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 analyze = new JMenuItem();
  JMenu defineMenu = new JMenu();
  JMenuItem groupName = new JMenuItem();
  JMenuItem groupAnnotation = 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();
  JMenu residueMenu = new JMenu();
  JMenuItem annotateResidue = new JMenuItem();

  Sequence sequence;
  JMenuItem unGroupMenuItem = new JMenuItem();
  JMenuItem pdbMenuItem = new JMenuItem();
  JMenuItem outline = new JMenuItem();

  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);
    }


    if(seq!=null)
      residueMenu.setVisible(false);
    else
      sequenceMenu.setVisible(false);

  }
  private void jbInit() throws Exception
  {
    groupMenu.setText("Group");
    analyze.setText("Analyze");
    analyze.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        analyze_actionPerformed(e);
      }
    });
    defineMenu.setText("Define");
    groupName.setText("Name");
    groupName.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        groupName_actionPerformed(e);
      }
    });
    groupAnnotation.setEnabled(false);
    groupAnnotation.setText("Annotation");
    groupAnnotation.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        groupAnnotation_actionPerformed(e);
      }
    });
    sequenceMenu.setText("Sequence");
    sequenceName.setText("Edit name");
    sequenceName.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        sequenceName_actionPerformed(e);
      }
    });
    residueMenu.setText("Residue");
    annotateResidue.setEnabled(false);
    annotateResidue.setActionCommand("annotate residue");
    annotateResidue.setText("annotate residue???");
    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);
      }
    });
    add(groupMenu);
    this.add(sequenceMenu);
    this.add(residueMenu);
    groupMenu.add(defineMenu);
    groupMenu.add(unGroupMenuItem);
    groupMenu.addSeparator();
    groupMenu.add(analyze);
    defineMenu.add(groupName);
    defineMenu.add(groupAnnotation);
    defineMenu.addSeparator();
    defineMenu.add(outline);
    defineMenu.addSeparator();
    defineMenu.add(noColourmenuItem);
    defineMenu.add(clustalColour);
    defineMenu.add(zappoColour);
    defineMenu.add(taylorColour);
    defineMenu.add(hydrophobicityColour);
    defineMenu.add(helixColour);
    defineMenu.add(strandColour);
    defineMenu.add(turnColour);
    defineMenu.add(buriedColour);
    defineMenu.add(userDefinedColour);
    defineMenu.add(PIDColour);
    defineMenu.add(BLOSUM62Colour);
    defineMenu.addSeparator();
    defineMenu.add(abovePIDColour);
    defineMenu.add(conservationMenuItem);

    sequenceMenu.add(sequenceName);
    sequenceMenu.add(pdbMenuItem);
    residueMenu.add(annotateResidue);

    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 colour scheme");
    zappoColour.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        zappoColour_actionPerformed(e);
      }
    });
    taylorColour.setText("Taylor colour scheme");
    taylorColour.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        taylorColour_actionPerformed(e);
      }
    });
    hydrophobicityColour.setText("By 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 PID threshold only");
    abovePIDColour.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        abovePIDColour_actionPerformed(e);
      }
    });
    userDefinedColour.setText("User defined colours");
    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 score");
    BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        BLOSUM62Colour_actionPerformed(e);
      }
    });
    conservationMenuItem.setText("By 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();
  }


  protected void abovePIDColour_actionPerformed(ActionEvent e)
  {
    if(abovePIDColour.isSelected())
{

   Desktop.setPIDSliderSource(ap, getGroup().cs, getGroup().getName());
   refresh();
}
else // remove PIDColouring
{
    ColourSchemeI cs = getGroup().cs;
      ResidueColourScheme rcs = (ResidueColourScheme)cs;
      rcs.setThreshold(0);
      getGroup().cs = rcs;
      refresh();
}



  }


  protected void userDefinedColour_actionPerformed(ActionEvent e)
  {
    JInternalFrame frame = new JInternalFrame();
    UserDefinedColours chooser = new UserDefinedColours( frame, ap, getGroup());
    frame.setContentPane(chooser);
    Desktop.addInternalFrame(frame,"User defined colours ("+getGroup().getName()+")", 450,540 );
    frame.setResizable(false);
    frame.setIconifiable(false);
    frame.setMaximizable(false);

  }

  protected void PIDColour_actionPerformed(ActionEvent e)
  {

  }

  protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
  {
    getGroup().cs = new Blosum62ColourScheme(ap.av);
    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, 100);
        ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);


      sg.cs = ccs;

      Desktop.setConservationSliderSource(ap, ccs, sg.getName());
    }
    else // remove ConservationColouring
    {
        ConservationColourScheme ccs = (ConservationColourScheme)sg.cs;
        sg.cs = ccs.cs;
    }

     refresh();
  }

  protected void groupAnnotation_actionPerformed(ActionEvent e)
  {

  }

  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(false);
     JInternalFrame frame = new JInternalFrame();
     cap.formatForOutput();
     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.RefreshPanels();
    }

  }

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

  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);
      sequence.setPDBfile(pdb);

      ( (PDBChain) pdb.chains.elementAt(sequence.maxchain)).isVisible = true;
      ( (PDBChain) pdb.chains.elementAt(sequence.maxchain)).sequence = sequence;
    //  ( (PDBChain)pdb.chains.elementAt(sequence.maxchain)).colourBySequence();

      rotCanvas rc = new rotCanvas(pdb);
      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);
  }

}