/*
 * Jalview - A Sequence Alignment Editor and Viewer
 * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
 *
 * This program 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 2
 * of the License, or (at your option) any later version.
 *
 * This program 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 this program; if not, write to the Free Software
 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
 */
package jalview.gui;

import jalview.datamodel.*;

import jalview.io.*;

import jalview.jbgui.*;

import jalview.schemes.*;

import java.awt.*;
import java.awt.event.*;

import java.io.*;

import java.util.*;

import javax.swing.*;
import javax.swing.event.*;



/**
 * DOCUMENT ME!
 *
 * @author $author$
 * @version $Revision$
 */
public class UserDefinedColours extends GUserDefinedColours
    implements ChangeListener
{
    AlignmentPanel ap;
    SequenceGroup seqGroup;
    Vector selectedButtons;
    ColourSchemeI oldColourScheme;
    JInternalFrame frame;
    MCview.PDBCanvas pdbcanvas;
    Vector upperCaseButtons;
    Vector lowerCaseButtons;


    /**
     * Creates a new UserDefinedColours object.
     *
     * @param ap DOCUMENT ME!
     * @param sg DOCUMENT ME!
     */
    public UserDefinedColours(AlignmentPanel ap, SequenceGroup sg)
    {
        super();

        lcaseColour.setEnabled(false);

        this.ap = ap;
        seqGroup = sg;

        if (seqGroup != null)
            oldColourScheme = seqGroup.cs;
        else
            oldColourScheme = ap.av.getGlobalColourScheme();

        if (oldColourScheme instanceof UserColourScheme)
        {
          schemeName.setText( ( (UserColourScheme) oldColourScheme).getName());
          if(( (UserColourScheme) oldColourScheme).getLowerCaseColours()!=null)
          {
            caseSensitive.setSelected(true);
            lcaseColour.setEnabled(true);
            resetButtonPanel(true);
          }
          else
            resetButtonPanel(false);
        }
        else
           resetButtonPanel(false);

        showFrame();
    }

    public UserDefinedColours(MCview.PDBCanvas pdb, ColourSchemeI oldcs)
    {
        super();
        pdbcanvas = pdb;

        colorChooser.getSelectionModel().addChangeListener(this);

        oldColourScheme = oldcs;

        if (oldColourScheme instanceof UserColourScheme)
        {
              schemeName.setText( ( (UserColourScheme) oldColourScheme).getName());
        }

        resetButtonPanel(false);

        showFrame();

    }

    void showFrame()
    {
      colorChooser.getSelectionModel().addChangeListener(this);
      frame = new JInternalFrame();
      frame.setContentPane(this);
      Desktop.addInternalFrame(frame, "User Defined Colours", 720, 370, true);

      if (seqGroup != null)
            frame.setTitle(frame.getTitle() + " (" + seqGroup.getName() + ")");

      if (System.getProperty("os.name").startsWith("Mac"))
      {
        frame.setSize(760, 370);
      }
    }

    void resetButtonPanel(boolean caseSensitive)
    {
      buttonPanel.removeAll();


      if(upperCaseButtons==null)
        upperCaseButtons = new Vector();

      JButton button;
      String label;
      for (int i = 0; i < 20; i++)
      {
        if(caseSensitive)
          label = ResidueProperties.aa[i];
        else
          label = ResidueProperties.aa2Triplet.get
              (ResidueProperties.aa[i]).toString();

        button = makeButton(label,
                              ResidueProperties.aa[i],
                              upperCaseButtons, i);

        buttonPanel.add(button);
      }

        buttonPanel.add(makeButton("B", "B", upperCaseButtons, 20));
        buttonPanel.add(makeButton("Z", "Z", upperCaseButtons, 21));
        buttonPanel.add(makeButton("X", "X", upperCaseButtons, 22));
        buttonPanel.add(makeButton("Gap", "-", upperCaseButtons, 23));

      if(!caseSensitive)
      {
        gridLayout.setRows(6);
        gridLayout.setColumns(4);
      }
      else
      {
        gridLayout.setRows(7);
        int cols = 7;
        gridLayout.setColumns(cols+1);

        if(lowerCaseButtons==null)
          lowerCaseButtons = new Vector();


          for (int i = 0; i < 20; i++)
          {
            int row = i / cols + 1;
            int index = (row * cols) + i;
            button = makeButton(
                ResidueProperties.aa[i].toLowerCase(),
                ResidueProperties.aa[i].toLowerCase(),
                lowerCaseButtons,
                i);

            buttonPanel.add(button, index);
          }
      }


      if(caseSensitive)
      {
        buttonPanel.add(makeButton("b", "b", lowerCaseButtons, 20));
        buttonPanel.add(makeButton("z", "z", lowerCaseButtons, 21));
        buttonPanel.add(makeButton("x", "x", lowerCaseButtons, 22));
      }

      buttonPanel.validate();
      validate();
    }


    /**
     * DOCUMENT ME!
     *
     * @param evt DOCUMENT ME!
     */
    public void stateChanged(ChangeEvent evt)
    {
        if (selectedButtons != null)
        {
          JButton button=null;
          for(int i=0; i<selectedButtons.size(); i++)
          {
            button = (JButton)selectedButtons.elementAt(i);
            button.setBackground(colorChooser.getColor());
            button.setForeground( button.getBackground().brighter().brighter().brighter());
          }
          if(button==lcaseColour)
          {
            for(int i=0; i<lowerCaseButtons.size(); i++)
            {
              button = (JButton)lowerCaseButtons.elementAt(i);
              button.setBackground(colorChooser.getColor());
              button.setForeground( button.getBackground().brighter().brighter().brighter());
            }
          }
        }
    }

    /**
     * DOCUMENT ME!
     *
     * @param e DOCUMENT ME!
     */
    public void colourButtonPressed(MouseEvent e)
    {
      if(selectedButtons == null)
        selectedButtons = new Vector();

      JButton pressed = (JButton) e.getSource();

      if(e.isShiftDown())
      {
        JButton start, end = (JButton) e.getSource();
        if(selectedButtons.size()>0)
          start = (JButton)selectedButtons.elementAt(selectedButtons.size()-1);
        else
          start = (JButton) e.getSource();

        int startIndex=0, endIndex=0;
        for(int b=0; b<buttonPanel.getComponentCount(); b++)
        {
          if(buttonPanel.getComponent(b)==start)
            startIndex = b;
          if(buttonPanel.getComponent(b)==end)
            endIndex = b;
        }

        if(startIndex > endIndex)
        {
          int temp = startIndex;
          startIndex = endIndex;
          endIndex = temp;
        }

        for(int b=startIndex; b<=endIndex; b++)
        {
          JButton button = (JButton)buttonPanel.getComponent(b);
          if(!selectedButtons.contains(button))
          {
            button.setForeground(button.getBackground().brighter().brighter());
            selectedButtons.add(button);
          }
        }
      }
      else if(!e.isControlDown())
      {
        for(int b=0; b<selectedButtons.size(); b++)
        {
          JButton button = (JButton)selectedButtons.elementAt(b);
          button.setForeground(button.getBackground().darker().darker());
        }
        selectedButtons.clear();
        pressed.setForeground( pressed.getBackground().brighter().brighter());
        selectedButtons.addElement(pressed);

      }
      else if(e.isControlDown())
      {
        if(selectedButtons.contains(pressed))
        {
          pressed.setForeground(pressed.getBackground().darker().darker());
          selectedButtons.remove(pressed);
        }
        else
        {
          pressed.setForeground( pressed.getBackground().brighter().brighter());
          selectedButtons.addElement(pressed);
        }
      }

      if(selectedButtons.size()>0)
      colorChooser.setColor( ((JButton)selectedButtons.elementAt(0)).getBackground());
    }

    /**
     * DOCUMENT ME!
     *
     * @param label DOCUMENT ME!
     * @param aa DOCUMENT ME!
     */
    JButton makeButton(String label,
                       String aa,
                       Vector caseSensitiveButtons,
                       int buttonIndex)
    {
        final JButton button;
        Color col;

        if(buttonIndex<caseSensitiveButtons.size())
        {
          button = (JButton) caseSensitiveButtons.elementAt(buttonIndex);
          col = button.getBackground();
        }
        else
        {
          button = new JButton();
          button.addMouseListener(new java.awt.event.MouseAdapter()
          {
            public void mouseClicked(MouseEvent e)
            {
              colourButtonPressed(e);
            }
          });

          caseSensitiveButtons.addElement(button);

          col = Color.white;

          try
          {
            col = oldColourScheme.findColour(aa, -1);
          }
          catch (Exception ex)
          {    }
        }

        if(caseSensitive.isSelected())
          button.setMargin(new java.awt.Insets(2,2,2,2));
        else
         button.setMargin(new java.awt.Insets(2,14,2,14));

        button.setBackground(col);
        button.setText(label);
        button.setForeground(col.darker().darker().darker());
        button.setFont(new java.awt.Font("Verdana", Font.BOLD, 10));

        return button;
    }

    /**
     * DOCUMENT ME!
     *
     * @param e DOCUMENT ME!
     */
    protected void okButton_actionPerformed(ActionEvent e)
    {
        applyButton_actionPerformed(null);

        try
        {
            frame.setClosed(true);
        }
        catch (Exception ex)
        {
        }
    }

    /**
     * DOCUMENT ME!
     *
     * @param e DOCUMENT ME!
     */
    protected void applyButton_actionPerformed(ActionEvent e)
    {
        UserColourScheme ucs = getSchemeFromButtons();
        ucs.setName(schemeName.getText());

        if (seqGroup != null)
        {
            seqGroup.cs = ucs;
            ap.repaint();
        }
        else if(ap!=null)
        {
            ap.alignFrame.changeColour(ucs);
        }
        else if(pdbcanvas!=null)
        {
          pdbcanvas.pdb.setColours(ucs);
          pdbcanvas.updateSeqColours();
        }
    }

    UserColourScheme getSchemeFromButtons()
    {

      Color[] newColours = new Color[24];

      for (int i = 0; i < 24; i++)
      {
        JButton button = (JButton) upperCaseButtons.elementAt(i);
        newColours[i] = button.getBackground();
      }

      UserColourScheme ucs = new UserColourScheme(newColours);


      if(caseSensitive.isSelected())
      {
        newColours = new Color[23];
        for (int i = 0; i < 23; i++)
        {
          JButton button = (JButton) lowerCaseButtons.elementAt(i);
          newColours[i] = button.getBackground();
        }
        ucs.setLowerCaseColours(newColours);
      }

      if(ap!=null)
        ucs.setThreshold(0, ap.av.getIgnoreGapsConsensus());


      return ucs;
    }



    /**
     * DOCUMENT ME!
     *
     * @param e DOCUMENT ME!
     */
    protected void loadbutton_actionPerformed(ActionEvent e)
    {
      upperCaseButtons = new Vector();
      lowerCaseButtons = new Vector();

        JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(
                    "LAST_DIRECTORY"), new String[] { "jc" },
                new String[] { "Jalview User Colours" }, "Jalview User Colours");
        chooser.setFileView(new jalview.io.JalviewFileView());
        chooser.setDialogTitle("Load colour scheme");
        chooser.setToolTipText("Load");

        int value = chooser.showOpenDialog(this);

        if (value == JalviewFileChooser.APPROVE_OPTION)
        {
            File choice = chooser.getSelectedFile();
            jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());
            String defaultColours = jalview.bin.Cache.getDefault("USER_DEFINED_COLOURS",
                choice.getPath());
            if (defaultColours.indexOf(choice.getPath()) == -1)
              defaultColours = defaultColours.concat("|").concat(choice.getPath());

            jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS", defaultColours);


            UserColourScheme ucs = loadColours(choice.getAbsolutePath());
            Color[] colors = ucs.getColours();
            schemeName.setText(ucs.getName());

            if(ucs.getLowerCaseColours()!=null)
            {
              caseSensitive.setSelected(true);
              lcaseColour.setEnabled(true);
              resetButtonPanel(true);
              for (int i = 0; i < lowerCaseButtons.size(); i++)
              {
                JButton button = (JButton) lowerCaseButtons.elementAt(i);
                button.setBackground(ucs.getLowerCaseColours()[i]);
              }

            }
            else
            {
              caseSensitive.setSelected(false);
              lcaseColour.setEnabled(false);
              resetButtonPanel(false);
            }

            for (int i = 0; i < upperCaseButtons.size(); i++)
            {
                JButton button = (JButton) upperCaseButtons.elementAt(i);
                button.setBackground(colors[i]);
            }

        }
    }

    /**
     * DOCUMENT ME!
     *
     * @return DOCUMENT ME!
     */
    public static UserColourScheme loadDefaultColours()
    {
        UserColourScheme ret = null;

        String colours = jalview.bin.Cache.getProperty("USER_DEFINED_COLOURS");
        if ( colours != null )
        {
          if(colours.indexOf("|")>-1)
            colours = colours.substring(0, colours.indexOf("|"));

          ret = loadColours(colours);
        }

        if(ret == null)
        {
          Color[] newColours = new Color[24];
          for (int i = 0; i < 24; i++)
          {
            newColours[i] = Color.white;
          }
          ret =  new UserColourScheme(newColours);
        }

        return ret;
    }

    /**
     * DOCUMENT ME!
     *
     * @param file DOCUMENT ME!
     *
     * @return DOCUMENT ME!
     */
    static UserColourScheme loadColours(String file)
    {
         UserColourScheme ucs = null;
         Color[]  newColours = null;
        try
        {
            InputStreamReader in = new InputStreamReader(new FileInputStream(
                        file), "UTF-8");

              jalview.schemabinding.version2.JalviewUserColours jucs
                  = new jalview.schemabinding.version2.JalviewUserColours();

              org.exolab.castor.xml.Unmarshaller unmar
                  = new org.exolab.castor.xml.Unmarshaller(jucs);
              jucs = (jalview.schemabinding.version2.JalviewUserColours) unmar.unmarshal( in );

              newColours = new Color[24];

              Color [] lowerCase = null;
              boolean caseSensitive = false;


            String name;
            int index;
            for (int i = 0; i < jucs.getColourCount(); i++)
            {
              name =  jucs.getColour(i).getName();
              if(ResidueProperties.aa3Hash.containsKey(name))
              {
                index = ((Integer)ResidueProperties.aa3Hash.get(name)).intValue();
              }
              else
              {
                index = ResidueProperties.aaIndex[name.charAt(0)];
              }
              if(index == -1)
                continue;

              if(name.toLowerCase().equals(name))
              {
                if(lowerCase==null)
                   lowerCase = new Color[23];
                caseSensitive = true;
                lowerCase[index] = new Color(Integer.parseInt(
                  jucs.getColour(i).getRGB(), 16));
              }
              else
              {
                newColours[index] = new Color(Integer.parseInt(
                    jucs.getColour(i).getRGB(), 16));
              }
            }

            if (newColours != null)
            {
              ucs = new UserColourScheme(newColours);
              ucs.setName( jucs.getSchemeName() );
              if(caseSensitive)
              {
                ucs.setLowerCaseColours(lowerCase);
              }
            }

        }
        catch (Exception ex)
        {
            //Could be Archive Jalview format
            try{
              InputStreamReader in = new InputStreamReader(new FileInputStream(
                  file), "UTF-8");

              jalview.binding.JalviewUserColours jucs
                  = new jalview.binding.JalviewUserColours();

              jucs = (jalview.binding.JalviewUserColours) jucs.unmarshal(in);

              newColours = new Color[jucs.getColourCount()];

              for (int i = 0; i < 24; i++)
              {
                newColours[i] = new Color(Integer.parseInt(
                    jucs.getColour(i).getRGB(), 16));
              }
              if (newColours != null)
              {
                ucs = new UserColourScheme(newColours);
                ucs.setName(jucs.getSchemeName());
              }
            }catch(Exception ex2)
            { ex2.printStackTrace(); }

            if(newColours==null)
              System.out.println("Error loading User ColourFile\n"+ex);
        }

       return ucs;
    }

    /**
     * DOCUMENT ME!
     *
     * @param e DOCUMENT ME!
     */
    protected void savebutton_actionPerformed(ActionEvent e)
    {
      if(schemeName.getText().trim().length()<1)
      {
        JOptionPane.showInternalMessageDialog(Desktop.desktop,
                                              "User colour scheme must have a name!",
                                              "No name for colour scheme",
                                              JOptionPane.WARNING_MESSAGE);
        return;
      }

      if(userColourSchemes!=null && userColourSchemes.containsKey(schemeName.getText()) )
      {
        int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop, "Colour scheme "+schemeName.getText()+ " exists."
            +"\nContinue saving colour scheme as "+schemeName.getText()+"?",
           "Duplicate scheme name", JOptionPane.YES_NO_OPTION);
        if(reply != JOptionPane.YES_OPTION)
          return;

         userColourSchemes.remove(schemeName.getText());
      }
        JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(
                    "LAST_DIRECTORY"), new String[] { "jc" },
                new String[] { "Jalview User Colours" }, "Jalview User Colours");

        chooser.setFileView(new jalview.io.JalviewFileView());
        chooser.setDialogTitle("Save colour scheme");
        chooser.setToolTipText("Save");

        int value = chooser.showSaveDialog(this);

        if (value == JalviewFileChooser.APPROVE_OPTION)
        {
            String choice = chooser.getSelectedFile().getPath();
            String defaultColours = jalview.bin.Cache.getDefault("USER_DEFINED_COLOURS", choice);
            if(defaultColours.indexOf(choice)==-1)
            {
              if(defaultColours.length()>0)
                defaultColours = defaultColours.concat("|");
              defaultColours = defaultColours.concat(choice);
            }

            userColourSchemes.put(schemeName.getText(), getSchemeFromButtons());

            ap.alignFrame.updateUserColourMenu();

            jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS", defaultColours);

            jalview.schemabinding.version2.JalviewUserColours ucs
                = new jalview.schemabinding.version2.JalviewUserColours();

            ucs.setSchemeName(schemeName.getText());
            try
            {
                PrintWriter out = new PrintWriter(new OutputStreamWriter(
                            new FileOutputStream(choice), "UTF-8"));

                for (int i = 0; i < buttonPanel.getComponentCount(); i++)
                {
                    JButton button = (JButton) buttonPanel.getComponent(i);
                    jalview.schemabinding.version2.Colour col
                        = new jalview.schemabinding.version2.Colour();
                    col.setName(button.getText());
                    col.setRGB(jalview.util.Format.getHexString(
                            button.getBackground()));
                    ucs.addColour(col);
                }

                ucs.marshal(out);
                out.close();
            }
            catch (Exception ex)
            {
                ex.printStackTrace();
            }
        }
    }

    /**
     * DOCUMENT ME!
     *
     * @param e DOCUMENT ME!
     */
    protected void cancelButton_actionPerformed(ActionEvent e)
    {
      if (ap != null)
      {
        if (seqGroup != null)
        {
          seqGroup.cs = oldColourScheme;
        }
        else if (ap != null)
        {
          ap.av.setGlobalColourScheme(oldColourScheme);
        }
        ap.repaint();
      }

      if(pdbcanvas!=null)
      {
        pdbcanvas.pdb.setColours(oldColourScheme);
      }

        try
        {
            frame.setClosed(true);
        }
        catch (Exception ex)
        {
        }
    }


    static Hashtable userColourSchemes;

    public static Hashtable getUserColourSchemes()
    {
      return userColourSchemes;
    }

    public static void initUserColourSchemes(String files)
    {
      userColourSchemes = new Hashtable();

      if(files==null || files.length()==0)
        return;


      // In case colours can't be loaded, we'll remove them
      // from the default list here.
      StringBuffer coloursFound = new StringBuffer();
      StringTokenizer st = new StringTokenizer(files, "|");
      while (st.hasMoreElements())
      {
        String file = st.nextToken();
        try
        {
          UserColourScheme ucs = loadColours(file);
          if (ucs != null)
          {
            if (coloursFound.length() > 0)
              coloursFound.append("|");
            coloursFound.append(file);
            userColourSchemes.put(ucs.getName(), ucs);
          }
        }
        catch (Exception ex)
        {
          System.out.println("Error loading User ColourFile\n" + ex);
        }
      }
      if (!files.equals(coloursFound.toString()))
      {
        if (coloursFound.toString().length() > 1)
          jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS",
                                        coloursFound.toString());
        else
          jalview.bin.Cache.applicationProperties.remove("USER_DEFINED_COLOURS");
      }
    }

    public static void removeColourFromDefaults(String target)
    {
      // The only way to find colours by name is to load them in
      // In case colours can't be loaded, we'll remove them
      // from the default list here.

      userColourSchemes = new Hashtable();

      StringBuffer coloursFound = new StringBuffer();
      StringTokenizer st = new StringTokenizer(
           jalview.bin.Cache.getProperty("USER_DEFINED_COLOURS"), "|");

      while (st.hasMoreElements())
      {
        String file = st.nextToken();
        try
        {
          UserColourScheme ucs = loadColours(file);
          if (ucs != null && !ucs.getName().equals(target))
          {
            if (coloursFound.length() > 0)
              coloursFound.append("|");
            coloursFound.append(file);
            userColourSchemes.put(ucs.getName(), ucs);
          }
        }
        catch (Exception ex)
        {
          System.out.println("Error loading User ColourFile\n" + ex);
        }
      }

      if (coloursFound.toString().length() > 1)
        jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS", coloursFound.toString());
      else
        jalview.bin.Cache.applicationProperties.remove("USER_DEFINED_COLOURS");

    }

    public void caseSensitive_actionPerformed(ActionEvent e)
    {
      resetButtonPanel(caseSensitive.isSelected());
      lcaseColour.setEnabled(caseSensitive.isSelected());
    }

    public void lcaseColour_actionPerformed(ActionEvent e)
    {
      if(selectedButtons==null)
        selectedButtons = new Vector();
      else
        selectedButtons.clear();
      selectedButtons.add(lcaseColour);
    }

}