X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAppletJmol.java;h=f3d7fa7b1f1f0ec9618a1facb72c6375c26e9234;hb=2026a420963f094072607c0495b6369ba96e60c0;hp=980985914e65256fe435aada4bd5d9d3f63c2242;hpb=f8456d4c0b253ae32a4b569e12bb8bf7f7096d65;p=jalview.git

diff --git a/src/jalview/appletgui/AppletJmol.java b/src/jalview/appletgui/AppletJmol.java
index 9809859..f3d7fa7 100644
--- a/src/jalview/appletgui/AppletJmol.java
+++ b/src/jalview/appletgui/AppletJmol.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -27,15 +27,15 @@ import jalview.structure.*;
 import jalview.io.*;
 
 import org.jmol.api.*;
-import org.jmol.adapter.smarter.SmarterJmolAdapter;
 
 import org.jmol.popup.*;
 import org.jmol.viewer.JmolConstants;
 
 import jalview.schemes.*;
 
-public class AppletJmol extends EmbmenuFrame implements StructureListener,
-        JmolStatusListener, KeyListener, ActionListener, ItemListener, SequenceStructureBinding
+public class AppletJmol extends EmbmenuFrame implements
+// StructureListener,
+        KeyListener, ActionListener, ItemListener, SequenceStructureBinding
 
 {
   Menu fileMenu = new Menu("File");
@@ -52,6 +52,8 @@ public class AppletJmol extends EmbmenuFrame implements StructureListener,
 
   CheckboxMenuItem seqColour = new CheckboxMenuItem("By Sequence", true);
 
+  CheckboxMenuItem jmolColour = new CheckboxMenuItem("Using Jmol", false);
+  
   MenuItem chain = new MenuItem("By Chain");
 
   MenuItem charge = new MenuItem("Charge & Cysteine");
@@ -69,54 +71,74 @@ public class AppletJmol extends EmbmenuFrame implements StructureListener,
   MenuItem turn = new MenuItem("Turn Propensity");
 
   MenuItem buried = new MenuItem("Buried Index");
+  
+  MenuItem purinepyrimidine = new MenuItem("Purine/Pyrimidine");
 
   MenuItem user = new MenuItem("User Defined Colours");
 
   MenuItem jmolHelp = new MenuItem("Jmol Help");
 
-  JmolViewer viewer;
-
-  JmolPopup jmolpopup;
-
   Panel scriptWindow;
 
   TextField inputLine;
 
   TextArea history;
 
-  SequenceI[] sequence;
-
-  String[] chains;
-
-  StructureSelectionManager ssm;
-
   RenderPanel renderPanel;
 
   AlignmentPanel ap;
+  ArrayList _aps = new ArrayList();
 
   String fileLoadingError;
 
   boolean loadedInline;
 
-  PDBEntry pdbentry;
+  // boolean colourBySequence = true;
 
-  boolean colourBySequence = true;
+  FeatureRenderer fr = null;
 
-  Vector atomsPicked = new Vector();
+  AppletJmolBinding jmb;
 
   /**
    * datasource protocol for access to PDBEntry
    */
   String protocol = null;
 
+  /**
+   * Load a bunch of pdb entries associated with sequences in the alignment and
+   * display them - aligning them if necessary.
+   * 
+   * @param pdbentries
+   *          each pdb file (at least one needed)
+   * @param boundseqs
+   *          each set of sequences for each pdb file (must match number of pdb
+   *          files)
+   * @param boundchains
+   *          the target pdb chain corresponding with each sequence associated
+   *          with each pdb file (may be null at any level)
+   * @param align
+   *          true/false
+   * @param ap
+   *          associated alignment
+   * @param protocol
+   *          how to get pdb data
+   */
+  public AppletJmol(PDBEntry[] pdbentries, SequenceI[][] boundseqs,
+          String[][] boundchains, boolean align, AlignmentPanel ap,
+          String protocol)
+  {
+    throw new Error("Not yet implemented.");
+  }
+
   public AppletJmol(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
           AlignmentPanel ap, String protocol)
   {
     this.ap = ap;
-    this.sequence = seq;
-    this.chains = chains;
-    this.pdbentry = pdbentry;
-    this.protocol = protocol;
+    jmb = new AppletJmolBinding(this, ap.getStructureSelectionManager(), new PDBEntry[]
+    { pdbentry }, new SequenceI[][]
+    { seq }, new String[][]
+    { chains }, protocol);
+    jmb.setColourBySequence(true);
     if (pdbentry.getId() == null || pdbentry.getId().length() < 1)
     {
       if (protocol.equals(AppletFormatAdapter.PASTE))
@@ -137,12 +159,12 @@ public class AppletJmol extends EmbmenuFrame implements StructureListener,
     }
 
     String alreadyMapped = StructureSelectionManager
-            .getStructureSelectionManager().alreadyMappedToFile(
+            .getStructureSelectionManager(ap.av.applet).alreadyMappedToFile(
                     pdbentry.getId());
     MCview.PDBfile reader = null;
     if (alreadyMapped != null)
     {
-      reader = StructureSelectionManager.getStructureSelectionManager()
+      reader = StructureSelectionManager.getStructureSelectionManager(ap.av.applet)
               .setMapping(seq, chains, pdbentry.getFile(), protocol);
       // PROMPT USER HERE TO ADD TO NEW OR EXISTING VIEW?
       // FOR NOW, LETS JUST OPEN A NEW WINDOW
@@ -160,14 +182,16 @@ public class AppletJmol extends EmbmenuFrame implements StructureListener,
     hydro.addActionListener(this);
     chain.addActionListener(this);
     seqColour.addItemListener(this);
+    jmolColour.addItemListener(this);
     zappo.addActionListener(this);
     taylor.addActionListener(this);
     helix.addActionListener(this);
     strand.addActionListener(this);
     turn.addActionListener(this);
     buried.addActionListener(this);
+    purinepyrimidine.addActionListener(this);
     user.addActionListener(this);
-
+    
     jmolHelp.addActionListener(this);
 
     coloursMenu.add(seqColour);
@@ -180,21 +204,38 @@ public class AppletJmol extends EmbmenuFrame implements StructureListener,
     coloursMenu.add(strand);
     coloursMenu.add(turn);
     coloursMenu.add(buried);
+    coloursMenu.add(purinepyrimidine);
     coloursMenu.add(user);
-
+    coloursMenu.add(jmolColour);
     helpMenu.add(jmolHelp);
+    this.setLayout(new BorderLayout());
 
     setMenuBar(menuBar);
 
     renderPanel = new RenderPanel();
     embedMenuIfNeeded(renderPanel);
     this.add(renderPanel, BorderLayout.CENTER);
-    viewer = JmolViewer.allocateViewer(renderPanel,
-            new SmarterJmolAdapter(), "jalviewJmol", ap.av.applet
-                    .getDocumentBase(), ap.av.applet.getCodeBase(), "",
-            this);
+    scriptWindow = new Panel();
+    scriptWindow.setVisible(false);
+    // this.add(scriptWindow, BorderLayout.SOUTH);
 
-    jmolpopup = JmolPopup.newJmolPopup(viewer, true, "Jmol", true);
+    try
+    {
+      jmb.allocateViewer(renderPanel, true, ap.av.applet.getName()
+              + "_jmol_", ap.av.applet.getDocumentBase(),
+              ap.av.applet.getCodeBase(), "-applet", scriptWindow, null);
+    } catch (Exception e)
+    {
+      System.err
+              .println("Couldn't create a jmol viewer. Args to allocate viewer were:\nDocumentBase="
+                      + ap.av.applet.getDocumentBase()
+                      + "\nCodebase="
+                      + ap.av.applet.getCodeBase());
+      e.printStackTrace();
+      dispose();
+      return;
+    }
+    jmb.newJmolPopup(true, "Jmol", true);
 
     this.addWindowListener(new WindowAdapter()
     {
@@ -203,18 +244,24 @@ public class AppletJmol extends EmbmenuFrame implements StructureListener,
         closeViewer();
       }
     });
-
+    if (pdbentry.getProperty() == null)
+    {
+      pdbentry.setProperty(new Hashtable());
+      pdbentry.getProperty().put("protocol", protocol);
+    }
     if (pdbentry.getFile() != null)
     {
       // import structure data from pdbentry.getFile based on given protocol
       if (protocol.equals(AppletFormatAdapter.PASTE))
       {
+        // TODO: JAL-623 : correctly record file contents for matching up later
+        // pdbentry.getProperty().put("pdbfilehash",""+pdbentry.getFile().hashCode());
         loadInline(pdbentry.getFile());
       }
       else if (protocol.equals(AppletFormatAdapter.FILE)
               || protocol.equals(AppletFormatAdapter.URL))
       {
-        viewer.openFile(pdbentry.getFile());
+        jmb.viewer.openFile(pdbentry.getFile());
       }
       else
       {
@@ -257,7 +304,8 @@ public class AppletJmol extends EmbmenuFrame implements StructureListener,
             throw new Exception(
                     "Invalid datasource. Could not obtain Reader.");
           }
-          viewer.openReader(pdbentry.getFile(), pdbentry.getId(), freader);
+          jmb.viewer.openReader(pdbentry.getFile(), pdbentry.getId(),
+                  freader);
         } catch (Exception e)
         {
           // give up!
@@ -269,28 +317,13 @@ public class AppletJmol extends EmbmenuFrame implements StructureListener,
       }
     }
 
-    jalview.bin.JalviewLite.addFrame(this, "Jmol", 400, 400);
-  }
-
-  /**
-   * create a new binding between structures in an existing jmol viewer instance and
-   * an alignpanel with sequences that have existing PDBFile entries. Note, this does not open a new Jmol window, 
-   * or modify the display of the structures in the original jmol window.
-   * @param viewer2
-   * @param alignPanel
-   * @param seqs - sequences to search for associations
-   */
-  public AppletJmol(JmolViewer viewer2, AlignmentPanel alignPanel,
-          SequenceI[] seqs)
-  {
-    
-    // TODO Auto-generated constructor stub
+    jalview.bin.JalviewLite.addFrame(this, jmb.getViewerTitle(), 400, 400);
   }
 
   public void loadInline(String string)
   {
     loadedInline = true;
-    viewer.openStringInline(string);
+    jmb.loadInline(string);
   }
 
   void setChainMenuItems(Vector chains)
@@ -316,10 +349,9 @@ public class AppletJmol extends EmbmenuFrame implements StructureListener,
 
   void centerViewer()
   {
-    jmolHistory(false);
-    StringBuffer cmd = new StringBuffer();
+    Vector toshow = new Vector();
     String lbl;
-    int mlength, p,mnum;
+    int mlength, p, mnum;
     for (int i = 0; i < chainMenu.getItemCount(); i++)
     {
       if (chainMenu.getItem(i) instanceof CheckboxMenuItem)
@@ -327,64 +359,22 @@ public class AppletJmol extends EmbmenuFrame implements StructureListener,
         CheckboxMenuItem item = (CheckboxMenuItem) chainMenu.getItem(i);
         if (item.getState())
         {
-          lbl = item.getLabel();
-          mlength = 0;
-          do
-          {
-            p = mlength;
-            mlength = lbl.indexOf(":", p);
-          } while (p < mlength && mlength < (lbl.length() - 2));
-                  mnum = 1+getModelNum(lbl.substring(0, mlength));
-        if (mnum>0)
-          {cmd.append(":" + lbl.substring(mlength + 1) + " /"
-                + mnum + " or ");
-          }
+          toshow.addElement(item.getLabel());
         }
       }
     }
-
-    if (cmd.length() > 0)
-      cmd.setLength(cmd.length() - 4);
-
-    viewer
-            .evalString("select *;restrict " + cmd + ";cartoon;center "
-                    + cmd);
-    jmolHistory(true);
-  }
-
-  private int getModelNum(String modelFileName)
-  {
-    String[] mfn = getPdbFile();
-    if (mfn == null)
-    {
-      return -1;
-    }
-    for (int i = 0; i < mfn.length; i++)
-    {
-      if (mfn[i].equalsIgnoreCase(modelFileName))
-        return i;
-    }
-    return -1;
+    jmb.centerViewer(toshow);
   }
 
   void closeViewer()
   {
-    viewer.setModeMouse(org.jmol.viewer.JmolConstants.MOUSE_NONE);
-    // remove listeners for all structures in viewer
-    StructureSelectionManager.getStructureSelectionManager()
-            .removeStructureViewerListener(this, this.getPdbFile());
-    // and shut down jmol
-    viewer.evalStringQuiet("zap");
-    viewer.setJmolStatusListener(null);
-
-    viewer = null;
-
+    jmb.closeViewer();
+    jmb = null;
     this.setVisible(false);
   }
 
   public void actionPerformed(ActionEvent evt)
   {
-    jmolHistory(false);
     if (evt.getSource() == mappingMenuItem)
     {
       jalview.appletgui.CutAndPasteTransfer cap = new jalview.appletgui.CutAndPasteTransfer(
@@ -392,56 +382,79 @@ public class AppletJmol extends EmbmenuFrame implements StructureListener,
       Frame frame = new Frame();
       frame.add(cap);
 
+      StringBuffer sb = new StringBuffer();
+      try
+      {
+        for (int s = 0; s < jmb.pdbentry.length; s++)
+        {
+          sb.append(jmb.printMapping(
+                          jmb.pdbentry[s].getFile()));
+          sb.append("\n");
+        }
+        cap.setText(sb.toString());
+      } catch (OutOfMemoryError ex)
+      {
+        frame.dispose();
+        System.err
+                .println("Out of memory when trying to create dialog box with sequence-structure mapping.");
+        return;
+      }
       jalview.bin.JalviewLite.addFrame(frame, "PDB - Sequence Mapping",
               550, 600);
-      cap.setText(StructureSelectionManager.getStructureSelectionManager()
-              .printMapping(pdbentry.getFile()));
     }
     else if (evt.getSource() == charge)
     {
-      colourBySequence = false;
-      seqColour.setState(false);
-      viewer
-              .evalStringQuiet("select *;color white;select ASP,GLU;color red;"
-                      + "select LYS,ARG;color blue;select CYS;color yellow");
+      setEnabled(charge);
+      jmb.colourByCharge();
     }
 
     else if (evt.getSource() == chain)
     {
-      colourBySequence = false;
-      seqColour.setState(false);
-      viewer.evalStringQuiet("select *;color chain");
+      setEnabled(chain);
+      jmb.colourByChain();
     }
     else if (evt.getSource() == zappo)
     {
-      setJalviewColourScheme(new ZappoColourScheme());
+      setEnabled(zappo);
+      jmb.setJalviewColourScheme(new ZappoColourScheme());
     }
     else if (evt.getSource() == taylor)
     {
-      setJalviewColourScheme(new TaylorColourScheme());
+      setEnabled(taylor);
+      jmb.setJalviewColourScheme(new TaylorColourScheme());
     }
     else if (evt.getSource() == hydro)
     {
-      setJalviewColourScheme(new HydrophobicColourScheme());
+      setEnabled(hydro);
+      jmb.setJalviewColourScheme(new HydrophobicColourScheme());
     }
     else if (evt.getSource() == helix)
     {
-      setJalviewColourScheme(new HelixColourScheme());
+      setEnabled(helix);
+      jmb.setJalviewColourScheme(new HelixColourScheme());
     }
     else if (evt.getSource() == strand)
     {
-      setJalviewColourScheme(new StrandColourScheme());
+      setEnabled(strand);
+      jmb.setJalviewColourScheme(new StrandColourScheme());
     }
     else if (evt.getSource() == turn)
     {
-      setJalviewColourScheme(new TurnColourScheme());
+      setEnabled(turn);
+      jmb.setJalviewColourScheme(new TurnColourScheme());
     }
     else if (evt.getSource() == buried)
     {
-      setJalviewColourScheme(new BuriedColourScheme());
+      setEnabled(buried);
+      jmb.setJalviewColourScheme(new BuriedColourScheme());
+    }
+    else if(evt.getSource() == purinepyrimidine)
+    {
+   	jmb.setJalviewColourScheme(new PurinePyrimidineColourScheme());
     }
     else if (evt.getSource() == user)
     {
+      setEnabled(user);
       new UserDefinedColours(this);
     }
     else if (evt.getSource() == jmolHelp)
@@ -464,54 +477,36 @@ public class AppletJmol extends EmbmenuFrame implements StructureListener,
         if (chainMenu.getItem(i) instanceof CheckboxMenuItem)
           ((CheckboxMenuItem) chainMenu.getItem(i)).setState(true);
       }
+
       centerViewer();
       allChainsSelected = false;
     }
-    jmolHistory(true);
   }
-  private void jmolHistory(boolean enable)
-  {
-    viewer.setBooleanProperty("history", enable);
-  }
-  public void setJalviewColourScheme(ColourSchemeI cs)
-  {
-    colourBySequence = false;
-    seqColour.setState(false);
-
-    if (cs == null)
-      return;
-
-    String res;
-    int index;
-    Color col;
-    jmolHistory(false);
-
-    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());
-    jmolHistory(true);
+  /**
+   * tick or untick the seqColour menu entry or jmoColour entry depending upon if it was selected
+   * or not.
+   * 
+   * @param itm
+   */
+  private void setEnabled(MenuItem itm)
+  {
+    jmolColour.setState(itm == jmolColour);
+    seqColour.setState(itm == seqColour);
+    jmb.setColourBySequence(itm == seqColour);
   }
 
   public void itemStateChanged(ItemEvent evt)
   {
+    if (evt.getSource() == jmolColour)
+    {
+      setEnabled(jmolColour);
+      jmb.setColourBySequence(false);
+    } else
     if (evt.getSource() == seqColour)
     {
-      lastCommand = null;
-      colourBySequence = seqColour.getState();
-      colourBySequence(ap);
+      setEnabled(seqColour);
+      jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap);
     }
     else if (!allChainsSelected)
       centerViewer();
@@ -521,7 +516,7 @@ public class AppletJmol extends EmbmenuFrame implements StructureListener,
   {
     if (evt.getKeyCode() == KeyEvent.VK_ENTER && scriptWindow.isVisible())
     {
-      viewer.evalString(inputLine.getText());
+      jmb.eval(inputLine.getText());
       history.append("\n$ " + inputLine.getText());
       inputLine.setText("");
     }
@@ -536,461 +531,23 @@ public class AppletJmol extends EmbmenuFrame implements StructureListener,
   {
   }
 
-  String[] modelFileNames = null;
-
-  // ////////////////////////////////
-  // /StructureListener
-  public String[] getPdbFile()
-  {
-    if (modelFileNames == null)
-    {
-      String mset[] = new String[viewer.getModelCount()];
-      for (int i = 0; i < mset.length; i++)
-      {
-        mset[i] = viewer.getModelFileName(i);
-      }
-      modelFileNames = mset;
-    }
-    return modelFileNames;
-  }
-
-  String lastMessage;
-
-  // jmol/ssm only
-  public void mouseOverStructure(int atomIndex, String strInfo)
-  {
-    int pdbResNum;
-    int mdlSep = strInfo.indexOf("/");
-    int chainSeparator = strInfo.indexOf(":"), chainSeparator1 = -1;
-
-    if (chainSeparator == -1)
-    {
-      chainSeparator = strInfo.indexOf(".");
-      if (mdlSep > -1 && mdlSep < chainSeparator)
-      {
-        chainSeparator1 = chainSeparator;
-        chainSeparator = mdlSep;
-      }
-    }
-    pdbResNum = Integer.parseInt(strInfo.substring(
-            strInfo.indexOf("]") + 1, chainSeparator));
-
-    String chainId;
-
-    if (strInfo.indexOf(":") > -1)
-      chainId = strInfo.substring(strInfo.indexOf(":") + 1, strInfo
-              .indexOf("."));
-    else
-    {
-      chainId = " ";
-    }
-
-    String pdbfilename = pdbentry.getFile();
-    if (mdlSep > -1)
-    {
-      if (chainSeparator1 == -1)
-      {
-        chainSeparator1 = strInfo.indexOf(".", mdlSep);
-      }
-      String mdlId = (chainSeparator1 > -1) ? strInfo.substring(mdlSep + 1,
-              chainSeparator1) : strInfo.substring(mdlSep + 1);
-      try
-      {
-        // recover PDB filename for the model hovered over.
-        pdbfilename = viewer
-                .getModelFileName(new Integer(mdlId).intValue() - 1);
-      } catch (Exception e)
-      {
-      }
-      ;
-    }
-    if (lastMessage == null || !lastMessage.equals(strInfo))
-      ssm.mouseOverStructure(pdbResNum, chainId, pdbfilename);
-
-    lastMessage = strInfo;
-  }
-
-  StringBuffer resetLastRes = new StringBuffer();
-
-  StringBuffer eval = new StringBuffer();
-
-  // jmol/ssm only
-  public void highlightAtom(int atomIndex, int pdbResNum, String chain,
-          String pdbfile)
-  {
-    int mdlNum = 1+getModelNum(pdbfile);
-    if (mdlNum==0)
-    {
-      return;
-    }
-
-    jmolHistory(false);
-    // if (!pdbfile.equals(pdbentry.getFile()))
-    // return;
-    if (resetLastRes.length() > 0)
-    {
-      viewer.evalStringQuiet(resetLastRes.toString());
-    }
-
-    eval.setLength(0);
-    eval.append("select " + pdbResNum); // +modelNum
-
-    resetLastRes.setLength(0);
-    resetLastRes.append("select " + pdbResNum); // +modelNum
-
-    if (!chain.equals(" "))
-    {
-    eval.append(":");
-    resetLastRes.append(":");
-      eval.append(chain);
-      resetLastRes.append(chain);
-    }
-    // if (mdlNum != 0)
-    {
-      eval.append(" /" + (mdlNum));
-      resetLastRes.append("/" + (mdlNum));
-    }
-    eval.append(";wireframe 100;" + eval.toString() + " and not hetero;");
-
-    resetLastRes.append(";wireframe 0;" + resetLastRes.toString()
-            + " and not hetero; spacefill 0;");
-
-    eval.append("spacefill 200;select none");
-
-    viewer.evalStringQuiet(eval.toString());
-    jmolHistory(true);
-
-  }
-
   public void updateColours(Object source)
   {
-    colourBySequence((AlignmentPanel) source);
+    AlignmentPanel ap = (AlignmentPanel) source;
+    jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap);
   }
 
-  // End StructureListener
-  // //////////////////////////
-
-  public Color getColour(int atomIndex, int pdbResNum, String chain,
-          String pdbfile)
+  public void updateTitleAndMenus()
   {
-    if (!pdbfile.equals(pdbentry.getFile()))
-      return null;
-
-    return new Color(viewer.getAtomArgb(atomIndex));
-  }
-
-  String lastCommand;
-
-  FeatureRenderer fr = null;
-
-  public void colourBySequence(AlignmentPanel sourceap)
-  {
-    this.ap = sourceap;
-
-    if (!colourBySequence)
-      return;
-    String[] files = getPdbFile();
-    SequenceRenderer sr = new SequenceRenderer(ap.av);
-
-    boolean showFeatures = false;
-
-    if (ap.av.showSequenceFeatures)
+    if (jmb.fileLoadingError != null && jmb.fileLoadingError.length() > 0)
     {
-      showFeatures = true;
-      if (fr == null)
-      {
-        fr = new jalview.appletgui.FeatureRenderer(ap.av);
-      }
-
-      fr.transferSettings(ap.seqPanel.seqCanvas.getFeatureRenderer());
-    }
-
-    StringBuffer command = new StringBuffer();
-
-    for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
-    {
-      StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
-
-      if (mapping == null || mapping.length < 1)
-        continue;
-
-      int lastPos = -1;
-      for (int s = 0; s < sequence.length; s++)
-      {
-        for (int sp, 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(sequence[s], r);
-
-              if (showFeatures)
-                col = fr.findFeatureColour(col, sequence[s], r);
-              String newSelcom = (mapping[m].getChain() != " " ? ":"
-                      + mapping[m].getChain() : "")
-                      + "/"
-                      + (pdbfnum + 1)
-                      + ".1"
-                      + ";color["
-                      + col.getRed()
-                      + ","
-                      + col.getGreen()
-                      + ","
-                      + col.getBlue() + "]";
-              if (command.toString().endsWith(newSelcom))
-              {
-                command = condenseCommand(command.toString(), pos);
-                continue;
-              }
-              // TODO: deal with case when buffer is too large for Jmol to parse
-              // - execute command and flush
-
-              command.append(";select " + pos);
-              command.append(newSelcom);
-            }
-            break;
-          }
-        }
-      }
-    }
-
-    jmolHistory(false);
-    if (lastCommand == null || !lastCommand.equals(command.toString()))
-    {
-      viewer.evalStringQuiet(command.toString());
-    }
-    jmolHistory(true);
-    lastCommand = command.toString();
-  }
-
-  StringBuffer condenseCommand(String command, int pos)
-  {
-
-    StringBuffer sb = new StringBuffer(command.substring(0, command
-            .lastIndexOf("select") + 7));
-
-    command = command.substring(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)
-  {
-  }
-
-  public void notifyFileLoaded(String fullPathName, String fileName2,
-          String modelName, String errorMsg, int modelParts)
-  {
-    if (errorMsg != null)
-    {
-      fileLoadingError = errorMsg;
       repaint();
       return;
     }
-    fileLoadingError = null;
-    modelFileNames = null;
-    
-    String[] modelfilenames = getPdbFile();
-    ssm = StructureSelectionManager.getStructureSelectionManager();
-    boolean modelsloaded=false;
-    for (int modelnum = 0; modelnum < modelfilenames.length; modelnum++)
-    {
-      String fileName = modelfilenames[modelnum];
-      if (fileName != null)
-      {
-        // search pdbentries and sequences to find correct pdbentry and sequence[] pair for this filename
-        if (pdbentry.getFile().equals(fileName))
-        {
-          modelsloaded=true;
-          MCview.PDBfile pdb;
-          if (loadedInline)
-          {
-            pdb = ssm.setMapping(sequence, chains, pdbentry.getFile(),
-                    AppletFormatAdapter.PASTE);
-            pdbentry.setFile("INLINE" + pdb.id);
-          }
-          else
-          {
-            // TODO: Jmol can in principle retrieve from CLASSLOADER but this
-            // needs
-            // to be tested. See mantis bug
-            // https://mantis.lifesci.dundee.ac.uk/view.php?id=36605
-
-            pdb = ssm.setMapping(sequence, chains, pdbentry.getFile(),
-                    AppletFormatAdapter.URL);
+    setChainMenuItems(jmb.chainNames);
+    jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap);
 
-          }
-
-          pdbentry.setId(pdb.id);
-
-          Vector chains = new Vector();
-          for (int i = 0; i < pdb.chains.size(); i++)
-          {
-            chains.addElement(new String(pdb.id + ":"
-                    + ((MCview.PDBChain) pdb.chains.elementAt(i)).id));
-          }
-          setChainMenuItems(chains);
-
-          colourBySequence(ap);
-
-          StringBuffer title = new StringBuffer(sequence[0].getName() + ":"
-                  + pdbentry.getId());
-
-          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"));
-            }
-          }
-
-          this.setTitle(title.toString());
-
-        }
-        else
-        {
-          // this is a foreign pdb file that jalview doesn't know about - add it to the dataset
-          // and try to find a home - either on a matching sequence or as a new sequence.
-          String pdbcontent = viewer.getData("/" + (modelnum + 1) + ".1",
-                  "PDB");
-          // parse pdb file into a chain, etc.
-          // locate best match for pdb in associated views and add mapping to
-          // ssm
-          modelsloaded=true;
-        }
-      }
-      }
-      if (modelsloaded) {
-      // FILE LOADED OK
-      jmolpopup.updateComputedMenus();
-      viewer
-              .evalStringQuiet("model 0; select backbone;restrict;cartoon;wireframe off;spacefill off");
-
-      ssm.addStructureViewerListener(this);
-    }
-  }
-
-  public void sendConsoleEcho(String strEcho)
-  {
-    if (scriptWindow == null)
-      showConsole(true);
-
-    history.append("\n" + strEcho);
-  }
-
-  public void sendConsoleMessage(String strStatus)
-  {
-    if (history != null && strStatus != null
-            && !strStatus.equals("Script completed"))
-    {
-      history.append("\n" + strStatus);
-    }
-  }
-
-  public void notifyScriptTermination(String strStatus, int 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)
-    {
-      System.err.println("Ignoring additional pick data string " + strData);
-    }
-    int chainSeparator = strInfo.indexOf(":");
-    int p=0;
-    if (chainSeparator == -1)
-      chainSeparator = strInfo.indexOf(".");
-
-    String picked = strInfo.substring(strInfo.indexOf("]") + 1,
-            chainSeparator);
-    String mdlString="";
-    if ((p=strInfo.indexOf(":")) > -1)
-      picked += strInfo.substring(p + 1, strInfo
-              .indexOf("."));
-
-    if ((p=strInfo.indexOf("/"))> -1)
-            {
-      mdlString += strInfo.substring(p, strInfo.indexOf(" #"));
-            }
-    picked = "((" + picked + ".CA" + mdlString+")|(" + picked + ".P" + mdlString+"))";
-    jmolHistory(false);
-
-    if (!atomsPicked.contains(picked))
-    {
-      viewer.evalStringQuiet("select " + picked + ";label %n %r:%c");
-      atomsPicked.addElement(picked);
-    }
-    else
-    {
-      viewer.evalString("select " + picked + ";label off");
-      atomsPicked.removeElement(picked);
-    }
-    jmolHistory(true);
-
-  }
-
-  public void notifyAtomHovered(int atomIndex, String strInfo, String data)
-  {
-    if (data != null)
-    {
-      System.err.println("Ignoring additional hover info: " + data);
-    }
-    mouseOverStructure(atomIndex, strInfo);
+    setTitle(jmb.getViewerTitle());
   }
 
   public void showUrl(String url)
@@ -1004,22 +561,30 @@ public class AppletJmol extends EmbmenuFrame implements StructureListener,
     }
   }
 
+  Panel splitPane = null;
+
   public void showConsole(boolean showConsole)
   {
-    if (scriptWindow == null)
+    if (showConsole)
+    {
+      remove(renderPanel);
+      splitPane = new Panel();
+
+      splitPane.setLayout(new java.awt.GridLayout(2, 1));
+      splitPane.add(renderPanel);
+      splitPane.add(scriptWindow);
+      scriptWindow.setVisible(true);
+      this.add(splitPane, BorderLayout.CENTER);
+      splitPane.setVisible(true);
+      splitPane.validate();
+    }
+    else
     {
-      scriptWindow = new Panel(new BorderLayout());
-      inputLine = new TextField();
-      history = new TextArea(5, 40);
-      scriptWindow.add(history, BorderLayout.CENTER);
-      scriptWindow.add(inputLine, BorderLayout.SOUTH);
-      add(scriptWindow, BorderLayout.SOUTH);
       scriptWindow.setVisible(false);
-      history.setEditable(false);
-      inputLine.addKeyListener(this);
+      remove(splitPane);
+      add(renderPanel, BorderLayout.CENTER);
+      splitPane = null;
     }
-
-    scriptWindow.setVisible(!scriptWindow.isVisible());
     validate();
   }
 
@@ -1047,7 +612,7 @@ public class AppletJmol extends EmbmenuFrame implements StructureListener,
       currentSize = this.getSize();
       rectClip = g.getClipBounds();
 
-      if (viewer == null)
+      if (jmb.viewer == null)
       {
         g.setColor(Color.black);
         g.fillRect(0, 0, currentSize.width, currentSize.height);
@@ -1057,102 +622,43 @@ public class AppletJmol extends EmbmenuFrame implements StructureListener,
       }
       else
       {
-        viewer.renderScreenImage(g, currentSize, rectClip);
+        jmb.viewer.renderScreenImage(g, currentSize, rectClip);
       }
     }
   }
 
-  public String createImage(String fileName, String type,
-          Object textOrBytes, int quality)
-  {
-    // TODO Auto-generated method stub
-    return null;
-  }
-
-  public float[][][] functionXYZ(String functionName, int nx, int ny, int nz)
-  {
-    // TODO Auto-generated method stub
-    return null;
-  }
-
-  public Hashtable getRegistryInfo()
+  /*
+   * @Override public Color getColour(int atomIndex, int pdbResNum, String
+   * chain, String pdbId) { return jmb.getColour(atomIndex, pdbResNum, chain,
+   * pdbId); }
+   * 
+   * @Override public String[] getPdbFile() { return jmb.getPdbFile(); }
+   * 
+   * @Override public void highlightAtom(int atomIndex, int pdbResNum, String
+   * chain, String pdbId) { jmb.highlightAtom(atomIndex, pdbResNum, chain,
+   * pdbId);
+   * 
+   * }
+   * 
+   * @Override public void mouseOverStructure(int atomIndex, String strInfo) {
+   * jmb.mouseOverStructure(atomIndex, strInfo);
+   * 
+   * }
+   */
+  public void setJalviewColourScheme(UserColourScheme ucs)
   {
-    // TODO Auto-generated method stub
-    return null;
+    jmb.setJalviewColourScheme(ucs);
   }
 
-  public void notifyCallback(int type, Object[] data)
+  public AlignmentPanel getAlignmentPanelFor(AlignmentI alignment)
   {
-    try
+    for (int i=0;i<_aps.size();i++)
     {
-      switch (type)
+      if (((AlignmentPanel)_aps.get(i)).av.getAlignment()==alignment)
       {
-      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;
+        return ((AlignmentPanel)_aps.get(i));
       }
-    } catch (Exception e)
-    {
-      System.err.println("Squashed Jmol callback handler error:");
-      e.printStackTrace();
     }
+    return ap;
   }
-
-  public boolean notifyEnabled(int callbackPick)
-  {
-    switch (callbackPick)
-    {
-    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:
-    }
-    return false;
-  }
-
-  public void setCallbackFunction(String callbackType,
-          String callbackFunction)
-  {
-    System.err.println("Ignoring set-callback request to associate "
-            + callbackType + " with function " + callbackFunction);
-
-  }
-
 }