After merge
[jalview.git] / src / jalview / jbappletgui / GAlignFrame.java
diff --git a/src/jalview/jbappletgui/GAlignFrame.java b/src/jalview/jbappletgui/GAlignFrame.java
deleted file mode 100755 (executable)
index 7775b65..0000000
+++ /dev/null
@@ -1,831 +0,0 @@
-/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
-*/\r
-package jalview.jbappletgui;\r
-\r
-import java.awt.*;\r
-import java.awt.event.*;\r
-\r
-\r
-public class GAlignFrame extends Frame {\r
-    protected MenuBar alignFrameMenuBar = new MenuBar();\r
-    protected Menu fileMenu = new Menu();\r
-    protected MenuItem closeMenuItem = new MenuItem();\r
-    protected Menu editMenu = new Menu();\r
-    protected Menu viewMenu = new Menu();\r
-    protected Menu colourMenu = new Menu();\r
-    protected Menu calculateMenu = new Menu();\r
-    protected MenuItem selectAllSequenceMenuItem = new MenuItem();\r
-    protected MenuItem deselectAllSequenceMenuItem = new MenuItem();\r
-    protected MenuItem invertSequenceMenuItem = new MenuItem();\r
-    protected MenuItem remove2LeftMenuItem = new MenuItem();\r
-    protected MenuItem remove2RightMenuItem = new MenuItem();\r
-    protected MenuItem removeGappedColumnMenuItem = new MenuItem();\r
-    protected MenuItem removeAllGapsMenuItem = new MenuItem();\r
-    protected CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();\r
-    protected CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();\r
-    protected MenuItem sortPairwiseMenuItem = new MenuItem();\r
-    protected MenuItem sortIDMenuItem = new MenuItem();\r
-    protected MenuItem sortGroupMenuItem = new MenuItem();\r
-    protected MenuItem removeRedundancyMenuItem = new MenuItem();\r
-    protected MenuItem pairwiseAlignmentMenuItem = new MenuItem();\r
-    protected MenuItem PCAMenuItem = new MenuItem();\r
-    protected MenuItem averageDistanceTreeMenuItem = new MenuItem();\r
-    protected MenuItem neighbourTreeMenuItem = new MenuItem();\r
-    BorderLayout borderLayout1 = new BorderLayout();\r
-    public Label statusBar = new Label();\r
-    protected Menu outputTextboxMenu = new Menu();\r
-    protected MenuItem clustalColour = new MenuItem();\r
-    protected MenuItem zappoColour = new MenuItem();\r
-    protected MenuItem taylorColour = new MenuItem();\r
-    protected MenuItem hydrophobicityColour = new MenuItem();\r
-    protected MenuItem helixColour = new MenuItem();\r
-    protected MenuItem strandColour = new MenuItem();\r
-    protected MenuItem turnColour = new MenuItem();\r
-    protected MenuItem buriedColour = new MenuItem();\r
-    protected MenuItem userDefinedColour = new MenuItem();\r
-    protected MenuItem PIDColour = new MenuItem();\r
-    protected MenuItem BLOSUM62Colour = new MenuItem();\r
-    MenuItem njTreeBlosumMenuItem = new MenuItem();\r
-    MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();\r
-    protected CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();\r
-    protected CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();\r
-    MenuItem overviewMenuItem = new MenuItem();\r
-    protected MenuItem undoMenuItem = new MenuItem();\r
-    protected MenuItem redoMenuItem = new MenuItem();\r
-    protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();\r
-    MenuItem noColourmenuItem = new MenuItem();\r
-    protected CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();\r
-    protected CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();\r
-    MenuItem findMenuItem = new MenuItem();\r
-    Menu searchMenu = new Menu();\r
-    protected CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();\r
-    protected MenuItem nucleotideColour = new MenuItem();\r
-    MenuItem deleteGroups = new MenuItem();\r
-    MenuItem delete = new MenuItem();\r
-    MenuItem copy = new MenuItem();\r
-    MenuItem cut = new MenuItem();\r
-    Menu Menu1 = new Menu();\r
-    MenuItem pasteNew = new MenuItem();\r
-    MenuItem pasteThis = new MenuItem();\r
-    protected CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();\r
-    protected MenuItem font = new MenuItem();\r
-    protected CheckboxMenuItem fullSeqId = new CheckboxMenuItem();\r
-    protected CheckboxMenuItem scaleAbove = new CheckboxMenuItem();\r
-    protected CheckboxMenuItem scaleLeft = new CheckboxMenuItem();\r
-    protected CheckboxMenuItem scaleRight = new CheckboxMenuItem();\r
-    MenuItem modifyPID = new MenuItem();\r
-    MenuItem modifyConservation = new MenuItem();\r
-    protected Menu sortByTreeMenu = new Menu();\r
-    Menu sort = new Menu();\r
-    Menu calculate = new Menu();\r
-    MenuItem inputText = new MenuItem();\r
-    Menu helpMenu = new Menu();\r
-    MenuItem documentation = new MenuItem();\r
-    MenuItem about = new MenuItem();\r
-\r
-    public GAlignFrame() {\r
-        try {\r
-            jbInit();\r
-            setMenuBar(alignFrameMenuBar);\r
-\r
-            MenuItem item;\r
-\r
-            // dynamically fill save as menu with available formats\r
-            for (int i = 0; i < jalview.io.FormatAdapter.formats.size(); i++) {\r
-                item = new MenuItem((String) jalview.io.FormatAdapter.formats.elementAt(\r
-                            i));\r
-                item.addActionListener(new java.awt.event.ActionListener() {\r
-                        public void actionPerformed(ActionEvent e) {\r
-                            saveAs_actionPerformed(e);\r
-                        }\r
-                    });\r
-\r
-                item = new MenuItem((String) jalview.io.FormatAdapter.formats.elementAt(\r
-                            i));\r
-                item.addActionListener(new java.awt.event.ActionListener() {\r
-                        public void actionPerformed(ActionEvent e) {\r
-                            outputText_actionPerformed(e);\r
-                        }\r
-                    });\r
-\r
-                outputTextboxMenu.add(item);\r
-            }\r
-        } catch (Exception e) {\r
-            e.printStackTrace();\r
-        }\r
-    }\r
-\r
-    private void jbInit() throws Exception {\r
-        fileMenu.setLabel("File");\r
-        closeMenuItem.setLabel("Close");\r
-        closeMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    closeMenuItem_actionPerformed(e);\r
-                }\r
-            });\r
-        editMenu.setLabel("Edit");\r
-        viewMenu.setLabel("View");\r
-        colourMenu.setLabel("Colour");\r
-        calculateMenu.setLabel("Calculate");\r
-        selectAllSequenceMenuItem.setLabel("Select all");\r
-        selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    selectAllSequenceMenuItem_actionPerformed(e);\r
-                }\r
-            });\r
-        deselectAllSequenceMenuItem.setLabel("Deselect All");\r
-        deselectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    deselectAllSequenceMenuItem_actionPerformed(e);\r
-                }\r
-            });\r
-        invertSequenceMenuItem.setLabel("Invert Selection");\r
-        invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    invertSequenceMenuItem_actionPerformed(e);\r
-                }\r
-            });\r
-        remove2LeftMenuItem.setLabel("Remove Left");\r
-        remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    remove2LeftMenuItem_actionPerformed(e);\r
-                }\r
-            });\r
-        remove2RightMenuItem.setLabel("Remove Right");\r
-        remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    remove2RightMenuItem_actionPerformed(e);\r
-                }\r
-            });\r
-        removeGappedColumnMenuItem.setLabel("Remove Empty Columns");\r
-        removeGappedColumnMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    removeGappedColumnMenuItem_actionPerformed(e);\r
-                }\r
-            });\r
-        removeAllGapsMenuItem.setLabel("Remove All Gaps");\r
-        removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    removeAllGapsMenuItem_actionPerformed(e);\r
-                }\r
-            });\r
-        viewBoxesMenuItem.setLabel("Boxes");\r
-        viewBoxesMenuItem.setState(true);\r
-        viewBoxesMenuItem.addItemListener(new java.awt.event.ItemListener() {\r
-                public void itemStateChanged(ItemEvent e) {\r
-                    viewBoxesMenuItem_actionPerformed(null);\r
-                }\r
-            });\r
-        viewTextMenuItem.setLabel("Text");\r
-        viewTextMenuItem.setState(true);\r
-        viewTextMenuItem.addItemListener(new java.awt.event.ItemListener() {\r
-                public void itemStateChanged(ItemEvent e) {\r
-                    viewTextMenuItem_actionPerformed(null);\r
-                }\r
-            });\r
-        sortPairwiseMenuItem.setLabel("by Pairwise Identity");\r
-        sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    sortPairwiseMenuItem_actionPerformed(e);\r
-                }\r
-            });\r
-        sortIDMenuItem.setLabel("by ID");\r
-        sortIDMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    sortIDMenuItem_actionPerformed(e);\r
-                }\r
-            });\r
-        sortGroupMenuItem.setLabel("by Group");\r
-        sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    sortGroupMenuItem_actionPerformed(e);\r
-                }\r
-            });\r
-        removeRedundancyMenuItem.setLabel("Remove Redundancy...");\r
-        removeRedundancyMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    removeRedundancyMenuItem_actionPerformed(e);\r
-                }\r
-            });\r
-        pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");\r
-        pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    pairwiseAlignmentMenuItem_actionPerformed(e);\r
-                }\r
-            });\r
-        PCAMenuItem.setLabel("Principal Component Analysis");\r
-        PCAMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    PCAMenuItem_actionPerformed(e);\r
-                }\r
-            });\r
-        averageDistanceTreeMenuItem.setLabel(\r
-            "Average Distance Using % Identity");\r
-        averageDistanceTreeMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    averageDistanceTreeMenuItem_actionPerformed(e);\r
-                }\r
-            });\r
-        neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");\r
-        neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    neighbourTreeMenuItem_actionPerformed(e);\r
-                }\r
-            });\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.setText("Status bar");\r
-        outputTextboxMenu.setLabel("Output to Textbox");\r
-        clustalColour.setLabel("Clustalx");\r
-\r
-        clustalColour.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    clustalColour_actionPerformed(e);\r
-                }\r
-            });\r
-        zappoColour.setLabel("Zappo");\r
-        zappoColour.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    zappoColour_actionPerformed(e);\r
-                }\r
-            });\r
-        taylorColour.setLabel("Taylor");\r
-        taylorColour.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    taylorColour_actionPerformed(e);\r
-                }\r
-            });\r
-        hydrophobicityColour.setLabel("Hydrophobicity");\r
-        hydrophobicityColour.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    hydrophobicityColour_actionPerformed(e);\r
-                }\r
-            });\r
-        helixColour.setLabel("Helix Propensity");\r
-        helixColour.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    helixColour_actionPerformed(e);\r
-                }\r
-            });\r
-        strandColour.setLabel("Strand Propensity");\r
-        strandColour.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    strandColour_actionPerformed(e);\r
-                }\r
-            });\r
-        turnColour.setLabel("Turn Propensity");\r
-        turnColour.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    turnColour_actionPerformed(e);\r
-                }\r
-            });\r
-        buriedColour.setLabel("Buried Index");\r
-        buriedColour.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    buriedColour_actionPerformed(e);\r
-                }\r
-            });\r
-        userDefinedColour.setLabel("User Defined...");\r
-        userDefinedColour.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    userDefinedColour_actionPerformed(e);\r
-                }\r
-            });\r
-        PIDColour.setLabel("Percentage Identity");\r
-        PIDColour.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    PIDColour_actionPerformed(e);\r
-                }\r
-            });\r
-        BLOSUM62Colour.setLabel("BLOSUM62 Score");\r
-        BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    BLOSUM62Colour_actionPerformed(e);\r
-                }\r
-            });\r
-        avDistanceTreeBlosumMenuItem.setLabel(\r
-            "Average Distance Using BLOSUM62");\r
-        avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    avTreeBlosumMenuItem_actionPerformed(e);\r
-                }\r
-            });\r
-        njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");\r
-        njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    njTreeBlosumMenuItem_actionPerformed(e);\r
-                }\r
-            });\r
-        annotationPanelMenuItem.setActionCommand("");\r
-        annotationPanelMenuItem.setState(true);\r
-        annotationPanelMenuItem.setLabel("Show Annotations");\r
-        annotationPanelMenuItem.addItemListener(new java.awt.event.ItemListener() {\r
-                public void itemStateChanged(ItemEvent e) {\r
-                    annotationPanelMenuItem_actionPerformed(null);\r
-                }\r
-            });\r
-        colourTextMenuItem.setLabel("Colour Text");\r
-        colourTextMenuItem.addItemListener(new java.awt.event.ItemListener() {\r
-                public void itemStateChanged(ItemEvent e) {\r
-                    colourTextMenuItem_actionPerformed(null);\r
-                }\r
-            });\r
-        overviewMenuItem.setLabel("Overview Window");\r
-        overviewMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    overviewMenuItem_actionPerformed(e);\r
-                }\r
-            });\r
-        undoMenuItem.setEnabled(false);\r
-        undoMenuItem.setLabel("Undo");\r
-        undoMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    undoMenuItem_actionPerformed(e);\r
-                }\r
-            });\r
-        redoMenuItem.setEnabled(false);\r
-        redoMenuItem.setLabel("Redo");\r
-        redoMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    redoMenuItem_actionPerformed(e);\r
-                }\r
-            });\r
-        conservationMenuItem.setLabel("by Conservation");\r
-        conservationMenuItem.addItemListener(new java.awt.event.ItemListener() {\r
-                public void itemStateChanged(ItemEvent e) {\r
-                    conservationMenuItem_actionPerformed(null);\r
-                }\r
-            });\r
-        noColourmenuItem.setLabel("None");\r
-        noColourmenuItem.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    noColourmenuItem_actionPerformed(e);\r
-                }\r
-            });\r
-        wrapMenuItem.setLabel("Wrap");\r
-        wrapMenuItem.addItemListener(new java.awt.event.ItemListener() {\r
-                public void itemStateChanged(ItemEvent e) {\r
-                    wrapMenuItem_actionPerformed(null);\r
-                }\r
-            });\r
-        renderGapsMenuItem.setLabel("Show Gaps");\r
-        renderGapsMenuItem.setState(true);\r
-        renderGapsMenuItem.addItemListener(new java.awt.event.ItemListener() {\r
-                public void itemStateChanged(ItemEvent e) {\r
-                    renderGapsMenuItem_actionPerformed(null);\r
-                }\r
-            });\r
-        findMenuItem.setLabel("Find...");\r
-        findMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    findMenuItem_actionPerformed(e);\r
-                }\r
-            });\r
-        searchMenu.setLabel("Search");\r
-\r
-        abovePIDThreshold.setLabel("Above Identity Threshold");\r
-        abovePIDThreshold.addItemListener(new java.awt.event.ItemListener() {\r
-                public void itemStateChanged(ItemEvent e) {\r
-                    abovePIDThreshold_actionPerformed(null);\r
-                }\r
-            });\r
-        nucleotideColour.setLabel("Nucleotide");\r
-        nucleotideColour.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    nucleotideColour_actionPerformed(e);\r
-                }\r
-            });\r
-        deleteGroups.setLabel("Undefine Groups");\r
-        deleteGroups.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    deleteGroups_actionPerformed(e);\r
-                }\r
-            });\r
-        copy.setLabel("Copy");\r
-        copy.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    copy_actionPerformed(e);\r
-                }\r
-            });\r
-        cut.setLabel("Cut");\r
-        cut.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    cut_actionPerformed(e);\r
-                }\r
-            });\r
-        delete.setLabel("Delete");\r
-        delete.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    delete_actionPerformed(e);\r
-                }\r
-            });\r
-        Menu1.setLabel("Paste");\r
-        pasteNew.setLabel("To New Alignment");\r
-        pasteNew.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    pasteNew_actionPerformed(e);\r
-                }\r
-            });\r
-        pasteThis.setLabel("Add To This Alignment");\r
-        pasteThis.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    pasteThis_actionPerformed(e);\r
-                }\r
-            });\r
-        applyToAllGroups.setLabel("Apply Colour To All Groups");\r
-        applyToAllGroups.setState(true);\r
-        applyToAllGroups.addItemListener(new java.awt.event.ItemListener() {\r
-                public void itemStateChanged(ItemEvent e) {\r
-                    applyToAllGroups_actionPerformed(null);\r
-                }\r
-            });\r
-        font.setLabel("Font...");\r
-        font.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    font_actionPerformed(e);\r
-                }\r
-            });\r
-        fullSeqId.setLabel("Show Full Sequence ID");\r
-        fullSeqId.setState(true);\r
-        fullSeqId.addItemListener(new java.awt.event.ItemListener() {\r
-                public void itemStateChanged(ItemEvent e) {\r
-                    fullSeqId_actionPerformed(null);\r
-                }\r
-            });\r
-        scaleAbove.setLabel("Scale Above");\r
-        scaleAbove.setState(true);\r
-        scaleAbove.addItemListener(new java.awt.event.ItemListener() {\r
-                public void itemStateChanged(ItemEvent e) {\r
-                    scaleAbove_actionPerformed(null);\r
-                }\r
-            });\r
-        scaleLeft.setEnabled(false);\r
-        scaleLeft.setState(true);\r
-        scaleLeft.setLabel("Scale Left");\r
-        scaleLeft.addItemListener(new java.awt.event.ItemListener() {\r
-                public void itemStateChanged(ItemEvent e) {\r
-                    scaleLeft_actionPerformed(null);\r
-                }\r
-            });\r
-        scaleRight.setEnabled(false);\r
-        scaleRight.setState(true);\r
-        scaleRight.setLabel("Scale Right");\r
-        scaleRight.addItemListener(new java.awt.event.ItemListener() {\r
-                public void itemStateChanged(ItemEvent e) {\r
-                    scaleRight_actionPerformed(null);\r
-                }\r
-            });\r
-        modifyPID.setLabel("Modify Identity Threshold...");\r
-        modifyPID.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    modifyPID_actionPerformed(e);\r
-                }\r
-            });\r
-        modifyConservation.setLabel("Modify Conservation Threshold...");\r
-        modifyConservation.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    modifyConservation_actionPerformed(e);\r
-                }\r
-            });\r
-        sortByTreeMenu.setLabel("By Tree Order");\r
-        sort.setLabel("Sort");\r
-        calculate.setLabel("Calculate Tree");\r
-        inputText.setLabel("Input from textbox");\r
-        inputText.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    inputText_actionPerformed(e);\r
-                }\r
-            });\r
-\r
-        helpMenu.setLabel("Help");\r
-        documentation.setLabel("Documentation");\r
-        documentation.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    documentation_actionPerformed(e);\r
-                }\r
-            });\r
-\r
-        about.setLabel("About...");\r
-        about.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    about_actionPerformed(e);\r
-                }\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(helpMenu);\r
-        fileMenu.add(inputText);\r
-        fileMenu.add(outputTextboxMenu);\r
-        fileMenu.addSeparator();\r
-        fileMenu.add(closeMenuItem);\r
-        editMenu.add(undoMenuItem);\r
-        editMenu.add(redoMenuItem);\r
-        editMenu.add(cut);\r
-        editMenu.add(copy);\r
-        editMenu.add(Menu1);\r
-        editMenu.add(delete);\r
-        editMenu.addSeparator();\r
-        editMenu.add(selectAllSequenceMenuItem);\r
-        editMenu.add(deselectAllSequenceMenuItem);\r
-        editMenu.add(invertSequenceMenuItem);\r
-        editMenu.add(deleteGroups);\r
-        editMenu.addSeparator();\r
-        editMenu.add(remove2LeftMenuItem);\r
-        editMenu.add(remove2RightMenuItem);\r
-        editMenu.add(removeGappedColumnMenuItem);\r
-        editMenu.add(removeAllGapsMenuItem);\r
-        editMenu.add(removeRedundancyMenuItem);\r
-        searchMenu.add(findMenuItem);\r
-        viewMenu.add(font);\r
-        viewMenu.addSeparator();\r
-        viewMenu.add(wrapMenuItem);\r
-        viewMenu.add(scaleAbove);\r
-        viewMenu.add(scaleLeft);\r
-        viewMenu.add(scaleRight);\r
-        viewMenu.addSeparator();\r
-        viewMenu.add(fullSeqId);\r
-        viewMenu.add(viewBoxesMenuItem);\r
-        viewMenu.add(viewTextMenuItem);\r
-        viewMenu.add(colourTextMenuItem);\r
-        viewMenu.add(renderGapsMenuItem);\r
-        viewMenu.add(annotationPanelMenuItem);\r
-        viewMenu.addSeparator();\r
-        viewMenu.add(overviewMenuItem);\r
-        colourMenu.add(applyToAllGroups);\r
-        colourMenu.addSeparator();\r
-        colourMenu.add(noColourmenuItem);\r
-        colourMenu.add(clustalColour);\r
-        colourMenu.add(BLOSUM62Colour);\r
-        colourMenu.add(PIDColour);\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.addSeparator();\r
-        colourMenu.add(conservationMenuItem);\r
-        colourMenu.add(modifyConservation);\r
-        colourMenu.add(abovePIDThreshold);\r
-        colourMenu.add(modifyPID);\r
-        calculateMenu.add(sort);\r
-        calculateMenu.add(calculate);\r
-        calculateMenu.addSeparator();\r
-        calculateMenu.add(pairwiseAlignmentMenuItem);\r
-        calculateMenu.add(PCAMenuItem);\r
-        this.add(statusBar, BorderLayout.SOUTH);\r
-        Menu1.add(pasteNew);\r
-        Menu1.add(pasteThis);\r
-        sort.add(sortIDMenuItem);\r
-        sort.add(sortByTreeMenu);\r
-        sort.add(sortGroupMenuItem);\r
-        sort.add(sortPairwiseMenuItem);\r
-        calculate.add(averageDistanceTreeMenuItem);\r
-        calculate.add(neighbourTreeMenuItem);\r
-        calculate.add(avDistanceTreeBlosumMenuItem);\r
-        calculate.add(njTreeBlosumMenuItem);\r
-        helpMenu.add(documentation);\r
-        helpMenu.add(about);\r
-    }\r
-\r
-    protected void saveAs_actionPerformed(ActionEvent e) {\r
-    }\r
-\r
-    protected void outputText_actionPerformed(ActionEvent e) {\r
-    }\r
-\r
-    protected void htmlMenuItem_actionPerformed(ActionEvent e) {\r
-    }\r
-\r
-    protected void closeMenuItem_actionPerformed(ActionEvent e) {\r
-    }\r
-\r
-    protected void redoMenuItem_actionPerformed(ActionEvent e) {\r
-    }\r
-\r
-    protected void undoMenuItem_actionPerformed(ActionEvent e) {\r
-    }\r
-\r
-    protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e) {\r
-    }\r
-\r
-    protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e) {\r
-    }\r
-\r
-    protected void invertSequenceMenuItem_actionPerformed(ActionEvent e) {\r
-    }\r
-\r
-    protected void remove2LeftMenuItem_actionPerformed(ActionEvent e) {\r
-    }\r
-\r
-    protected void remove2RightMenuItem_actionPerformed(ActionEvent e) {\r
-    }\r
-\r
-    protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e) {\r
-    }\r
-\r
-    protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e) {\r
-    }\r
-\r
-    protected void wrapMenuItem_actionPerformed(ActionEvent e) {\r
-    }\r
-\r
-    protected void viewBoxesMenuItem_actionPerformed(ActionEvent e) {\r
-    }\r
-\r
-    protected void viewTextMenuItem_actionPerformed(ActionEvent e) {\r
-    }\r
-\r
-    protected void colourTextMenuItem_actionPerformed(ActionEvent e) {\r
-    }\r
-\r
-    protected void annotationPanelMenuItem_actionPerformed(ActionEvent e) {\r
-    }\r
-\r
-    protected void overviewMenuItem_actionPerformed(ActionEvent e) {\r
-    }\r
-\r
-    protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e) {\r
-    }\r
-\r
-    protected void sortIDMenuItem_actionPerformed(ActionEvent e) {\r
-    }\r
-\r
-    protected void sortGroupMenuItem_actionPerformed(ActionEvent e) {\r
-    }\r
-\r
-    protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e) {\r
-    }\r
-\r
-    protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e) {\r
-    }\r
-\r
-    protected void PCAMenuItem_actionPerformed(ActionEvent e) {\r
-    }\r
-\r
-    protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e) {\r
-    }\r
-\r
-    protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e) {\r
-    }\r
-\r
-    protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e) {\r
-    }\r
-\r
-    protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e) {\r
-    }\r
-\r
-    protected void clustalAlignMenuItem_actionPerformed(ActionEvent e) {\r
-    }\r
-\r
-    protected void clustalColour_actionPerformed(ActionEvent e) {\r
-    }\r
-\r
-    protected void zappoColour_actionPerformed(ActionEvent e) {\r
-    }\r
-\r
-    protected void taylorColour_actionPerformed(ActionEvent e) {\r
-    }\r
-\r
-    protected void hydrophobicityColour_actionPerformed(ActionEvent e) {\r
-    }\r
-\r
-    protected void helixColour_actionPerformed(ActionEvent e) {\r
-    }\r
-\r
-    protected void strandColour_actionPerformed(ActionEvent e) {\r
-    }\r
-\r
-    protected void turnColour_actionPerformed(ActionEvent e) {\r
-    }\r
-\r
-    protected void buriedColour_actionPerformed(ActionEvent e) {\r
-    }\r
-\r
-    protected void userDefinedColour_actionPerformed(ActionEvent e) {\r
-    }\r
-\r
-    protected void PIDColour_actionPerformed(ActionEvent e) {\r
-    }\r
-\r
-    protected void BLOSUM62Colour_actionPerformed(ActionEvent e) {\r
-    }\r
-\r
-    protected void noColourmenuItem_actionPerformed(ActionEvent e) {\r
-    }\r
-\r
-    protected void conservationMenuItem_actionPerformed(ActionEvent e) {\r
-    }\r
-\r
-    protected void printMenuItem_actionPerformed(ActionEvent e) {\r
-    }\r
-\r
-    protected void renderGapsMenuItem_actionPerformed(ActionEvent e) {\r
-    }\r
-\r
-    protected void findMenuItem_actionPerformed(ActionEvent e) {\r
-    }\r
-\r
-    protected void abovePIDThreshold_actionPerformed(ActionEvent e) {\r
-    }\r
-\r
-    public void sequenceFeatures_actionPerformed(ActionEvent actionEvent) {\r
-    }\r
-\r
-    protected void nucleotideColour_actionPerformed(ActionEvent e) {\r
-    }\r
-\r
-    protected void deleteGroups_actionPerformed(ActionEvent e) {\r
-    }\r
-\r
-    protected void copy_actionPerformed(ActionEvent e) {\r
-    }\r
-\r
-    protected void cut_actionPerformed(ActionEvent e) {\r
-    }\r
-\r
-    protected void delete_actionPerformed(ActionEvent e) {\r
-    }\r
-\r
-    protected void pasteNew_actionPerformed(ActionEvent e) {\r
-    }\r
-\r
-    protected void pasteThis_actionPerformed(ActionEvent e) {\r
-    }\r
-\r
-    protected void applyToAllGroups_actionPerformed(ActionEvent e) {\r
-    }\r
-\r
-    protected void createPNG_actionPerformed(ActionEvent e) {\r
-    }\r
-\r
-    protected void font_actionPerformed(ActionEvent e) {\r
-    }\r
-\r
-    protected void fullSeqId_actionPerformed(ActionEvent e) {\r
-    }\r
-\r
-    protected void epsFile_actionPerformed(ActionEvent e) {\r
-    }\r
-\r
-    protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) {\r
-    }\r
-\r
-    protected void jpred_actionPerformed(ActionEvent e) {\r
-    }\r
-\r
-    protected void scaleAbove_actionPerformed(ActionEvent e) {\r
-    }\r
-\r
-    protected void scaleLeft_actionPerformed(ActionEvent e) {\r
-    }\r
-\r
-    protected void scaleRight_actionPerformed(ActionEvent e) {\r
-    }\r
-\r
-    protected void modifyPID_actionPerformed(ActionEvent e) {\r
-    }\r
-\r
-    protected void modifyConservation_actionPerformed(ActionEvent e) {\r
-    }\r
-\r
-    protected void preferences_actionPerformed(ActionEvent e) {\r
-    }\r
-\r
-    protected void msaAlignMenuItem_actionPerformed(ActionEvent e) {\r
-    }\r
-\r
-    protected void inputText_actionPerformed(ActionEvent e) {\r
-    }\r
-\r
-    protected void documentation_actionPerformed(ActionEvent e) {\r
-    }\r
-\r
-    protected void about_actionPerformed(ActionEvent e) {\r
-    }\r
-}\r