/********************
 * 2004 Jalview Reengineered
 * Barton Group
 * Dundee University
 *
 * AM Waterhouse
 *******************/

package jalview.jbgui;

import javax.swing.*;
import java.awt.event.*;
import java.awt.*;

import jalview.gui.Preferences;
import jalview.schemes.ColourSchemeProperty;

public class GAlignFrame extends JInternalFrame
{
  protected JMenuBar alignFrameMenuBar = new JMenuBar();
  protected JMenu fileMenu = new JMenu();
  protected JMenuItem closeMenuItem = new JMenuItem();
  protected JMenu editMenu = new JMenu();
  protected JMenu viewMenu = new JMenu();
  protected JMenu colourMenu = new JMenu();
  protected JMenu calculateMenu = new JMenu();
  protected JMenu webService = new JMenu();
  protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();
  protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();
  protected JMenuItem invertSequenceMenuItem = new JMenuItem();
  protected JMenuItem remove2LeftMenuItem = new JMenuItem();
  protected JMenuItem remove2RightMenuItem = new JMenuItem();
  protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();
  protected JMenuItem removeAllGapsMenuItem = new JMenuItem();
  protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
  protected JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
  protected JMenuItem sortPairwiseMenuItem = new JMenuItem();
  protected JMenuItem sortIDMenuItem = new JMenuItem();
  protected JMenuItem sortGroupMenuItem = new JMenuItem();
  protected JMenuItem removeRedundancyMenuItem = new JMenuItem();
  protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();
  protected JMenuItem PCAMenuItem = new JMenuItem();
  protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();
  protected JMenuItem neighbourTreeMenuItem = new JMenuItem();
  protected JMenuItem clustalAlignMenuItem = new JMenuItem();
  BorderLayout borderLayout1 = new BorderLayout();
  public JLabel statusBar = new JLabel();
  protected JMenu saveAlignmentMenu = new JMenu();
  protected JMenu outputTextboxMenu = new JMenu();
  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 userDefinedColour = new JRadioButtonMenuItem();
  protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
  protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
  JMenuItem njTreeBlosumMenuItem = new JMenuItem();
  JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
  protected JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
  protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
  JMenuItem htmlMenuItem = new JMenuItem();
  JMenuItem overviewMenuItem = new JMenuItem();
  protected JMenuItem undoMenuItem = new JMenuItem();
  protected JMenuItem redoMenuItem = new JMenuItem();
  protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
  JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
  protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
  JMenuItem printMenuItem = new JMenuItem();
  protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
  JMenuItem findMenuItem = new JMenuItem();
  JMenu searchMenu = new JMenu();
  protected JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
  protected JCheckBoxMenuItem sequenceFeatures = new JCheckBoxMenuItem();
  protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
  JMenuItem deleteGroups = new JMenuItem();
  JMenuItem delete = new JMenuItem();
  JMenuItem copy = new JMenuItem();
  JMenuItem cut = new JMenuItem();
  JMenu jMenu1 = new JMenu();
  JMenuItem pasteNew = new JMenuItem();
  JMenuItem pasteThis = new JMenuItem();
  protected JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
  JMenuItem createPNG = new JMenuItem();
  protected JMenuItem font = new JMenuItem();
  protected JCheckBoxMenuItem fullSeqId = new JCheckBoxMenuItem();
  JMenuItem epsFile = new JMenuItem();
  JMenuItem LoadtreeMenuItem = new JMenuItem();
  JMenuItem jpred = new JMenuItem();
  protected JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
  protected JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
  protected JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
  JMenuItem modifyPID = new JMenuItem();
  JMenuItem modifyConservation = new JMenuItem();
  protected JMenu sortByTreeMenu = new JMenu();
  JMenu jMenu2 = new JMenu();
  JMenu sort = new JMenu();
  JMenu calculate = new JMenu();
  JMenuItem msaAlignMenuItem = new JMenuItem();
  public GAlignFrame()
  {
    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(userDefinedColour);
    colours.add(PIDColour);
    colours.add(BLOSUM62Colour);
    colours.add(nucleotideColour);

   noColourmenuItem.setSelected(true);
   String defaultColour = Preferences.defaultColour;
   if(defaultColour!=null)
   {
   int index = ColourSchemeProperty.getColourIndexFromName(defaultColour);
   switch(index)
   {
     case ColourSchemeProperty.CLUSTAL : clustalColour.setSelected(true); break;
     case ColourSchemeProperty.BLOSUM : BLOSUM62Colour.setSelected(true); break;
     case ColourSchemeProperty.PID : PIDColour.setSelected(true); break;
     case ColourSchemeProperty.ZAPPO : zappoColour.setSelected(true); break;
     case ColourSchemeProperty.HYDROPHOBIC: hydrophobicityColour.setSelected(true); break;
     case ColourSchemeProperty.HELIX: helixColour.setSelected(true); break;
     case ColourSchemeProperty.STRAND: strandColour.setSelected(true); break;
     case ColourSchemeProperty.TURN : turnColour.setSelected(true); break;
     case ColourSchemeProperty.BURIED: buriedColour.setSelected(true); break;
     case ColourSchemeProperty.NUCLEOTIDE: nucleotideColour.setSelected(true); break;
     case ColourSchemeProperty.USER_DEFINED : userDefinedColour.setSelected(true); break;
   }
   }


    try
    {
      jbInit();
      setJMenuBar(alignFrameMenuBar);

      JMenuItem item;
      // dynamically fill save as menu with available formats
      for (int i = 0; i < jalview.io.FormatAdapter.formats.size(); i++) {
        item = new JMenuItem((String) jalview.io.FormatAdapter.formats.elementAt(i));
        saveAlignmentMenu.add( item );
        item.addActionListener(new java.awt.event.ActionListener()
        {
          public void actionPerformed(ActionEvent e)
          {
            saveAs_actionPerformed(e);
          }
        });

        item = new JMenuItem((String) jalview.io.FormatAdapter.formats.elementAt(i));
        item.addActionListener(new java.awt.event.ActionListener()
        {
          public void actionPerformed(ActionEvent e)
          {
            outputText_actionPerformed(e);
          }
        });

        outputTextboxMenu.add( item );
      }

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

  }
  private void jbInit() throws Exception
  {
    fileMenu.setMnemonic('F');
    fileMenu.setText("File");
    saveAlignmentMenu.setMnemonic('L');
    saveAlignmentMenu.setText("Save");
    closeMenuItem.setMnemonic('C');
    closeMenuItem.setText("Close");
    closeMenuItem.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        closeMenuItem_actionPerformed(e);
      }
    });
    editMenu.setText("Edit");
    viewMenu.setText("View");
    colourMenu.setText("Colour");
    calculateMenu.setText("Calculate");
    webService.setText("Web Service");
    selectAllSequenceMenuItem.setText("Select all");
    selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
        java.awt.event.KeyEvent.VK_A, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
    selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        selectAllSequenceMenuItem_actionPerformed(e);
      }
    });
    deselectAllSequenceMenuItem.setText("Deselect All");
    deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.
                                               getKeyStroke(java.awt.event.
        KeyEvent.VK_ESCAPE, 0, false));
    deselectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        deselectAllSequenceMenuItem_actionPerformed(e);
      }
    });
    invertSequenceMenuItem.setText("Invert Selection");
    invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        invertSequenceMenuItem_actionPerformed(e);
      }
    });
    remove2LeftMenuItem.setText("Remove Left");
    remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        remove2LeftMenuItem_actionPerformed(e);
      }
    });
    remove2RightMenuItem.setText("Remove Right");
    remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        remove2RightMenuItem_actionPerformed(e);
      }
    });
    removeGappedColumnMenuItem.setText("Remove Empty Columns");
    removeGappedColumnMenuItem.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        removeGappedColumnMenuItem_actionPerformed(e);
      }
    });
    removeAllGapsMenuItem.setText("Remove All Gaps");
    removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        removeAllGapsMenuItem_actionPerformed(e);
      }
    });
    viewBoxesMenuItem.setText("Boxes");
    viewBoxesMenuItem.setState(true);
    viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        viewBoxesMenuItem_actionPerformed(e);
      }
    });
    viewTextMenuItem.setText("Text");
    viewTextMenuItem.setState(true);
    viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        viewTextMenuItem_actionPerformed(e);
      }
    });
    sortPairwiseMenuItem.setText("Pairwise Identity");
    sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        sortPairwiseMenuItem_actionPerformed(e);
      }
    });
    sortIDMenuItem.setText("ID");
    sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        sortIDMenuItem_actionPerformed(e);
      }
    });
    sortGroupMenuItem.setText("Group");
    sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        sortGroupMenuItem_actionPerformed(e);
      }
    });
    removeRedundancyMenuItem.setText("Remove Redundancy...");
    removeRedundancyMenuItem.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        removeRedundancyMenuItem_actionPerformed(e);
      }
    });
    pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");
    pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        pairwiseAlignmentMenuItem_actionPerformed(e);
      }
    });
    PCAMenuItem.setText("Principal Component Analysis...");
    PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        PCAMenuItem_actionPerformed(e);
      }
    });
    averageDistanceTreeMenuItem.setText("Average Distance Using % Identity...");
    averageDistanceTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        averageDistanceTreeMenuItem_actionPerformed(e);
      }
    });
    neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity...");
    neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        neighbourTreeMenuItem_actionPerformed(e);
      }
    });
    clustalAlignMenuItem.setText("Clustal Alignment...");
    clustalAlignMenuItem.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        clustalAlignMenuItem_actionPerformed(e);
      }
    });
    this.getContentPane().setLayout(borderLayout1);
    alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
    statusBar.setBackground(Color.white);
    statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
    statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
    statusBar.setText("Status bar");
    outputTextboxMenu.setMnemonic('T');
    outputTextboxMenu.setText("Output to Textbox");
    clustalColour.setText("Clustalx");

    clustalColour.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        clustalColour_actionPerformed(e);
      }
    });
    zappoColour.setText("Zappo");
    zappoColour.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        zappoColour_actionPerformed(e);
      }
    });
    taylorColour.setText("Taylor");
    taylorColour.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        taylorColour_actionPerformed(e);
      }
    });
    hydrophobicityColour.setText("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);
      }
    });
    userDefinedColour.setText("User Defined...");
    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);
      }
    });
    avDistanceTreeBlosumMenuItem.setText("Average Distance using BLOSUM62...");
    avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        avTreeBlosumMenuItem_actionPerformed(e);
      }
    });
    njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62...");
    njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        njTreeBlosumMenuItem_actionPerformed(e);
      }
    });
    annotationPanelMenuItem.setActionCommand("");
    annotationPanelMenuItem.setText("Show Annotations");
    annotationPanelMenuItem.setState( jalview.gui.Preferences.showAnnotation );
    annotationPanelMenuItem.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        annotationPanelMenuItem_actionPerformed(e);
      }
    });
    colourTextMenuItem.setText("Colour Text");
    colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        colourTextMenuItem_actionPerformed(e);
      }
    });
    htmlMenuItem.setText("HTML");
    htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        htmlMenuItem_actionPerformed(e);
      }
    });
    overviewMenuItem.setText("Overview Window...");
    overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        overviewMenuItem_actionPerformed(e);
      }
    });
    undoMenuItem.setEnabled(false);
    undoMenuItem.setMnemonic('Z');
    undoMenuItem.setText("Undo");
    undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
        event.KeyEvent.VK_Z, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
    undoMenuItem.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        undoMenuItem_actionPerformed(e);
      }
    });
    redoMenuItem.setEnabled(false);
    redoMenuItem.setMnemonic('0');
    redoMenuItem.setText("Redo");
    redoMenuItem.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        redoMenuItem_actionPerformed(e);
      }
    });
    conservationMenuItem.setText("By Conservation");
    conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        conservationMenuItem_actionPerformed(e);
      }
    });
    noColourmenuItem.setText("None");
    noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        noColourmenuItem_actionPerformed(e);
      }
    });
    wrapMenuItem.setText("Wrap");
    wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        wrapMenuItem_actionPerformed(e);
      }
    });
    printMenuItem.setText("Print");
    printMenuItem.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        printMenuItem_actionPerformed(e);
      }
    });
    renderGapsMenuItem.setText("Show Gaps");
    renderGapsMenuItem.setState(true);
    renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        renderGapsMenuItem_actionPerformed(e);
      }
    });
    findMenuItem.setText("Find...");
    findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
        event.KeyEvent.VK_F, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
    findMenuItem.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        findMenuItem_actionPerformed(e);
      }
    });
    searchMenu.setText("Search");

    abovePIDThreshold.setText("Above Identity threshold");
    abovePIDThreshold.addActionListener(new java.awt.event.ActionListener() {
      public void actionPerformed(ActionEvent e) {
        abovePIDThreshold_actionPerformed(e);
      }
    });
    sequenceFeatures.setText("Sequence Features");
    sequenceFeatures.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent actionEvent)
      {
        sequenceFeatures_actionPerformed(actionEvent);
      }
    });
    nucleotideColour.setText("Nucleotide");
    nucleotideColour.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        nucleotideColour_actionPerformed(e);
      }
    });
    deleteGroups.setText("Undefine groups");
    deleteGroups.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        deleteGroups_actionPerformed(e);
      }
    });
    copy.setText("Copy");
    copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
        KeyEvent.VK_C, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
    copy.setMnemonic(KeyEvent.VK_C);

    copy.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        copy_actionPerformed(e);
      }
    });
    cut.setText("Cut");
    cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
        KeyEvent.VK_X, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
    cut.setMnemonic(KeyEvent.VK_X);
    cut.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        cut_actionPerformed(e);
      }
    });
    delete.setText("Delete");
    delete.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        delete_actionPerformed(e);
      }
    });
    jMenu1.setMnemonic('V');
    jMenu1.setText("Paste");
    pasteNew.setText("to new alignment");
    pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
        KeyEvent.VK_V, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
    pasteNew.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        pasteNew_actionPerformed(e);
      }
    });
    pasteThis.setText("add to this alignment");
    pasteThis.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        pasteThis_actionPerformed(e);
      }
    });
    applyToAllGroups.setText("Apply Colour To All Groups");
    applyToAllGroups.setState(true);
    applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        applyToAllGroups_actionPerformed(e);
      }
    });
    createPNG.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        createPNG_actionPerformed(e);
      }
    });
    createPNG.setActionCommand("Save as PNG Image");
    createPNG.setText("PNG");
    font.setText("Font...");
    font.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        font_actionPerformed(e);
      }
    });
    fullSeqId.setText("Show Full Sequence ID");
    fullSeqId.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        fullSeqId_actionPerformed(e);
      }
    });
    epsFile.setText("EPS");
    epsFile.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        epsFile_actionPerformed(e);
      }
    });
    LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");
    LoadtreeMenuItem.setText("Load Assocated Tree");
    LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener() {
      public void actionPerformed(ActionEvent e)
      {
        LoadtreeMenuItem_actionPerformed(e);
      }
    });
    jpred.setText("JPred...");
    jpred.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        jpred_actionPerformed(e);
      }
    });
    scaleAbove.setVisible(false);
    scaleAbove.setText("Scale Above");
    scaleAbove.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        scaleAbove_actionPerformed(e);
      }
    });
    scaleLeft.setVisible(false);
    scaleLeft.setSelected(true);
    scaleLeft.setText("Scale Left");
    scaleLeft.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        scaleLeft_actionPerformed(e);
      }
    });
    scaleRight.setVisible(false);
    scaleRight.setSelected(true);
    scaleRight.setText("Scale Right");
    scaleRight.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        scaleRight_actionPerformed(e);
      }
    });
    modifyPID.setText("Modify Identity Threshold...");
    modifyPID.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        modifyPID_actionPerformed(e);
      }
    });
    modifyConservation.setText("Modify Conservation Threshold...");
    modifyConservation.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        modifyConservation_actionPerformed(e);
      }
    });
    sortByTreeMenu.setText("Tree Order");
    jMenu2.setText("Save as");
    sort.setText("Sort");
    calculate.setText("Calculate Tree");
    msaAlignMenuItem.setText("Muscle Alignment...");
    msaAlignMenuItem.addActionListener(new java.awt.event.ActionListener() {
      public void actionPerformed(ActionEvent e) {
        msaAlignMenuItem_actionPerformed(e);
      }
    });
    alignFrameMenuBar.add(fileMenu);
    alignFrameMenuBar.add(editMenu);
    alignFrameMenuBar.add(searchMenu);
    alignFrameMenuBar.add(viewMenu);
    alignFrameMenuBar.add(colourMenu);
    alignFrameMenuBar.add(calculateMenu);
    fileMenu.add(saveAlignmentMenu);
    fileMenu.add(jMenu2);
    fileMenu.add(outputTextboxMenu);
    fileMenu.add(printMenuItem);
    fileMenu.addSeparator();
    fileMenu.add(LoadtreeMenuItem);
    fileMenu.addSeparator();
    fileMenu.add(closeMenuItem);
    editMenu.add(undoMenuItem);
    editMenu.add(redoMenuItem);
    editMenu.add(cut);
    editMenu.add(copy);
    editMenu.add(jMenu1);
    editMenu.add(delete);
    editMenu.addSeparator();
    editMenu.add(selectAllSequenceMenuItem);
    editMenu.add(deselectAllSequenceMenuItem);
    editMenu.add(invertSequenceMenuItem);
    editMenu.add(deleteGroups);
    editMenu.addSeparator();
    editMenu.add(remove2LeftMenuItem);
    editMenu.add(remove2RightMenuItem);
    editMenu.add(removeGappedColumnMenuItem);
    editMenu.add(removeAllGapsMenuItem);
    editMenu.add(removeRedundancyMenuItem);
    searchMenu.add(findMenuItem);
    viewMenu.add(font);
    viewMenu.add(fullSeqId);
    viewMenu.addSeparator();
    viewMenu.add(wrapMenuItem);
    viewMenu.add(scaleAbove);
    viewMenu.add(scaleLeft);
    viewMenu.add(scaleRight);
    viewMenu.addSeparator();
    viewMenu.add(viewBoxesMenuItem);
    viewMenu.add(viewTextMenuItem);
    viewMenu.add(colourTextMenuItem);
    viewMenu.add(renderGapsMenuItem);
    viewMenu.add(annotationPanelMenuItem);
    viewMenu.add(sequenceFeatures);
    viewMenu.addSeparator();
    viewMenu.add(overviewMenuItem);
    colourMenu.add(applyToAllGroups);
    colourMenu.add(noColourmenuItem);
    colourMenu.addSeparator();
    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(nucleotideColour);
    colourMenu.add(userDefinedColour);
    colourMenu.addSeparator();
    colourMenu.add(conservationMenuItem);
    colourMenu.add(modifyConservation);
    colourMenu.add(abovePIDThreshold);
    colourMenu.add(modifyPID);
    calculateMenu.add(sort);
    calculateMenu.add(calculate);
    calculateMenu.addSeparator();
    calculateMenu.add(pairwiseAlignmentMenuItem);
    calculateMenu.add(PCAMenuItem);
    calculateMenu.addSeparator();
    calculateMenu.add(webService);
    webService.add(clustalAlignMenuItem);
    webService.add(jpred);
    webService.add(msaAlignMenuItem);
    this.getContentPane().add(statusBar, BorderLayout.SOUTH);
    jMenu1.add(pasteNew);
    jMenu1.add(pasteThis);
    jMenu2.add(htmlMenuItem);
    jMenu2.add(epsFile);
    jMenu2.add(createPNG);
    sort.add(sortIDMenuItem);
    sort.add(sortGroupMenuItem);
    sort.add(sortByTreeMenu);
    sort.add(sortPairwiseMenuItem);
    calculate.add(averageDistanceTreeMenuItem);
    calculate.add(neighbourTreeMenuItem);
    calculate.add(avDistanceTreeBlosumMenuItem);
    calculate.add(njTreeBlosumMenuItem);
  }

  protected void saveAs_actionPerformed(ActionEvent e)
  {

  }

  protected void outputText_actionPerformed(ActionEvent e)
  {

  }

  protected void htmlMenuItem_actionPerformed(ActionEvent e)
  {

  }


  protected void closeMenuItem_actionPerformed(ActionEvent e)
  {

  }

  protected void redoMenuItem_actionPerformed(ActionEvent e)
  {

  }

  protected void undoMenuItem_actionPerformed(ActionEvent e)
  {

  }


  protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
  {

  }

  protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
  {

  }

  protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
  {

  }

  protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
  {

  }

  protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
  {

  }

  protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
  {

  }

  protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
  {

  }


  protected void wrapMenuItem_actionPerformed(ActionEvent e)
  {

  }


  protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
  {

  }

  protected void viewTextMenuItem_actionPerformed(ActionEvent e)
  {

  }


  protected void colourTextMenuItem_actionPerformed(ActionEvent e)
  {

  }

  protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
  {

  }

  protected void overviewMenuItem_actionPerformed(ActionEvent e)
  {

  }

  protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
  {

  }

  protected void sortIDMenuItem_actionPerformed(ActionEvent e)
  {

  }

  protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
  {

  }


  protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
  {

  }

  protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
  {

  }

  protected void PCAMenuItem_actionPerformed(ActionEvent e)
  {

  }

  protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
  {

  }

  protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
  {

  }


  protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
  {

  }

  protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
  {

  }



  protected void clustalAlignMenuItem_actionPerformed(ActionEvent e)
  {

  }




  protected void clustalColour_actionPerformed(ActionEvent e)
  {

  }

  protected void zappoColour_actionPerformed(ActionEvent e)
  {

  }

  protected void taylorColour_actionPerformed(ActionEvent e)
  {

  }


  protected void hydrophobicityColour_actionPerformed(ActionEvent e)
  {

  }

  protected void helixColour_actionPerformed(ActionEvent e)
  {

  }

  protected void strandColour_actionPerformed(ActionEvent e)
  {

  }

  protected void turnColour_actionPerformed(ActionEvent e)
  {

  }

  protected void buriedColour_actionPerformed(ActionEvent e)
  {

  }



  protected void userDefinedColour_actionPerformed(ActionEvent e)
  {

  }

  protected void PIDColour_actionPerformed(ActionEvent e)
  {

  }

  protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
  {

  }


  protected void noColourmenuItem_actionPerformed(ActionEvent e)
  {

  }

  protected  void conservationMenuItem_actionPerformed(ActionEvent e)
  {

  }


  protected void printMenuItem_actionPerformed(ActionEvent e)
  {

  }

  protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
  {

  }

  protected void findMenuItem_actionPerformed(ActionEvent e)
  {

  }


  protected void abovePIDThreshold_actionPerformed(ActionEvent e) {

  }

  public void sequenceFeatures_actionPerformed(ActionEvent actionEvent)
  {

  }

  protected void nucleotideColour_actionPerformed(ActionEvent e)
  {

  }

  protected void deleteGroups_actionPerformed(ActionEvent e)
  {

  }

 protected void copy_actionPerformed(ActionEvent e)
  {

  }


  protected void cut_actionPerformed(ActionEvent e)
  {

  }

  protected void delete_actionPerformed(ActionEvent e)
  {

  }

  protected void pasteNew_actionPerformed(ActionEvent e)
  {

  }

  protected void pasteThis_actionPerformed(ActionEvent e)
  {

  }

  protected void applyToAllGroups_actionPerformed(ActionEvent e)
  {

  }

  protected void createPNG_actionPerformed(ActionEvent e)
  {

  }

  protected void font_actionPerformed(ActionEvent e)
  {

  }

  protected void fullSeqId_actionPerformed(ActionEvent e)
  {

  }

  protected void epsFile_actionPerformed(ActionEvent e)
  {

  }

  protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) {

  }

  protected void jpred_actionPerformed(ActionEvent e)
  {

  }

  protected void scaleAbove_actionPerformed(ActionEvent e)
  {

  }

  protected void scaleLeft_actionPerformed(ActionEvent e)
  {

  }

  protected void scaleRight_actionPerformed(ActionEvent e)
  {

  }

  protected void modifyPID_actionPerformed(ActionEvent e)
  {

  }

  protected void modifyConservation_actionPerformed(ActionEvent e)
  {

  }

  protected void preferences_actionPerformed(ActionEvent e)
  {

  }

  protected void msaAlignMenuItem_actionPerformed(ActionEvent e) {

  }

}