package jalview.gui;

import jalview.datamodel.*;
import jalview.analysis.*;
import jalview.schemes.*;
import javax.swing.*;
import java.awt.event.*;


public class PopupMenu extends JPopupMenu
{
  JMenuItem residueMenu = new JMenuItem();
  JMenu groupMenu = new JMenu();
  JMenuItem copyGroup = new JMenuItem();
  JMenuItem moveGroup = new JMenuItem();
  JMenuItem deleteSequences = new JMenuItem();
  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 JRadioButtonMenuItem abovePIDColour = new JRadioButtonMenuItem();
  protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
  protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
  protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
  JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
  protected JMenuItem conservationColourIncMenuItem = new JMenuItem();
  protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();


  AlignViewport av;
  SeqPanel seqPanel;

  public PopupMenu(AlignViewport av, SeqPanel sp)
  {
    this.av = av;
    seqPanel = sp;

    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 = av.getRubberbandGroup();
    groupName.setText( sg.getName() );
  }
  private void jbInit() throws Exception
  {
    residueMenu.setText("Residue");
    groupMenu.setText("Group");
    copyGroup.setText("Copy region to new Alignment");
    copyGroup.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        copyGroup_actionPerformed(e);
      }
    });
    moveGroup.setText("Move sequences to new Alignment");
    moveGroup.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        moveGroup_actionPerformed(e);
      }
    });
    deleteSequences.setText("Delete sequences");
    deleteSequences.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        deleteSequences_actionPerformed(e);
      }
    });
    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.setText("Annotation");
    groupAnnotation.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        groupAnnotation_actionPerformed(e);
      }
    });
    add(groupMenu);
    add(residueMenu);
    groupMenu.add(defineMenu);
    groupMenu.addSeparator();
    groupMenu.add(copyGroup);
    groupMenu.add(moveGroup);
    groupMenu.add(deleteSequences);
    groupMenu.addSeparator();
    groupMenu.add(analyze);
    defineMenu.add(groupName);
    defineMenu.add(groupAnnotation);
    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.addSeparator();
    defineMenu.add(conservationMenuItem);
    defineMenu.add(conservationColourIncMenuItem);
    defineMenu.addSeparator();
    defineMenu.add(abovePIDColour);
    defineMenu.add(PIDColour);
    defineMenu.add(BLOSUM62Colour);

    noColourmenuItem.setText("None");
    noColourmenuItem.setSelected(true);
    noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        noColourmenuItem_actionPerformed(e);
      }
    });

    clustalColour.setEnabled(false);
    clustalColour.setSelected(false);
    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.setEnabled(false);
    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.setEnabled(false);
    PIDColour.setText("By PID");
    PIDColour.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        PIDColour_actionPerformed(e);
      }
    });
    BLOSUM62Colour.setText("By 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);
     }
   });

    conservationColourIncMenuItem.setEnabled(false);
    conservationColourIncMenuItem.setText("Conservation Colour Increment");
    conservationColourIncMenuItem.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        conservationColourIncMenuItem_actionPerformed(e);
      }
    });


  }

  void refresh()
  {
    seqPanel.seqCanvas.paintFlag=true;
    seqPanel.repaint();
  }

  protected void clustalColour_actionPerformed(ActionEvent e)
  {

  }

  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 conservationColourIncMenuItem_actionPerformed(ActionEvent e)
 {

}
/*
public void conservationColourIncMenuItem_actionPerformed(ActionEvent e)
{
ConservationIncrementPanel cip = new ConservationIncrementPanel(viewport, alignPanel);
JInternalFrame frame = new JInternalFrame();
frame.setContentPane(cip);
Desktop.addInternalFrame(frame, "Conservation Colour Increment", 400,90);
frame.setMaximizable(false);

 }*/


  protected void abovePIDColour_actionPerformed(ActionEvent e)
  {

  }


  protected void userDefinedColour_actionPerformed(ActionEvent e)
  {
    JInternalFrame frame = new JInternalFrame();
    UserDefinedColours chooser = new UserDefinedColours( frame, seqPanel.parent, getGroup());
    frame.setContentPane(chooser);
    Desktop.addInternalFrame(frame,"User defined colours", 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(av);
    refresh();
  }


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

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

    Conservation c = new Conservation("Group",
                          ResidueProperties.propHash, 3, sg.sequences, sg.getStartRes(),
                          sg.getEndRes() );

     c.calculate();
     c.verdict(false, 100);
     ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);

     sg.cs = ccs;

     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);
  }
  /*  public void deleteSelectedMenuItem_actionPerformed(ActionEvent e)
    {
      addHistoryItem("delete selection");

      for (int i=0;i < viewport.getSelection().size(); i++)
              viewport.getAlignment().deleteSequence(viewport.getSelection().sequenceAt(i));

      viewport.getSelection().clear();
      viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getHeight());
      alignPanel.RefreshPanels();
    }

    public void moveSelectedMenuItem_actionPerformed(ActionEvent e)
    {
      copySelectedMenuItem_actionPerformed(null);
      deleteSelectedMenuItem_actionPerformed(null);
      alignPanel.repaint();
    }

    public void copySelectedMenuItem_actionPerformed(ActionEvent e)
    {
      if(viewport.getSelection().size()==0)
        return;

     SequenceI[] s = new Sequence[viewport.getSelection().size()];
     for (int i=0; i < viewport.getSelection().size(); i++) {
       s[i] = new Sequence(viewport.getSelection().sequenceAt(i));
      }
      AlignFrame af = new AlignFrame(new Alignment(s));
      int newHeight = s.length * af.viewport.getCharHeight() + 200;
      if(newHeight>500)
        newHeight=500;
      Desktop.addInternalFrame(af, "Copied sequences", 700,newHeight);
    }
*/
  protected void copyGroup_actionPerformed(ActionEvent e)
  {
    SequenceGroup sg = av.getRubberbandGroup();

    SequenceI[] s = new Sequence[sg.sequences.size()];
     for (int i=0; i < sg.sequences.size(); i++)
     {
       s[i] = new Sequence( sg.getSequenceAt(i));
       s[i].setSequence( s[i].getSequence(sg.getStartRes(), sg.getEndRes()+1) );
     }
     AlignFrame af = new AlignFrame(new Alignment(s));
     int newHeight = s.length * af.viewport.getCharHeight() + 200;
     if (newHeight > 500)
       newHeight = 500;
     Desktop.addInternalFrame(af, "Copied sequences", 700, newHeight);
  }

  protected  void moveGroup_actionPerformed(ActionEvent e)
  {

  }

  protected void deleteSequences_actionPerformed(ActionEvent e)
  {
    SequenceGroup sg = av.getRubberbandGroup();
    for (int i=0;i < sg.sequences.size(); i++)
            av.getAlignment().deleteSequence(sg.getSequenceAt(i));

    av.alignment.deleteGroup(sg);
    av.resetSeqLimits(seqPanel.seqCanvas.getHeight());
    seqPanel.parent.RefreshPanels();

  }

  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 = av.getRubberbandGroup();

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