/*
 * 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.appletgui;

import java.awt.*;
import java.awt.event.*;
import java.util.Vector;

import jalview.analysis.*;
import jalview.datamodel.*;
import jalview.schemes.*;

public class APopupMenu
    extends java.awt.PopupMenu
{
  Menu groupMenu = new Menu();
  protected MenuItem clustalColour = new MenuItem();
  protected MenuItem zappoColour = new MenuItem();
  protected MenuItem taylorColour = new MenuItem();
  protected MenuItem hydrophobicityColour = new MenuItem();
  protected MenuItem helixColour = new MenuItem();
  protected MenuItem strandColour = new MenuItem();
  protected MenuItem turnColour = new MenuItem();
  protected MenuItem buriedColour = new MenuItem();
  protected CheckboxMenuItem abovePIDColour = new CheckboxMenuItem();
  protected MenuItem userDefinedColour = new MenuItem();
  protected MenuItem PIDColour = new MenuItem();
  protected MenuItem BLOSUM62Colour = new MenuItem();
  MenuItem noColourmenuItem = new MenuItem();
  protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();

  AlignmentPanel ap;
  MenuItem unGroupMenuItem = new MenuItem();
  MenuItem nucleotideMenuItem = new MenuItem();
  Menu colourMenu = new Menu();
  CheckboxMenuItem showBoxes = new CheckboxMenuItem();
  CheckboxMenuItem showText = new CheckboxMenuItem();
  CheckboxMenuItem showColourText = new CheckboxMenuItem();

  public APopupMenu(AlignmentPanel ap, Sequence seq, Vector links)
  {
    ///////////////////////////////////////////////////////////
    // 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;

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

    SequenceGroup sg = ap.av.getSelectionGroup();
    if (sg != null)
    {
      showText.setState(sg.getDisplayText());
      showColourText.setState(sg.getColourText());
      showBoxes.setState(sg.getDisplayBoxes());
    }

    if (!ap.av.alignment.getGroups().contains(sg))
    {
      groupMenu.remove(unGroupMenuItem);
    }

    if (seq != null && links!=null)
    {
      Menu linkMenu = new Menu("Link");
      MenuItem item;
      String link;
      for(int i=0; i<links.size(); i++)
      {
        link = links.elementAt(i).toString();
        final String target = link.substring(0, link.indexOf("|"));
        item = new MenuItem(target);
        final String url = link.substring(link.indexOf("|")+1, link.indexOf("$SEQUENCE_ID$"))
               + seq.getName() +
               link.substring(link.indexOf("$SEQUENCE_ID$") + 13);

           item.addActionListener(new java.awt.event.ActionListener()
           {
               public void actionPerformed(ActionEvent e)
               {
                  jalview.bin.JalviewLite.showURL(url, target);
               }
           });
          linkMenu.add(item);
      }
      add(linkMenu);
    }
  }

  private void jbInit()
      throws Exception
  {
    groupMenu.setLabel("Group");
    groupMenu.setLabel("Define");

    unGroupMenuItem.setLabel("Remove Group");
    unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        unGroupMenuItem_actionPerformed(e);
      }
    });

    nucleotideMenuItem.setLabel("Nucleotide");
    nucleotideMenuItem.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        nucleotideMenuItem_actionPerformed(e);
      }
    });
    conservationMenuItem.addItemListener(new ItemListener()
    {
      public void itemStateChanged(ItemEvent itemEvent)
      {
        conservationMenuItem_itemStateChanged(itemEvent);
      }
    });
    abovePIDColour.addItemListener(new ItemListener()
    {
      public void itemStateChanged(ItemEvent itemEvent)
      {
        abovePIDColour_itemStateChanged(itemEvent);
      }
    });
    colourMenu.setLabel("Group Colour");
    showBoxes.setLabel("Boxes");
    showBoxes.setState(true);
    showBoxes.addItemListener(new ItemListener()
    {
      public void itemStateChanged(ItemEvent itemEvent)
      {
        showBoxes_itemStateChanged(itemEvent);
      }
    });

    showText.setLabel("Text");
    showText.addItemListener(new ItemListener()
    {
      public void itemStateChanged(ItemEvent itemEvent)
      {
        showText_itemStateChanged(itemEvent);
      }
    });
    showColourText.setLabel("Colour Text");
    showColourText.addItemListener(new ItemListener()
    {
      public void itemStateChanged(ItemEvent itemEvent)
      {
        showColourText_itemStateChanged(itemEvent);
      }
    });

    add(groupMenu);
    groupMenu.add(unGroupMenuItem);
    groupMenu.add(colourMenu);
    groupMenu.addSeparator();
    groupMenu.add(showBoxes);
    groupMenu.add(showText);
    groupMenu.add(showColourText);
    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.setLabel("None");
    noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        noColourmenuItem_actionPerformed(e);
      }
    });

    clustalColour.setLabel("Clustalx colours");
    clustalColour.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        clustalColour_actionPerformed(e);
      }
    });
    zappoColour.setLabel("Zappo");
    zappoColour.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        zappoColour_actionPerformed(e);
      }
    });
    taylorColour.setLabel("Taylor");
    taylorColour.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        taylorColour_actionPerformed(e);
      }
    });
    hydrophobicityColour.setLabel("Hydrophobicity");
    hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        hydrophobicityColour_actionPerformed(e);
      }
    });
    helixColour.setLabel("Helix propensity");
    helixColour.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        helixColour_actionPerformed(e);
      }
    });
    strandColour.setLabel("Strand propensity");
    strandColour.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        strandColour_actionPerformed(e);
      }
    });
    turnColour.setLabel("Turn propensity");
    turnColour.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        turnColour_actionPerformed(e);
      }
    });
    buriedColour.setLabel("Buried Index");
    buriedColour.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        buriedColour_actionPerformed(e);
      }
    });
    abovePIDColour.setLabel("Above % Identity");

    userDefinedColour.setLabel("User Defined");
    userDefinedColour.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        userDefinedColour_actionPerformed(e);
      }
    });
    PIDColour.setLabel("Percentage Identity");
    PIDColour.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        PIDColour_actionPerformed(e);
      }
    });
    BLOSUM62Colour.setLabel("BLOSUM62");
    BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        BLOSUM62Colour_actionPerformed(e);
      }
    });
    conservationMenuItem.setLabel("Conservation");

  }

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

      if (superG != null)
      {
        superG.setSuperGroupProperties(sg);
      }
        }
    ap.seqPanel.seqCanvas.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_itemStateChanged(ItemEvent ie)
  {
    SequenceGroup sg = getGroup();
    if(sg.cs==null)
          return;

    if (abovePIDColour.getState())
    {
      sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
                                               ap.av.alignment.getWidth()));
      int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,
          getGroup().getName());

      sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());

      SliderPanel.showPIDSlider();

    }
    else // remove PIDColouring
    {
      sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
    }

    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_itemStateChanged(ItemEvent ie)
  {
    SequenceGroup sg = getGroup();
    if(sg.cs==null)
          return;

    if (conservationMenuItem.getState())
    {

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

      c.calculate();
      c.verdict(false, ap.av.ConsPercGaps);

      sg.cs.setConservation(c);

      SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
      SliderPanel.showConservationSlider();
    }
    else // remove ConservationColouring
    {
      sg.cs.setConservation(null);
    }

    refresh();
  }

  protected void analyze_actionPerformed(ActionEvent e)
  {
    CutAndPasteTransfer cap = new CutAndPasteTransfer(false);
    Frame frame = new Frame();
    frame.add(cap);
    jalview.bin.JalviewLite.addFrame(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.elementAt(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
    if(sg!=null)
      ap.av.alignment.addGroup(sg);

    return sg;
  }

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

  public void showColourText_itemStateChanged(ItemEvent itemEvent)
  {
    getGroup().setColourText(showColourText.getState());
    refresh();
  }

  public void showText_itemStateChanged(ItemEvent itemEvent)
  {
    getGroup().setDisplayText(showText.getState());
    refresh();
  }

  public void showBoxes_itemStateChanged(ItemEvent itemEvent)
  {
    getGroup().setDisplayBoxes(showBoxes.getState());
    refresh();
  }

}