/*
* Jalview - A Sequence Alignment Editor and Viewer
* Copyright (C) 2005 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.analysis.*;
import jalview.schemes.*;
import java.awt.*;
import javax.swing.*;
import java.awt.event.*;
import jalview.io.*;
import MCview.*;

public class PopupMenu extends JPopupMenu
{
  JMenu groupMenu = new JMenu();
  JMenuItem groupName = new JMenuItem();
  protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
  protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
  protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
  protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
  protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
  protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
  protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
  protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
  protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();
  protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
  protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
  protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
  JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
  protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();


  AlignmentPanel ap;
  JMenu sequenceMenu = new JMenu();
  JMenuItem sequenceName = new JMenuItem();
  Sequence sequence;
  JMenuItem unGroupMenuItem = new JMenuItem();
  JMenuItem pdbMenuItem = new JMenuItem();
  JMenuItem outline = new JMenuItem();
  JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem();
  JMenu colourMenu = new JMenu();
  JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();
  JCheckBoxMenuItem showText = new JCheckBoxMenuItem();
  JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();

  public PopupMenu(AlignmentPanel ap, Sequence seq)
  {
    ///////////////////////////////////////////////////////////
    // If this is activated from the sequence panel, the user may want to
    // edit or annotate a particular residue. Therefore display the residue menu
    //
    // If from the IDPanel, we must display the sequence menu
    //////////////////////////////////////////////////////////

    this.ap = ap;
    sequence = seq;

    ButtonGroup colours = new ButtonGroup();
    colours.add(noColourmenuItem);
    colours.add(clustalColour);
    colours.add(zappoColour);
    colours.add(taylorColour);
    colours.add(hydrophobicityColour);
    colours.add(helixColour);
    colours.add(strandColour);
    colours.add(turnColour);
    colours.add(buriedColour);
    colours.add(abovePIDColour);
    colours.add(userDefinedColour);
    colours.add(PIDColour);
    colours.add(BLOSUM62Colour);

    try
    {     jbInit();   }
    catch(Exception e)
    {    e.printStackTrace();    }

    SequenceGroup sg = ap.av.getSelectionGroup();
    if(sg!=null)
    {
      groupName.setText(sg.getName());
      if(sg.cs instanceof ZappoColourScheme)
        zappoColour.setSelected(true);
      else if(sg.cs instanceof TaylorColourScheme)
        taylorColour.setSelected(true);
      else if (sg.cs instanceof PIDColourScheme)
        PIDColour.setSelected(true);
      else if (sg.cs instanceof Blosum62ColourScheme)
        BLOSUM62Colour.setSelected(true);
      else if (sg.cs instanceof UserColourScheme)
        userDefinedColour.setSelected(true);
      else if (sg.cs instanceof HydrophobicColourScheme)
        hydrophobicityColour.setSelected(true);
      else if (sg.cs instanceof HelixColourScheme)
        helixColour.setSelected(true);
      else if (sg.cs instanceof StrandColourScheme)
        strandColour.setSelected(true);
      else if (sg.cs instanceof TurnColourScheme)
        turnColour.setSelected(true);
      else if (sg.cs instanceof BuriedColourScheme)
        buriedColour.setSelected(true);
      else if (sg.cs instanceof ClustalxColourScheme)
        clustalColour.setSelected(true);
      else
        noColourmenuItem.setSelected(true);

      if (sg.cs instanceof ConservationColourScheme)
        conservationMenuItem.setSelected(true);

      showText.setSelected(sg.getDisplayText());
      showColourText.setSelected(sg.getColourText());
      showBoxes.setSelected(sg.getDisplayBoxes());
    }

    if( !ap.av.alignment.getGroups().contains(sg))
      unGroupMenuItem.setVisible(false);
    else
      groupMenu.insertSeparator(3);

    if(seq==null)
       sequenceMenu.setVisible(false);

  }
  private void jbInit() throws Exception
  {
    groupMenu.setText("Group");
    groupMenu.setText("Define");
    groupName.setText("Name");
    groupName.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        groupName_actionPerformed(e);
      }
    });
    sequenceMenu.setText("Sequence");
    sequenceName.setText("Edit name");
    sequenceName.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        sequenceName_actionPerformed(e);
      }
    });
    PIDColour.setFocusPainted(false);
    unGroupMenuItem.setText("Remove Group");
    unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        unGroupMenuItem_actionPerformed(e);
      }
    });
    pdbMenuItem.setText("View PDB structure");
    pdbMenuItem.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        pdbMenuItem_actionPerformed(e);
      }
    });
    outline.setText("Border colour");
    outline.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        outline_actionPerformed(e);
      }
    });
    nucleotideMenuItem.setText("Nucleotide");
    nucleotideMenuItem.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        nucleotideMenuItem_actionPerformed(e);
      }
    });
    colourMenu.setText("Group Colour");
    showBoxes.setText("Boxes");
    showBoxes.setState(true);
    showBoxes.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        showBoxes_actionPerformed(e);
      }
    });
    showText.setText("Text");
    showText.setState(true);
    showText.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        showText_actionPerformed(e);
      }
    });
    showColourText.setText("Colour Text");
    showColourText.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        showColourText_actionPerformed(e);
      }
    });
    add(groupMenu);
    add(sequenceMenu);
    groupMenu.add(groupName);
    groupMenu.addSeparator();
    groupMenu.add(unGroupMenuItem);
    groupMenu.add(colourMenu);
    groupMenu.addSeparator();
    groupMenu.add(showBoxes);
    groupMenu.add(showText);
    groupMenu.add(showColourText);
    groupMenu.addSeparator();
    groupMenu.add(outline);
    sequenceMenu.add(sequenceName);
    sequenceMenu.add(pdbMenuItem);
    colourMenu.add(noColourmenuItem);
    colourMenu.add(clustalColour);
    colourMenu.add(BLOSUM62Colour);
    colourMenu.add(PIDColour);
    colourMenu.add(zappoColour);
    colourMenu.add(taylorColour);
    colourMenu.add(hydrophobicityColour);
    colourMenu.add(helixColour);
    colourMenu.add(strandColour);
    colourMenu.add(turnColour);
    colourMenu.add(buriedColour);
    colourMenu.add(nucleotideMenuItem);
    colourMenu.add(userDefinedColour);
    colourMenu.addSeparator();
    colourMenu.add(abovePIDColour);
    colourMenu.add(conservationMenuItem);
    noColourmenuItem.setText("None");
    noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        noColourmenuItem_actionPerformed(e);
      }
    });

    clustalColour.setText("Clustalx colours");
    clustalColour.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        clustalColour_actionPerformed(e);
      }
    });
    zappoColour.setText("Zappo");
    zappoColour.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        zappoColour_actionPerformed(e);
      }
    });
    taylorColour.setText("Taylor");
    taylorColour.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        taylorColour_actionPerformed(e);
      }
    });
    hydrophobicityColour.setText("Hydrophobicity");
    hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        hydrophobicityColour_actionPerformed(e);
      }
    });
    helixColour.setText("Helix propensity");
    helixColour.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        helixColour_actionPerformed(e);
      }
    });
    strandColour.setText("Strand propensity");
    strandColour.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        strandColour_actionPerformed(e);
      }
    });
    turnColour.setText("Turn propensity");
    turnColour.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        turnColour_actionPerformed(e);
      }
    });
    buriedColour.setText("Buried Index");
    buriedColour.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        buriedColour_actionPerformed(e);
      }
    });
    abovePIDColour.setText("Above % Identity");
    abovePIDColour.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        abovePIDColour_actionPerformed(e);
      }
    });
    userDefinedColour.setText("User Defined");
    userDefinedColour.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        userDefinedColour_actionPerformed(e);
      }
    });
    PIDColour.setText("Percentage Identity");
    PIDColour.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        PIDColour_actionPerformed(e);
      }
    });
    BLOSUM62Colour.setText("BLOSUM62");
    BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        BLOSUM62Colour_actionPerformed(e);
      }
    });
    conservationMenuItem.setText("Conservation");
   conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
   {
     public void actionPerformed(ActionEvent e)
     {
       conservationMenuItem_actionPerformed(e);
     }
   });



  }

  void refresh()
  {
    SequenceGroup sg = getGroup();
    SuperGroup superG = ap.av.alignment.getSuperGroup( sg );
    if( superG !=null)
      superG.setSuperGroupProperties( sg );

    ap.seqPanel.repaint();
  }

  protected void clustalColour_actionPerformed(ActionEvent e)
  {
    SequenceGroup sg = getGroup();
    sg.cs = new ClustalxColourScheme(sg.sequences, ap.av.alignment.getWidth());
    refresh();
  }

  protected void zappoColour_actionPerformed(ActionEvent e)
  {
    getGroup().cs = new ZappoColourScheme();
    refresh();
  }

  protected void taylorColour_actionPerformed(ActionEvent e)
  {
    getGroup().cs = new TaylorColourScheme();
    refresh();
  }


  protected void hydrophobicityColour_actionPerformed(ActionEvent e)
  {
    getGroup().cs = new HydrophobicColourScheme();
    refresh();
  }

  protected void helixColour_actionPerformed(ActionEvent e)
  {
    getGroup().cs = new HelixColourScheme();
    refresh();
  }

  protected void strandColour_actionPerformed(ActionEvent e)
  {
    getGroup().cs = new StrandColourScheme();
    refresh();
  }

  protected void turnColour_actionPerformed(ActionEvent e)
  {
    getGroup().cs = new TurnColourScheme();
    refresh();
  }

  protected void buriedColour_actionPerformed(ActionEvent e)
  {
    getGroup().cs = new BuriedColourScheme();
    refresh();
  }

  public void nucleotideMenuItem_actionPerformed(ActionEvent e)
  {
    getGroup().cs = new NucleotideColourScheme();
    refresh();
  }



  protected void abovePIDColour_actionPerformed(ActionEvent e)
  {
    SequenceGroup sg = getGroup();
    if (abovePIDColour.isSelected())
    {
      sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
                                               ap.av.alignment.getWidth()));
      int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup().getName());
      if (sg.cs instanceof ResidueColourScheme)
        ( (ResidueColourScheme)sg. cs).setThreshold(threshold);
      else if (sg.cs instanceof ScoreColourScheme)
        ( (ScoreColourScheme) sg.cs).setThreshold(threshold);

      SliderPanel.showPIDSlider();


    }
    else // remove PIDColouring
    {
      ResidueColourScheme rcs = (ResidueColourScheme) sg.cs;
      rcs.setThreshold(0);
      sg.cs = rcs;
    }

    refresh();

  }


  protected void userDefinedColour_actionPerformed(ActionEvent e)
  {
    new UserDefinedColours( ap, getGroup());
  }

  protected void PIDColour_actionPerformed(ActionEvent e)
  {
    SequenceGroup sg = getGroup();
    sg.cs = new PIDColourScheme();
    sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
                                               ap.av.alignment.getWidth()));
    refresh();
  }

  protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
  {
    SequenceGroup sg = getGroup();

    sg.cs = new Blosum62ColourScheme();

    sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
                                               ap.av.alignment.getWidth()));

    refresh();
  }


  protected void noColourmenuItem_actionPerformed(ActionEvent e)
  {
    getGroup().cs = null;
    refresh();
  }

  protected  void conservationMenuItem_actionPerformed(ActionEvent e)
  {
    SequenceGroup sg = getGroup();

    if(conservationMenuItem.isSelected())
    {

        Conservation c = new Conservation("Group",
                                          ResidueProperties.propHash, 3,
                                          sg.sequences, 0,
                                          ap.av.alignment.getWidth());

        c.calculate();
        c.verdict(false, ap.av.ConsPercGaps);
        ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);


      sg.cs = ccs;

      SliderPanel.setConservationSlider(ap, ccs, sg.getName());
      SliderPanel.showConservationSlider();
    }
    else // remove ConservationColouring
    {
        ConservationColourScheme ccs = (ConservationColourScheme)sg.cs;
        sg.cs = ccs.cs;
    }

     refresh();
  }


  protected void groupName_actionPerformed(ActionEvent e)
  {
    SequenceGroup sg = getGroup();
    String reply = JOptionPane.showInternalInputDialog(Desktop.desktop, "Enter new group name", "Edit group name", JOptionPane.QUESTION_MESSAGE);
    if(reply==null)
      return;

    sg.setName(reply);
    groupName.setText(reply);
  }


  protected void analyze_actionPerformed(ActionEvent e)
  {
     CutAndPasteTransfer cap = new CutAndPasteTransfer();
     JInternalFrame frame = new JInternalFrame();
     frame.setContentPane(cap);
     Desktop.addInternalFrame(frame, "Analyze this - ", 400, 300);
     SequenceGroup sg = getGroup();
     StringBuffer sb = new StringBuffer();

     for(int i=0; i<sg.sequences.size(); i++)
     {
       Sequence tmp = (Sequence)sg.sequences.get(i);
       sb.append(  tmp.getSequence(sg.getStartRes(), sg.getEndRes()+1));
       sb.append("\n");
     }

     sb.append("Something amazing will happen soon");
     cap.setText( sb.toString() );

  }

  SequenceGroup getGroup()
  {
    SequenceGroup sg = ap.av.getSelectionGroup();

    // this method won't add a new group if it already exists
    ap.av.alignment.addGroup(sg);

    return sg;
  }

  void sequenceName_actionPerformed(ActionEvent e)
  {
    String id = sequence.getName();
    String s = (String)JOptionPane.showInternalInputDialog(
                ap,
                "Edit sequence name",
                "Edit sequence name ("+sequence.getName()+")",
                JOptionPane.PLAIN_MESSAGE,
                null,
                null,
                id);

    if(s!=null)
    {
      sequence.setName(s);
      ap.repaint();
    }

  }

  void unGroupMenuItem_actionPerformed(ActionEvent e)
  {
     SequenceGroup sg = ap.av.getSelectionGroup();
     ap.av.alignment.deleteGroup(sg);
     ap.av.setSelectionGroup(null);
     ap.repaint();
  }

  void pdbMenuItem_actionPerformed(ActionEvent e)
  {
    if(sequence.getPDBId()==null)
      return;

    try
    {
      EBIFetchClient ebi = new EBIFetchClient();
      String[] result = ebi.fetchData("pdb:" + sequence.getPDBId(), null, null);

      PDBfile pdb = new PDBfile(result);

      rotCanvas rc = new rotCanvas(pdb, sequence, ap.av);
      JInternalFrame frame = new JInternalFrame();
      frame.setContentPane(rc);
      Desktop.addInternalFrame(frame,sequence.getName()+" "+ sequence.getPDBId(), 400, 400);
    }
    catch (Exception ex)
    {
      ex.printStackTrace();
    }
  }

  protected void outline_actionPerformed(ActionEvent e)
  {
    SequenceGroup sg = getGroup();
    Color col = JColorChooser.showDialog(this, "Select Outline Colour", Color.BLUE);
    if(col!=null)
      sg.setOutlineColour(col);
    ap.repaint();
  }

  public void showBoxes_actionPerformed(ActionEvent e)
  {
    getGroup().setDisplayBoxes(showBoxes.isSelected());
    refresh();
  }

  public void showText_actionPerformed(ActionEvent e)
  {
    getGroup().setDisplayText(showText.isSelected());
    refresh();
  }

  public void showColourText_actionPerformed(ActionEvent e)
  {
    getGroup().setColourText(showColourText.isSelected());
    refresh();
  }

}