lastMessage.equals(strInfo))
-    {
-      ssm.mouseOverStructure(pdbResNum, chainId, pdbentry.getFile());
-    }
-    lastMessage = strInfo;
-  }
-
-  StringBuffer resetLastRes = new StringBuffer();
-
-  StringBuffer eval = new StringBuffer();
-
-  public void highlightAtom(int atomIndex, int pdbResNum, String chain,
-          String pdbfile)
-  {
-    // TODO: rna: remove CA dependency in select string
-    if (!pdbfile.equals(pdbentry.getFile()))
-      return;
-
-    if (resetLastRes.length() > 0)
-    {
-      viewer.evalStringQuiet(resetLastRes.toString());
-    }
-
-    eval.setLength(0);
-    eval.append("select " + pdbResNum);
-
-    resetLastRes.setLength(0);
-    resetLastRes.append("select " + pdbResNum);
-
-    eval.append(":");
-    resetLastRes.append(":");
-    if (!chain.equals(" "))
-    {
-      eval.append(chain);
-      resetLastRes.append(chain);
-    }
-
-    eval.append(";wireframe 100;" + eval.toString() + " and not hetero;"); // ".*;");
-
-    resetLastRes.append(";wireframe 0;" + resetLastRes.toString()
-    // + ".*;spacefill 0;");
-            + " and not hetero;spacefill 0;");
-
-    eval.append("spacefill 200;select none");
-    // System.out.println("jmol:\n"+eval+"\n");
-    viewer.evalStringQuiet(eval.toString());
-  }
-
-  public Color getColour(int atomIndex, int pdbResNum, String chain,
-          String pdbfile)
-  {
-    if (!pdbfile.equals(pdbentry.getFile()))
-      return null;
-
-    return new Color(viewer.getAtomArgb(atomIndex));
-  }
-
-  public void updateColours(Object source)
-  {
-    colourBySequence((AlignmentPanel) source);
-  }
-
-  // End StructureListener
-  // //////////////////////////
-
-  String lastCommand;
-
-  FeatureRenderer fr = null;
-
-  public void colourBySequence(AlignmentPanel sourceap)
-  {
-    this.ap = sourceap;
-
-    if (!colourBySequence || ap.alignFrame.getCurrentView() != ap.av)
-      return;
-
-    StructureMapping[] mapping = ssm.getMapping(pdbentry.getFile());
-
-    if (mapping.length < 1)
-      return;
-
-    SequenceRenderer sr = new SequenceRenderer(ap.av);
-
-    boolean showFeatures = false;
-
-    if (ap.av.showSequenceFeatures)
-    {
-      showFeatures = true;
-      if (fr == null)
-      {
-        fr = new jalview.gui.FeatureRenderer(ap);
-      }
-
-      fr.transferSettings(ap.seqPanel.seqCanvas.getFeatureRenderer());
-    }
-
-    StringBuffer command = new StringBuffer();
-
-    int lastPos = -1;
-    for (int sp, s = 0; s < sequence.length; s++)
-    {
-      for (int m = 0; m < mapping.length; m++)
-      {
-        if (mapping[m].getSequence() == sequence[s]
-                && (sp = ap.av.alignment.findIndex(sequence[s])) > -1)
-        {
-          SequenceI asp = ap.av.alignment.getSequenceAt(sp);
-          for (int r = 0; r < asp.getLength(); r++)
-          {
-            // No mapping to gaps in sequence.
-            if (jalview.util.Comparison.isGap(asp.getCharAt(r)))
-            {
-              continue;
-            }
-            int pos = mapping[m].getPDBResNum(asp.findPosition(r));
-
-            if (pos < 1 || pos == lastPos)
-              continue;
-
-            lastPos = pos;
-
-            Color col = sr.getResidueBoxColour(asp, r);
-
-            if (showFeatures)
-              col = fr.findFeatureColour(col, asp, r);
-
-            if (command.toString().endsWith(
-                    ":" + mapping[m].getChain() + ";color[" + col.getRed()
-                            + "," + col.getGreen() + "," + col.getBlue()
-                            + "]"))
-            {
-              command = condenseCommand(command, pos);
-              continue;
-            }
-
-            command.append(";select " + pos);
-
-            if (!mapping[m].getChain().equals(" "))
-            {
-              command.append(":" + mapping[m].getChain());
-            }
-
-            command.append(";color[" + col.getRed() + "," + col.getGreen()
-                    + "," + col.getBlue() + "]");
-
-          }
-          break;
-        }
-      }
-    }
-
-    if (lastCommand == null || !lastCommand.equals(command.toString()))
-    {
-      viewer.evalStringQuiet(command.toString());
-    }
-    lastCommand = command.toString();
-  }
-
-  StringBuffer condenseCommand(StringBuffer command, int pos)
-  {
-    StringBuffer sb = new StringBuffer(command.substring(0, command
-            .lastIndexOf("select") + 7));
-
-    command.delete(0, sb.length());
-
-    String start;
-
-    if (command.indexOf("-") > -1)
-    {
-      start = command.substring(0, command.indexOf("-"));
-    }
-    else
-    {
-      start = command.substring(0, command.indexOf(":"));
-    }
-
-    sb.append(start + "-" + pos + command.substring(command.indexOf(":")));
-
-    return sb;
-  }
-
-  // ///////////////////////////////
-  // JmolStatusListener
-
-  public String eval(String strEval)
-  {
-    // System.out.println(strEval);
-    // "# 'eval' is implemented only for the applet.";
-    return null;
-  }
-
-  public void createImage(String file, String type, int quality)
-  {
-    System.out.println("JMOL CREATE IMAGE");
-  }
-
-  public void notifyFileLoaded(String fullPathName, String fileName,
-          String modelName, String errorMsg, int modelParts)
-  {
-    if (errorMsg != null)
-    {
-      fileLoadingError = errorMsg;
-      repaint();
-      return;
-    }
-
-    fileLoadingError = null;
-
-    if (fileName != null)
-    {
-      // TODO: do some checking using the modelPts number of parts against our own estimate of the number of chains
-      // FILE LOADED OK
-      ssm = StructureSelectionManager.getStructureSelectionManager();
-      MCview.PDBfile pdbFile = ssm.setMapping(sequence, chains, pdbentry
-              .getFile(), AppletFormatAdapter.FILE);
-      ssm.addStructureViewerListener(this);
-      Vector chains = new Vector();
-      for (int i = 0; i < pdbFile.chains.size(); i++)
-      {
-        chains
-                .addElement(((MCview.PDBChain) pdbFile.chains.elementAt(i)).id);
-      }
-      setChainMenuItems(chains);
-
-      jmolpopup.updateComputedMenus();
-
-      if (!loadingFromArchive)
-      {
-        viewer
-                .evalStringQuiet("select backbone;restrict;cartoon;wireframe off;spacefill off");
-
-        colourBySequence(ap);
-      }
-      if (fr != null)
-        fr.featuresAdded();
-
-      loadingFromArchive = false;
-    }
-    else
-      return;
-  }
-
-  public void sendConsoleEcho(String strEcho)
-  {
-    if (scriptWindow != null)
-      scriptWindow.sendConsoleEcho(strEcho);
-  }
-
-  public void sendConsoleMessage(String strStatus)
-  {
-    if (scriptWindow != null)
-      scriptWindow.sendConsoleMessage(strStatus);
-  }
-
-  public void notifyScriptTermination(String strStatus, int msWalltime)
-  {
-    if (scriptWindow != null)
-      scriptWindow.notifyScriptTermination(strStatus, msWalltime);
-  }
-
-  public void handlePopupMenu(int x, int y)
-  {
-    jmolpopup.show(x, y);
-  }
-
-  public void notifyNewPickingModeMeasurement(int iatom, String strMeasure)
-  {
-    notifyAtomPicked(iatom, strMeasure, null);
-  }
-
-  public void notifyAtomPicked(int atomIndex, String strInfo, String strData)
-  {
-    if (strData!=null)
-    {
-      Cache.log.info("Non null pick data string: "+strData+" (other info: '"+strInfo+"' pos "+atomIndex+")");
-    }
-    Matcher matcher = pattern.matcher(strInfo);
-    matcher.find();
-
-    matcher.group(1);
-    String resnum = new String(matcher.group(2));
-    String chainId = matcher.group(3);
-
-    String picked = resnum;
-
-    if (chainId != null)
-      picked += (":" + chainId.substring(1, chainId.length()));
-
-    picked = "(("+picked+".CA" + ")|("+picked+".P"+"))";
-
-    if (!atomsPicked.contains(picked))
-    {
-      if (chainId != null)
-        viewer.evalString("select " + picked + ";label %n %r:%c");
-      else
-        viewer.evalString("select " + picked + ";label %n %r");
-      atomsPicked.addElement(picked);
-    }
-    else
-    {
-      viewer.evalString("select " + picked + ";label off");
-      atomsPicked.removeElement(picked);
-    }
-
-    if (scriptWindow != null)
-    {
-      scriptWindow.sendConsoleMessage(strInfo);
-      scriptWindow.sendConsoleMessage("\n");
-    }
-  }
-
-  public void notifyAtomHovered(int atomIndex, String strInfo, String data)
-  {
-    if (data!=null)
-    {
-      Cache.log.info("Non null hover data string: "+data+" (other info: '"+strInfo+"' pos "+atomIndex+")");
-    }
-    mouseOverStructure(atomIndex, strInfo);
-  }
-
-  @Override
-  public void showUrl(String url)
-  {
-    try {
-      jalview.util.BrowserLauncher.openURL(url);
-    } catch (IOException e)
-    {
-      Cache.log.error("Failed to launch Jmol-associated url "+url,e);
-      // TODO: 2.6 : warn user if browser was not configured.
-    }
-  }
-
   public void showConsole(boolean showConsole)
   {
-    if (scriptWindow == null)
-      scriptWindow = new ScriptWindow(this);
 
     if (showConsole)
     {
@@ -927,15 +797,19 @@ public class AppJmol extends GStructureViewer implements StructureListener,
         splitPane.setTopComponent(renderPanel);
         splitPane.setBottomComponent(scriptWindow);
         this.getContentPane().add(splitPane, BorderLayout.CENTER);
+        splitPane.setDividerLocation(getHeight() - 200);
+        scriptWindow.setVisible(true);
+        scriptWindow.validate();
+        splitPane.validate();
       }
 
-      splitPane.setDividerLocation(getHeight() - 200);
-      splitPane.validate();
     }
     else
     {
       if (splitPane != null)
-        splitPane.setVisible(false);
+        {
+          splitPane.setVisible(false);
+        }
 
       splitPane = null;
 
@@ -945,14 +819,6 @@ public class AppJmol extends GStructureViewer implements StructureListener,
     validate();
   }
 
-  public float[][] functionXY(String functionName, int x, int y)
-  {
-    return null;
-  }
-
-  // /End JmolStatusListener
-  // /////////////////////////////
-
   class RenderPanel extends JPanel
   {
     final Dimension currentSize = new Dimension();
@@ -964,26 +830,42 @@ public class AppJmol extends GStructureViewer implements StructureListener,
       getSize(currentSize);
       g.getClipBounds(rectClip);
 
-      if (viewer == null)
+      if (jmb.fileLoadingError != null)
       {
         g.setColor(Color.black);
         g.fillRect(0, 0, currentSize.width, currentSize.height);
         g.setColor(Color.white);
         g.setFont(new Font("Verdana", Font.BOLD, 14));
-        g.drawString("Retrieving PDB data....", 20, currentSize.height / 2);
+        g.drawString("Error loading file...", 20, currentSize.height / 2);
+        StringBuffer sb = new StringBuffer();
+        int lines = 0;
+        for (int e = 0; e < jmb.pdbentry.length; e++)
+        {
+          sb.append(jmb.pdbentry[e].getId());
+          if (e < jmb.pdbentry.length - 1)
+          {
+            sb.append(",");
+          }
+
+          if (e == jmb.pdbentry.length - 1 || sb.length() > 20)
+          {
+            lines++;
+            g.drawString(sb.toString(), 20, currentSize.height / 2 - lines
+                    * g.getFontMetrics().getHeight());
+          }
+        }
       }
-      else if (fileLoadingError != null)
+      else if (jmb == null || jmb.viewer == null || !jmb.isFinishedInit())
       {
         g.setColor(Color.black);
         g.fillRect(0, 0, currentSize.width, currentSize.height);
         g.setColor(Color.white);
         g.setFont(new Font("Verdana", Font.BOLD, 14));
-        g.drawString("Error loading file..." + pdbentry.getId(), 20,
-                currentSize.height / 2);
+        g.drawString("Retrieving PDB data....", 20, currentSize.height / 2);
       }
       else
       {
-        viewer.renderScreenImage(g, currentSize, rectClip);
+        jmb.viewer.renderScreenImage(g, currentSize, rectClip);
       }
     }
   }
@@ -999,96 +881,50 @@ public class AppJmol extends GStructureViewer implements StructureListener,
     return viewId;
   }
 
-  @Override
-  public String createImage(String fileName, String type,
-          Object textOrBytes, int quality)
+  public void updateTitleAndMenus()
   {
-    // TODO Auto-generated method stub
-    return null;
-  }
-
-  @Override
-  public float[][][] functionXYZ(String functionName, int nx, int ny, int nz)
-  {
-    // TODO Auto-generated method stub
-    return null;
-  }
-
-  @Override
-  public Hashtable getRegistryInfo()
-  {
-    // TODO Auto-generated method stub
-    return null;
-  }
-
-  @Override
-  public void notifyCallback(int type, Object[] data)
-  {
-    try {
-    switch (type)
+    if (jmb.fileLoadingError != null && jmb.fileLoadingError.length() > 0)
     {
-    case JmolConstants.CALLBACK_LOADSTRUCT:
-      notifyFileLoaded((String) data[1], (String) data[2], 
-              (String) data[3], (String) data[4], ((Integer) data[5]).intValue());
-              
-      break;
-    case JmolConstants.CALLBACK_PICK:
-      notifyAtomPicked(((Integer) data[2]).intValue(), (String) data[1], (String) data[0]);
-      // also highlight in alignment
-    case JmolConstants.CALLBACK_HOVER:
-      notifyAtomHovered(((Integer) data[2]).intValue(), (String) data[1], (String) data[0]);
-      break;
-    case JmolConstants.CALLBACK_SCRIPT:
-      notifyScriptTermination((String)data[2], ((Integer)data[3]).intValue());
-      break;
-    case JmolConstants.CALLBACK_ECHO:
-      sendConsoleEcho((String)data[1]);
-      break;
-    case JmolConstants.CALLBACK_MESSAGE:
-      sendConsoleMessage((data==null) ? ((String) null) : (String)data[1]);
-      break;
-    case JmolConstants.CALLBACK_MEASURE:
-    case JmolConstants.CALLBACK_CLICK:
-      default:
-        System.err.println("Unhandled callback "+type+" "+data);
-        break;
-    }
+      repaint();
+      return;
     }
-    catch (Exception e)
+    setChainMenuItems(jmb.chainNames);
+    jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap.av.alignment);
+
+    this.setTitle(jmb.getViewerTitle());
+    if (jmb.getPdbFile().length > 1 && jmb.sequence.length > 1)
     {
-      Cache.log.warn("Squashed Jmol callback handler error: ",e);
+      jmolActionMenu.setVisible(true);
     }
   }
 
+  /*
+   * (non-Javadoc)
+   * 
+   * @see
+   * jalview.jbgui.GStructureViewer#alignStructs_actionPerformed(java.awt.event
+   * .ActionEvent)
+   */
   @Override
-  public boolean notifyEnabled(int callbackPick)
+  protected void alignStructs_actionPerformed(ActionEvent actionEvent)
   {
-    switch (callbackPick)
+
+    try
     {
-    case JmolConstants.CALLBACK_ECHO:
-    case JmolConstants.CALLBACK_LOADSTRUCT:
-    case JmolConstants.CALLBACK_MEASURE:
-    case JmolConstants.CALLBACK_MESSAGE:
-    case JmolConstants.CALLBACK_PICK:
-    case JmolConstants.CALLBACK_SCRIPT:
-    case JmolConstants.CALLBACK_HOVER:
-    case JmolConstants.CALLBACK_ERROR:
-      return true;
-    case JmolConstants.CALLBACK_CLICK:
-      case JmolConstants.CALLBACK_ANIMFRAME:
-    case JmolConstants.CALLBACK_MINIMIZATION:
-    case JmolConstants.CALLBACK_RESIZE:
-    case JmolConstants.CALLBACK_SYNC:
+      jmb.superposeStructures(ap.av.getAlignment(), -1,
+              ap.av.getColumnSelection());
+    } catch (Exception e)
+    {
+      Cache.log.info("Couldn't align structures in alignframe "
+              + ap.alignFrame.getTitle(), e);
+
     }
-    return false;
   }
 
-  @Override
-  public void setCallbackFunction(String callbackType,
-          String callbackFunction)
+  public void setJalviewColourScheme(ColourSchemeI ucs)
   {
-    Cache.log.debug("Ignoring set-callback request to associate "+callbackType+" with function "+callbackFunction);
-    
+    jmb.setJalviewColourScheme(ucs);
+
   }
 
 }