/*
* Jalview - A Sequence Alignment Editor and Viewer
* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
*/

package jalview.jbappletgui;

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

public class GAlignFrame extends Frame
{
  protected MenuBar alignFrameMenuBar = new MenuBar();
  protected Menu fileMenu = new Menu();
  protected MenuItem closeMenuItem = new MenuItem();
  protected Menu editMenu = new Menu();
  protected Menu viewMenu = new Menu();
  protected Menu colourMenu = new Menu();
  protected Menu calculateMenu = new Menu();
  protected MenuItem selectAllSequenceMenuItem = new MenuItem();
  protected MenuItem deselectAllSequenceMenuItem = new MenuItem();
  protected MenuItem invertSequenceMenuItem = new MenuItem();
  protected MenuItem remove2LeftMenuItem = new MenuItem();
  protected MenuItem remove2RightMenuItem = new MenuItem();
  protected MenuItem removeGappedColumnMenuItem = new MenuItem();
  protected MenuItem removeAllGapsMenuItem = new MenuItem();
  protected CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
  protected CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
  protected MenuItem sortPairwiseMenuItem = new MenuItem();
  protected MenuItem sortIDMenuItem = new MenuItem();
  protected MenuItem sortGroupMenuItem = new MenuItem();
  protected MenuItem removeRedundancyMenuItem = new MenuItem();
  protected MenuItem pairwiseAlignmentMenuItem = new MenuItem();
  protected MenuItem PCAMenuItem = new MenuItem();
  protected MenuItem averageDistanceTreeMenuItem = new MenuItem();
  protected MenuItem neighbourTreeMenuItem = new MenuItem();
  BorderLayout borderLayout1 = new BorderLayout();
  public Label statusBar = new Label();
  protected Menu outputTextboxMenu = new Menu();
  protected MenuItem clustalColour = new MenuItem();
  protected MenuItem zappoColour = new MenuItem();
  protected MenuItem taylorColour = new MenuItem();
  protected MenuItem hydrophobicityColour = new MenuItem();
  protected MenuItem helixColour = new MenuItem();
  protected MenuItem strandColour = new MenuItem();
  protected MenuItem turnColour = new MenuItem();
  protected MenuItem buriedColour = new MenuItem();
  protected MenuItem userDefinedColour = new MenuItem();
  protected MenuItem PIDColour = new MenuItem();
  protected MenuItem BLOSUM62Colour = new MenuItem();
  MenuItem njTreeBlosumMenuItem = new MenuItem();
  MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
  protected CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
  protected CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
  MenuItem overviewMenuItem = new MenuItem();
  protected MenuItem undoMenuItem = new MenuItem();
  protected MenuItem redoMenuItem = new MenuItem();
  protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
  MenuItem noColourmenuItem = new MenuItem();
  protected CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
  protected CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
  MenuItem findMenuItem = new MenuItem();
  Menu searchMenu = new Menu();
  protected CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
  protected MenuItem nucleotideColour = new MenuItem();
  MenuItem deleteGroups = new MenuItem();
  MenuItem delete = new MenuItem();
  MenuItem copy = new MenuItem();
  MenuItem cut = new MenuItem();
  Menu Menu1 = new Menu();
  MenuItem pasteNew = new MenuItem();
  MenuItem pasteThis = new MenuItem();
  protected CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
  protected MenuItem font = new MenuItem();
  protected CheckboxMenuItem fullSeqId = new CheckboxMenuItem();
  protected CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
  protected CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
  protected CheckboxMenuItem scaleRight = new CheckboxMenuItem();
  MenuItem modifyPID = new MenuItem();
  MenuItem modifyConservation = new MenuItem();
  protected Menu sortByTreeMenu = new Menu();
  Menu sort = new Menu();
  Menu calculate = new Menu();
  MenuItem inputText = new MenuItem();
  Menu helpMenu = new Menu();
  MenuItem documentation = new MenuItem();
  MenuItem about = new MenuItem();
  public GAlignFrame()
  {
    try
    {
      jbInit();
      setMenuBar(alignFrameMenuBar);

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

        item = new MenuItem((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.setLabel("File");
    closeMenuItem.setLabel("Close");
    closeMenuItem.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        closeMenuItem_actionPerformed(e);
      }
    });
    editMenu.setLabel("Edit");
    viewMenu.setLabel("View");
    colourMenu.setLabel("Colour");
    calculateMenu.setLabel("Calculate");
    selectAllSequenceMenuItem.setLabel("Select all");
    selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        selectAllSequenceMenuItem_actionPerformed(e);
      }
    });
    deselectAllSequenceMenuItem.setLabel("Deselect All");
    deselectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        deselectAllSequenceMenuItem_actionPerformed(e);
      }
    });
    invertSequenceMenuItem.setLabel("Invert Selection");
    invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        invertSequenceMenuItem_actionPerformed(e);
      }
    });
    remove2LeftMenuItem.setLabel("Remove Left");
    remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        remove2LeftMenuItem_actionPerformed(e);
      }
    });
    remove2RightMenuItem.setLabel("Remove Right");
    remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        remove2RightMenuItem_actionPerformed(e);
      }
    });
    removeGappedColumnMenuItem.setLabel("Remove Empty Columns");
    removeGappedColumnMenuItem.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        removeGappedColumnMenuItem_actionPerformed(e);
      }
    });
    removeAllGapsMenuItem.setLabel("Remove All Gaps");
    removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        removeAllGapsMenuItem_actionPerformed(e);
      }
    });
    viewBoxesMenuItem.setLabel("Boxes");
    viewBoxesMenuItem.setState(true);
    viewBoxesMenuItem.addItemListener(new java.awt.event.ItemListener()
    {
      public void itemStateChanged(ItemEvent e)
      {
        viewBoxesMenuItem_actionPerformed(null);
      }
    });
    viewTextMenuItem.setLabel("Text");
    viewTextMenuItem.setState(true);
    viewTextMenuItem.addItemListener(new java.awt.event.ItemListener()
    {
      public void itemStateChanged(ItemEvent e)
      {
        viewTextMenuItem_actionPerformed(null);
      }
    });
    sortPairwiseMenuItem.setLabel("by Pairwise Identity");
    sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        sortPairwiseMenuItem_actionPerformed(e);
      }
    });
    sortIDMenuItem.setLabel("by ID");
    sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        sortIDMenuItem_actionPerformed(e);
      }
    });
    sortGroupMenuItem.setLabel("by Group");
    sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        sortGroupMenuItem_actionPerformed(e);
      }
    });
    removeRedundancyMenuItem.setLabel("Remove Redundancy...");
    removeRedundancyMenuItem.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        removeRedundancyMenuItem_actionPerformed(e);
      }
    });
    pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");
    pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        pairwiseAlignmentMenuItem_actionPerformed(e);
      }
    });
    PCAMenuItem.setLabel("Principal Component Analysis...");
    PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        PCAMenuItem_actionPerformed(e);
      }
    });
    averageDistanceTreeMenuItem.setLabel("Average Distance Using % Identity...");
    averageDistanceTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        averageDistanceTreeMenuItem_actionPerformed(e);
      }
    });
    neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity...");
    neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        neighbourTreeMenuItem_actionPerformed(e);
      }
    });
    alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
    statusBar.setBackground(Color.white);
    statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
    statusBar.setText("Status bar");
    outputTextboxMenu.setLabel("Output to Textbox");
    clustalColour.setLabel("Clustalx");

    clustalColour.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        clustalColour_actionPerformed(e);
      }
    });
    zappoColour.setLabel("Zappo");
    zappoColour.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        zappoColour_actionPerformed(e);
      }
    });
    taylorColour.setLabel("Taylor");
    taylorColour.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        taylorColour_actionPerformed(e);
      }
    });
    hydrophobicityColour.setLabel("Hydrophobicity");
    hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        hydrophobicityColour_actionPerformed(e);
      }
    });
    helixColour.setLabel("Helix Propensity");
    helixColour.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        helixColour_actionPerformed(e);
      }
    });
    strandColour.setLabel("Strand Propensity");
    strandColour.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        strandColour_actionPerformed(e);
      }
    });
    turnColour.setLabel("Turn Propensity");
    turnColour.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        turnColour_actionPerformed(e);
      }
    });
    buriedColour.setLabel("Buried Index");
    buriedColour.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        buriedColour_actionPerformed(e);
      }
    });
    userDefinedColour.setLabel("User Defined...");
    userDefinedColour.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        userDefinedColour_actionPerformed(e);
      }
    });
    PIDColour.setLabel("Percentage Identity");
    PIDColour.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        PIDColour_actionPerformed(e);
      }
    });
    BLOSUM62Colour.setLabel("BLOSUM62 Score");
    BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        BLOSUM62Colour_actionPerformed(e);
      }
    });
    avDistanceTreeBlosumMenuItem.setLabel("Average Distance Using BLOSUM62...");
    avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        avTreeBlosumMenuItem_actionPerformed(e);
      }
    });
    njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62...");
    njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        njTreeBlosumMenuItem_actionPerformed(e);
      }
    });
    annotationPanelMenuItem.setActionCommand("");
    annotationPanelMenuItem.setState(true);
    annotationPanelMenuItem.setLabel("Show Annotations");
    annotationPanelMenuItem.addItemListener(new java.awt.event.ItemListener()
    {
      public void itemStateChanged(ItemEvent e)
      {
        annotationPanelMenuItem_actionPerformed(null);
      }
    });
    colourTextMenuItem.setLabel("Colour Text");
    colourTextMenuItem.addItemListener(new java.awt.event.ItemListener()
    {
      public void itemStateChanged(ItemEvent e)
      {
        colourTextMenuItem_actionPerformed(null);
      }
    });
    overviewMenuItem.setLabel("Overview Window...");
    overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        overviewMenuItem_actionPerformed(e);
      }
    });
    undoMenuItem.setEnabled(false);
    undoMenuItem.setLabel("Undo");
    undoMenuItem.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        undoMenuItem_actionPerformed(e);
      }
    });
    redoMenuItem.setEnabled(false);
    redoMenuItem.setLabel("Redo");
    redoMenuItem.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        redoMenuItem_actionPerformed(e);
      }
    });
    conservationMenuItem.setLabel("by Conservation");
    conservationMenuItem.addItemListener(new java.awt.event.ItemListener()
    {
      public void itemStateChanged(ItemEvent e)
      {
        conservationMenuItem_actionPerformed(null);
      }
    });
    noColourmenuItem.setLabel("None");
    noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        noColourmenuItem_actionPerformed(e);
      }
    });
    wrapMenuItem.setLabel("Wrap");
    wrapMenuItem.addItemListener(new java.awt.event.ItemListener()
    {
      public void itemStateChanged(ItemEvent e)
      {
        wrapMenuItem_actionPerformed(null);
      }
    });
    renderGapsMenuItem.setLabel("Show Gaps");
    renderGapsMenuItem.setState(true);
    renderGapsMenuItem.addItemListener(new java.awt.event.ItemListener()
    {

      public void itemStateChanged(ItemEvent e)
      {

        renderGapsMenuItem_actionPerformed(null);
      }
    });
    findMenuItem.setLabel("Find...");
    findMenuItem.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        findMenuItem_actionPerformed(e);
      }
    });
    searchMenu.setLabel("Search");

    abovePIDThreshold.setLabel("Above Identity Threshold");
    abovePIDThreshold.addItemListener(new java.awt.event.ItemListener()
    {
      public void itemStateChanged(ItemEvent e)
      {
        abovePIDThreshold_actionPerformed(null);
      }
    });
    nucleotideColour.setLabel("Nucleotide");
    nucleotideColour.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        nucleotideColour_actionPerformed(e);
      }
    });
    deleteGroups.setLabel("Undefine Groups");
    deleteGroups.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        deleteGroups_actionPerformed(e);
      }
    });
    copy.setLabel("Copy");
    copy.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        copy_actionPerformed(e);
      }
    });
    cut.setLabel("Cut");
    cut.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        cut_actionPerformed(e);
      }
    });
    delete.setLabel("Delete");
    delete.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        delete_actionPerformed(e);
      }
    });
    Menu1.setLabel("Paste");
    pasteNew.setLabel("To New Alignment");
    pasteNew.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        pasteNew_actionPerformed(e);
      }
    });
    pasteThis.setLabel("Add To This Alignment");
    pasteThis.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        pasteThis_actionPerformed(e);
      }
    });
    applyToAllGroups.setLabel("Apply Colour To All Groups");
    applyToAllGroups.setState(true);
    applyToAllGroups.addItemListener(new java.awt.event.ItemListener()
   {
     public void itemStateChanged(ItemEvent e)
     {
        applyToAllGroups_actionPerformed(null);
      }
    });
    font.setLabel("Font...");
    font.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        font_actionPerformed(e);
      }
    });
    fullSeqId.setLabel("Show Full Sequence ID");
    fullSeqId.setState(true);
    fullSeqId.addItemListener(new java.awt.event.ItemListener()
    {

      public void itemStateChanged(ItemEvent e)
      {
        fullSeqId_actionPerformed(null);
      }
    });
    scaleAbove.setLabel("Scale Above");
    scaleAbove.setState(true);
    scaleAbove.addItemListener(new java.awt.event.ItemListener()
    {

      public void itemStateChanged(ItemEvent e)
      {

        scaleAbove_actionPerformed(null);
      }
    });
    scaleLeft.setEnabled(false);
    scaleLeft.setState(true);
    scaleLeft.setLabel("Scale Left");
    scaleLeft.addItemListener(new java.awt.event.ItemListener()
    {

      public void itemStateChanged(ItemEvent e)
      {

        scaleLeft_actionPerformed(null);
      }
    });
    scaleRight.setEnabled(false);
    scaleRight.setState(true);
    scaleRight.setLabel("Scale Right");
    scaleRight.addItemListener(new java.awt.event.ItemListener()
    {

      public void itemStateChanged(ItemEvent e)
      {

        scaleRight_actionPerformed(null);
      }
    });
    modifyPID.setLabel("Modify Identity Threshold...");
    modifyPID.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        modifyPID_actionPerformed(e);
      }
    });
    modifyConservation.setLabel("Modify Conservation Threshold...");
    modifyConservation.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        modifyConservation_actionPerformed(e);
      }
    });
    sortByTreeMenu.setLabel("By Tree Order");
    sort.setLabel("Sort");
    calculate.setLabel("Calculate Tree");
    inputText.setLabel("Input from textbox");
    inputText.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        inputText_actionPerformed(e);
      }
    });

    helpMenu.setLabel("Help");
    documentation.setLabel("Documentation");
    documentation.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        documentation_actionPerformed(e);
      }
    });

    about.setLabel("About...");
    about.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        about_actionPerformed(e);
      }
    });

    alignFrameMenuBar.add(fileMenu);
    alignFrameMenuBar.add(editMenu);
    alignFrameMenuBar.add(searchMenu);
    alignFrameMenuBar.add(viewMenu);
    alignFrameMenuBar.add(colourMenu);
    alignFrameMenuBar.add(calculateMenu);
    alignFrameMenuBar.add(helpMenu);
    fileMenu.add(inputText);
    fileMenu.add(outputTextboxMenu);
    fileMenu.addSeparator();
    fileMenu.add(closeMenuItem);
    editMenu.add(undoMenuItem);
    editMenu.add(redoMenuItem);
    editMenu.add(cut);
    editMenu.add(copy);
    editMenu.add(Menu1);
    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.addSeparator();
    viewMenu.add(wrapMenuItem);
    viewMenu.add(scaleAbove);
    viewMenu.add(scaleLeft);
    viewMenu.add(scaleRight);
    viewMenu.addSeparator();
    viewMenu.add(fullSeqId);
    viewMenu.add(viewBoxesMenuItem);
    viewMenu.add(viewTextMenuItem);
    viewMenu.add(colourTextMenuItem);
    viewMenu.add(renderGapsMenuItem);
    viewMenu.add(annotationPanelMenuItem);
    viewMenu.addSeparator();
    viewMenu.add(overviewMenuItem);
    colourMenu.add(applyToAllGroups);
    colourMenu.addSeparator();
    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(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);
    this.add(statusBar, BorderLayout.SOUTH);
    Menu1.add(pasteNew);
    Menu1.add(pasteThis);
    sort.add(sortIDMenuItem);
    sort.add(sortByTreeMenu);
    sort.add(sortGroupMenuItem);
    sort.add(sortPairwiseMenuItem);
    calculate.add(averageDistanceTreeMenuItem);
    calculate.add(neighbourTreeMenuItem);
    calculate.add(avDistanceTreeBlosumMenuItem);
    calculate.add(njTreeBlosumMenuItem);
    helpMenu.add(documentation);
    helpMenu.add(about);
  }

  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) {

  }

  protected void inputText_actionPerformed(ActionEvent e) {

  }

  protected void documentation_actionPerformed(ActionEvent e) {

  }

  protected void about_actionPerformed(ActionEvent e) {

  }


}