/*
 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
 * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
 * 
 * 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/>.
 */
package jalview.gui;

import java.util.regex.*;
import java.util.*;
import java.awt.*;
import javax.swing.*;
import javax.swing.event.*;
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.*;
import jalview.structure.*;
import jalview.datamodel.PDBEntry;
import jalview.io.*;
import jalview.schemes.*;
import jalview.ws.ebi.EBIFetchClient;

import org.jmol.api.*;
import org.jmol.adapter.smarter.SmarterJmolAdapter;
import org.jmol.popup.*;
import org.jmol.viewer.JmolConstants;

public class AppJmol extends GStructureViewer implements StructureListener,
        JmolStatusListener, Runnable, SequenceStructureBinding

{
  JmolViewer viewer;

  JmolPopup jmolpopup;

  ScriptWindow scriptWindow;

  PDBEntry pdbentry;

  SequenceI[] sequence;

  String[] chains;

  StructureSelectionManager ssm;

  JSplitPane splitPane;

  RenderPanel renderPanel;

  AlignmentPanel ap;

  String fileLoadingError;

  boolean colourBySequence = true;

  boolean loadingFromArchive = false;

  Vector atomsPicked = new Vector();

  public AppJmol(String file, String id, SequenceI[] seq,
          AlignmentPanel ap, String loadStatus, Rectangle bounds)
  {
    this(file, id, seq, ap, loadStatus, bounds, null);
  }

  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.ap = ap;
    this.setBounds(bounds);
    colourBySequence = 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)
      {
        closeViewer();
      }
    });
  }

  public synchronized void addSequence(SequenceI[] seq)
  {
    Vector v = new Vector();
    for (int i = 0; i < sequence.length; i++)
      v.addElement(sequence[i]);

    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;
  }

  public AppJmol(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
          AlignmentPanel ap)
  {
    // ////////////////////////////////
    // Is the pdb file already loaded?
    String alreadyMapped = StructureSelectionManager
            .getStructureSelectionManager().alreadyMappedToFile(
                    pdbentry.getId());

    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);

      if (option == JOptionPane.YES_OPTION)
      {
        StructureSelectionManager.getStructureSelectionManager()
                .setMapping(seq, chains, alreadyMapped,
                        AppletFormatAdapter.FILE);
        if (ap.seqPanel.seqCanvas.fr != null)
        {
          ap.seqPanel.seqCanvas.fr.featuresAdded();
          ap.paintAlignment(true);
        }

        // Now this AppJmol is mapped to new sequences. We must add them to
        // the exisiting array
        JInternalFrame[] frames = Desktop.instance.getAllFrames();

        for (int i = 0; i < frames.length; i++)
        {
          if (frames[i] instanceof AppJmol)
          {
            AppJmol topJmol = ((AppJmol) frames[i]);
            if (topJmol.pdbentry.getFile().equals(alreadyMapped))
            {
              topJmol.addSequence(seq);
              break;
            }
          }
        }

        return;
      }
    }
    // /////////////////////////////////

    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);

    if (pdbentry.getFile() != null)
    {
      initJmol("load \"" + pdbentry.getFile() + "\"");
    }
    else
    {
      Thread worker = new Thread(this);
      worker.start();
    }

    this.addInternalFrameListener(new InternalFrameAdapter()
    {
      public void internalFrameClosing(InternalFrameEvent internalFrameEvent)
      {
        closeViewer();
      }
    });
  }

  void initJmol(String command)
  {
    renderPanel = new RenderPanel();

    this.getContentPane().add(renderPanel, java.awt.BorderLayout.CENTER);

    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());
    jalview.gui.Desktop.addInternalFrame(this, title.toString(),
            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);
  }

  void setChainMenuItems(Vector chains)
  {
    chainMenu.removeAll();

    JMenuItem menuItem = new JMenuItem("All");
    menuItem.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent evt)
      {
        allChainsSelected = true;
        for (int i = 0; i < chainMenu.getItemCount(); i++)
        {
          if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem)
            ((JCheckBoxMenuItem) chainMenu.getItem(i)).setSelected(true);
        }
        centerViewer();
        allChainsSelected = false;
      }
    });

    chainMenu.add(menuItem);

    for (int c = 0; c < chains.size(); c++)
    {
      menuItem = new JCheckBoxMenuItem(chains.elementAt(c).toString(), true);
      menuItem.addItemListener(new ItemListener()
      {
        public void itemStateChanged(ItemEvent evt)
        {
          if (!allChainsSelected)
            centerViewer();
        }
      });

      chainMenu.add(menuItem);
    }
  }

  boolean allChainsSelected = false;

  void centerViewer()
  {
    jmolHistory(false);
    StringBuffer cmd = new StringBuffer();
    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())
        {          lbl = item.getText();
        mlength = 0;
        do
        {
          p = mlength;
          mlength = lbl.indexOf(":", p);
        } while (p < mlength && mlength < (lbl.length() - 2));
        if (pdbentry.getId().equals(lbl.substring(0,mlength)))
        {
          mnum = 1+getModelNum(pdbentry.getFile());
        if (mnum>0)
          {cmd.append(":" + lbl.substring(mlength + 1) + " /"
                + mnum + " or ");
          }
        }
        }
      }
    }

    if (cmd.length() > 0)
      cmd.setLength(cmd.length() - 4);

    viewer.evalStringQuiet("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;
  }

  void closeViewer()
  {
    viewer.setModeMouse(org.jmol.viewer.JmolConstants.MOUSE_NONE);
    // remove listeners for all structures in viewer
    StructureSelectionManager.getStructureSelectionManager()
            .removeStructureViewerListener(this, getPdbFile());
    // and shut down jmol
    viewer.evalStringQuiet("zap");
    viewer.setJmolStatusListener(null);
    viewer = null;
  }

  public void run()
  {
    try
    {
      // 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
      {
        JOptionPane
                .showInternalMessageDialog(
                        Desktop.desktop,
                        pdbentry.getId()
                                + " could not be retrieved. Please try downloading the file manually.",
                        "Couldn't load file", JOptionPane.ERROR_MESSAGE);

      }
    } catch (OutOfMemoryError oomerror)
    {
      new OOMWarning("Retrieving PDB id " + pdbentry.getId() + " from MSD",
              oomerror);
    } catch (Exception ex)
    {
      ex.printStackTrace();
    }
  }

  public void pdbFile_actionPerformed(ActionEvent actionEvent)
  {
    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
            .getProperty("LAST_DIRECTORY"));

    chooser.setFileView(new JalviewFileView());
    chooser.setDialogTitle("Save PDB File");
    chooser.setToolTipText("Save");

    int value = chooser.showSaveDialog(this);

    if (value == JalviewFileChooser.APPROVE_OPTION)
    {
      try
      {
        BufferedReader in = new BufferedReader(new FileReader(pdbentry
                .getFile()));
        File outFile = chooser.getSelectedFile();

        PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
        String data;
        while ((data = in.readLine()) != null)
        {
          if (!(data.indexOf("<PRE>") > -1 || data.indexOf("</PRE>") > -1))
          {
            out.println(data);
          }
        }
        out.close();
      } catch (Exception ex)
      {
        ex.printStackTrace();
      }
    }
  }

  public void viewMapping_actionPerformed(ActionEvent actionEvent)
  {
    jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();
    jalview.gui.Desktop.addInternalFrame(cap, "PDB - Sequence Mapping",
            550, 600);
    cap.setText(StructureSelectionManager.getStructureSelectionManager()
            .printMapping(pdbentry.getFile()));
  }

  /**
   * 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 = getWidth();
    int height = 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)
    {
      Rectangle rect = new Rectangle(width, height);
      viewer.renderScreenImage(im.getGraphics(), rect.getSize(), rect);
      im.writeImage();
    }
  }

  public void seqColour_actionPerformed(ActionEvent actionEvent)
  {
    lastCommand = null;
    colourBySequence = seqColour.isSelected();
    colourBySequence(ap.alignFrame.alignPanel);
  }

  public void chainColour_actionPerformed(ActionEvent actionEvent)
  {
    colourBySequence = false;
    seqColour.setSelected(false);
    jmolHistory(false);
    viewer.evalStringQuiet("select *;color chain");
    jmolHistory(true);
  }

  public void chargeColour_actionPerformed(ActionEvent actionEvent)
  {
    colourBySequence = false;
    seqColour.setSelected(false);
    jmolHistory(false);
    viewer.evalStringQuiet("select *;color white;select ASP,GLU;color red;"
            + "select LYS,ARG;color blue;select CYS;color yellow");
    jmolHistory(true);
  }

  public void zappoColour_actionPerformed(ActionEvent actionEvent)
  {
    setJalviewColourScheme(new ZappoColourScheme());
  }

  public void taylorColour_actionPerformed(ActionEvent actionEvent)
  {
    setJalviewColourScheme(new TaylorColourScheme());
  }

  public void hydroColour_actionPerformed(ActionEvent actionEvent)
  {
    setJalviewColourScheme(new HydrophobicColourScheme());
  }

  public void helixColour_actionPerformed(ActionEvent actionEvent)
  {
    setJalviewColourScheme(new HelixColourScheme());
  }

  public void strandColour_actionPerformed(ActionEvent actionEvent)
  {
    setJalviewColourScheme(new StrandColourScheme());
  }

  public void turnColour_actionPerformed(ActionEvent actionEvent)
  {
    setJalviewColourScheme(new TurnColourScheme());
  }

  public void buriedColour_actionPerformed(ActionEvent actionEvent)
  {
    setJalviewColourScheme(new BuriedColourScheme());
  }

  public void setJalviewColourScheme(ColourSchemeI cs)
  {
    jmolHistory(false);
    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());
    jmolHistory(true);
  }

  public void userColour_actionPerformed(ActionEvent actionEvent)
  {
    new UserDefinedColours(this, null);
  }

  public void backGround_actionPerformed(ActionEvent actionEvent)
  {
    java.awt.Color col = JColorChooser.showDialog(this,
            "Select Background Colour", null);

    if (col != null)
    {
      jmolHistory(false);
      viewer.evalStringQuiet("background [" + col.getRed() + ","
              + col.getGreen() + "," + col.getBlue() + "];");
      jmolHistory(true);
    }
  }
  private void jmolHistory(boolean enable)
  {
    viewer.setBooleanProperty("history", enable);
  }

  public void jmolHelp_actionPerformed(ActionEvent actionEvent)
  {
    try
    {
      jalview.util.BrowserLauncher
              .openURL("http://jmol.sourceforge.net/docs/JmolUserGuide/");
    } catch (Exception ex)
    {
    }
  }
  String[] modelFileNames = null;

  // ////////////////////////////////
  // /StructureListener
  public String[] getPdbFile()
  {
    if (modelFileNames == null)
    {
      String mset[] = new String[viewer.getModelCount()];
      for (int i = 0; i < mset.length; i++)
      {
        try {
          String mname = viewer.getModelFileName(i);
          if (mname==null)
          {
            System.err.println("Model "+i+" has no filename!");
            continue;
          }
          File fpath = new File(mname);
          mset[i] = fpath.toString();
        } catch (Exception e)
        {
          System.err.println("Couldn't parse "+viewer.getModelFileName(i)+" as a file!");
        }
      }
      modelFileNames = mset;
    }
    return modelFileNames;
  }

  Pattern pattern = Pattern
          .compile("\\[(.*)\\]([0-9]+)(:[a-zA-Z]*)?\\.([a-zA-Z]+).*(/[0-9]*)?");

  String lastMessage;

  public void mouseOverStructure(int atomIndex, String strInfo)
  {
    // copied from AppJmol - will be refactored to binding eventually
    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;
/*
 * Old Implementation based on Pattern regex.
    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 = " ";
    }
    String mdlId = matcher.group(4);
    String pdbfilename = pdbentry.getFile();

    if (mdlId!=null && mdlId.length()>0)
    {
      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();

  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 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;

    String[] files = getPdbFile();
    
    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();
    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 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);
            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, pos);
              continue;
            }

            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(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 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)
    {
      modelsloaded=true;
      // search pdbentries and sequences to find correct pdbentry and sequence[] pair for this filename
      if (pdbentry.getFile().equals(fileName))
      {
      // TODO: do some checking using the modelPts number of parts against our
      // own estimate of the number of chains
      // FILE LOADED OK
      MCview.PDBfile pdbFile = ssm.setMapping(sequence, chains, pdbentry
              .getFile(), AppletFormatAdapter.FILE);
      Vector chains = new Vector();
      for (int i = 0; i < pdbFile.chains.size(); i++)
      {
        chains
                .addElement(new String(pdbFile.id+":"+((MCview.PDBChain) pdbFile.chains.elementAt(i)).id));
      }
      setChainMenuItems(chains);

      if (!loadingFromArchive)
      {
        viewer
                .evalStringQuiet("model 0; select backbone;restrict;cartoon;wireframe off;spacefill off");

        colourBySequence(ap);
      }
      if (fr != null)
        fr.featuresAdded();

      loadingFromArchive = false;
    }
    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)
    {
      ssm.addStructureViewerListener(this);
      jmolpopup.updateComputedMenus();
    }
  }

  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()));
*/
    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))
    {
      // TODO: re-instate chain ID separator dependent labelling for both applet and application
//      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);
    }
    jmolHistory(true);
    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)
    {
      if (splitPane == null)
      {
        splitPane = new JSplitPane(JSplitPane.VERTICAL_SPLIT);
        splitPane.setTopComponent(renderPanel);
        splitPane.setBottomComponent(scriptWindow);
        this.getContentPane().add(splitPane, BorderLayout.CENTER);
      }

      splitPane.setDividerLocation(getHeight() - 200);
      splitPane.validate();
    }
    else
    {
      if (splitPane != null)
        splitPane.setVisible(false);

      splitPane = null;

      this.getContentPane().add(renderPanel, BorderLayout.CENTER);
    }

    validate();
  }

  public float[][] functionXY(String functionName, int x, int y)
  {
    return null;
  }

  // /End JmolStatusListener
  // /////////////////////////////

  class RenderPanel extends JPanel
  {
    final Dimension currentSize = new Dimension();

    final Rectangle rectClip = new Rectangle();

    public void paintComponent(Graphics g)
    {
      getSize(currentSize);
      g.getClipBounds(rectClip);

      if (viewer == 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);
      }
      else if (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("Error loading file..." + pdbentry.getId(), 20,
                currentSize.height / 2);
      }
      else
      {
        viewer.renderScreenImage(g, currentSize, rectClip);
      }
    }
  }

  String viewId = null;

  public String getViewId()
  {
    if (viewId == null)
    {
      viewId = System.currentTimeMillis() + "." + this.hashCode();
    }
    return viewId;
  }

  @Override
  public String createImage(String fileName, String type,
          Object textOrBytes, int quality)
  {
    // 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)
      {
      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;
      }
    } catch (Exception e)
    {
      Cache.log.warn("Squashed Jmol callback handler error: ", e);
    }
  }

  @Override
  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;
  }

  @Override
  public void setCallbackFunction(String callbackType,
          String callbackFunction)
  {
    Cache.log.debug("Ignoring set-callback request to associate "
            + callbackType + " with function " + callbackFunction);

  }

}