After merge
authoramwaterhouse <Andrew Waterhouse>
Tue, 6 Dec 2005 11:42:19 +0000 (11:42 +0000)
committeramwaterhouse <Andrew Waterhouse>
Tue, 6 Dec 2005 11:42:19 +0000 (11:42 +0000)
src/jalview/jbappletgui/GAlignFrame.java [deleted file]
src/jalview/jbappletgui/GAlignmentPanel.java [deleted file]
src/jalview/jbappletgui/GCutAndPasteTransfer.java [deleted file]
src/jalview/jbappletgui/GFinder.java [deleted file]
src/jalview/jbappletgui/GFontChooser.java [deleted file]
src/jalview/jbappletgui/GPCAPanel.java [deleted file]
src/jalview/jbappletgui/GPairwiseAlignPanel.java [deleted file]
src/jalview/jbappletgui/GSliderPanel.java [deleted file]
src/jalview/jbappletgui/GTreePanel.java [deleted file]
src/jalview/jbappletgui/GUserDefinedColours.java [deleted file]

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
diff --git a/src/jalview/jbappletgui/GAlignmentPanel.java b/src/jalview/jbappletgui/GAlignmentPanel.java
deleted file mode 100755 (executable)
index 683c9c1..0000000
+++ /dev/null
@@ -1,100 +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
-\r
-\r
-public class GAlignmentPanel extends Panel {\r
-    protected Panel sequenceHolderPanel = new Panel();\r
-    protected Scrollbar vscroll = new Scrollbar();\r
-    protected Scrollbar hscroll = new Scrollbar();\r
-    protected Panel seqPanelHolder = new Panel();\r
-    BorderLayout borderLayout1 = new BorderLayout();\r
-    BorderLayout borderLayout3 = new BorderLayout();\r
-    protected Panel scalePanelHolder = new Panel();\r
-    protected Panel idPanelHolder = new Panel();\r
-    BorderLayout borderLayout5 = new BorderLayout();\r
-    protected Panel idSpaceFillerPanel1 = new Panel();\r
-    public Panel annotationSpaceFillerHolder = new Panel();\r
-    BorderLayout borderLayout6 = new BorderLayout();\r
-    BorderLayout borderLayout7 = new BorderLayout();\r
-    Panel hscrollHolder = new Panel();\r
-    BorderLayout borderLayout10 = new BorderLayout();\r
-    protected Panel hscrollFillerPanel = new Panel();\r
-    BorderLayout borderLayout11 = new BorderLayout();\r
-    public Panel annotationScroller = new Panel();\r
-    BorderLayout borderLayout4 = new BorderLayout();\r
-    BorderLayout borderLayout2 = new BorderLayout();\r
-\r
-    public GAlignmentPanel() {\r
-        try {\r
-            jbInit();\r
-        } catch (Exception e) {\r
-            e.printStackTrace();\r
-        }\r
-    }\r
-\r
-    private void jbInit() throws Exception {\r
-        //  idPanelHolder.setPreferredSize(new Dimension(70, 10));\r
-        this.setLayout(borderLayout7);\r
-\r
-        //   sequenceHolderPanel.setPreferredSize(new Dimension(150, 150));\r
-        sequenceHolderPanel.setLayout(borderLayout3);\r
-        seqPanelHolder.setLayout(borderLayout1);\r
-        scalePanelHolder.setBackground(Color.white);\r
-\r
-        // scalePanelHolder.setPreferredSize(new Dimension(10, 30));\r
-        scalePanelHolder.setLayout(borderLayout6);\r
-        idPanelHolder.setLayout(borderLayout5);\r
-        idSpaceFillerPanel1.setBackground(Color.white);\r
-\r
-        //  idSpaceFillerPanel1.setPreferredSize(new Dimension(10, 30));\r
-        idSpaceFillerPanel1.setLayout(borderLayout11);\r
-        annotationSpaceFillerHolder.setBackground(Color.white);\r
-\r
-        //  annotationSpaceFillerHolder.setPreferredSize(new Dimension(10, 80));\r
-        annotationSpaceFillerHolder.setLayout(borderLayout4);\r
-        hscroll.setOrientation(Scrollbar.HORIZONTAL);\r
-        hscrollHolder.setLayout(borderLayout10);\r
-        hscrollFillerPanel.setBackground(Color.white);\r
-\r
-        //  hscrollFillerPanel.setPreferredSize(new Dimension(70, 10));\r
-        hscrollHolder.setBackground(Color.white);\r
-\r
-        //    annotationScroller.setPreferredSize(new Dimension(10, 80));\r
-        //  this.setPreferredSize(new Dimension(220, 166));\r
-        seqPanelHolder.setBackground(Color.white);\r
-        idPanelHolder.setBackground(Color.white);\r
-        annotationScroller.setLayout(borderLayout2);\r
-        sequenceHolderPanel.add(scalePanelHolder, BorderLayout.NORTH);\r
-        sequenceHolderPanel.add(seqPanelHolder, BorderLayout.CENTER);\r
-        seqPanelHolder.add(vscroll, BorderLayout.EAST);\r
-        sequenceHolderPanel.add(annotationScroller, BorderLayout.SOUTH);\r
-\r
-        //  Panel3.add(secondaryPanelHolder,  BorderLayout.SOUTH);\r
-        this.add(idPanelHolder, BorderLayout.WEST);\r
-        idPanelHolder.add(idSpaceFillerPanel1, BorderLayout.NORTH);\r
-        idPanelHolder.add(annotationSpaceFillerHolder, BorderLayout.SOUTH);\r
-        this.add(hscrollHolder, BorderLayout.SOUTH);\r
-        hscrollHolder.add(hscroll, BorderLayout.CENTER);\r
-        hscrollHolder.add(hscrollFillerPanel, BorderLayout.WEST);\r
-        this.add(sequenceHolderPanel, BorderLayout.CENTER);\r
-    }\r
-}\r
diff --git a/src/jalview/jbappletgui/GCutAndPasteTransfer.java b/src/jalview/jbappletgui/GCutAndPasteTransfer.java
deleted file mode 100755 (executable)
index 907ec0a..0000000
+++ /dev/null
@@ -1,78 +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 GCutAndPasteTransfer extends Panel {\r
-    protected TextArea textarea = new TextArea();\r
-    Button ok = new Button();\r
-    Button cancel = new Button();\r
-    protected Panel buttonPanel = new Panel();\r
-    BorderLayout borderLayout1 = new BorderLayout();\r
-\r
-    public GCutAndPasteTransfer() {\r
-        try {\r
-            jbInit();\r
-        } catch (Exception e) {\r
-            e.printStackTrace();\r
-        }\r
-    }\r
-\r
-    private void jbInit() throws Exception {\r
-        textarea.setFont(new java.awt.Font("Monospaced", Font.PLAIN, 10));\r
-        textarea.setText("Paste your alignment file here");\r
-        textarea.addMouseListener(new java.awt.event.MouseAdapter() {\r
-                public void mousePressed(MouseEvent e) {\r
-                    textarea_mousePressed(e);\r
-                }\r
-            });\r
-        this.setLayout(borderLayout1);\r
-        ok.setLabel("OK");\r
-        ok.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    ok_actionPerformed(e);\r
-                }\r
-            });\r
-        cancel.setLabel("Cancel");\r
-        cancel.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    cancel_actionPerformed(e);\r
-                }\r
-            });\r
-        this.add(buttonPanel, BorderLayout.SOUTH);\r
-        buttonPanel.add(ok, null);\r
-        buttonPanel.add(cancel, null);\r
-        this.add(textarea, java.awt.BorderLayout.CENTER);\r
-    }\r
-\r
-    void textarea_mousePressed(MouseEvent e) {\r
-        if (textarea.getText().equals("Paste your alignment file here")) {\r
-            textarea.setText("");\r
-        }\r
-    }\r
-\r
-    protected void ok_actionPerformed(ActionEvent e) {\r
-    }\r
-\r
-    protected void cancel_actionPerformed(ActionEvent e) {\r
-    }\r
-}\r
diff --git a/src/jalview/jbappletgui/GFinder.java b/src/jalview/jbappletgui/GFinder.java
deleted file mode 100755 (executable)
index 434c8ea..0000000
+++ /dev/null
@@ -1,111 +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 GFinder extends Panel {\r
-    Label jLabel1 = new Label();\r
-    protected TextField textfield = new TextField();\r
-    protected Button findAll = new Button();\r
-    protected Button findNext = new Button();\r
-    Panel jPanel1 = new Panel();\r
-    GridLayout gridLayout1 = new GridLayout();\r
-    protected Button createNewGroup = new Button();\r
-\r
-    public GFinder() {\r
-        try {\r
-            jbInit();\r
-        } catch (Exception e) {\r
-            e.printStackTrace();\r
-        }\r
-    }\r
-\r
-    private void jbInit() throws Exception {\r
-        jLabel1.setFont(new java.awt.Font("Verdana", 0, 12));\r
-        jLabel1.setText("Find");\r
-        jLabel1.setBounds(new Rectangle(3, 30, 34, 15));\r
-        this.setLayout(null);\r
-        textfield.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));\r
-        textfield.setText("");\r
-        textfield.setBounds(new Rectangle(40, 27, 133, 21));\r
-        textfield.addKeyListener(new java.awt.event.KeyAdapter() {\r
-                public void keyTyped(KeyEvent e) {\r
-                    textfield_keyTyped(e);\r
-                }\r
-            });\r
-        textfield.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    textfield_actionPerformed(e);\r
-                }\r
-            });\r
-        findAll.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));\r
-        findAll.setLabel("Find all");\r
-        findAll.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    findAll_actionPerformed(e);\r
-                }\r
-            });\r
-        findNext.setEnabled(false);\r
-        findNext.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));\r
-        findNext.setLabel("Find Next");\r
-        findNext.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    findNext_actionPerformed(e);\r
-                }\r
-            });\r
-        jPanel1.setBounds(new Rectangle(180, 5, 141, 64));\r
-        jPanel1.setLayout(gridLayout1);\r
-        gridLayout1.setHgap(0);\r
-        gridLayout1.setRows(3);\r
-        gridLayout1.setVgap(2);\r
-        createNewGroup.setEnabled(false);\r
-        createNewGroup.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));\r
-        createNewGroup.setLabel("Create new group");\r
-        createNewGroup.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    createNewGroup_actionPerformed(e);\r
-                }\r
-            });\r
-        jPanel1.add(findNext, null);\r
-        jPanel1.add(findAll, null);\r
-        jPanel1.add(createNewGroup, null);\r
-        this.add(textfield, null);\r
-        this.add(jLabel1, null);\r
-        this.add(jPanel1, null);\r
-    }\r
-\r
-    protected void findNext_actionPerformed(ActionEvent e) {\r
-    }\r
-\r
-    protected void findAll_actionPerformed(ActionEvent e) {\r
-    }\r
-\r
-    protected void textfield_actionPerformed(ActionEvent e) {\r
-    }\r
-\r
-    void textfield_keyTyped(KeyEvent e) {\r
-        findNext.setEnabled(true);\r
-    }\r
-\r
-    public void createNewGroup_actionPerformed(ActionEvent e) {\r
-    }\r
-}\r
diff --git a/src/jalview/jbappletgui/GFontChooser.java b/src/jalview/jbappletgui/GFontChooser.java
deleted file mode 100755 (executable)
index 794dbbb..0000000
+++ /dev/null
@@ -1,133 +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 GFontChooser extends Panel {\r
-    Label label1 = new Label();\r
-    protected Choice fontSize = new Choice();\r
-    protected Choice fontStyle = new Choice();\r
-    Label label2 = new Label();\r
-    Label label3 = new Label();\r
-    protected Choice fontName = new Choice();\r
-    Button ok = new Button();\r
-    Button cancel = new Button();\r
-    Panel panel1 = new Panel();\r
-    Panel panel2 = new Panel();\r
-    Panel panel3 = new Panel();\r
-    BorderLayout borderLayout1 = new BorderLayout();\r
-    BorderLayout borderLayout2 = new BorderLayout();\r
-    BorderLayout borderLayout3 = new BorderLayout();\r
-    Panel panel4 = new Panel();\r
-    Panel panel5 = new Panel();\r
-    BorderLayout borderLayout4 = new BorderLayout();\r
-\r
-    public GFontChooser() {\r
-        try {\r
-            jbInit();\r
-        } catch (Exception e) {\r
-            e.printStackTrace();\r
-        }\r
-    }\r
-\r
-    private void jbInit() throws Exception {\r
-        label1.setFont(new java.awt.Font("Verdana", 0, 11));\r
-        label1.setAlignment(Label.RIGHT);\r
-        label1.setText("Font: ");\r
-        this.setLayout(borderLayout4);\r
-        fontSize.setFont(new java.awt.Font("Verdana", 0, 11));\r
-        fontSize.addItemListener(new java.awt.event.ItemListener() {\r
-                public void itemStateChanged(ItemEvent e) {\r
-                    fontSize_actionPerformed();\r
-                }\r
-            });\r
-        fontStyle.setFont(new java.awt.Font("Verdana", 0, 11));\r
-        fontStyle.addItemListener(new java.awt.event.ItemListener() {\r
-                public void itemStateChanged(ItemEvent e) {\r
-                    fontStyle_actionPerformed();\r
-                }\r
-            });\r
-        label2.setAlignment(Label.RIGHT);\r
-        label2.setFont(new java.awt.Font("Verdana", 0, 11));\r
-        label2.setText("Size: ");\r
-        label3.setAlignment(Label.RIGHT);\r
-        label3.setFont(new java.awt.Font("Verdana", 0, 11));\r
-        label3.setText("Style: ");\r
-        fontName.setFont(new java.awt.Font("Verdana", 0, 11));\r
-        fontName.addItemListener(new java.awt.event.ItemListener() {\r
-                public void itemStateChanged(ItemEvent e) {\r
-                    fontName_actionPerformed();\r
-                }\r
-            });\r
-        ok.setFont(new java.awt.Font("Verdana", 0, 11));\r
-        ok.setLabel("OK");\r
-        ok.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    ok_actionPerformed();\r
-                }\r
-            });\r
-        cancel.setFont(new java.awt.Font("Verdana", 0, 11));\r
-        cancel.setLabel("Cancel");\r
-        cancel.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    cancel_actionPerformed();\r
-                }\r
-            });\r
-        this.setBackground(Color.white);\r
-        panel1.setLayout(borderLayout1);\r
-        panel2.setLayout(borderLayout3);\r
-        panel3.setLayout(borderLayout2);\r
-        panel5.setBackground(Color.white);\r
-        panel4.setBackground(Color.white);\r
-        panel1.setBackground(Color.white);\r
-        panel2.setBackground(Color.white);\r
-        panel3.setBackground(Color.white);\r
-        panel1.add(label1, BorderLayout.WEST);\r
-        panel1.add(fontName, BorderLayout.CENTER);\r
-        panel5.add(panel1, null);\r
-        panel5.add(panel3, null);\r
-        panel5.add(panel2, null);\r
-        panel2.add(label3, BorderLayout.WEST);\r
-        panel2.add(fontStyle, BorderLayout.CENTER);\r
-        panel3.add(label2, BorderLayout.WEST);\r
-        panel3.add(fontSize, BorderLayout.CENTER);\r
-        this.add(panel4, BorderLayout.SOUTH);\r
-        panel4.add(ok, null);\r
-        panel4.add(cancel, null);\r
-        this.add(panel5, BorderLayout.CENTER);\r
-    }\r
-\r
-    protected void ok_actionPerformed() {\r
-    }\r
-\r
-    protected void cancel_actionPerformed() {\r
-    }\r
-\r
-    protected void fontName_actionPerformed() {\r
-    }\r
-\r
-    protected void fontSize_actionPerformed() {\r
-    }\r
-\r
-    protected void fontStyle_actionPerformed() {\r
-    }\r
-}\r
diff --git a/src/jalview/jbappletgui/GPCAPanel.java b/src/jalview/jbappletgui/GPCAPanel.java
deleted file mode 100755 (executable)
index d67d1c3..0000000
+++ /dev/null
@@ -1,133 +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 GPCAPanel extends Frame {\r
-    Panel jPanel2 = new Panel();\r
-    Label jLabel1 = new Label();\r
-    Label jLabel2 = new Label();\r
-    Label jLabel3 = new Label();\r
-    protected Choice xCombobox = new Choice();\r
-    protected Choice yCombobox = new Choice();\r
-    protected Choice zCombobox = new Choice();\r
-    FlowLayout flowLayout1 = new FlowLayout();\r
-    BorderLayout borderLayout1 = new BorderLayout();\r
-  MenuBar menuBar1 = new MenuBar();\r
-  Menu menu1 = new Menu();\r
-  Menu menu2 = new Menu();\r
-  protected CheckboxMenuItem labels = new CheckboxMenuItem();\r
-  MenuItem values = new MenuItem();\r
-\r
-  public GPCAPanel() {\r
-        try {\r
-            jbInit();\r
-        } catch (Exception e) {\r
-            e.printStackTrace();\r
-        }\r
-\r
-        for (int i = 1; i < 8; i++) {\r
-            xCombobox.addItem("dim " + i);\r
-            yCombobox.addItem("dim " + i);\r
-            zCombobox.addItem("dim " + i);\r
-        }\r
-    }\r
-\r
-    private void jbInit() throws Exception {\r
-        this.setLayout(borderLayout1);\r
-        jPanel2.setLayout(flowLayout1);\r
-        jLabel1.setFont(new java.awt.Font("Verdana", 0, 12));\r
-        jLabel1.setText("x=");\r
-        jLabel2.setFont(new java.awt.Font("Verdana", 0, 12));\r
-        jLabel2.setText("y=");\r
-        jLabel3.setFont(new java.awt.Font("Verdana", 0, 12));\r
-        jLabel3.setText("z=");\r
-        jPanel2.setBackground(Color.white);\r
-        zCombobox.setFont(new java.awt.Font("Verdana", 0, 12));\r
-        zCombobox.addItemListener(new java.awt.event.ItemListener() {\r
-                public void itemStateChanged(ItemEvent e) {\r
-                    zCombobox_actionPerformed(null);\r
-                }\r
-            });\r
-        yCombobox.setFont(new java.awt.Font("Verdana", 0, 12));\r
-        yCombobox.addItemListener(new java.awt.event.ItemListener() {\r
-                public void itemStateChanged(ItemEvent e) {\r
-                    yCombobox_actionPerformed(null);\r
-                }\r
-            });\r
-        xCombobox.setFont(new java.awt.Font("Verdana", 0, 12));\r
-        xCombobox.addItemListener(new java.awt.event.ItemListener() {\r
-                public void itemStateChanged(ItemEvent e) {\r
-                    xCombobox_actionPerformed(null);\r
-                }\r
-            });\r
-    this.setMenuBar(menuBar1);\r
-    menu1.setLabel("File");\r
-    menu2.setLabel("View");\r
-    labels.setLabel("Labels");\r
-    labels.addItemListener(new ItemListener()\r
-    {\r
-      public void itemStateChanged(ItemEvent itemEvent)\r
-      {\r
-        labels_itemStateChanged(itemEvent);\r
-      }\r
-    });\r
-    values.setLabel("Output Values...");\r
-    values.addActionListener(new ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent actionEvent)\r
-      {\r
-        values_actionPerformed(actionEvent);\r
-      }\r
-    });\r
-    this.add(jPanel2, BorderLayout.SOUTH);\r
-        jPanel2.add(jLabel1, null);\r
-        jPanel2.add(xCombobox, null);\r
-        jPanel2.add(jLabel2, null);\r
-        jPanel2.add(yCombobox, null);\r
-        jPanel2.add(jLabel3, null);\r
-        jPanel2.add(zCombobox, null);\r
-    menuBar1.add(menu1);\r
-    menuBar1.add(menu2);\r
-    menu2.add(labels);\r
-    menu1.add(values);\r
-  }\r
-\r
-    protected void xCombobox_actionPerformed(ActionEvent e) {\r
-    }\r
-\r
-    protected void yCombobox_actionPerformed(ActionEvent e) {\r
-    }\r
-\r
-    protected void zCombobox_actionPerformed(ActionEvent e) {\r
-    }\r
-\r
-  public void values_actionPerformed(ActionEvent actionEvent)\r
-  {\r
-\r
-  }\r
-\r
-  public void labels_itemStateChanged(ItemEvent itemEvent)\r
-  {\r
-\r
-  }\r
-}\r
diff --git a/src/jalview/jbappletgui/GPairwiseAlignPanel.java b/src/jalview/jbappletgui/GPairwiseAlignPanel.java
deleted file mode 100755 (executable)
index 10bd01e..0000000
+++ /dev/null
@@ -1,59 +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 GPairwiseAlignPanel extends Panel {\r
-    protected ScrollPane scrollPane = new ScrollPane();\r
-    protected TextArea textarea = new TextArea();\r
-    protected Button viewInEditorButton = new Button();\r
-    Panel jPanel1 = new Panel();\r
-    BorderLayout borderLayout1 = new BorderLayout();\r
-\r
-    public GPairwiseAlignPanel() {\r
-        try {\r
-            jbInit();\r
-        } catch (Exception e) {\r
-            e.printStackTrace();\r
-        }\r
-    }\r
-\r
-    private void jbInit() throws Exception {\r
-        this.setLayout(borderLayout1);\r
-        textarea.setFont(new java.awt.Font("Monospaced", 0, 12));\r
-        textarea.setText("");\r
-        viewInEditorButton.setFont(new java.awt.Font("Verdana", 0, 12));\r
-        viewInEditorButton.setLabel("View in alignment editor");\r
-        viewInEditorButton.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    viewInEditorButton_actionPerformed(e);\r
-                }\r
-            });\r
-        this.add(scrollPane, BorderLayout.CENTER);\r
-        scrollPane.add(textarea);\r
-        this.add(jPanel1, BorderLayout.SOUTH);\r
-        jPanel1.add(viewInEditorButton, null);\r
-    }\r
-\r
-    protected void viewInEditorButton_actionPerformed(ActionEvent e) {\r
-    }\r
-}\r
diff --git a/src/jalview/jbappletgui/GSliderPanel.java b/src/jalview/jbappletgui/GSliderPanel.java
deleted file mode 100755 (executable)
index 5e33300..0000000
+++ /dev/null
@@ -1,115 +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 GSliderPanel extends Panel {\r
-    // this is used for conservation colours, PID colours and redundancy threshold\r
-    protected Scrollbar slider = new Scrollbar();\r
-    protected TextField valueField = new TextField();\r
-    protected Label label = new Label();\r
-    Panel jPanel1 = new Panel();\r
-    Panel jPanel2 = new Panel();\r
-    protected Button applyButton = new Button();\r
-    protected Button undoButton = new Button();\r
-    FlowLayout flowLayout1 = new FlowLayout();\r
-    protected Checkbox allGroupsCheck = new Checkbox();\r
-    BorderLayout borderLayout1 = new BorderLayout();\r
-    BorderLayout borderLayout2 = new BorderLayout();\r
-    FlowLayout flowLayout2 = new FlowLayout();\r
-\r
-    public GSliderPanel() {\r
-        try {\r
-            jbInit();\r
-        } catch (Exception e) {\r
-            e.printStackTrace();\r
-        }\r
-    }\r
-\r
-    private void jbInit() throws Exception {\r
-        this.setLayout(borderLayout2);\r
-\r
-        // slider.setMajorTickSpacing(10);\r
-        //  slider.setMinorTickSpacing(1);\r
-        //  slider.setPaintTicks(true);\r
-        slider.setBackground(Color.white);\r
-        slider.setFont(new java.awt.Font("Verdana", 0, 11));\r
-        slider.setOrientation(0);\r
-        valueField.setFont(new java.awt.Font("Verdana", 0, 11));\r
-        valueField.setText("      ");\r
-        valueField.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    valueField_actionPerformed(e);\r
-                }\r
-            });\r
-        label.setFont(new java.awt.Font("Verdana", 0, 11));\r
-        label.setText("set this label text");\r
-        jPanel1.setLayout(borderLayout1);\r
-        jPanel2.setLayout(flowLayout1);\r
-        applyButton.setFont(new java.awt.Font("Verdana", 0, 11));\r
-        applyButton.setLabel("Apply");\r
-        applyButton.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    applyButton_actionPerformed(e);\r
-                }\r
-            });\r
-        undoButton.setEnabled(false);\r
-        undoButton.setFont(new java.awt.Font("Verdana", 0, 11));\r
-        undoButton.setLabel("Undo");\r
-        undoButton.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    undoButton_actionPerformed(e);\r
-                }\r
-            });\r
-        allGroupsCheck.setEnabled(false);\r
-        allGroupsCheck.setFont(new java.awt.Font("Verdana", 0, 11));\r
-        allGroupsCheck.setLabel("Apply threshold to all groups");\r
-        allGroupsCheck.setName("Apply to all Groups");\r
-        allGroupsCheck.addItemListener(new java.awt.event.ItemListener() {\r
-                public void itemStateChanged(ItemEvent e) {\r
-                    allGroupsCheck_actionPerformed();\r
-                }\r
-            });\r
-        this.setBackground(Color.white);\r
-        this.setForeground(Color.black);\r
-        jPanel2.add(label, null);\r
-        jPanel2.add(applyButton, null);\r
-        jPanel2.add(undoButton, null);\r
-        jPanel2.add(allGroupsCheck);\r
-        jPanel1.add(valueField, java.awt.BorderLayout.EAST);\r
-        jPanel1.add(slider, java.awt.BorderLayout.CENTER);\r
-        this.add(jPanel1, java.awt.BorderLayout.SOUTH);\r
-        this.add(jPanel2, java.awt.BorderLayout.CENTER);\r
-    }\r
-\r
-    protected void valueField_actionPerformed(ActionEvent e) {\r
-    }\r
-\r
-    protected void applyButton_actionPerformed(ActionEvent e) {\r
-    }\r
-\r
-    protected void undoButton_actionPerformed(ActionEvent e) {\r
-    }\r
-\r
-    protected void allGroupsCheck_actionPerformed() {\r
-    }\r
-}\r
diff --git a/src/jalview/jbappletgui/GTreePanel.java b/src/jalview/jbappletgui/GTreePanel.java
deleted file mode 100755 (executable)
index bfe6b2b..0000000
+++ /dev/null
@@ -1,121 +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 GTreePanel extends Frame {\r
-    BorderLayout borderLayout1 = new BorderLayout();\r
-    protected ScrollPane scrollPane = new ScrollPane();\r
-    MenuBar jMenuBar1 = new MenuBar();\r
-    Menu jMenu2 = new Menu();\r
-    protected MenuItem fontSize = new MenuItem();\r
-    protected CheckboxMenuItem bootstrapMenu = new CheckboxMenuItem();\r
-    protected CheckboxMenuItem distanceMenu = new CheckboxMenuItem();\r
-    protected CheckboxMenuItem placeholdersMenu = new CheckboxMenuItem();\r
-    protected CheckboxMenuItem fitToWindow = new CheckboxMenuItem();\r
-    Menu fileMenu = new Menu();\r
-    MenuItem newickOutput = new MenuItem();\r
-\r
-    public GTreePanel() {\r
-        try {\r
-            jbInit();\r
-            this.setMenuBar(jMenuBar1);\r
-        } catch (Exception e) {\r
-            e.printStackTrace();\r
-        }\r
-    }\r
-\r
-    private void jbInit() throws Exception {\r
-        setLayout(borderLayout1);\r
-        this.setBackground(Color.white);\r
-        this.setFont(new java.awt.Font("Verdana", 0, 12));\r
-        jMenu2.setLabel("View");\r
-        fontSize.setLabel("Font...");\r
-        fontSize.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    fontSize_actionPerformed(e);\r
-                }\r
-            });\r
-        bootstrapMenu.setLabel("Show Bootstrap Values");\r
-        bootstrapMenu.addItemListener(new java.awt.event.ItemListener() {\r
-                public void itemStateChanged(ItemEvent e) {\r
-                    bootstrapMenu_actionPerformed(null);\r
-                }\r
-            });\r
-        distanceMenu.setLabel("Show Distances");\r
-        distanceMenu.addItemListener(new java.awt.event.ItemListener() {\r
-                public void itemStateChanged(ItemEvent e) {\r
-                    distanceMenu_actionPerformed(null);\r
-                }\r
-            });\r
-        placeholdersMenu.setLabel("Mark Unassociated Leaves");\r
-        placeholdersMenu.addItemListener(new java.awt.event.ItemListener() {\r
-                public void itemStateChanged(ItemEvent e) {\r
-                    placeholdersMenu_actionPerformed(null);\r
-                }\r
-            });\r
-        fitToWindow.setState(true);\r
-        fitToWindow.setLabel("Fit To Window");\r
-        fitToWindow.addItemListener(new java.awt.event.ItemListener() {\r
-                public void itemStateChanged(ItemEvent e) {\r
-                    fitToWindow_actionPerformed(null);\r
-                }\r
-            });\r
-        fileMenu.setLabel("File");\r
-        newickOutput.setLabel("Newick Format");\r
-        newickOutput.addActionListener(new ActionListener() {\r
-                public void actionPerformed(ActionEvent actionEvent) {\r
-                    newickOutput_actionPerformed(actionEvent);\r
-                }\r
-            });\r
-        add(scrollPane, BorderLayout.CENTER);\r
-        jMenuBar1.add(fileMenu);\r
-        jMenuBar1.add(jMenu2);\r
-        jMenu2.add(fitToWindow);\r
-        jMenu2.add(fontSize);\r
-        jMenu2.add(distanceMenu);\r
-        jMenu2.add(bootstrapMenu);\r
-        jMenu2.add(placeholdersMenu);\r
-        fileMenu.add(newickOutput);\r
-    }\r
-\r
-    protected void printMenu_actionPerformed(ActionEvent e) {\r
-    }\r
-\r
-    protected void fontSize_actionPerformed(ActionEvent e) {\r
-    }\r
-\r
-    protected void distanceMenu_actionPerformed(ActionEvent e) {\r
-    }\r
-\r
-    protected void bootstrapMenu_actionPerformed(ActionEvent e) {\r
-    }\r
-\r
-    protected void placeholdersMenu_actionPerformed(ActionEvent e) {\r
-    }\r
-\r
-    protected void fitToWindow_actionPerformed(ActionEvent e) {\r
-    }\r
-\r
-    public void newickOutput_actionPerformed(ActionEvent actionEvent) {\r
-    }\r
-}\r
diff --git a/src/jalview/jbappletgui/GUserDefinedColours.java b/src/jalview/jbappletgui/GUserDefinedColours.java
deleted file mode 100755 (executable)
index b26dd9a..0000000
+++ /dev/null
@@ -1,191 +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 GUserDefinedColours extends Panel {\r
-    protected Panel buttonPanel = new Panel();\r
-    protected GridLayout gridLayout = new GridLayout();\r
-    Panel jPanel2 = new Panel();\r
-    protected Button okButton = new Button();\r
-    protected Button applyButton = new Button();\r
-    protected Button cancelButton = new Button();\r
-    protected Scrollbar rScroller = new Scrollbar();\r
-    Label label1 = new Label();\r
-  protected TextField rText = new TextField();\r
-  Label label4 = new Label();\r
-    protected Scrollbar gScroller = new Scrollbar();\r
-    protected TextField gText = new TextField();\r
-  Label label5 = new Label();\r
-    protected Scrollbar bScroller = new Scrollbar();\r
-    protected TextField bText = new TextField();\r
-  protected Panel target = new Panel();\r
-\r
-    public GUserDefinedColours() {\r
-        try {\r
-            jbInit();\r
-        } catch (Exception e) {\r
-            e.printStackTrace();\r
-        }\r
-    }\r
-\r
-    private void jbInit() throws Exception {\r
-        this.setLayout(null);\r
-        buttonPanel.setLayout(gridLayout);\r
-        gridLayout.setColumns(6);\r
-        gridLayout.setRows(4);\r
-        okButton.setFont(new java.awt.Font("Verdana", 0, 11));\r
-        okButton.setLabel("OK");\r
-        okButton.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    okButton_actionPerformed(e);\r
-                }\r
-            });\r
-        applyButton.setFont(new java.awt.Font("Verdana", 0, 11));\r
-        applyButton.setLabel("Apply");\r
-        applyButton.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    applyButton_actionPerformed(e);\r
-                }\r
-            });\r
-        cancelButton.setFont(new java.awt.Font("Verdana", 0, 11));\r
-        cancelButton.setLabel("Cancel");\r
-        cancelButton.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    cancelButton_actionPerformed(e);\r
-                }\r
-            });\r
-        this.setBackground(new Color(212, 208, 223));\r
-        jPanel2.setBounds(new Rectangle(0, 265, 400, 35));\r
-        buttonPanel.setBounds(new Rectangle(0, 123, 400, 142));\r
-        rScroller.setMaximum(256);\r
-        rScroller.setMinimum(0);\r
-        rScroller.setOrientation(0);\r
-        rScroller.setUnitIncrement(1);\r
-    rScroller.setVisibleAmount(1);\r
-    rScroller.setBounds(new Rectangle(36, 27, 119, 19));\r
-    rScroller.addAdjustmentListener(new java.awt.event.AdjustmentListener() {\r
-                public void adjustmentValueChanged(AdjustmentEvent e) {\r
-                    rScroller_adjustmentValueChanged(e);\r
-                }\r
-            });\r
-    label1.setAlignment(Label.RIGHT);\r
-    label1.setText("R");\r
-    label1.setBounds(new Rectangle(19, 30, 16, 15));\r
-    rText.setFont(new java.awt.Font("Dialog", Font.PLAIN, 10));\r
-    rText.setText("0        ");\r
-    rText.setBounds(new Rectangle(156, 27, 53, 19));\r
-    rText.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    rText_actionPerformed(e);\r
-                }\r
-            });\r
-    label4.setAlignment(Label.RIGHT);\r
-    label4.setText("G");\r
-    label4.setBounds(new Rectangle(15, 56, 20, 15));\r
-    gScroller.setMaximum(256);\r
-        gScroller.setMinimum(0);\r
-        gScroller.setOrientation(0);\r
-        gScroller.setUnitIncrement(1);\r
-    gScroller.setVisibleAmount(1);\r
-    gScroller.setBounds(new Rectangle(35, 52, 120, 20));\r
-    gScroller.addAdjustmentListener(new java.awt.event.AdjustmentListener() {\r
-                public void adjustmentValueChanged(AdjustmentEvent e) {\r
-                    gScroller_adjustmentValueChanged(e);\r
-                }\r
-            });\r
-    gText.setFont(new java.awt.Font("Dialog", Font.PLAIN, 10));\r
-    gText.setText("0        ");\r
-    gText.setBounds(new Rectangle(156, 52, 53, 20));\r
-    gText.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    gText_actionPerformed(e);\r
-                }\r
-            });\r
-    label5.setAlignment(Label.RIGHT);\r
-    label5.setText("B");\r
-    label5.setBounds(new Rectangle(14, 82, 20, 15));\r
-    bScroller.setMaximum(256);\r
-        bScroller.setMinimum(0);\r
-        bScroller.setOrientation(0);\r
-        bScroller.setUnitIncrement(1);\r
-    bScroller.setVisibleAmount(1);\r
-    bScroller.setBounds(new Rectangle(35, 78, 120, 20));\r
-    bScroller.addAdjustmentListener(new java.awt.event.AdjustmentListener() {\r
-                public void adjustmentValueChanged(AdjustmentEvent e) {\r
-                    bScroller_adjustmentValueChanged(e);\r
-                }\r
-            });\r
-    bText.setFont(new java.awt.Font("Dialog", Font.PLAIN, 10));\r
-    bText.setText("0        ");\r
-    bText.setBounds(new Rectangle(157, 78, 52, 20));\r
-    bText.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    bText_actionPerformed(e);\r
-                }\r
-            });\r
-    target.setBackground(Color.black);\r
-        target.setBounds(new Rectangle(229, 26, 134, 79));\r
-        this.add(jPanel2, null);\r
-        jPanel2.add(okButton, null);\r
-        jPanel2.add(applyButton, null);\r
-        jPanel2.add(cancelButton, null);\r
-        this.add(buttonPanel, null);\r
-    this.add(target, null);\r
-    this.add(gScroller);\r
-    this.add(rScroller);\r
-    this.add(bScroller);\r
-    this.add(label5);\r
-    this.add(label4);\r
-    this.add(label1);\r
-    this.add(gText);\r
-    this.add(rText);\r
-    this.add(bText);\r
-  }\r
-\r
-    protected void okButton_actionPerformed(ActionEvent e) {\r
-    }\r
-\r
-    protected void applyButton_actionPerformed(ActionEvent e) {\r
-    }\r
-\r
-    protected void cancelButton_actionPerformed(ActionEvent e) {\r
-    }\r
-\r
-    protected void rScroller_adjustmentValueChanged(AdjustmentEvent e) {\r
-    }\r
-\r
-    protected void gScroller_adjustmentValueChanged(AdjustmentEvent e) {\r
-    }\r
-\r
-    protected void bScroller_adjustmentValueChanged(AdjustmentEvent e) {\r
-    }\r
-\r
-    protected void rText_actionPerformed(ActionEvent e) {\r
-    }\r
-\r
-    protected void gText_actionPerformed(ActionEvent e) {\r
-    }\r
-\r
-    protected void bText_actionPerformed(ActionEvent e) {\r
-    }\r
-}\r