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

package jalview.jbgui;

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

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 fontMenu = new JMenu();
  protected JMenu viewMenu = new JMenu();
  protected JMenu colourMenu = new JMenu();
  protected JMenu calculateMenu = new JMenu();
  protected JMenu alignMenu = new JMenu();
  protected JMenuItem groupsMenuItem = new JMenuItem();
  protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();
  protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();
  protected JMenuItem invertSequenceMenuItem = new JMenuItem();
  protected JMenuItem deselectAllColumnsMenuItem = new JMenuItem();
  protected JMenuItem remove2LeftMenuItem = new JMenuItem();
  protected JMenuItem remove2RightMenuItem = new JMenuItem();
  protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();
  protected JMenuItem removeAllGapsMenuItem = new JMenuItem();
  protected JMenuItem setGapCharMenuItem = new JMenuItem();
  protected JMenuItem fontNameMenuItem = new JMenuItem();
  protected JMenuItem fontSizeMenuItem = new JMenuItem();
  protected JMenuItem fontStyleMenuItem = 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 sortTreeOrderMenuItem = 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 consensusGraphMenuItem = new JCheckBoxMenuItem();
  protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
  JMenuItem htmlMenuItem = new JMenuItem();
  JMenuItem schemeKeyMenuItem = 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 pdbTest = new JMenuItem();
  JMenuItem printMenuItem = new JMenuItem();
  protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
  JMenuItem findMenuItem = new JMenuItem();
  JMenu searchMenu = new JMenu();
  protected JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
  protected JCheckBoxMenuItem secondaryStructure = new JCheckBoxMenuItem();
  protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
  JMenuItem deleteGroups = new JMenuItem();
  public GAlignFrame()
  {
    try
    {
      jbInit();
      setJMenuBar(alignFrameMenuBar);

      JMenuItem item;
      // dynamically fill save as menu with available formats
      for (int i = 0; i < jalview.io.FormatProperties.getFormats().size(); i++) {
        item = new JMenuItem((String) jalview.io.FormatProperties.getFormats().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.FormatProperties.getFormats().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();
    }

    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);
  }
  private void jbInit() throws Exception
  {
    fileMenu.setMnemonic('F');
    fileMenu.setText("File");
    saveAlignmentMenu.setMnemonic('L');
    saveAlignmentMenu.setText("Save alignment to local file");
    closeMenuItem.setMnemonic('C');
    closeMenuItem.setText("Close");
    closeMenuItem.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        closeMenuItem_actionPerformed(e);
      }
    });
    editMenu.setText("Edit");
    fontMenu.setText("Font");
    viewMenu.setText("View");
    colourMenu.setText("Colour");
    calculateMenu.setText("Calculate");
    alignMenu.setText("Web Service");
    groupsMenuItem.setText("Groups");
    groupsMenuItem.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        groupsMenuItem_actionPerformed(e);
      }
    });
    selectAllSequenceMenuItem.setText("Select all sequences");
    selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        selectAllSequenceMenuItem_actionPerformed(e);
      }
    });
    deselectAllSequenceMenuItem.setText("Clear sequence selection");
    deselectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        deselectAllSequenceMenuItem_actionPerformed(e);
      }
    });
    invertSequenceMenuItem.setText("Invert sequence selection");
    invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        invertSequenceMenuItem_actionPerformed(e);
      }
    });
    deselectAllColumnsMenuItem.setText("Deselect all columns");
    deselectAllColumnsMenuItem.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        deselectAllColumnsMenuItem_actionPerformed(e);
      }
    });
    remove2LeftMenuItem.setText("Remove sequence <- left of selected column");
    remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        remove2LeftMenuItem_actionPerformed(e);
      }
    });
    remove2RightMenuItem.setText("Remove sequence -> right of selected column");
    remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        remove2RightMenuItem_actionPerformed(e);
      }
    });
    removeGappedColumnMenuItem.setText("Remove gapped 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);
      }
    });
    setGapCharMenuItem.setText("Set gap character to \".\"");
    setGapCharMenuItem.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        setGapCharMenuItem_actionPerformed(e);
      }
    });
    fontNameMenuItem.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        fontNameMenuItem_actionPerformed(e);
      }
    });
    fontSizeMenuItem.setText("10");
    fontSizeMenuItem.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        fontSizeMenuItem_actionPerformed(e);
      }
    });
    fontStyleMenuItem.setText("Plain");
    fontStyleMenuItem.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        fontStyleMenuItem_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("Sort by pairwise identity");
    sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        sortPairwiseMenuItem_actionPerformed(e);
      }
    });
    sortIDMenuItem.setText("Sort by ID");
    sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        sortIDMenuItem_actionPerformed(e);
      }
    });
    sortGroupMenuItem.setText("Sort by group");
    sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        sortGroupMenuItem_actionPerformed(e);
      }
    });
    sortTreeOrderMenuItem.setText("Sort by tree order");
    sortTreeOrderMenuItem.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        sortTreeOrderMenuItem_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 tree using PID");
    averageDistanceTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        averageDistanceTreeMenuItem_actionPerformed(e);
      }
    });
    neighbourTreeMenuItem.setText("Neighbour joining tree using PID");
    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 alignment via textbox");
    clustalColour.setSelected(false);
    clustalColour.setText("Clustalx colours");
    clustalColour.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        clustalColour_actionPerformed(e);
      }
    });
    zappoColour.setText("Zappo colour scheme");
    zappoColour.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        zappoColour_actionPerformed(e);
      }
    });
    taylorColour.setText("Taylor colour scheme");
    taylorColour.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        taylorColour_actionPerformed(e);
      }
    });
    hydrophobicityColour.setText("By hydrophobicity");
    hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        hydrophobicityColour_actionPerformed(e);
      }
    });
    helixColour.setText("Helix propensity");
    helixColour.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        helixColour_actionPerformed(e);
      }
    });
    strandColour.setText("Strand propensity");
    strandColour.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        strandColour_actionPerformed(e);
      }
    });
    turnColour.setText("Turn propensity");
    turnColour.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        turnColour_actionPerformed(e);
      }
    });
    buriedColour.setText("Buried index");
    buriedColour.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        buriedColour_actionPerformed(e);
      }
    });
    userDefinedColour.setText("User defined colours");
    userDefinedColour.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        userDefinedColour_actionPerformed(e);
      }
    });
    PIDColour.setText("Percentage Identity");
    PIDColour.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        PIDColour_actionPerformed(e);
      }
    });
    BLOSUM62Colour.setText("BLOSUM62 score");
    BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        BLOSUM62Colour_actionPerformed(e);
      }
    });
    avDistanceTreeBlosumMenuItem.setText("Average distance tree using BLOSUM62");
    avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        avTreeBlosumMenuItem_actionPerformed(e);
      }
    });
    njTreeBlosumMenuItem.setText("Neighbour joining tree using BLOSUM62");
    njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        njTreeBlosumMenuItem_actionPerformed(e);
      }
    });
    consensusGraphMenuItem.setActionCommand("");
    consensusGraphMenuItem.setText("Consensus graph");
    consensusGraphMenuItem.setState(true);
    consensusGraphMenuItem.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        consensusGraphMenuItem_actionPerformed(e);
      }
    });
    colourTextMenuItem.setText("Colour text");
    colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        colourTextMenuItem_actionPerformed(e);
      }
    });
    htmlMenuItem.setText("Output as HTML");
    htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        htmlMenuItem_actionPerformed(e);
      }
    });
    schemeKeyMenuItem.setText("Colour Scheme Key");
    schemeKeyMenuItem.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        schemeKeyMenuItem_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.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.setSelected(true);
    noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        noColourmenuItem_actionPerformed(e);
      }
    });
    wrapMenuItem.setEnabled(false);
    wrapMenuItem.setText("Wrap alignment");
    wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        wrapMenuItem_actionPerformed(e);
      }
    });
    pdbTest.setText("PDB Test Viewer");
    pdbTest.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        pdbTest_actionPerformed(e);
      }
    });
    printMenuItem.setText("Print");
    printMenuItem.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        printMenuItem_actionPerformed(e);
      }
    });
    renderGapsMenuItem.setText("Render gaps");
    renderGapsMenuItem.setState(true);
    renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        renderGapsMenuItem_actionPerformed(e);
      }
    });
    findMenuItem.setText("Find");
    findMenuItem.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        findMenuItem_actionPerformed(e);
      }
    });
    searchMenu.setText("Search");

    abovePIDThreshold.setText("Above PID threshold");
    abovePIDThreshold.addActionListener(new java.awt.event.ActionListener() {
      public void actionPerformed(ActionEvent e) {
        abovePIDThreshold_actionPerformed(e);
      }
    });
    secondaryStructure.setSelected(true);
    secondaryStructure.setText("Secondary Structure");
    secondaryStructure.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent actionEvent)
      {
        secondaryStructure_actionPerformed(actionEvent);
      }
    });
    nucleotideColour.setText("Nucleotide colours");
    nucleotideColour.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        nucleotideColour_actionPerformed(e);
      }
    });
    deleteGroups.setSelected(false);
    deleteGroups.setText("Delete all groups");
    deleteGroups.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        deleteGroups_actionPerformed(e);
      }
    });
    alignFrameMenuBar.add(fileMenu);
    alignFrameMenuBar.add(editMenu);
    alignFrameMenuBar.add(searchMenu);
    alignFrameMenuBar.add(fontMenu);
    alignFrameMenuBar.add(viewMenu);
    alignFrameMenuBar.add(colourMenu);
    alignFrameMenuBar.add(calculateMenu);
    alignFrameMenuBar.add(alignMenu);
    fileMenu.add(saveAlignmentMenu);
    fileMenu.add(outputTextboxMenu);
    fileMenu.add(htmlMenuItem);
    fileMenu.add(printMenuItem);
    fileMenu.addSeparator();
    fileMenu.add(closeMenuItem);
    editMenu.add(undoMenuItem);
    editMenu.add(redoMenuItem);
    editMenu.addSeparator();
    editMenu.add(deleteGroups);
    editMenu.add(groupsMenuItem);
    editMenu.addSeparator();
    editMenu.add(selectAllSequenceMenuItem);
    editMenu.add(deselectAllSequenceMenuItem);
    editMenu.add(invertSequenceMenuItem);
    editMenu.addSeparator();
    editMenu.add(deselectAllColumnsMenuItem);
    editMenu.add(remove2LeftMenuItem);
    editMenu.add(remove2RightMenuItem);
    editMenu.addSeparator();
    editMenu.add(removeGappedColumnMenuItem);
    editMenu.add(removeAllGapsMenuItem);
    editMenu.add(setGapCharMenuItem);
    searchMenu.add(findMenuItem);
    fontMenu.add(fontNameMenuItem);
    fontMenu.add(fontSizeMenuItem);
    fontMenu.add(fontStyleMenuItem);
    viewMenu.add(wrapMenuItem);
    viewMenu.add(viewBoxesMenuItem);
    viewMenu.add(viewTextMenuItem);
    viewMenu.add(colourTextMenuItem);
    viewMenu.add(renderGapsMenuItem);
    viewMenu.add(consensusGraphMenuItem);
    viewMenu.add(overviewMenuItem);
    viewMenu.add(secondaryStructure);
    colourMenu.add(noColourmenuItem);
    colourMenu.add(clustalColour);
    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.add(PIDColour);
    colourMenu.add(BLOSUM62Colour);
    colourMenu.addSeparator();
    colourMenu.add(abovePIDThreshold);
    colourMenu.add(conservationMenuItem);
    colourMenu.addSeparator();
    colourMenu.add(schemeKeyMenuItem);
    calculateMenu.add(sortPairwiseMenuItem);
    calculateMenu.add(sortIDMenuItem);
    calculateMenu.add(sortGroupMenuItem);
    calculateMenu.add(sortTreeOrderMenuItem);
    calculateMenu.add(removeRedundancyMenuItem);
    calculateMenu.addSeparator();
    calculateMenu.add(pairwiseAlignmentMenuItem);
    calculateMenu.add(PCAMenuItem);
    calculateMenu.addSeparator();
    calculateMenu.add(averageDistanceTreeMenuItem);
    calculateMenu.add(neighbourTreeMenuItem);
    calculateMenu.add(avDistanceTreeBlosumMenuItem);
    calculateMenu.add(njTreeBlosumMenuItem);
    alignMenu.add(clustalAlignMenuItem);
    alignMenu.add(pdbTest);
    this.getContentPane().add(statusBar, BorderLayout.SOUTH);
  }

  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 groupsMenuItem_actionPerformed(ActionEvent e)
  {

  }


  protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
  {

  }

  protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
  {

  }

  protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
  {

  }


  protected void deselectAllColumnsMenuItem_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 setGapCharMenuItem_actionPerformed(ActionEvent e)
  {

  }


  protected void fontNameMenuItem_actionPerformed(ActionEvent e)
  {

  }

  protected void fontSizeMenuItem_actionPerformed(ActionEvent e)
  {

  }

  protected void fontStyleMenuItem_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 consensusGraphMenuItem_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 sortTreeOrderMenuItem_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 schemeKeyMenuItem_actionPerformed(ActionEvent e)
  {

  }

  protected void noColourmenuItem_actionPerformed(ActionEvent e)
  {

  }

  protected  void conservationMenuItem_actionPerformed(ActionEvent e)
  {

  }

  protected void pdbTest_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 secondaryStructure_actionPerformed(ActionEvent actionEvent)
  {

  }

  protected void nucleotideColour_actionPerformed(ActionEvent e)
  {

  }

  protected void deleteGroups_actionPerformed(ActionEvent e)
  {

  }


}