/*
 * Jalview - A Sequence Alignment Editor and Viewer
 * Copyright (C) 2006 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 implements ActionListener, ItemListener
{
  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();

  final 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();
  Menu editMenu = new Menu("Edit");
  MenuItem copy = new MenuItem("Copy (Jalview Only)");
  MenuItem cut = new MenuItem("Cut (Jalview Only)");
  MenuItem toUpper = new MenuItem("To Upper Case");
  MenuItem toLower = new MenuItem("To Lower Case");
  MenuItem toggleCase = new MenuItem("Toggle Case");
  Menu outputmenu = new Menu();
  Menu seqMenu = new Menu();
  MenuItem pdb = new MenuItem();
  MenuItem hideSeqs = new MenuItem();
  MenuItem repGroup = new MenuItem();

  Sequence seq;
  MenuItem revealAll = new MenuItem();

  public APopupMenu(AlignmentPanel apanel, final 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 = apanel;
    this.seq = seq;

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

    for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
    {
      MenuItem item = new MenuItem( jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i] );

      item.addActionListener(this);
      outputmenu.add(item);
    }

    SequenceGroup sg = ap.av.getSelectionGroup();

    if (sg != null && sg.getSize(false)>0)
    {
      showText.setState(sg.getDisplayText());
      showColourText.setState(sg.getColourText());
      showBoxes.setState(sg.getDisplayBoxes());
      if (!ap.av.alignment.getGroups().contains(sg))
      {
        groupMenu.remove(unGroupMenuItem);
      }

    }
    else
    {
      remove(hideSeqs);
      remove(groupMenu);
    }

    if (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;

        if (link.indexOf("$SEQUENCE_ID$") > -1)
        {
          String id = seq.getName();
          if (id.indexOf("|") > -1)
            id = id.substring(id.lastIndexOf("|") + 1);

          url = link.substring(link.indexOf("|") + 1,
                               link.indexOf("$SEQUENCE_ID$"))
              + id +
              link.substring(link.indexOf("$SEQUENCE_ID$") + 13);
        }
        else
          url = link.substring(link.lastIndexOf("|")+1);

        System.out.println("add "+url +" "+target);
           item.addActionListener(new java.awt.event.ActionListener()
           {
               public void actionPerformed(ActionEvent e)
               {
                  ap.alignFrame.showURL(url, target);
               }
           });
          linkMenu.add(item);
      }
      if(seq!=null)
        seqMenu.add(linkMenu);
      else
        add(linkMenu);
    }
    if(seq!=null)
    {
      seqMenu.setLabel(seq.getName());
      repGroup.setLabel("Represent Group with " + seq.getName());
    }
    else
      remove(seqMenu);

    if(!ap.av.hasHiddenRows)
      remove(revealAll);
  }

  public void itemStateChanged(ItemEvent evt)
  {
    if(evt.getSource()==abovePIDColour)
      abovePIDColour_itemStateChanged();
    else if(evt.getSource()==showColourText)
      showColourText_itemStateChanged();
    else if(evt.getSource()==showText)
      showText_itemStateChanged();
    else if(evt.getSource()==showBoxes)
       showBoxes_itemStateChanged()   ;
  }

  public void actionPerformed(ActionEvent evt)
  {
    Object source = evt.getSource();
    if(source==clustalColour)
      clustalColour_actionPerformed();
    else if(source==zappoColour)
      zappoColour_actionPerformed();
    else if(source==taylorColour)
      taylorColour_actionPerformed();
    else if(source==hydrophobicityColour)
      hydrophobicityColour_actionPerformed();
    else if(source==helixColour)
      helixColour_actionPerformed();
    else if(source==strandColour)
      strandColour_actionPerformed();
    else if(source==clustalColour)
      turnColour_actionPerformed();
    else if(source==buriedColour)
      buriedColour_actionPerformed();
    else if(source==nucleotideMenuItem)
      nucleotideMenuItem_actionPerformed();

    else if (source == userDefinedColour)
      userDefinedColour_actionPerformed();
    else if (source == PIDColour)
      PIDColour_actionPerformed();
    else if (source == BLOSUM62Colour)
      BLOSUM62Colour_actionPerformed();
    else if (source == noColourmenuItem)
      noColourmenuItem_actionPerformed();
    else if (source == conservationMenuItem)
      conservationMenuItem_itemStateChanged();
    else if (source == unGroupMenuItem)
      unGroupMenuItem_actionPerformed();

    else if(source == pdb)
      addPDB();
    else if(source == hideSeqs)
      hideSequences(false);
    else if(source == repGroup)
      hideSequences(true);
    else if(source == revealAll)
    {
        ap.av.showAllHiddenSeqs();
    }

    else if(source==copy)
      ap.alignFrame.copy_actionPerformed();
    else if(source==cut)
      ap.alignFrame.cut_actionPerformed();
    else if(source==toUpper || source==toLower || source==toggleCase)
    {
      SequenceGroup sg = ap.av.getSelectionGroup();
      if (sg != null)
      {
        for (int g = 0; g < sg.getSize(true); g++)
        {
          if (source == toggleCase)
           ((SequenceI) sg.getSequences(true).elementAt(g))
          .toggleCase(sg.getStartRes(), sg.getEndRes() + 1);
          else
            ((SequenceI) sg.getSequences(true).elementAt(g))
                .changeCase(source == toUpper, sg.getStartRes(),
                                           sg.getEndRes() + 1);
        }
        ap.seqPanel.seqCanvas.repaint();
      }
    }
    else
      outputText(evt);

  }

  void outputText(ActionEvent e)
  {
    CutAndPasteTransfer cap = new CutAndPasteTransfer(false, ap.alignFrame);
    Vector vseqs = new Vector();

      String [] selection = ap.av.getViewAsString(true);
      SequenceI [] seqs = ap.av.getSelectionAsNewSequence();
      if (selection != null)
      {
        for (int i = 0; i < selection.length; i++)
        {
          Sequence seq = new Sequence(
              seqs[i].getName(),
              selection[i],
              seqs[i].getStart(), seqs[i].getEnd());
          seq.setDescription(seqs[i].getDescription());
          vseqs.addElement( seq );
      }
    }

    Frame frame = new Frame();
    frame.add(cap);
    jalview.bin.JalviewLite.addFrame(frame,
                                     "Selection output - " + e.getActionCommand(),
                                     600, 500);

    cap.setText(new jalview.io.AppletFormatAdapter().formatSequences(
        e.getActionCommand(),
        vseqs,
        ap.av.showJVSuffix));

  }

  void addPDB()
  {
    CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame);
    cap.setText("Paste your PDB file here.");
    cap.setPDBImport(seq);
    Frame frame = new Frame();
    frame.add(cap);
    jalview.bin.JalviewLite.addFrame(frame, "Paste PDB file ", 400, 300);
  }

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

    unGroupMenuItem.setLabel("Remove Group");
    unGroupMenuItem.addActionListener(this);

    nucleotideMenuItem.setLabel("Nucleotide");
    nucleotideMenuItem.addActionListener(this);
    conservationMenuItem.addItemListener(this);
    abovePIDColour.addItemListener(this);
    colourMenu.setLabel("Group Colour");
    showBoxes.setLabel("Boxes");
    showBoxes.setState(true);
    showBoxes.addItemListener(this);

    showText.setLabel("Text");
    showText.addItemListener(this);
    showColourText.setLabel("Colour Text");
    showColourText.addItemListener(this);
    outputmenu.setLabel("Output to Textbox...");
    seqMenu.setLabel("Sequence");
    pdb.setLabel("View PDB Structure");
    hideSeqs.setLabel("Hide Sequences");
    repGroup.setLabel("Represent Group with");
    revealAll.setLabel("Reveal All");

    add(groupMenu);
    this.add(seqMenu);
    this.add(hideSeqs);
    this.add(revealAll);
    groupMenu.add(editMenu);
    groupMenu.add(outputmenu);
    groupMenu.addSeparator();
    groupMenu.add(unGroupMenuItem);
    groupMenu.add(colourMenu);
    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(this);

    clustalColour.setLabel("Clustalx colours");
    clustalColour.addActionListener(this);
    zappoColour.setLabel("Zappo");
    zappoColour.addActionListener(this);
    taylorColour.setLabel("Taylor");
    taylorColour.addActionListener(this);
    hydrophobicityColour.setLabel("Hydrophobicity");
    hydrophobicityColour.addActionListener(this);
    helixColour.setLabel("Helix propensity");
    helixColour.addActionListener(this);
    strandColour.setLabel("Strand propensity");
    strandColour.addActionListener(this);
    turnColour.setLabel("Turn propensity");
    turnColour.addActionListener(this);
    buriedColour.setLabel("Buried Index");
    buriedColour.addActionListener(this);
    abovePIDColour.setLabel("Above % Identity");

    userDefinedColour.setLabel("User Defined");
    userDefinedColour.addActionListener(this);
    PIDColour.setLabel("Percentage Identity");
    PIDColour.addActionListener(this);
    BLOSUM62Colour.setLabel("BLOSUM62");
    BLOSUM62Colour.addActionListener(this);
    conservationMenuItem.setLabel("Conservation");

    editMenu.add(copy);
    copy.addActionListener(this);
    editMenu.add(cut);
    cut.addActionListener(this);
    editMenu.add(toUpper);
    toUpper.addActionListener(this);
    editMenu.add(toLower);
    toLower.addActionListener(this);
    editMenu.add(toggleCase);
    seqMenu.add(pdb);
    seqMenu.add(repGroup);
    toggleCase.addActionListener(this);
    pdb.addActionListener(this);
    hideSeqs.addActionListener(this);
    repGroup.addActionListener(this);
    revealAll.addActionListener(this);

  }

  void refresh()
  {
    ap.seqPanel.seqCanvas.repaint();
    if(ap.overviewPanel!=null)
      ap.overviewPanel.updateOverviewImage();
  }

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

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

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

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

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

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

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

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

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

  protected void abovePIDColour_itemStateChanged()
  {
    SequenceGroup sg = getGroup();
    if(sg.cs==null)
          return;

    if (abovePIDColour.getState())
    {
      sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 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()
  {
    new UserDefinedColours(ap, getGroup());
  }

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

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

    sg.cs = new Blosum62ColourScheme();

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

    refresh();
  }

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

  protected void conservationMenuItem_itemStateChanged()
  {
    SequenceGroup sg = getGroup();
    if(sg.cs==null)
          return;

    if (conservationMenuItem.getState())
    {

      Conservation c = new Conservation("Group",
                                        ResidueProperties.propHash, 3,
                                        sg.getSequences(true), 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();
  }


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

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

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

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

  void hideSequences(boolean representGroup)
  {
    SequenceGroup sg = ap.av.getSelectionGroup();
    if(sg==null || sg.getSize(false)<1)
    {
      ap.av.hideSequence(seq);
      return;
    }

      int index = 0;
      while(index < sg.getSize(false))
      {
        if(representGroup && sg.getSequenceAt(index)!=seq)
        {
          seq.addHiddenSequence(sg.getSequenceAt(index));
          ap.av.hideSequence(sg.getSequenceAt(index));
        }
        else if(!representGroup)
        {
          ap.av.hideSequence(sg.getSequenceAt(index));
        }
        index ++;
      }

      ap.av.setSelectionGroup(null);
    }

}