merged Loadtree and EPSfile and changed crlf.
authorjprocter <Jim Procter>
Fri, 18 Mar 2005 17:08:17 +0000 (17:08 +0000)
committerjprocter <Jim Procter>
Fri, 18 Mar 2005 17:08:17 +0000 (17:08 +0000)
src/jalview/jbgui/GAlignFrame.java

index 44cb8b7..a256133 100755 (executable)
-/********************\r
- * 2004 Jalview Reengineered\r
- * Barton Group\r
- * Dundee University\r
- *\r
- * AM Waterhouse\r
- *******************/\r
-\r
-package jalview.jbgui;\r
-\r
-import javax.swing.*;\r
-import java.awt.event.*;\r
-import java.awt.*;\r
-\r
-public class GAlignFrame extends JInternalFrame\r
-{\r
-  protected JMenuBar alignFrameMenuBar = new JMenuBar();\r
-  protected JMenu fileMenu = new JMenu();\r
-  protected JMenuItem closeMenuItem = new JMenuItem();\r
-  protected JMenu editMenu = new JMenu();\r
-  protected JMenu viewMenu = new JMenu();\r
-  protected JMenu colourMenu = new JMenu();\r
-  protected JMenu calculateMenu = new JMenu();\r
-  protected JMenu alignMenu = new JMenu();\r
-  protected JMenuItem groupsMenuItem = new JMenuItem();\r
-  protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();\r
-  protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();\r
-  protected JMenuItem invertSequenceMenuItem = new JMenuItem();\r
-  protected JMenuItem deselectAllColumnsMenuItem = new JMenuItem();\r
-  protected JMenuItem remove2LeftMenuItem = new JMenuItem();\r
-  protected JMenuItem remove2RightMenuItem = new JMenuItem();\r
-  protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();\r
-  protected JMenuItem removeAllGapsMenuItem = new JMenuItem();\r
-  protected JMenuItem setGapCharMenuItem = new JMenuItem();\r
-  protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();\r
-  protected JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();\r
-  protected JMenuItem sortPairwiseMenuItem = new JMenuItem();\r
-  protected JMenuItem sortIDMenuItem = new JMenuItem();\r
-  protected JMenuItem sortGroupMenuItem = new JMenuItem();\r
-  protected JMenuItem sortTreeOrderMenuItem = new JMenuItem();\r
-  protected JMenuItem removeRedundancyMenuItem = new JMenuItem();\r
-  protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();\r
-  protected JMenuItem PCAMenuItem = new JMenuItem();\r
-  protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();\r
-  protected JMenuItem neighbourTreeMenuItem = new JMenuItem();\r
-  protected JMenuItem clustalAlignMenuItem = new JMenuItem();\r
-  BorderLayout borderLayout1 = new BorderLayout();\r
-  public JLabel statusBar = new JLabel();\r
-  protected JMenu saveAlignmentMenu = new JMenu();\r
-  protected JMenu outputTextboxMenu = new JMenu();\r
-  protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();\r
-  protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();\r
-  protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();\r
-  protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();\r
-  protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();\r
-  protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();\r
-  protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();\r
-  protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();\r
-  protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();\r
-  protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();\r
-  protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();\r
-  JMenuItem njTreeBlosumMenuItem = new JMenuItem();\r
-  JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();\r
-  protected JCheckBoxMenuItem consensusGraphMenuItem = new JCheckBoxMenuItem();\r
-  protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();\r
-  JMenuItem htmlMenuItem = new JMenuItem();\r
-  JMenuItem overviewMenuItem = new JMenuItem();\r
-  protected JMenuItem undoMenuItem = new JMenuItem();\r
-  protected JMenuItem redoMenuItem = new JMenuItem();\r
-  protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();\r
-  JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();\r
-  protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();\r
-  JMenuItem printMenuItem = new JMenuItem();\r
-  protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();\r
-  JMenuItem findMenuItem = new JMenuItem();\r
-  JMenu searchMenu = new JMenu();\r
-  protected JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();\r
-  protected JCheckBoxMenuItem sequenceFeatures = new JCheckBoxMenuItem();\r
-  protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();\r
-  JMenuItem deleteGroups = new JMenuItem();\r
-  JMenuItem delete = new JMenuItem();\r
-  JMenuItem copy = new JMenuItem();\r
-  JMenuItem cut = new JMenuItem();\r
-  JMenu jMenu1 = new JMenu();\r
-  JMenuItem pasteNew = new JMenuItem();\r
-  JMenuItem pasteThis = new JMenuItem();\r
-  protected JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();\r
-  JMenuItem createPNG = new JMenuItem();\r
-  protected JMenuItem font = new JMenuItem();\r
-  protected JCheckBoxMenuItem fullSeqId = new JCheckBoxMenuItem();\r
-  JMenuItem epsFile = new JMenuItem();\r
-  public GAlignFrame()\r
-  {\r
-\r
-\r
-    try\r
-    {\r
-      jbInit();\r
-      setJMenuBar(alignFrameMenuBar);\r
-\r
-      JMenuItem item;\r
-      // dynamically fill save as menu with available formats\r
-      for (int i = 0; i < jalview.io.FormatProperties.getFormats().size(); i++) {\r
-        item = new JMenuItem((String) jalview.io.FormatProperties.getFormats().elementAt(i));\r
-        saveAlignmentMenu.add( item );\r
-        item.addActionListener(new java.awt.event.ActionListener()\r
-        {\r
-          public void actionPerformed(ActionEvent e)\r
-          {\r
-            saveAs_actionPerformed(e);\r
-          }\r
-        });\r
-\r
-        item = new JMenuItem((String) jalview.io.FormatProperties.getFormats().elementAt(i));\r
-        item.addActionListener(new java.awt.event.ActionListener()\r
-        {\r
-          public void actionPerformed(ActionEvent e)\r
-          {\r
-            outputText_actionPerformed(e);\r
-          }\r
-        });\r
-\r
-        outputTextboxMenu.add( item );\r
-      }\r
-\r
-    }\r
-    catch(Exception e)\r
-    {\r
-      e.printStackTrace();\r
-    }\r
-\r
-    ButtonGroup colours = new ButtonGroup();\r
-    colours.add(noColourmenuItem);\r
-    colours.add(clustalColour);\r
-    colours.add(zappoColour);\r
-    colours.add(taylorColour);\r
-    colours.add(hydrophobicityColour);\r
-    colours.add(helixColour);\r
-    colours.add(strandColour);\r
-    colours.add(turnColour);\r
-    colours.add(buriedColour);\r
-    colours.add(userDefinedColour);\r
-    colours.add(PIDColour);\r
-    colours.add(BLOSUM62Colour);\r
-    colours.add(nucleotideColour);\r
-  }\r
-  private void jbInit() throws Exception\r
-  {\r
-    fileMenu.setMnemonic('F');\r
-    fileMenu.setText("File");\r
-    saveAlignmentMenu.setMnemonic('L');\r
-    saveAlignmentMenu.setText("Save alignment to local file");\r
-    closeMenuItem.setMnemonic('C');\r
-    closeMenuItem.setText("Close");\r
-    closeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        closeMenuItem_actionPerformed(e);\r
-      }\r
-    });\r
-    editMenu.setText("Edit");\r
-    viewMenu.setText("View");\r
-    colourMenu.setText("Colour");\r
-    calculateMenu.setText("Calculate");\r
-    alignMenu.setText("Web Service");\r
-    groupsMenuItem.setVisible(false);\r
-    groupsMenuItem.setText("Groups");\r
-    groupsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        groupsMenuItem_actionPerformed(e);\r
-      }\r
-    });\r
-    selectAllSequenceMenuItem.setText("Select all");\r
-    selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        selectAllSequenceMenuItem_actionPerformed(e);\r
-      }\r
-    });\r
-    deselectAllSequenceMenuItem.setText("Clear selection");\r
-    deselectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        deselectAllSequenceMenuItem_actionPerformed(e);\r
-      }\r
-    });\r
-    invertSequenceMenuItem.setText("Invert sequence selection");\r
-    invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        invertSequenceMenuItem_actionPerformed(e);\r
-      }\r
-    });\r
-    deselectAllColumnsMenuItem.setText("Deselect all columns");\r
-    deselectAllColumnsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        deselectAllColumnsMenuItem_actionPerformed(e);\r
-      }\r
-    });\r
-    remove2LeftMenuItem.setText("Remove sequence <- left of selected column");\r
-    remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        remove2LeftMenuItem_actionPerformed(e);\r
-      }\r
-    });\r
-    remove2RightMenuItem.setText("Remove sequence -> right of selected column");\r
-    remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        remove2RightMenuItem_actionPerformed(e);\r
-      }\r
-    });\r
-    removeGappedColumnMenuItem.setText("Remove gapped columns");\r
-    removeGappedColumnMenuItem.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        removeGappedColumnMenuItem_actionPerformed(e);\r
-      }\r
-    });\r
-    removeAllGapsMenuItem.setText("Remove all gaps");\r
-    removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        removeAllGapsMenuItem_actionPerformed(e);\r
-      }\r
-    });\r
-    setGapCharMenuItem.setText("Set gap character to \".\"");\r
-    setGapCharMenuItem.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        setGapCharMenuItem_actionPerformed(e);\r
-      }\r
-    });\r
-    viewBoxesMenuItem.setText("Boxes");\r
-    viewBoxesMenuItem.setState(true);\r
-    viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        viewBoxesMenuItem_actionPerformed(e);\r
-      }\r
-    });\r
-    viewTextMenuItem.setText("Text");\r
-    viewTextMenuItem.setState(true);\r
-    viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        viewTextMenuItem_actionPerformed(e);\r
-      }\r
-    });\r
-    sortPairwiseMenuItem.setText("Sort by pairwise identity");\r
-    sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        sortPairwiseMenuItem_actionPerformed(e);\r
-      }\r
-    });\r
-    sortIDMenuItem.setText("Sort by ID");\r
-    sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        sortIDMenuItem_actionPerformed(e);\r
-      }\r
-    });\r
-    sortGroupMenuItem.setText("Sort by group");\r
-    sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        sortGroupMenuItem_actionPerformed(e);\r
-      }\r
-    });\r
-    sortTreeOrderMenuItem.setText("Sort by tree order");\r
-    sortTreeOrderMenuItem.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        sortTreeOrderMenuItem_actionPerformed(e);\r
-      }\r
-    });\r
-    removeRedundancyMenuItem.setText("Remove redundancy");\r
-    removeRedundancyMenuItem.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        removeRedundancyMenuItem_actionPerformed(e);\r
-      }\r
-    });\r
-    pairwiseAlignmentMenuItem.setText("Pairwise alignments");\r
-    pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        pairwiseAlignmentMenuItem_actionPerformed(e);\r
-      }\r
-    });\r
-    PCAMenuItem.setText("Principal component analysis");\r
-    PCAMenuItem.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        PCAMenuItem_actionPerformed(e);\r
-      }\r
-    });\r
-    averageDistanceTreeMenuItem.setText("Average distance tree using PID");\r
-    averageDistanceTreeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        averageDistanceTreeMenuItem_actionPerformed(e);\r
-      }\r
-    });\r
-    neighbourTreeMenuItem.setText("Neighbour joining tree using PID");\r
-    neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        neighbourTreeMenuItem_actionPerformed(e);\r
-      }\r
-    });\r
-    clustalAlignMenuItem.setText("Clustal alignment");\r
-    clustalAlignMenuItem.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        clustalAlignMenuItem_actionPerformed(e);\r
-      }\r
-    });\r
-    this.getContentPane().setLayout(borderLayout1);\r
-    alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
-    statusBar.setBackground(Color.white);\r
-    statusBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
-    statusBar.setBorder(BorderFactory.createLineBorder(Color.black));\r
-    statusBar.setText("Status bar");\r
-    outputTextboxMenu.setMnemonic('T');\r
-    outputTextboxMenu.setText("Output alignment via textbox");\r
-    clustalColour.setSelected(false);\r
-    clustalColour.setText("Clustalx colours");\r
-    clustalColour.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        clustalColour_actionPerformed(e);\r
-      }\r
-    });\r
-    zappoColour.setText("Zappo colour scheme");\r
-    zappoColour.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        zappoColour_actionPerformed(e);\r
-      }\r
-    });\r
-    taylorColour.setText("Taylor colour scheme");\r
-    taylorColour.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        taylorColour_actionPerformed(e);\r
-      }\r
-    });\r
-    hydrophobicityColour.setText("By hydrophobicity");\r
-    hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        hydrophobicityColour_actionPerformed(e);\r
-      }\r
-    });\r
-    helixColour.setText("Helix propensity");\r
-    helixColour.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        helixColour_actionPerformed(e);\r
-      }\r
-    });\r
-    strandColour.setText("Strand propensity");\r
-    strandColour.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        strandColour_actionPerformed(e);\r
-      }\r
-    });\r
-    turnColour.setText("Turn propensity");\r
-    turnColour.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        turnColour_actionPerformed(e);\r
-      }\r
-    });\r
-    buriedColour.setText("Buried index");\r
-    buriedColour.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        buriedColour_actionPerformed(e);\r
-      }\r
-    });\r
-    userDefinedColour.setText("User defined colours");\r
-    userDefinedColour.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        userDefinedColour_actionPerformed(e);\r
-      }\r
-    });\r
-    PIDColour.setText("Percentage Identity");\r
-    PIDColour.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        PIDColour_actionPerformed(e);\r
-      }\r
-    });\r
-    BLOSUM62Colour.setText("BLOSUM62 score");\r
-    BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        BLOSUM62Colour_actionPerformed(e);\r
-      }\r
-    });\r
-    avDistanceTreeBlosumMenuItem.setText("Average distance tree using BLOSUM62");\r
-    avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        avTreeBlosumMenuItem_actionPerformed(e);\r
-      }\r
-    });\r
-    njTreeBlosumMenuItem.setText("Neighbour joining tree using BLOSUM62");\r
-    njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        njTreeBlosumMenuItem_actionPerformed(e);\r
-      }\r
-    });\r
-    consensusGraphMenuItem.setActionCommand("");\r
-    consensusGraphMenuItem.setText("Consensus graph");\r
-    consensusGraphMenuItem.setState(true);\r
-    consensusGraphMenuItem.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        consensusGraphMenuItem_actionPerformed(e);\r
-      }\r
-    });\r
-    colourTextMenuItem.setText("Colour text");\r
-    colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        colourTextMenuItem_actionPerformed(e);\r
-      }\r
-    });\r
-    htmlMenuItem.setText("Output as HTML");\r
-    htmlMenuItem.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        htmlMenuItem_actionPerformed(e);\r
-      }\r
-    });\r
-    overviewMenuItem.setText("Overview window");\r
-    overviewMenuItem.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        overviewMenuItem_actionPerformed(e);\r
-      }\r
-    });\r
-    undoMenuItem.setEnabled(false);\r
-    undoMenuItem.setMnemonic('Z');\r
-    undoMenuItem.setText("Undo");\r
-    undoMenuItem.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        undoMenuItem_actionPerformed(e);\r
-      }\r
-    });\r
-    redoMenuItem.setEnabled(false);\r
-    redoMenuItem.setMnemonic('0');\r
-    redoMenuItem.setText("Redo");\r
-    redoMenuItem.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        redoMenuItem_actionPerformed(e);\r
-      }\r
-    });\r
-    conservationMenuItem.setText("By conservation");\r
-    conservationMenuItem.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        conservationMenuItem_actionPerformed(e);\r
-      }\r
-    });\r
-    noColourmenuItem.setText("None");\r
-    noColourmenuItem.setSelected(true);\r
-    noColourmenuItem.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        noColourmenuItem_actionPerformed(e);\r
-      }\r
-    });\r
-    wrapMenuItem.setText("Wrap alignment");\r
-    wrapMenuItem.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        wrapMenuItem_actionPerformed(e);\r
-      }\r
-    });\r
-    printMenuItem.setText("Print");\r
-    printMenuItem.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        printMenuItem_actionPerformed(e);\r
-      }\r
-    });\r
-    renderGapsMenuItem.setText("Render gaps");\r
-    renderGapsMenuItem.setState(true);\r
-    renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        renderGapsMenuItem_actionPerformed(e);\r
-      }\r
-    });\r
-    findMenuItem.setText("Find");\r
-    findMenuItem.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        findMenuItem_actionPerformed(e);\r
-      }\r
-    });\r
-    searchMenu.setText("Search");\r
-\r
-    abovePIDThreshold.setText("Above PID threshold");\r
-    abovePIDThreshold.addActionListener(new java.awt.event.ActionListener() {\r
-      public void actionPerformed(ActionEvent e) {\r
-        abovePIDThreshold_actionPerformed(e);\r
-      }\r
-    });\r
-    sequenceFeatures.setText("Sequence Features");\r
-    sequenceFeatures.addActionListener(new ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent actionEvent)\r
-      {\r
-        sequenceFeatures_actionPerformed(actionEvent);\r
-      }\r
-    });\r
-    nucleotideColour.setText("Nucleotide colours");\r
-    nucleotideColour.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        nucleotideColour_actionPerformed(e);\r
-      }\r
-    });\r
-    deleteGroups.setSelected(false);\r
-    deleteGroups.setText("Delete all groups");\r
-    deleteGroups.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        deleteGroups_actionPerformed(e);\r
-      }\r
-    });\r
-    copy.setText("Copy");\r
-    copy.setMnemonic(KeyEvent.VK_C);\r
-\r
-    copy.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        copy_actionPerformed(e);\r
-      }\r
-    });\r
-    cut.setText("Cut");\r
-    cut.setMnemonic(KeyEvent.VK_X);\r
-    cut.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        cut_actionPerformed(e);\r
-      }\r
-    });\r
-    delete.setText("Delete");\r
-    delete.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        delete_actionPerformed(e);\r
-      }\r
-    });\r
-    jMenu1.setMnemonic('V');\r
-    jMenu1.setText("Paste");\r
-    pasteNew.setText("to new alignment");\r
-    pasteNew.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        pasteNew_actionPerformed(e);\r
-      }\r
-    });\r
-    pasteThis.setText("add to this alignment");\r
-    pasteThis.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        pasteThis_actionPerformed(e);\r
-      }\r
-    });\r
-    applyToAllGroups.setText("Apply colour to all groups");\r
-    applyToAllGroups.setState(true);\r
-    applyToAllGroups.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        applyToAllGroups_actionPerformed(e);\r
-      }\r
-    });\r
-    createPNG.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        createPNG_actionPerformed(e);\r
-      }\r
-    });\r
-    createPNG.setActionCommand("Save as PNG Image");\r
-    createPNG.setText("Save as PNG Image");\r
-    font.setText("Change Font");\r
-    font.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        font_actionPerformed(e);\r
-      }\r
-    });\r
-    fullSeqId.setText("Show full sequence id");\r
-    fullSeqId.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        fullSeqId_actionPerformed(e);\r
-      }\r
-    });\r
-    epsFile.setText("Save as EPS file");\r
-    epsFile.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        epsFile_actionPerformed(e);\r
-      }\r
-    });\r
-    alignFrameMenuBar.add(fileMenu);\r
-    alignFrameMenuBar.add(editMenu);\r
-    alignFrameMenuBar.add(searchMenu);\r
-    alignFrameMenuBar.add(viewMenu);\r
-    alignFrameMenuBar.add(colourMenu);\r
-    alignFrameMenuBar.add(calculateMenu);\r
-    alignFrameMenuBar.add(alignMenu);\r
-    fileMenu.add(saveAlignmentMenu);\r
-    fileMenu.add(outputTextboxMenu);\r
-    fileMenu.add(htmlMenuItem);\r
-    fileMenu.add(epsFile);\r
-    fileMenu.add(createPNG);\r
-    fileMenu.add(printMenuItem);\r
-    fileMenu.addSeparator();\r
-    fileMenu.add(closeMenuItem);\r
-    editMenu.add(copy);\r
-    editMenu.add(jMenu1);\r
-    editMenu.add(cut);\r
-    editMenu.add(delete);\r
-    editMenu.addSeparator();\r
-    editMenu.add(undoMenuItem);\r
-    editMenu.add(redoMenuItem);\r
-    editMenu.addSeparator();\r
-    editMenu.add(deselectAllSequenceMenuItem);\r
-    editMenu.add(selectAllSequenceMenuItem);\r
-    editMenu.add(invertSequenceMenuItem);\r
-    editMenu.add(deleteGroups);\r
-    editMenu.add(groupsMenuItem);\r
-    editMenu.addSeparator();\r
-    editMenu.add(deselectAllColumnsMenuItem);\r
-    editMenu.add(remove2LeftMenuItem);\r
-    editMenu.add(remove2RightMenuItem);\r
-    editMenu.addSeparator();\r
-    editMenu.add(removeGappedColumnMenuItem);\r
-    editMenu.add(removeAllGapsMenuItem);\r
-    editMenu.add(setGapCharMenuItem);\r
-    searchMenu.add(findMenuItem);\r
-    viewMenu.add(font);\r
-    viewMenu.add(fullSeqId);\r
-    viewMenu.add(wrapMenuItem);\r
-    viewMenu.add(viewBoxesMenuItem);\r
-    viewMenu.add(viewTextMenuItem);\r
-    viewMenu.add(colourTextMenuItem);\r
-    viewMenu.add(renderGapsMenuItem);\r
-    viewMenu.add(consensusGraphMenuItem);\r
-    viewMenu.add(overviewMenuItem);\r
-    viewMenu.add(sequenceFeatures);\r
-    colourMenu.add(applyToAllGroups);\r
-    colourMenu.add(noColourmenuItem);\r
-    colourMenu.add(clustalColour);\r
-    colourMenu.add(zappoColour);\r
-    colourMenu.add(taylorColour);\r
-    colourMenu.add(hydrophobicityColour);\r
-    colourMenu.add(helixColour);\r
-    colourMenu.add(strandColour);\r
-    colourMenu.add(turnColour);\r
-    colourMenu.add(buriedColour);\r
-    colourMenu.add(nucleotideColour);\r
-    colourMenu.add(userDefinedColour);\r
-    colourMenu.add(PIDColour);\r
-    colourMenu.add(BLOSUM62Colour);\r
-    colourMenu.addSeparator();\r
-    colourMenu.add(abovePIDThreshold);\r
-    colourMenu.add(conservationMenuItem);\r
-    calculateMenu.add(sortPairwiseMenuItem);\r
-    calculateMenu.add(sortIDMenuItem);\r
-    calculateMenu.add(sortGroupMenuItem);\r
-    calculateMenu.add(sortTreeOrderMenuItem);\r
-    calculateMenu.add(removeRedundancyMenuItem);\r
-    calculateMenu.addSeparator();\r
-    calculateMenu.add(pairwiseAlignmentMenuItem);\r
-    calculateMenu.add(PCAMenuItem);\r
-    calculateMenu.addSeparator();\r
-    calculateMenu.add(averageDistanceTreeMenuItem);\r
-    calculateMenu.add(neighbourTreeMenuItem);\r
-    calculateMenu.add(avDistanceTreeBlosumMenuItem);\r
-    calculateMenu.add(njTreeBlosumMenuItem);\r
-    alignMenu.add(clustalAlignMenuItem);\r
-    this.getContentPane().add(statusBar, BorderLayout.SOUTH);\r
-    jMenu1.add(pasteNew);\r
-    jMenu1.add(pasteThis);\r
-  }\r
-\r
-  protected void saveAs_actionPerformed(ActionEvent e)\r
-  {\r
-\r
-  }\r
-\r
-  protected void outputText_actionPerformed(ActionEvent e)\r
-  {\r
-\r
-  }\r
-\r
-  protected void htmlMenuItem_actionPerformed(ActionEvent e)\r
-  {\r
-\r
-  }\r
-\r
-\r
-\r
-\r
-\r
-  protected void closeMenuItem_actionPerformed(ActionEvent e)\r
-  {\r
-\r
-  }\r
-\r
-  protected void redoMenuItem_actionPerformed(ActionEvent e)\r
-  {\r
-\r
-  }\r
-\r
-  protected void undoMenuItem_actionPerformed(ActionEvent e)\r
-  {\r
-\r
-  }\r
-\r
-\r
-  protected void groupsMenuItem_actionPerformed(ActionEvent e)\r
-  {\r
-\r
-  }\r
-\r
-\r
-  protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
-  {\r
-\r
-  }\r
-\r
-  protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
-  {\r
-\r
-  }\r
-\r
-  protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
-  {\r
-\r
-  }\r
-\r
-\r
-  protected void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)\r
-  {\r
-\r
-  }\r
-\r
-  protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
-  {\r
-\r
-  }\r
-\r
-  protected void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
-  {\r
-\r
-  }\r
-\r
-  protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
-  {\r
-\r
-  }\r
-\r
-  protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
-  {\r
-\r
-  }\r
-\r
-  protected void setGapCharMenuItem_actionPerformed(ActionEvent e)\r
-  {\r
-\r
-  }\r
-\r
-\r
-\r
-\r
-\r
-  protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
-  {\r
-\r
-  }\r
-\r
-\r
-  protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
-  {\r
-\r
-  }\r
-\r
-  protected void viewTextMenuItem_actionPerformed(ActionEvent e)\r
-  {\r
-\r
-  }\r
-\r
-\r
-  protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
-  {\r
-\r
-  }\r
-\r
-\r
-\r
-  protected void consensusGraphMenuItem_actionPerformed(ActionEvent e)\r
-  {\r
-\r
-  }\r
-\r
-  protected void overviewMenuItem_actionPerformed(ActionEvent e)\r
-  {\r
-\r
-  }\r
-\r
-  protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
-  {\r
-\r
-  }\r
-\r
-  protected void sortIDMenuItem_actionPerformed(ActionEvent e)\r
-  {\r
-\r
-  }\r
-\r
-  protected void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
-  {\r
-\r
-  }\r
-\r
-  protected void sortTreeOrderMenuItem_actionPerformed(ActionEvent e)\r
-  {\r
-\r
-  }\r
-\r
-  protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
-  {\r
-\r
-  }\r
-\r
-  protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
-  {\r
-\r
-  }\r
-\r
-  protected void PCAMenuItem_actionPerformed(ActionEvent e)\r
-  {\r
-\r
-  }\r
-\r
-  protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
-  {\r
-\r
-  }\r
-\r
-  protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
-  {\r
-\r
-  }\r
-\r
-\r
-  protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
-  {\r
-\r
-  }\r
-\r
-  protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
-  {\r
-\r
-  }\r
-\r
-\r
-\r
-  protected void clustalAlignMenuItem_actionPerformed(ActionEvent e)\r
-  {\r
-\r
-  }\r
-\r
-\r
-\r
-\r
-  protected void clustalColour_actionPerformed(ActionEvent e)\r
-  {\r
-\r
-  }\r
-\r
-  protected void zappoColour_actionPerformed(ActionEvent e)\r
-  {\r
-\r
-  }\r
-\r
-  protected void taylorColour_actionPerformed(ActionEvent e)\r
-  {\r
-\r
-  }\r
-\r
-\r
-  protected void hydrophobicityColour_actionPerformed(ActionEvent e)\r
-  {\r
-\r
-  }\r
-\r
-  protected void helixColour_actionPerformed(ActionEvent e)\r
-  {\r
-\r
-  }\r
-\r
-  protected void strandColour_actionPerformed(ActionEvent e)\r
-  {\r
-\r
-  }\r
-\r
-  protected void turnColour_actionPerformed(ActionEvent e)\r
-  {\r
-\r
-  }\r
-\r
-  protected void buriedColour_actionPerformed(ActionEvent e)\r
-  {\r
-\r
-  }\r
-\r
-\r
-\r
-  protected void userDefinedColour_actionPerformed(ActionEvent e)\r
-  {\r
-\r
-  }\r
-\r
-  protected void PIDColour_actionPerformed(ActionEvent e)\r
-  {\r
-\r
-  }\r
-\r
-  protected void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
-  {\r
-\r
-  }\r
-\r
-\r
-  protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
-  {\r
-\r
-  }\r
-\r
-  protected  void conservationMenuItem_actionPerformed(ActionEvent e)\r
-  {\r
-\r
-  }\r
-\r
-\r
-  protected void printMenuItem_actionPerformed(ActionEvent e)\r
-  {\r
-\r
-  }\r
-\r
-  protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
-  {\r
-\r
-  }\r
-\r
-  protected void findMenuItem_actionPerformed(ActionEvent e)\r
-  {\r
-\r
-  }\r
-\r
-\r
-  protected void abovePIDThreshold_actionPerformed(ActionEvent e) {\r
-\r
-  }\r
-\r
-  public void sequenceFeatures_actionPerformed(ActionEvent actionEvent)\r
-  {\r
-\r
-  }\r
-\r
-  protected void nucleotideColour_actionPerformed(ActionEvent e)\r
-  {\r
-\r
-  }\r
-\r
-  protected void deleteGroups_actionPerformed(ActionEvent e)\r
-  {\r
-\r
-  }\r
-\r
- protected void copy_actionPerformed(ActionEvent e)\r
-  {\r
-\r
-  }\r
-\r
-\r
-  protected void cut_actionPerformed(ActionEvent e)\r
-  {\r
-\r
-  }\r
-\r
-  protected void delete_actionPerformed(ActionEvent e)\r
-  {\r
-\r
-  }\r
-\r
-  protected void pasteNew_actionPerformed(ActionEvent e)\r
-  {\r
-\r
-  }\r
-\r
-  protected void pasteThis_actionPerformed(ActionEvent e)\r
-  {\r
-\r
-  }\r
-\r
-  protected void applyToAllGroups_actionPerformed(ActionEvent e)\r
-  {\r
-\r
-  }\r
-\r
-  protected void createPNG_actionPerformed(ActionEvent e)\r
-  {\r
-\r
-  }\r
-\r
-  protected void font_actionPerformed(ActionEvent e)\r
-  {\r
-\r
-  }\r
-\r
-  protected void fullSeqId_actionPerformed(ActionEvent e)\r
-  {\r
-\r
-  }\r
-\r
-  protected void epsFile_actionPerformed(ActionEvent e)\r
-  {\r
-\r
-  }\r
-\r
-\r
-\r
-}\r
+/********************
+ * 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 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 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 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();
+  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");
+    viewMenu.setText("View");
+    colourMenu.setText("Colour");
+    calculateMenu.setText("Calculate");
+    alignMenu.setText("Web Service");
+    groupsMenuItem.setVisible(false);
+    groupsMenuItem.setText("Groups");
+    groupsMenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        groupsMenuItem_actionPerformed(e);
+      }
+    });
+    selectAllSequenceMenuItem.setText("Select all");
+    selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        selectAllSequenceMenuItem_actionPerformed(e);
+      }
+    });
+    deselectAllSequenceMenuItem.setText("Clear 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);
+      }
+    });
+    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);
+      }
+    });
+    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.setText("Wrap alignment");
+    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("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);
+      }
+    });
+    sequenceFeatures.setText("Sequence Features");
+    sequenceFeatures.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent actionEvent)
+      {
+        sequenceFeatures_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);
+      }
+    });
+    copy.setText("Copy");
+    copy.setMnemonic(KeyEvent.VK_C);
+
+    copy.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        copy_actionPerformed(e);
+      }
+    });
+    cut.setText("Cut");
+    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.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("Save as PNG Image");
+    font.setText("Change 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("Save as EPS file");
+    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);
+      }
+    });
+    alignFrameMenuBar.add(fileMenu);
+    alignFrameMenuBar.add(editMenu);
+    alignFrameMenuBar.add(searchMenu);
+    alignFrameMenuBar.add(viewMenu);
+    alignFrameMenuBar.add(colourMenu);
+    alignFrameMenuBar.add(calculateMenu);
+    alignFrameMenuBar.add(alignMenu);
+    fileMenu.add(saveAlignmentMenu);
+    fileMenu.add(outputTextboxMenu);
+    fileMenu.add(htmlMenuItem);
+    fileMenu.add(epsFile);
+    fileMenu.add(createPNG);
+    fileMenu.add(printMenuItem);
+    fileMenu.addSeparator();
+    fileMenu.add(LoadtreeMenuItem);
+    fileMenu.addSeparator();
+    fileMenu.add(closeMenuItem);
+    editMenu.add(copy);
+    editMenu.add(jMenu1);
+    editMenu.add(cut);
+    editMenu.add(delete);
+    editMenu.addSeparator();
+    editMenu.add(undoMenuItem);
+    editMenu.add(redoMenuItem);
+    editMenu.addSeparator();
+    editMenu.add(deselectAllSequenceMenuItem);
+    editMenu.add(selectAllSequenceMenuItem);
+    editMenu.add(invertSequenceMenuItem);
+    editMenu.add(deleteGroups);
+    editMenu.add(groupsMenuItem);
+    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);
+    viewMenu.add(font);
+    viewMenu.add(fullSeqId);
+    viewMenu.add(wrapMenuItem);
+    viewMenu.add(viewBoxesMenuItem);
+    viewMenu.add(viewTextMenuItem);
+    viewMenu.add(colourTextMenuItem);
+    viewMenu.add(renderGapsMenuItem);
+    viewMenu.add(consensusGraphMenuItem);
+    viewMenu.add(overviewMenuItem);
+    viewMenu.add(sequenceFeatures);
+    colourMenu.add(applyToAllGroups);
+    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);
+    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);
+    this.getContentPane().add(statusBar, BorderLayout.SOUTH);
+    jMenu1.add(pasteNew);
+    jMenu1.add(pasteThis);
+  }
+
+  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 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 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) {
+
+  }
+
+}