/*
 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
 * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
 * 
 * This file is part of Jalview.
 * 
 * Jalview 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 3 of the License, or (at your option) any later version.
 * 
 * Jalview 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 Jalview.  If not, see <http://www.gnu.org/licenses/>.
 */
package jalview.appletgui;

import java.util.*;

import java.awt.*;
import java.awt.event.*;

import jalview.analysis.*;
import jalview.commands.*;
import jalview.datamodel.*;
import jalview.schemes.*;
import jalview.util.UrlLink;
import jalview.io.AppletFormatAdapter;

public class APopupMenu extends java.awt.PopupMenu implements
        ActionListener, ItemListener
{
  Menu groupMenu = new Menu();

  MenuItem editGroupName = new MenuItem();

  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();

  CheckboxMenuItem displayNonconserved = 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();

  MenuItem sequenceName = new MenuItem("Edit Name/Description");

  MenuItem sequenceFeature = new MenuItem("Create Sequence Feature");

  MenuItem editSequence = new MenuItem("Edit Sequence");

  Sequence seq;

  MenuItem revealAll = new MenuItem();

  MenuItem revealSeq = new MenuItem();
  /**
   * index of sequence to be revealed
   */
  int revealSeq_index=-1;
  Menu menu1 = new Menu();

  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() > 0)
    {
      editGroupName.setLabel("Name: "+sg.getName());
      showText.setState(sg.getDisplayText());
      showColourText.setState(sg.getColourText());
      showBoxes.setState(sg.getDisplayBoxes());
      displayNonconserved.setState(sg.getShowNonconserved());
      if (!ap.av.getAlignment().getGroups().contains(sg))
      {
        groupMenu.remove(unGroupMenuItem);
      }

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

    if (links != null && links.size() > 0)
    {
      Menu linkMenu = new Menu("Link");
      String link;
      for (int i = 0; i < links.size(); i++)
      {
        link = links.elementAt(i).toString();
        UrlLink urlLink = new UrlLink(link);
        if (!urlLink.isValid())
        {
          System.err.println(urlLink.getInvalidMessage());
          continue;
        }
        final String target = urlLink.getTarget(); // link.substring(0,
        // link.indexOf("|"));
        final String label = urlLink.getLabel();
        if (seq!=null && urlLink.isDynamic())
        {

          // collect matching db-refs
          DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(
                  seq.getDBRef(), new String[]
                  { target });
          // collect id string too
          String id = seq.getName();
          String descr = seq.getDescription();
          if (descr != null && descr.length() < 1)
          {
            descr = null;
          }
          if (dbr != null)
          {
            for (int r = 0; r < dbr.length; r++)
            {
              if (id != null && dbr[r].getAccessionId().equals(id))
              {
                // suppress duplicate link creation for the bare sequence ID
                // string with this link
                id = null;
              }
              // create Bare ID link for this RUL
              String[] urls = urlLink.makeUrls(dbr[r].getAccessionId(),
                      true);
              if (urls != null)
              {
                for (int u = 0; u < urls.length; u += 2)
                {
                  addshowLink(linkMenu, label + "|" + urls[u], urls[u + 1]);
                }
              }
            }
          }
          if (id != null)
          {
            // create Bare ID link for this RUL
            String[] urls = urlLink.makeUrls(id, true);
            if (urls != null)
            {
              for (int u = 0; u < urls.length; u += 2)
              {
                addshowLink(linkMenu, label, urls[u + 1]);
              }
            }
            // addshowLink(linkMenu, target, url_pref + id + url_suff);
          }
          // Now construct URLs from description but only try to do it for regex
          // URL links
          if (descr != null && urlLink.getRegexReplace() != null)
          {
            // create link for this URL from description only if regex matches
            String[] urls = urlLink.makeUrls(descr, true);
            if (urls != null)
            {
              for (int u = 0; u < urls.length; u += 2)
              {
                addshowLink(linkMenu, label, urls[u + 1]);
              }
            }
          }
        }
        else
        {
          addshowLink(linkMenu, target, urlLink.getUrl_prefix()); // link.substring(link.lastIndexOf("|")+1));
        }
        /*
         * final String url;
         * 
         * if (link.indexOf("$SEQUENCE_ID$") > -1) { // Substitute SEQUENCE_ID
         * string and any matching database reference accessions String url_pref
         * = link.substring(link.indexOf("|") + 1,
         * link.indexOf("$SEQUENCE_ID$"));
         * 
         * String url_suff = link.substring(link.indexOf("$SEQUENCE_ID$") + 13);
         * // collect matching db-refs DBRefEntry[] dbr =
         * jalview.util.DBRefUtils.selectRefs(seq.getDBRef(), new
         * String[]{target}); // collect id string too String id =
         * seq.getName(); if (id.indexOf("|") > -1) { id =
         * id.substring(id.lastIndexOf("|") + 1); } if (dbr!=null) { for (int
         * r=0;r<dbr.length; r++) { if (dbr[r].getAccessionId().equals(id)) { //
         * suppress duplicate link creation for the bare sequence ID string with
         * this link id = null; } addshowLink(linkMenu,
         * dbr[r].getSource()+"|"+dbr[r].getAccessionId(), target,
         * url_pref+dbr[r].getAccessionId()+url_suff); } } if (id!=null) { //
         * create Bare ID link for this RUL addshowLink(linkMenu, target,
         * url_pref + id + url_suff); } } else { addshowLink(linkMenu, target,
         * link.substring(link.lastIndexOf("|")+1)); }
         */
      }
      if (linkMenu.getItemCount() > 0)
      {
        if (seq != null)
        {
          seqMenu.add(linkMenu);
        }
        else
        {
          add(linkMenu);
        }
      }
    }
    // TODO: add group link menu entry here
    if (seq != null)
    {
      seqMenu.setLabel(seq.getName());
      repGroup.setLabel("Represent Group with " + seq.getName());
    }
    else
    {
      remove(seqMenu);
    }

    if (!ap.av.hasHiddenRows())
    {
      remove(revealAll);
      remove(revealSeq);
    } else {
      final int index = ap.av.getAlignment().findIndex(seq);

      if (ap.av.adjustForHiddenSeqs(index)
              - ap.av.adjustForHiddenSeqs(index - 1) > 1)
      {
        revealSeq_index=index;
      } else {
        remove(revealSeq);
      }
    }
  }

  /**
   * add a show URL menu item to the given linkMenu
   * 
   * @param linkMenu
   * @param target
   *          - menu label string
   * @param url
   *          - url to open
   */
  private void addshowLink(Menu linkMenu, final String target,
          final String url)
  {
    addshowLink(linkMenu, target, target, url);
  }

  /**
   * add a show URL menu item to the given linkMenu
   * 
   * @param linkMenu
   * @param target
   *          - URL target window
   * @param label
   *          - menu label string
   * @param url
   *          - url to open
   */
  private void addshowLink(Menu linkMenu, final String target,
          final String label, final String url)
  {
    MenuItem item = new MenuItem(label);
    item.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        ap.alignFrame.showURL(url, target);
      }
    });
    linkMenu.add(item);
  }

  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();
    }
    else if (evt.getSource() == displayNonconserved)
    {
      this.showNonconserved_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 == turnColour)
    {
      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 == sequenceName)
    {
      editName();
    }
    else if (source == pdb)
    {
      addPDB();
    }
    else if (source == hideSeqs)
    {
      hideSequences(false);
    }
    else if (source == repGroup)
    {
      hideSequences(true);
    }
    else if (source == revealSeq)
    {
      ap.av.showSequence(revealSeq_index);
    }
    else if (source == revealAll)
    {
      ap.av.showAllHiddenSeqs();
    }

    else if (source == editGroupName)
    {
      EditNameDialog dialog = new EditNameDialog(getGroup().getName(),
              getGroup().getDescription(), "       Group Name",
              "Group Description", ap.alignFrame,
              "Edit Group Name / Description", 500, 100, true);

      if (dialog.accept)
      {
        getGroup().setName(dialog.getName().replace(' ', '_'));
        getGroup().setDescription(dialog.getDescription());
      }

    }
    else if (source == copy)
    {
      ap.alignFrame.copy_actionPerformed();
    }
    else if (source == cut)
    {
      ap.alignFrame.cut_actionPerformed();
    }
    else if (source == editSequence)
    {
      SequenceGroup sg = ap.av.getSelectionGroup();

      if (sg != null)
      {
        if (seq == null)
          seq = (Sequence) sg.getSequenceAt(0);

        EditNameDialog dialog = new EditNameDialog(seq.getSequenceAsString(
                sg.getStartRes(), sg.getEndRes() + 1), null,
                "Edit Sequence ", null,

                ap.alignFrame, "Edit Sequence", 500, 100, true);

        if (dialog.accept)
        {
          EditCommand editCommand = new EditCommand("Edit Sequences",
                  EditCommand.REPLACE, dialog.getName().replace(' ',
                          ap.av.getGapCharacter()),
                  sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
                  sg.getStartRes(), sg.getEndRes() + 1, ap.av.getAlignment());

          ap.alignFrame.addHistoryItem(editCommand);

          ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
                  .getSequences());
        }
      }
    }
    else if (source == toUpper || source == toLower || source == toggleCase)
    {
      SequenceGroup sg = ap.av.getSelectionGroup();
      Vector regions = new Vector();
      if (sg != null)
      {
        int[][] startEnd = ap.av.getVisibleRegionBoundaries(sg.getStartRes(),
                sg.getEndRes() + 1);

        String description;
        int caseChange;

        if (source == toggleCase)
        {
          description = "Toggle Case";
          caseChange = ChangeCaseCommand.TOGGLE_CASE;
        }
        else if (source == toUpper)
        {
          description = "To Upper Case";
          caseChange = ChangeCaseCommand.TO_UPPER;
        }
        else
        {
          description = "To Lower Case";
          caseChange = ChangeCaseCommand.TO_LOWER;
        }

        ChangeCaseCommand caseCommand = new ChangeCaseCommand(description,
                sg.getSequencesAsArray(ap.av.getHiddenRepSequences()), startEnd,
                caseChange);

        ap.alignFrame.addHistoryItem(caseCommand);

        ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
                .getSequences());

      }
    }
    else if (source == sequenceFeature)
    {
      SequenceGroup sg = ap.av.getSelectionGroup();
      if (sg == null)
      {
        return;
      }

      int rsize = 0, gSize = sg.getSize();
      SequenceI[] rseqs, seqs = new SequenceI[gSize];
      SequenceFeature[] tfeatures, features = new SequenceFeature[gSize];

      for (int i = 0; i < gSize; i++)
      {
        int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
        int end = sg.findEndRes(sg.getSequenceAt(i));
        if (start <= end)
        {
          seqs[rsize] = sg.getSequenceAt(i);
          features[rsize] = new SequenceFeature(null, null, null, start,
                  end, "Jalview");
          rsize++;
        }
      }
      rseqs = new SequenceI[rsize];
      tfeatures = new SequenceFeature[rsize];
      System.arraycopy(seqs, 0, rseqs, 0, rsize);
      System.arraycopy(features, 0, tfeatures, 0, rsize);
      features = tfeatures;
      seqs = rseqs;

      if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs,
              features, true, ap))
      {
        ap.alignFrame.sequenceFeatures.setState(true);
        ap.av.showSequenceFeatures(true);
        ap.highlightSearchResults(null);
      }
    }
    else
    {
      outputText(evt);
    }

  }

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

    Frame frame = new Frame();
    frame.add(cap);
    jalview.bin.JalviewLite.addFrame(frame,
            "Selection output - " + e.getActionCommand(), 600, 500);
    // JBPNote: getSelectionAsNewSequence behaviour has changed - this method now returns a full copy of sequence data
    // TODO consider using getSequenceSelection instead here

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

  }

  void editName()
  {
    EditNameDialog dialog = new EditNameDialog(seq.getName(),
            seq.getDescription(), "       Sequence Name",
            "Sequence Description", ap.alignFrame,
            "Edit Sequence Name / Description", 500, 100, true);

    if (dialog.accept)
    {
      seq.setName(dialog.getName());
      seq.setDescription(dialog.getDescription());
      ap.paintAlignment(false);
    }
  }

  void addPDB()
  {
    if (seq.getPDBId() != null)
    {
      PDBEntry entry = (PDBEntry) seq.getPDBId().firstElement();

      if (ap.av.applet.jmolAvailable)
        new jalview.appletgui.AppletJmol(entry, new Sequence[]
        { seq }, null, ap, AppletFormatAdapter.URL);
      else
        new MCview.AppletPDBViewer(entry, new Sequence[]
        { seq }, null, ap, AppletFormatAdapter.URL);

    }
    else
    {
      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 for sequence "+seq.getName(), 400, 300);
    }
  }

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

    editGroupName.addActionListener(this);
    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);
    sequenceName.addActionListener(this);
    displayNonconserved.setLabel("Show Nonconserved");
    displayNonconserved.setState(false);
    displayNonconserved.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");
    revealSeq.setLabel("Reveal Sequences");
    menu1.setLabel("Group");
    add(groupMenu);
    this.add(seqMenu);
    this.add(hideSeqs);
    this.add(revealSeq);
    this.add(revealAll);
    groupMenu.add(editGroupName);
    groupMenu.add(editMenu);
    groupMenu.add(outputmenu);
    groupMenu.add(sequenceFeature);
    groupMenu.add(menu1);

    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(editSequence);
    editSequence.addActionListener(this);

    editMenu.add(toUpper);
    toUpper.addActionListener(this);
    editMenu.add(toLower);
    toLower.addActionListener(this);
    editMenu.add(toggleCase);
    seqMenu.add(sequenceName);
    if (!ap.av.applet.useXtrnalSviewer)
    {
      seqMenu.add(pdb);
    }
    seqMenu.add(repGroup);
    menu1.add(unGroupMenuItem);
    menu1.add(colourMenu);
    menu1.add(showBoxes);
    menu1.add(showText);
    menu1.add(showColourText);
    menu1.add(displayNonconserved);
    toggleCase.addActionListener(this);
    pdb.addActionListener(this);
    hideSeqs.addActionListener(this);
    repGroup.addActionListener(this);
    revealAll.addActionListener(this);
    revealSeq.addActionListener(this);
  }

  void refresh()
  {
    ap.paintAlignment(true);
  }

  protected void clustalColour_actionPerformed()
  {
    SequenceGroup sg = getGroup();
    sg.cs = new ClustalxColourScheme(
            sg.getSequences(ap.av.getHiddenRepSequences()),
            ap.av.getAlignment().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(ap.av.getHiddenRepSequences()), 0,
              ap.av.getAlignment().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(ap.av.getHiddenRepSequences()), 0,
            ap.av.getAlignment().getWidth()));
    refresh();
  }

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

    sg.cs = new Blosum62ColourScheme();

    sg.cs.setConsensus(AAFrequency.calculate(
            sg.getSequences(ap.av.getHiddenRepSequences()), 0,
            ap.av.getAlignment().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())
    {

      sg.cs.setConservation(Conservation.calculateConservation("Group",
              ResidueProperties.propHash, 3,
              sg.getSequences(ap.av.getHiddenRepSequences()), 0,
              ap.av.getAlignment().getWidth(),
              false, ap.av.getConsPercGaps(),false));
      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.getAlignment().addGroup(sg);
    }

    return sg;
  }

  void unGroupMenuItem_actionPerformed()
  {
    SequenceGroup sg = ap.av.getSelectionGroup();
    ap.av.getAlignment().deleteGroup(sg);
    ap.av.setSelectionGroup(null);
    ap.paintAlignment(true);
  }

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

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

  public void showNonconserved_itemStateChanged()
  {
    getGroup().setShowNonconserved(this.displayNonconserved.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() < 1)
    {
      ap.av.hideSequence(new SequenceI[]
      { seq });
      return;
    }

    ap.av.setSelectionGroup(null);

    if (representGroup)
    {
      ap.av.hideRepSequences(seq, sg);

      return;
    }

    int gsize = sg.getSize();
    SequenceI[] hseqs;

    hseqs = new SequenceI[gsize];

    int index = 0;
    for (int i = 0; i < gsize; i++)
    {
      hseqs[index++] = sg.getSequenceAt(i);
    }

    ap.av.hideSequence(hseqs);
    ap.av.sendSelection();
  }

}