package jalview.gui;

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


public class PopupMenu extends JPopupMenu
{
  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 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();

  SequenceI sequence;

  public PopupMenu(AlignmentPanel ap, SequenceI 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.getRubberbandGroup();
    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);
      sequenceName.setText( sequence.getName() );
    }
    else
      sequenceMenu.setVisible(false);

  }
  private void jbInit() throws Exception
  {
    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);
      }
    });
    sequenceMenu.setText("Sequence");
    sequenceName.setText("sequenceName");
    sequenceName.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        sequenceName_actionPerformed(e);
      }
    });
    residueMenu.setText("Residue");
    annotateResidue.setText("annotate residue???");
    PIDColour.setFocusPainted(false);
    add(groupMenu);
    this.add(sequenceMenu);
    this.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.add(PIDColour);
    defineMenu.add(BLOSUM62Colour);
    defineMenu.addSeparator();
    defineMenu.add(abovePIDColour);
    defineMenu.add(conservationMenuItem);

    sequenceMenu.add(sequenceName);
    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()
  {
    ap.seqPanel.seqCanvas.paintFlag=true;
    ap.seqPanel.repaint();
  }

  protected void clustalColour_actionPerformed(ActionEvent e)
  {
    getGroup().cs = new ClustalxColourScheme();
    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 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)
  {
    SliderPanel sp = new SliderPanel(ap, 70, false, getGroup().cs );
    JInternalFrame frame = new JInternalFrame();
    frame.setContentPane(sp);
    Desktop.addInternalFrame(frame, "Percentage Identity Threshold ("+getGroup().getName()+")" , 400,90);
    frame.setMaximizable(false);

  }


  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();

    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 noColourmenuItem_actionPerformed(ActionEvent e)
  {
    viewport.setGlobalColourScheme( null );
    changeColour();
  }


  public void clustalColour_actionPerformed(ActionEvent e)
  {
    viewport.setGlobalColourScheme(new ClustalxColourScheme( ));
    conservationMenuItem.setSelected(false);
    abovePIDThreshold.setSelected(false);
    changeColour();
  }

  public void zappoColour_actionPerformed(ActionEvent e)
  {
    viewport.setGlobalColourScheme(new ZappoColourScheme() );
    changeColour();
  }

  public void taylorColour_actionPerformed(ActionEvent e)
  {
    viewport.setGlobalColourScheme(new TaylorColourScheme() );
    changeColour();
  }


  public void hydrophobicityColour_actionPerformed(ActionEvent e)
  {
    viewport.setGlobalColourScheme( new HydrophobicColourScheme() );
    changeColour();
  }

  public void helixColour_actionPerformed(ActionEvent e)
  {
    viewport.setGlobalColourScheme( new HelixColourScheme()  );
    changeColour();
  }


  public void strandColour_actionPerformed(ActionEvent e)
  {
    viewport.setGlobalColourScheme(new StrandColourScheme() );
    changeColour();
  }


  public void turnColour_actionPerformed(ActionEvent e)
  {
    viewport.setGlobalColourScheme(new TurnColourScheme() );
    changeColour();
  }


  public void buriedColour_actionPerformed(ActionEvent e)
  {
    viewport.setGlobalColourScheme( new BuriedColourScheme() );
    changeColour();
  }

  void changeColour()
  {
    if(abovePIDThreshold.isSelected())
      abovePIDThreshold_actionPerformed(null);
    else if(conservationMenuItem.isSelected())
      conservationMenuItem_actionPerformed(null);

     alignPanel.seqPanel.seqCanvas.paintFlag = true;
     alignPanel.repaint();
  }

  void addConservationOrPIDColour()
  {
    int x=0, y=0, threshold = 70;

    if(sliderFrame!=null)
       try
       {
         x = sliderFrame.getX();
         y = sliderFrame.getY();
         SliderPanel sp = (SliderPanel) sliderFrame.getContentPane();
         threshold = sp.getValue();
         sliderFrame.setClosed(true);
       }
       catch (Exception ex)
       {    ex.printStackTrace();   }

     ColourSchemeI oldCs = viewport.getGlobalColourScheme();

     ConservationColourScheme ccs = null;
     if (oldCs instanceof ConservationColourScheme)
       ccs = (ConservationColourScheme) oldCs;

     if(conservationMenuItem.isSelected())
     {
       Alignment al = (Alignment)viewport.alignment;
       Conservation c = new Conservation("All",
                            ResidueProperties.propHash, 3, al.getSequences(), 0,
                            al.getWidth() );

       c.calculate();
       c.verdict(false, 100);

       if(ccs!=null)
         ccs = new ConservationColourScheme(c, ccs.cs);
       else
         ccs = new ConservationColourScheme(c, oldCs);

        viewport.setGlobalColourScheme( ccs );

     }
     else if(oldCs instanceof ConservationColourScheme)
     {
       oldCs = ccs.cs;
       viewport.setGlobalColourScheme( oldCs );
     }


     if( conservationMenuItem.isSelected() || abovePIDThreshold.isSelected() )
     {
       sliderFrame = new JInternalFrame();
       sliderFrame.setMaximizable(false);
       sliderFrame.setResizable(false);

       SliderPanel sp = null;
       if (conservationMenuItem.isSelected())
       {
        if(threshold > 50)
          threshold = 30;
        sp = new SliderPanel(alignPanel, threshold, true,ccs);
        Desktop.addInternalFrame(sliderFrame, "Conservation Colour Increment  (Global colour)", 400, 90);
        threshold = 0;
       }
       else if (abovePIDThreshold.isSelected())
       {
         sp = new SliderPanel(alignPanel, threshold, false, oldCs);
         sp.cs = oldCs;
         Desktop.addInternalFrame(sliderFrame, "Percentage Identity Threshold (Global colour)", 400, 90);
       }

       sliderFrame.setContentPane(sp);
       if(x!=0 && y!=0)
               sliderFrame.setLocation(x,y);

     }
     else
       threshold = 0;


     if (oldCs instanceof ResidueColourScheme)
     {
       ResidueColourScheme rcs = (ResidueColourScheme) oldCs;
       rcs.setThreshold(threshold);
     }
     else if (oldCs instanceof ScoreColourScheme)
     {
       ScoreColourScheme scs = (ScoreColourScheme) oldCs;
       scs.setThreshold(threshold);
     }

     alignPanel.seqPanel.seqCanvas.paintFlag = true;
     alignPanel.repaint();

  }

  protected  void conservationMenuItem_actionPerformed(ActionEvent e)
  {
   if(abovePIDThreshold.isSelected())
    abovePIDThreshold.setSelected(false);

   viewport.setConservationSelected(conservationMenuItem.isSelected());

   addConservationOrPIDColour();
  }

  JInternalFrame sliderFrame;
  public void abovePIDThreshold_actionPerformed(ActionEvent e)
  {
      if(conservationMenuItem.isSelected())
        conservationMenuItem.setSelected(false);

      addConservationOrPIDColour();
  }



  public void userDefinedColour_actionPerformed(ActionEvent e)
  {
    JInternalFrame frame = new JInternalFrame();
    UserDefinedColours chooser = new UserDefinedColours( frame, alignPanel, null);
    frame.setContentPane(chooser);
    Desktop.addInternalFrame(frame,"User defined colours", 450,540 );
    frame.setResizable(false);
    frame.setIconifiable(false);
    frame.setMaximizable(false);
  }

  public void PIDColour_actionPerformed(ActionEvent e)
  {
    viewport.setGlobalColourScheme( new PIDColourScheme() );
    alignPanel.setColourScheme( );
  }


  public void BLOSUM62Colour_actionPerformed(ActionEvent e)
  {
    viewport.setGlobalColourScheme( new Blosum62ColourScheme(viewport)  );
    alignPanel.setColourScheme();
  }
*/
//////////////////////////////////////
  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 copyGroup_actionPerformed(ActionEvent e)
  {
    SequenceGroup sg = ap.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)
  {
    SequenceGroup sg = ap.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));

     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);


     for (int i=0; i < sg.sequences.size(); i++)
       ap.av.alignment.deleteSequence(sg.getSequenceAt(i));


     ap.av.resetSeqLimits(ap.seqPanel.seqCanvas.getHeight());
     ap.RefreshPanels();


  }

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

    ap.av.alignment.deleteGroup(sg);
    ap.av.resetSeqLimits(ap.seqPanel.seqCanvas.getHeight());
    ap.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 = ap.av.getRubberbandGroup();

    // 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",
                JOptionPane.PLAIN_MESSAGE,
                null,
                null,
                id);

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

  }
}