/*
 * 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 Runnable,
        SequenceStructureBinding

{
  AppJmolBinding jmb;

  ScriptWindow scriptWindow;

  JSplitPane splitPane;

  RenderPanel renderPanel;

  AlignmentPanel ap;

  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)
  {
    PDBEntry pdbentry = new PDBEntry();
    pdbentry.setFile(file);
    pdbentry.setId(id);
    // / TODO: check if protocol is needed to be set, and if chains are
    // autodiscovered.
    jmb = new AppJmolBinding(this, new PDBEntry[]
    { pdbentry }, seq, null, null);

    jmb.setLoadingFromArchive(true);
    this.ap = ap;
    this.setBounds(bounds);
    jmb.setColourBySequence(false);
    seqColour.setSelected(false);
    viewId = viewid;
    // jalview.gui.Desktop.addInternalFrame(this, "Loading File",
    // bounds.width,bounds.height);

    this.addInternalFrameListener(new InternalFrameAdapter()
    {
      public void internalFrameClosing(InternalFrameEvent internalFrameEvent)
      {
        closeViewer();
      }
    });
    initJmol(loadStatus); // pdbentry, seq, JBPCHECK!

  }

  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 re-use this viewer ?",
                      "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]);
            // JBPNOTE: this looks like a binding routine, rather than a gui
            // routine
            for (int pe = 0; pe < topJmol.jmb.pdbentry.length; pe++)
            {
              if (topJmol.jmb.pdbentry[pe].getFile().equals(alreadyMapped))
              {
                topJmol.jmb.addSequence(seq);
                break;
              }
            }
          }
        }

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

    jmb = new AppJmolBinding(this, new PDBEntry[]
    { pdbentry }, seq, null, null);
    this.ap = ap;
    setSize(400, 400); // probably should be a configurable/dynamic default here

    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)
  {
    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);
    jmb.allocateViewer(renderPanel, true, "", null, 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()
    {
      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()
  {
    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())
        {
          toshow.addElement(item.getText());
        }
      }
    }
    jmb.centerViewer(toshow);
  }

  void closeViewer()
  {
    jmb.closeViewer();
    // TODO: check for memory leaks where instance isn't finalised because jmb
    // holds a reference to the window
    jmb = null;
  }

  public void run()
  {
    String pdbid = "";
    // todo - record which pdbids were successfuly imported.
    StringBuffer errormsgs = new StringBuffer(), files = new StringBuffer();
    try
    {
      // TODO: replace with reference fetching/transfer code (validate PDBentry
      // as a DBRef?)
      jalview.ws.dbsources.Pdb pdbclient = new jalview.ws.dbsources.Pdb();
      for (int pi = 0; pi < jmb.pdbentry.length; pi++)
      {
        AlignmentI pdbseq;
        if ((pdbseq = pdbclient.getSequenceRecords(pdbid = jmb.pdbentry[pi]
                .getId())) != null)
        {
          String file;
          // 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 + "' ");
        }
      }
    } catch (OutOfMemoryError oomerror)
    {
      new OOMWarning("Retrieving PDB id " + pdbid, oomerror);
    } catch (Exception ex)
    {
      ex.printStackTrace();
      errormsgs.append("'" + 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)
    {
      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);
      }
    }
  }

  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
      {
        // 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));
        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();
    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);
  }

  /**
   * 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);
      jmb.viewer.renderScreenImage(im.getGraphics(), rect.getSize(), rect);
      im.writeImage();
    }
  }

  public void seqColour_actionPerformed(ActionEvent actionEvent)
  {
    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)
  {
    chainColour.setSelected(true);
    jmb.colourByChain();
  }

  public void chargeColour_actionPerformed(ActionEvent actionEvent)
  {
    chargeColour.setSelected(true);
    jmb.colourByCharge();
  }

  public void zappoColour_actionPerformed(ActionEvent actionEvent)
  {
    zappoColour.setSelected(true);
    jmb.setJalviewColourScheme(new ZappoColourScheme());
  }

  public void taylorColour_actionPerformed(ActionEvent actionEvent)
  {
    taylorColour.setSelected(true);
    jmb.setJalviewColourScheme(new TaylorColourScheme());
  }

  public void hydroColour_actionPerformed(ActionEvent actionEvent)
  {
    hydroColour.setSelected(true);
    jmb.setJalviewColourScheme(new HydrophobicColourScheme());
  }

  public void helixColour_actionPerformed(ActionEvent actionEvent)
  {
    helixColour.setSelected(true);
    jmb.setJalviewColourScheme(new HelixColourScheme());
  }

  public void strandColour_actionPerformed(ActionEvent actionEvent)
  {
    strandColour.setSelected(true);
    jmb.setJalviewColourScheme(new StrandColourScheme());
  }

  public void turnColour_actionPerformed(ActionEvent actionEvent)
  {
    turnColour.setSelected(true);
    jmb.setJalviewColourScheme(new TurnColourScheme());
  }

  public void buriedColour_actionPerformed(ActionEvent actionEvent)
  {
    buriedColour.setSelected(true);
    jmb.setJalviewColourScheme(new BuriedColourScheme());
  }


  public void userColour_actionPerformed(ActionEvent actionEvent)
  {
    userColour.setSelected(true);
    new UserDefinedColours(this, null);
  }

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

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

  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();
  }

  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 (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("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 (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("Retrieving PDB data....", 20, currentSize.height / 2);
        }
        else 
      {
        jmb.viewer.renderScreenImage(g, currentSize, rectClip);
      }
    }
  }

  String viewId = null;

  public String getViewId()
  {
    if (viewId == null)
    {
      viewId = System.currentTimeMillis() + "." + this.hashCode();
    }
    return viewId;
  }
  public void updateTitleAndMenus()
  {
    if (jmb.fileLoadingError != null && jmb.fileLoadingError.length() > 0)
    {
      repaint();
      return;
    }
    setChainMenuItems(jmb.chainNames);
    jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap.av.alignment);

    this.setTitle(jmb.getViewerTitle());
  }

  public void setJalviewColourScheme(ColourSchemeI ucs)
  {
    jmb.setJalviewColourScheme(ucs);
    
  }

}