/*
 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
 * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
 * 
 * This file is part of Jalview.
 * 
 * Jalview is free software: you can redistribute it and/or
 * modify it under the terms of the GNU General Public License 
 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
 * 
 * Jalview is distributed in the hope that it will be useful, but 
 * WITHOUT ANY WARRANTY; without even the implied warranty 
 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
 * PURPOSE.  See the GNU General Public License for more details.
 * 
 * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
 */
package jalview.jbgui;

import jalview.gui.JvSwingUtils;

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

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

/**
 * DOCUMENT ME!
 * 
 * @author $author$
 * @version $Revision$
 */
public class GPreferences extends JPanel
{
  JTabbedPane tabbedPane = new JTabbedPane();

  JButton ok = new JButton();

  JButton cancel = new JButton();

  JPanel okCancelPanel = new JPanel();

  BorderLayout borderLayout1 = new BorderLayout();

  protected JCheckBox quality = new JCheckBox();

  JPanel visualTab = new JPanel();
  JPanel visual2Tab = new JPanel();

  protected JCheckBox fullScreen = new JCheckBox();

  protected JCheckBox conservation = new JCheckBox();

  protected JCheckBox identity = new JCheckBox();

  protected JCheckBox annotations = new JCheckBox();

  protected JPanel minColour = new JPanel();
  JLabel mincolourLabel = new JLabel();

  protected JPanel maxColour = new JPanel();
  JLabel maxcolourLabel = new JLabel();

  JLabel gapLabel = new JLabel();

  protected JComboBox colour = new JComboBox();

  JLabel colourLabel = new JLabel();

  JLabel fontLabel = new JLabel();

  protected JComboBox fontSizeCB = new JComboBox();

  protected JComboBox fontStyleCB = new JComboBox();

  protected JComboBox fontNameCB = new JComboBox();

  protected JComboBox gapSymbolCB = new JComboBox();

  protected JCheckBox startupCheckbox = new JCheckBox();

  protected JTextField startupFileTextfield = new JTextField();

  JPanel connectTab = new JPanel();

  JLabel serverLabel = new JLabel();

  protected JList linkURLList = new JList();

  protected JTextField proxyServerTB = new JTextField();

  protected JTextField proxyPortTB = new JTextField();

  JLabel portLabel = new JLabel();

  JLabel browserLabel = new JLabel();

  protected JTextField defaultBrowser = new JTextField();

  JButton newLink = new JButton();

  JButton editLink = new JButton();

  JButton deleteLink = new JButton();

  JScrollPane linkScrollPane = new JScrollPane();

  JPanel linkPanel = new JPanel();

  BorderLayout borderLayout2 = new BorderLayout();

  JPanel editLinkButtons = new JPanel();

  GridLayout gridLayout1 = new GridLayout();

  protected JList linkNameList = new JList();

  JPanel linkPanel2 = new JPanel();

  BorderLayout borderLayout3 = new BorderLayout();

  protected JCheckBox useProxy = new JCheckBox();

  JPanel jPanel1 = new JPanel();

  TitledBorder titledBorder1 = new TitledBorder("Proxy Server");

  TitledBorder titledBorder2 = new TitledBorder("File Output");

  GridBagLayout gridBagLayout2 = new GridBagLayout();

  GridBagLayout gridBagLayout1 = new GridBagLayout();

  GridBagLayout gridBagLayout3 = new GridBagLayout();

  protected JComboBox sortby = new JComboBox();

  JLabel sortLabel = new JLabel();

  JPanel jPanel2 = new JPanel();
  JPanel visual2panel = new JPanel();

  GridLayout gridLayout2 = new GridLayout();

  GridLayout gridLayout4 = new GridLayout();

  JPanel annsettingsPanel = new JPanel();

  JPanel autoAnnotSettings1 = new JPanel();

  JPanel autoAnnotSettings2 = new JPanel();

  JPanel autoAnnotSettings3 = new JPanel();

  JPanel exportTab = new JPanel();

  JLabel epsLabel = new JLabel();

  protected JComboBox epsRendering = new JComboBox();

  JLabel jLabel1 = new JLabel();

  protected JCheckBox blcjv = new JCheckBox();

  protected JCheckBox pileupjv = new JCheckBox();

  protected JCheckBox clustaljv = new JCheckBox();

  protected JCheckBox msfjv = new JCheckBox();

  protected JCheckBox fastajv = new JCheckBox();

  protected JCheckBox pfamjv = new JCheckBox();

  FlowLayout flowLayout1 = new FlowLayout();

  protected JCheckBox pirjv = new JCheckBox();

  JPanel jPanel11 = new JPanel();

  Font verdana11 = JvSwingUtils.getLabelFont();

  protected JCheckBox seqLimit = new JCheckBox();

  GridLayout gridLayout3 = new GridLayout();

  protected JCheckBox smoothFont = new JCheckBox();

  JPanel calcTab = new JPanel();

  protected JCheckBox autoCalculateConsCheck = new JCheckBox();

  protected JCheckBox padGaps = new JCheckBox();

  protected JCheckBox modellerOutput = new JCheckBox();

  protected JPanel dasPanel = new JPanel();

  BorderLayout borderLayout4 = new BorderLayout();

  protected JPanel wsPanel = new JPanel();

  BorderLayout borderLayout5 = new BorderLayout();

  protected JCheckBox wrap = new JCheckBox();

  protected JCheckBox rightAlign = new JCheckBox();

  protected JCheckBox showUnconserved = new JCheckBox();

  protected JCheckBox showDbRefTooltip = new JCheckBox();

  protected JCheckBox showNpTooltip = new JCheckBox();

  protected JCheckBox idItalics = new JCheckBox();

  protected JCheckBox openoverv = new JCheckBox();

  protected JCheckBox usagestats = new JCheckBox();

  protected JCheckBox questionnaire = new JCheckBox();

  protected JCheckBox versioncheck = new JCheckBox();

  protected JLabel showGroupbits = new JLabel();

  protected JLabel showConsensbits = new JLabel();

  protected JCheckBox showConsensLogo = new JCheckBox();

  protected JCheckBox showConsensHistogram = new JCheckBox();

  protected JCheckBox showGroupConsensus = new JCheckBox();

  protected JCheckBox showGroupConservation = new JCheckBox();

  protected JCheckBox shareSelections = new JCheckBox();

  protected JCheckBox followHighlight = new JCheckBox();

  protected JCheckBox sortByTree= new JCheckBox();

  /**
   * Creates a new GPreferences object.
   */
  public GPreferences()
  {
    try
    {
      jbInit();
    } catch (Exception ex)
    {
      ex.printStackTrace();
    }
  }

  /**
   * DOCUMENT ME!
   * 
   * @throws Exception
   *           DOCUMENT ME!
   */
  private void jbInit() throws Exception
  {
    this.setLayout(borderLayout1);
    ok.setText("OK");
    ok.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        ok_actionPerformed(e);
      }
    });
    cancel.setText("Cancel");
    cancel.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        cancel_actionPerformed(e);
      }
    });
    quality.setEnabled(false);
    quality.setFont(verdana11);
    quality.setHorizontalAlignment(SwingConstants.RIGHT);
    quality.setHorizontalTextPosition(SwingConstants.LEFT);
    quality.setSelected(true);
    quality.setText("Quality");
    visualTab.setBorder(new TitledBorder("Open new alignment"));
    visualTab.setLayout(null);
    visual2Tab.setBorder(new TitledBorder("Open new alignment"));
    visual2Tab.setLayout(new FlowLayout());
    fullScreen.setFont(verdana11);
    fullScreen.setHorizontalAlignment(SwingConstants.RIGHT);
    fullScreen.setHorizontalTextPosition(SwingConstants.LEFT);
    fullScreen.setText("Maximise Window");
    conservation.setEnabled(false);
    conservation.setFont(verdana11);
    conservation.setHorizontalAlignment(SwingConstants.RIGHT);
    conservation.setHorizontalTextPosition(SwingConstants.LEFT);
    conservation.setSelected(true);
    conservation.setText("Conservation");
    identity.setEnabled(false);
    identity.setFont(verdana11);
    identity.setHorizontalAlignment(SwingConstants.RIGHT);
    identity.setHorizontalTextPosition(SwingConstants.LEFT);
    identity.setSelected(true);
    identity.setText("Consensus");
    showGroupbits.setFont(verdana11);
    showGroupbits.setHorizontalAlignment(SwingConstants.RIGHT);
    showGroupbits.setHorizontalTextPosition(SwingConstants.LEFT);
    showGroupbits.setText("Show group:");
    showConsensbits.setFont(verdana11);
    showConsensbits.setHorizontalAlignment(SwingConstants.RIGHT);
    showConsensbits.setHorizontalTextPosition(SwingConstants.LEFT);
    showConsensbits.setText("Consensus:");
    showConsensHistogram.setEnabled(false);
    showConsensHistogram.setFont(verdana11);
    showConsensHistogram.setHorizontalAlignment(SwingConstants.RIGHT);
    showConsensHistogram.setHorizontalTextPosition(SwingConstants.LEFT);
    showConsensHistogram.setSelected(true);
    showConsensHistogram.setText("Histogram");
    showConsensLogo.setEnabled(false);
    showConsensLogo.setFont(verdana11);
    showConsensLogo.setHorizontalAlignment(SwingConstants.RIGHT);
    showConsensLogo.setHorizontalTextPosition(SwingConstants.LEFT);
    showConsensLogo.setSelected(true);
    showConsensLogo.setText("Logo");
    showGroupConsensus.setEnabled(false);
    showGroupConsensus.setFont(verdana11);
    showGroupConsensus.setHorizontalAlignment(SwingConstants.RIGHT);
    showGroupConsensus.setHorizontalTextPosition(SwingConstants.LEFT);
    showGroupConsensus.setSelected(true);
    showGroupConsensus.setText("Consensus");
    showGroupConservation.setEnabled(false);
    showGroupConservation.setFont(verdana11);
    showGroupConservation.setHorizontalAlignment(SwingConstants.RIGHT);
    showGroupConservation.setHorizontalTextPosition(SwingConstants.LEFT);
    showGroupConservation.setSelected(true);
    showGroupConservation.setText("Conservation");
    showNpTooltip.setEnabled(true);
    showNpTooltip.setFont(verdana11);
    showNpTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
    showNpTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
    showNpTooltip.setSelected(true);
    showNpTooltip.setText("Non-positional Features");
    showDbRefTooltip.setEnabled(true);
    showDbRefTooltip.setFont(verdana11);
    showDbRefTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
    showDbRefTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
    showDbRefTooltip.setSelected(true);
    showDbRefTooltip.setText("Database References");
    annotations.setFont(verdana11);
    annotations.setHorizontalAlignment(SwingConstants.RIGHT);
    annotations.setHorizontalTextPosition(SwingConstants.LEADING);
    annotations.setSelected(true);
    annotations.setText("Show Annotations");
    annotations.setBounds(new Rectangle(169, 12, 200, 23));
    annotations.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        annotations_actionPerformed(e);
      }
    });
    identity.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        annotations_actionPerformed(e);
      }
    });
    showGroupConsensus.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        annotations_actionPerformed(e);
      }
    });
    showUnconserved.setFont(verdana11);
    showUnconserved.setHorizontalAlignment(SwingConstants.RIGHT);
    showUnconserved.setHorizontalTextPosition(SwingConstants.LEFT);
    showUnconserved.setSelected(true);
    showUnconserved.setText("Show Unconserved");
    showUnconserved.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        showunconserved_actionPerformed(e);
      }
    });
    // / TODO: fit these in to preferences panel!!!!!
    shareSelections.setFont(verdana11);
    shareSelections.setHorizontalAlignment(SwingConstants.RIGHT);
    shareSelections.setHorizontalTextPosition(SwingConstants.LEFT);
    shareSelections.setSelected(true);
    shareSelections.setText("Share selection across views");
    followHighlight.setFont(verdana11);
    followHighlight.setHorizontalAlignment(SwingConstants.RIGHT);
    followHighlight.setHorizontalTextPosition(SwingConstants.LEFT);
    // showUnconserved.setBounds(new Rectangle(169, 40, 200, 23));
    followHighlight.setSelected(true);
    followHighlight.setText("Scroll to highlighted regions");

    gapLabel.setFont(verdana11);
    gapLabel.setHorizontalAlignment(SwingConstants.RIGHT);
    gapLabel.setText("Gap Symbol ");
    colour.setFont(verdana11);
    colour.setBounds(new Rectangle(172, 225, 155, 21));
    colourLabel.setFont(verdana11);
    colourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
    colourLabel.setText("Alignment Colour ");
    fontLabel.setFont(verdana11);
    fontLabel.setHorizontalAlignment(SwingConstants.RIGHT);
    fontLabel.setText("Font ");
    fontSizeCB.setFont(verdana11);
    fontSizeCB.setBounds(new Rectangle(319, 104, 49, 23));
    fontStyleCB.setFont(verdana11);
    fontStyleCB.setBounds(new Rectangle(367, 104, 70, 23));
    fontNameCB.setFont(verdana11);
    fontNameCB.setBounds(new Rectangle(172, 104, 147, 23));
    gapSymbolCB.setFont(verdana11);
    gapSymbolCB.setBounds(new Rectangle(172, 204, 69, 23));
    mincolourLabel.setFont(verdana11);
    mincolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
    mincolourLabel.setText("Minimum Colour");
    minColour.setFont(verdana11);
    minColour.setBorder(BorderFactory.createEtchedBorder());
    minColour.setPreferredSize(new Dimension(40, 20));
    minColour.addMouseListener(new MouseAdapter()
    {
      public void mousePressed(MouseEvent e)
      {
          minColour_actionPerformed();
      }
    });
    maxcolourLabel.setFont(verdana11);
    maxcolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
    maxcolourLabel.setText("Maximum Colour ");
    maxColour.setFont(verdana11);
    maxColour.setBorder(BorderFactory.createEtchedBorder());
    maxColour.setPreferredSize(new Dimension(40, 20));
    maxColour.addMouseListener(new MouseAdapter()
    {
      public void mousePressed(MouseEvent e)
      {
          maxColour_actionPerformed();
      }
    });
    
    startupCheckbox.setText("Open file");
    startupCheckbox.setFont(verdana11);
    startupCheckbox.setHorizontalAlignment(SwingConstants.RIGHT);
    startupCheckbox.setHorizontalTextPosition(SwingConstants.LEFT);
    startupCheckbox.setSelected(true);
    startupFileTextfield.setFont(verdana11);
    startupFileTextfield.setBounds(new Rectangle(172, 273, 270, 20));
    startupFileTextfield.addMouseListener(new MouseAdapter()
    {
      public void mouseClicked(MouseEvent e)
      {
        if (e.getClickCount() > 1)
        {
          startupFileTextfield_mouseClicked();
        }
      }
    });

    connectTab.setLayout(gridBagLayout3);
    serverLabel.setText("Address");
    serverLabel.setHorizontalAlignment(SwingConstants.RIGHT);
    serverLabel.setFont(verdana11);
    proxyServerTB.setFont(verdana11);
    proxyPortTB.setFont(verdana11);
    portLabel.setFont(verdana11);
    portLabel.setHorizontalAlignment(SwingConstants.RIGHT);
    portLabel.setText("Port");
    browserLabel.setFont(new java.awt.Font("SansSerif", 0, 11));
    browserLabel.setHorizontalAlignment(SwingConstants.TRAILING);
    browserLabel.setText("Default Browser (Unix)");
    defaultBrowser.setFont(verdana11);
    defaultBrowser.setText("");
    usagestats.setText("Send usage statistics");
    usagestats.setFont(verdana11);
    usagestats.setHorizontalAlignment(SwingConstants.RIGHT);
    usagestats.setHorizontalTextPosition(SwingConstants.LEADING);
    questionnaire.setText("Check for questionnaires");
    questionnaire.setFont(verdana11);
    questionnaire.setHorizontalAlignment(SwingConstants.RIGHT);
    questionnaire.setHorizontalTextPosition(SwingConstants.LEADING);
    versioncheck.setText("Check for latest version");
    versioncheck.setFont(verdana11);
    versioncheck.setHorizontalAlignment(SwingConstants.RIGHT);
    versioncheck.setHorizontalTextPosition(SwingConstants.LEADING);
    newLink.setText("New");
    newLink.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        newLink_actionPerformed(e);
      }
    });
    editLink.setText("Edit");
    editLink.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        editLink_actionPerformed(e);
      }
    });
    deleteLink.setText("Delete");
    deleteLink.addActionListener(new java.awt.event.ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        deleteLink_actionPerformed(e);
      }
    });

    linkURLList.addListSelectionListener(new ListSelectionListener()
    {
      public void valueChanged(ListSelectionEvent e)
      {
        int index = linkURLList.getSelectedIndex();
        linkNameList.setSelectedIndex(index);
      }
    });

    linkNameList.addListSelectionListener(new ListSelectionListener()
    {
      public void valueChanged(ListSelectionEvent e)
      {
        int index = linkNameList.getSelectedIndex();
        linkURLList.setSelectedIndex(index);
      }
    });

    linkScrollPane.setBorder(null);
    linkPanel.setBorder(new TitledBorder("URL link from Sequence ID"));
    linkPanel.setLayout(borderLayout2);
    editLinkButtons.setLayout(gridLayout1);
    gridLayout1.setRows(3);
    linkNameList.setFont(verdana11);
    linkNameList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
    linkPanel2.setLayout(borderLayout3);
    linkURLList.setFont(verdana11);
    linkURLList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);

    defaultBrowser.addMouseListener(new MouseAdapter()
    {
      public void mouseClicked(MouseEvent e)
      {
        if (e.getClickCount() > 1)
        {
          defaultBrowser_mouseClicked(e);
        }
      }
    });
    useProxy.setFont(verdana11);
    useProxy.setHorizontalAlignment(SwingConstants.RIGHT);
    useProxy.setHorizontalTextPosition(SwingConstants.LEADING);
    useProxy.setText("Use a proxy server");
    useProxy.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        useProxy_actionPerformed();
      }
    });
    jPanel1.setBorder(titledBorder1);
    jPanel1.setLayout(gridBagLayout1);
    sortby.setFont(verdana11);
    sortby.setBounds(new Rectangle(172, 249, 155, 21));
    sortLabel.setFont(verdana11);
    sortLabel.setHorizontalAlignment(SwingConstants.RIGHT);
    sortLabel.setText("Sort by ");
    jPanel2.setBounds(new Rectangle(7, 17, 158, 278));
    jPanel2.setLayout(gridLayout2);
    gridLayout2.setRows(12);
    exportTab.setLayout(null);
    epsLabel.setFont(verdana11);
    epsLabel.setHorizontalAlignment(SwingConstants.RIGHT);
    epsLabel.setText("EPS Rendering Style");
    epsLabel.setBounds(new Rectangle(9, 31, 140, 24));
    epsRendering.setFont(verdana11);
    epsRendering.setBounds(new Rectangle(154, 34, 187, 21));
    jLabel1.setFont(verdana11);
    jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
    jLabel1.setText("Append /start-end (/15-380)");
    jLabel1.setFont(verdana11);
    fastajv.setFont(verdana11);
    fastajv.setHorizontalAlignment(SwingConstants.LEFT);
    clustaljv.setText("Clustal     ");
    blcjv.setText("BLC     ");
    fastajv.setText("Fasta     ");
    msfjv.setText("MSF     ");
    pfamjv.setText("PFAM     ");
    pileupjv.setText("Pileup     ");
    msfjv.setFont(verdana11);
    msfjv.setHorizontalAlignment(SwingConstants.LEFT);
    pirjv.setText("PIR     ");
    jPanel11.setFont(verdana11);
    jPanel11.setBorder(titledBorder2);
    jPanel11.setBounds(new Rectangle(30, 72, 196, 182));
    jPanel11.setLayout(gridLayout3);
    blcjv.setFont(verdana11);
    blcjv.setHorizontalAlignment(SwingConstants.LEFT);
    clustaljv.setFont(verdana11);
    clustaljv.setHorizontalAlignment(SwingConstants.LEFT);
    pfamjv.setFont(verdana11);
    pfamjv.setHorizontalAlignment(SwingConstants.LEFT);
    pileupjv.setFont(verdana11);
    pileupjv.setHorizontalAlignment(SwingConstants.LEFT);
    pirjv.setFont(verdana11);
    pirjv.setHorizontalAlignment(SwingConstants.LEFT);
    seqLimit.setFont(verdana11);
    seqLimit.setHorizontalAlignment(SwingConstants.RIGHT);
    seqLimit.setHorizontalTextPosition(SwingConstants.LEFT);
    seqLimit.setText("Full Sequence Id");
    gridLayout3.setRows(8);
    smoothFont.setFont(verdana11);
    smoothFont.setHorizontalAlignment(SwingConstants.RIGHT);
    smoothFont.setHorizontalTextPosition(SwingConstants.LEADING);
    smoothFont.setText("Smooth Font");
    calcTab.setLayout(null);
    autoCalculateConsCheck.setFont(JvSwingUtils.getLabelFont());
    autoCalculateConsCheck.setText("AutoCalculate Consensus");
    autoCalculateConsCheck.setBounds(new Rectangle(21, 52, 209, 23));
    padGaps.setFont(JvSwingUtils.getLabelFont());
    padGaps.setText("Pad Gaps When Editing");
    padGaps.setBounds(new Rectangle(22, 94, 168, 23));
    sortByTree.setFont(JvSwingUtils.getLabelFont());
    sortByTree.setText("Sort With New Tree");
    sortByTree.setToolTipText("When selected, any trees calculated or loaded onto the alignment will automatically sort the alignment.");
    sortByTree.setBounds(new Rectangle(22, 136, 168, 23));
    modellerOutput.setFont(JvSwingUtils.getLabelFont());
    modellerOutput.setText("Use Modeller Output");
    modellerOutput.setBounds(new Rectangle(228, 226, 168, 23));
    dasPanel.setLayout(borderLayout4);
    wsPanel.setLayout(borderLayout5);
    wrap.setFont(JvSwingUtils.getLabelFont());
    wrap.setHorizontalAlignment(SwingConstants.TRAILING);
    wrap.setHorizontalTextPosition(SwingConstants.LEADING);
    wrap.setText("Wrap Alignment");
    rightAlign.setFont(JvSwingUtils.getLabelFont());
    rightAlign.setForeground(Color.black);
    rightAlign.setHorizontalAlignment(SwingConstants.RIGHT);
    rightAlign.setHorizontalTextPosition(SwingConstants.LEFT);
    rightAlign.setText("Right Align Ids");
    idItalics.setFont(JvSwingUtils.getLabelFont());
    idItalics.setHorizontalAlignment(SwingConstants.RIGHT);
    idItalics.setHorizontalTextPosition(SwingConstants.LEADING);
    idItalics.setText("Sequence Name Italics");
    openoverv.setFont(JvSwingUtils.getLabelFont());
    openoverv.setActionCommand("Open Overview");
    openoverv.setHorizontalAlignment(SwingConstants.RIGHT);
    openoverv.setHorizontalTextPosition(SwingConstants.LEFT);
    openoverv.setText("Open Overview");
    jPanel2.add(fullScreen);
    jPanel2.add(openoverv);
    jPanel2.add(seqLimit);
    jPanel2.add(rightAlign);
    jPanel2.add(fontLabel);
    jPanel2.add(showUnconserved);
    jPanel2.add(idItalics);
    jPanel2.add(smoothFont);
    jPanel2.add(gapLabel);
    jPanel2.add(wrap);
    jPanel2.add(sortLabel);
    jPanel2.add(startupCheckbox);
    visualTab.add(annotations);
    visualTab.add(startupFileTextfield);
    visualTab.add(sortby);
    visualTab.add(gapSymbolCB);
    visualTab.add(fontNameCB);
    visualTab.add(fontSizeCB);
    visualTab.add(fontStyleCB);
    annsettingsPanel.setBounds(new Rectangle(173, 34, 300, 61));
    annsettingsPanel.setLayout(new FlowLayout(FlowLayout.LEFT, 0, 0));
    annsettingsPanel.add(autoAnnotSettings1);
    annsettingsPanel.add(autoAnnotSettings2);
    annsettingsPanel.add(autoAnnotSettings3);
    autoAnnotSettings1.setLayout(new GridLayout(3, 1, 0, 0));
    autoAnnotSettings2.setLayout(new GridLayout(3, 1, 0, 0));
    autoAnnotSettings3.setLayout(new GridLayout(3, 1, 0, 0));
    visualTab.add(annsettingsPanel);
    Border jb = new EmptyBorder(1, 1, 4, 5);
    quality.setBorder(jb);
    conservation.setBorder(jb);
    identity.setBorder(jb);
    showConsensbits.setBorder(jb);
    showGroupbits.setBorder(jb);
    showGroupConsensus.setBorder(jb);
    showGroupConservation.setBorder(jb);
    showConsensHistogram.setBorder(jb);
    showConsensLogo.setBorder(jb);

    autoAnnotSettings2.add(conservation);
    autoAnnotSettings1.add(quality);
    autoAnnotSettings3.add(identity);
    autoAnnotSettings1.add(showGroupbits);
    autoAnnotSettings3.add(showGroupConsensus);
    autoAnnotSettings2.add(showGroupConservation);
    autoAnnotSettings1.add(showConsensbits);
    autoAnnotSettings2.add(showConsensHistogram);
    autoAnnotSettings3.add(showConsensLogo);

    JPanel tooltipSettings = new JPanel();
    tooltipSettings.setBorder(new TitledBorder("Sequence ID Tooltip"));
    tooltipSettings.setBounds(173, 130, 200, 62);
    tooltipSettings.setLayout(new GridLayout(2, 1));
    tooltipSettings.add(showDbRefTooltip);
    tooltipSettings.add(showNpTooltip);
    visualTab.add(tooltipSettings);
    visualTab.add(jPanel2);
    JvSwingUtils.addtoLayout(visual2Tab, "Default Colourscheme for alignment", colourLabel, colour);
    JPanel annotationShding=new JPanel();
    annotationShding.setBorder(new TitledBorder("Annotation Shading Default"));
    annotationShding.setLayout(new GridLayout(1,2));
    JvSwingUtils.addtoLayout(annotationShding, "Default Minimum Colour for annotation shading", mincolourLabel,minColour);
    JvSwingUtils.addtoLayout(annotationShding,"Default Maximum Colour for annotation shading", maxcolourLabel, maxColour);
    visual2Tab.add(annotationShding); // , FlowLayout.LEFT);

//    visual2panel.add(minColour);
//    visual2panel.add(maxColour);
//    visual2Tab.add(visual2panel);

    linkPanel.add(editLinkButtons, BorderLayout.EAST);
    editLinkButtons.add(newLink, null);
    editLinkButtons.add(editLink, null);
    editLinkButtons.add(deleteLink, null);
    linkPanel.add(linkScrollPane, BorderLayout.CENTER);
    linkScrollPane.getViewport().add(linkPanel2, null);
    linkPanel2.add(linkURLList, BorderLayout.CENTER);
    linkPanel2.add(linkNameList, BorderLayout.WEST);
    okCancelPanel.add(ok);
    okCancelPanel.add(cancel);
    this.add(tabbedPane, java.awt.BorderLayout.CENTER);

    this.add(okCancelPanel, java.awt.BorderLayout.SOUTH);
    jPanel1.add(serverLabel, new GridBagConstraints(0, 1, 1, 1, 0.0, 0.0,
            GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
                    2, 4, 0), 5, 0));
    jPanel1.add(portLabel, new GridBagConstraints(2, 1, 1, 1, 0.0, 0.0,
            GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
                    0, 4, 0), 11, 6));
    connectTab.add(linkPanel, new GridBagConstraints(0, 0, 2, 1, 1.0, 1.0,
            GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(
                    16, 0, 0, 12), 359, -17));
    connectTab.add(jPanel1, new GridBagConstraints(0, 2, 2, 1, 1.0, 1.0,
            GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(
                    21, 0, 35, 12), 4, 6));
    connectTab.add(browserLabel, new GridBagConstraints(0, 1, 1, 1, 0.0,
            0.0, GridBagConstraints.WEST, GridBagConstraints.NONE,
            new Insets(16, 0, 0, 0), 5, 1));
    jPanel1.add(proxyPortTB, new GridBagConstraints(3, 1, 1, 1, 1.0, 0.0,
            GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
            new Insets(0, 2, 4, 2), 54, 1));
    jPanel1.add(proxyServerTB, new GridBagConstraints(1, 1, 1, 1, 1.0, 0.0,
            GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
            new Insets(0, 2, 4, 0), 263, 1));
    connectTab.add(defaultBrowser, new GridBagConstraints(1, 1, 1, 1, 1.0,
            0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
            new Insets(15, 0, 0, 15), 307, 1));
    connectTab.add(usagestats, new GridBagConstraints(0, 4, 1, 1, 1.0, 0.0,
            GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
            new Insets(0, 2, 4, 2), 70, 1));
    connectTab.add(questionnaire, new GridBagConstraints(1, 4, 1, 1, 1.0,
            0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
            new Insets(0, 2, 4, 2), 70, 1));
    connectTab.add(versioncheck, new GridBagConstraints(0, 5, 1, 1, 1.0,
            0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
            new Insets(0, 2, 4, 2), 70, 1));

    jPanel1.add(useProxy, new GridBagConstraints(0, 0, 2, 1, 0.0, 0.0,
            GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
                    2, 5, 185), 2, -4));
    DefaultListCellRenderer dlcr = new DefaultListCellRenderer();
    dlcr.setHorizontalAlignment(DefaultListCellRenderer.CENTER);
    gapSymbolCB.setRenderer(dlcr);

    tabbedPane.add(visualTab, "Visual");
    tabbedPane.add(visual2Tab,"Colours");
    tabbedPane.add(connectTab, "Connections");
    tabbedPane.add(exportTab, "Output");
    jPanel11.add(jLabel1);
    jPanel11.add(blcjv);
    jPanel11.add(clustaljv);
    jPanel11.add(fastajv);
    jPanel11.add(msfjv);
    jPanel11.add(pfamjv);
    jPanel11.add(pileupjv);
    jPanel11.add(pirjv);
    exportTab.add(modellerOutput);
    tabbedPane.add(calcTab, "Editing");
    calcTab.add(autoCalculateConsCheck);
    calcTab.add(padGaps);
    calcTab.add(sortByTree);
    
    tabbedPane.add(dasPanel, "DAS Settings");
    tabbedPane.add(wsPanel, "Web Services");

    exportTab.add(epsLabel);
    exportTab.add(epsRendering);
    exportTab.add(jPanel11);
  }

  protected void maxColour_actionPerformed()
  {
    // TODO Auto-generated method stub
    
  }

  protected void minColour_actionPerformed()
  {
    // TODO Auto-generated method stub
    
  }

  protected void showunconserved_actionPerformed(ActionEvent e)
  {
    // TODO Auto-generated method stub

  }

  /**
   * DOCUMENT ME!
   * 
   * @param e
   *          DOCUMENT ME!
   */
  public void ok_actionPerformed(ActionEvent e)
  {
  }

  /**
   * DOCUMENT ME!
   * 
   * @param e
   *          DOCUMENT ME!
   */
  public void cancel_actionPerformed(ActionEvent e)
  {
  }

  /**
   * DOCUMENT ME!
   * 
   * @param e
   *          DOCUMENT ME!
   */
  public void annotations_actionPerformed(ActionEvent e)
  {
  }

  /**
   * DOCUMENT ME!
   */
  public void startupFileTextfield_mouseClicked()
  {
  }

  public void newLink_actionPerformed(ActionEvent e)
  {

  }

  public void editLink_actionPerformed(ActionEvent e)
  {

  }

  public void deleteLink_actionPerformed(ActionEvent e)
  {

  }

  public void defaultBrowser_mouseClicked(MouseEvent e)
  {

  }

  public void linkURLList_keyTyped(KeyEvent e)
  {

  }

  public void useProxy_actionPerformed()
  {
    proxyServerTB.setEnabled(useProxy.isSelected());
    proxyPortTB.setEnabled(useProxy.isSelected());
  }

}