/* * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) * Copyright (C) 2014 The Jalview Authors * * 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 . * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.jbgui; import jalview.gui.JvSwingUtils; import jalview.util.MessageManager; 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( MessageManager.getString("label.proxy_server")); TitledBorder titledBorder2 = new TitledBorder( MessageManager.getString("label.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(); protected JLabel userIdWidthlabel = new JLabel(); protected JCheckBox autoIdWidth = new JCheckBox(); protected JTextField userIdWidth = new JTextField(); 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(MessageManager.getString("action.ok")); ok.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { ok_actionPerformed(e); } }); cancel.setText(MessageManager.getString("action.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(MessageManager.getString("label.quality")); visualTab.setBorder(new TitledBorder(MessageManager .getString("action.open_new_aligmnent"))); visualTab.setLayout(null); visual2Tab.setBorder(new TitledBorder(MessageManager .getString("action.open_new_aligmnent"))); visual2Tab.setLayout(new FlowLayout()); fullScreen.setFont(verdana11); fullScreen.setHorizontalAlignment(SwingConstants.RIGHT); fullScreen.setHorizontalTextPosition(SwingConstants.LEFT); fullScreen.setText(MessageManager.getString("label.maximize_window")); conservation.setEnabled(false); conservation.setFont(verdana11); conservation.setHorizontalAlignment(SwingConstants.RIGHT); conservation.setHorizontalTextPosition(SwingConstants.LEFT); conservation.setSelected(true); conservation.setText(MessageManager.getString("label.conservation")); identity.setEnabled(false); identity.setFont(verdana11); identity.setHorizontalAlignment(SwingConstants.RIGHT); identity.setHorizontalTextPosition(SwingConstants.LEFT); identity.setSelected(true); identity.setText(MessageManager.getString("label.consensus")); showGroupbits.setFont(verdana11); showGroupbits.setHorizontalAlignment(SwingConstants.RIGHT); showGroupbits.setHorizontalTextPosition(SwingConstants.LEFT); showGroupbits.setText(MessageManager.getString("action.show_group") + ":"); showConsensbits.setFont(verdana11); showConsensbits.setHorizontalAlignment(SwingConstants.RIGHT); showConsensbits.setHorizontalTextPosition(SwingConstants.LEFT); showConsensbits.setText(MessageManager.getString("label.consensus") + ":"); showConsensHistogram.setEnabled(false); showConsensHistogram.setFont(verdana11); showConsensHistogram.setHorizontalAlignment(SwingConstants.RIGHT); showConsensHistogram.setHorizontalTextPosition(SwingConstants.LEFT); showConsensHistogram.setSelected(true); showConsensHistogram.setText(MessageManager .getString("label.histogram")); showConsensLogo.setEnabled(false); showConsensLogo.setFont(verdana11); showConsensLogo.setHorizontalAlignment(SwingConstants.RIGHT); showConsensLogo.setHorizontalTextPosition(SwingConstants.LEFT); showConsensLogo.setSelected(true); showConsensLogo.setText(MessageManager.getString("label.logo")); showGroupConsensus.setEnabled(false); showGroupConsensus.setFont(verdana11); showGroupConsensus.setHorizontalAlignment(SwingConstants.RIGHT); showGroupConsensus.setHorizontalTextPosition(SwingConstants.LEFT); showGroupConsensus.setSelected(true); showGroupConsensus.setText(MessageManager.getString("label.consensus")); showGroupConservation.setEnabled(false); showGroupConservation.setFont(verdana11); showGroupConservation.setHorizontalAlignment(SwingConstants.RIGHT); showGroupConservation.setHorizontalTextPosition(SwingConstants.LEFT); showGroupConservation.setSelected(true); showGroupConservation.setText(MessageManager .getString("label.conservation")); showNpTooltip.setEnabled(true); showNpTooltip.setFont(verdana11); showNpTooltip.setHorizontalAlignment(SwingConstants.RIGHT); showNpTooltip.setHorizontalTextPosition(SwingConstants.LEFT); showNpTooltip.setSelected(true); showNpTooltip.setText(MessageManager .getString("label.non_positional_features")); showDbRefTooltip.setEnabled(true); showDbRefTooltip.setFont(verdana11); showDbRefTooltip.setHorizontalAlignment(SwingConstants.RIGHT); showDbRefTooltip.setHorizontalTextPosition(SwingConstants.LEFT); showDbRefTooltip.setSelected(true); showDbRefTooltip.setText(MessageManager .getString("label.database_references")); annotations.setFont(verdana11); annotations.setHorizontalAlignment(SwingConstants.RIGHT); annotations.setHorizontalTextPosition(SwingConstants.LEADING); annotations.setSelected(true); annotations.setText(MessageManager.getString("label.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(MessageManager .getString("action.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(MessageManager .getString("label.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(MessageManager .getString("label.scroll_highlighted_regions")); gapLabel.setFont(verdana11); gapLabel.setHorizontalAlignment(SwingConstants.RIGHT); gapLabel.setText(MessageManager.getString("label.gap_symbol") + " "); colour.setFont(verdana11); colour.setBounds(new Rectangle(172, 225, 155, 21)); colourLabel.setFont(verdana11); colourLabel.setHorizontalAlignment(SwingConstants.RIGHT); colourLabel.setText(MessageManager.getString("label.alignment_colour") + " "); fontLabel.setFont(verdana11); fontLabel.setHorizontalAlignment(SwingConstants.RIGHT); fontLabel.setText(MessageManager.getString("label.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(MessageManager.getString("label.min_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(MessageManager.getString("label.max_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(MessageManager.getString("action.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(MessageManager.getString("label.address")); serverLabel.setHorizontalAlignment(SwingConstants.RIGHT); serverLabel.setFont(verdana11); proxyServerTB.setFont(verdana11); proxyPortTB.setFont(verdana11); portLabel.setFont(verdana11); portLabel.setHorizontalAlignment(SwingConstants.RIGHT); portLabel.setText(MessageManager.getString("label.port")); browserLabel.setFont(new java.awt.Font("SansSerif", 0, 11)); browserLabel.setHorizontalAlignment(SwingConstants.TRAILING); browserLabel.setText(MessageManager .getString("label.default_browser_unix")); defaultBrowser.setFont(verdana11); defaultBrowser.setText(""); usagestats.setText(MessageManager .getString("label.send_usage_statistics")); usagestats.setFont(verdana11); usagestats.setHorizontalAlignment(SwingConstants.RIGHT); usagestats.setHorizontalTextPosition(SwingConstants.LEADING); questionnaire.setText(MessageManager .getString("label.check_for_questionnaires")); questionnaire.setFont(verdana11); questionnaire.setHorizontalAlignment(SwingConstants.RIGHT); questionnaire.setHorizontalTextPosition(SwingConstants.LEADING); versioncheck.setText(MessageManager .getString("label.check_for_latest_version")); versioncheck.setFont(verdana11); versioncheck.setHorizontalAlignment(SwingConstants.RIGHT); versioncheck.setHorizontalTextPosition(SwingConstants.LEADING); newLink.setText(MessageManager.getString("action.new")); newLink.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { newLink_actionPerformed(e); } }); editLink.setText(MessageManager.getString("action.edit")); editLink.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { editLink_actionPerformed(e); } }); deleteLink.setText(MessageManager.getString("action.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(MessageManager .getString("label.url_linkfrom_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(MessageManager.getString("label.use_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(MessageManager.getString("label.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(MessageManager.getString("label.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(MessageManager.getString("label.append_start_end")); jLabel1.setFont(verdana11); fastajv.setFont(verdana11); fastajv.setHorizontalAlignment(SwingConstants.LEFT); clustaljv.setText(MessageManager.getString("label.clustal") + " "); blcjv.setText(MessageManager.getString("label.blc") + " "); fastajv.setText(MessageManager.getString("label.fasta") + " "); msfjv.setText(MessageManager.getString("label.msf") + " "); pfamjv.setText(MessageManager.getString("label.pfam") + " "); pileupjv.setText(MessageManager.getString("label.pileup") + " "); msfjv.setFont(verdana11); msfjv.setHorizontalAlignment(SwingConstants.LEFT); pirjv.setText(MessageManager.getString("label.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(MessageManager.getString("label.full_sequence_id")); gridLayout3.setRows(8); smoothFont.setFont(verdana11); smoothFont.setHorizontalAlignment(SwingConstants.RIGHT); smoothFont.setHorizontalTextPosition(SwingConstants.LEADING); smoothFont.setText(MessageManager.getString("label.smooth_font")); calcTab.setLayout(null); autoCalculateConsCheck.setFont(JvSwingUtils.getLabelFont()); autoCalculateConsCheck.setText(MessageManager .getString("label.autocalculate_consensus")); autoCalculateConsCheck.setBounds(new Rectangle(21, 52, 209, 23)); padGaps.setFont(JvSwingUtils.getLabelFont()); padGaps.setText(MessageManager.getString("label.pad_gaps_when_editing")); padGaps.setBounds(new Rectangle(22, 94, 168, 23)); sortByTree.setFont(JvSwingUtils.getLabelFont()); sortByTree .setText(MessageManager.getString("label.sort_with_new_tree")); sortByTree .setToolTipText(MessageManager .getString("label.any_trees_calculated_or_loaded_alignment_automatically_sort")); sortByTree.setBounds(new Rectangle(22, 136, 168, 23)); autoIdWidth.setFont(JvSwingUtils.getLabelFont()); autoIdWidth.setText(MessageManager .getString("label.automatically_set_id_width")); autoIdWidth .setToolTipText(JvSwingUtils.wrapTooltip(MessageManager.getString("label.adjusts_width_generated_eps_png"))); autoIdWidth.setBounds(new Rectangle(228, 96, 188, 23)); autoIdWidth.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { autoIdWidth_actionPerformed(); } }); userIdWidthlabel.setFont(JvSwingUtils.getLabelFont()); userIdWidthlabel.setText(MessageManager .getString("label.figure_id_column_width")); userIdWidth .setToolTipText(JvSwingUtils.wrapTooltip(MessageManager.getString("label.manually_specify_width_left_column"))); userIdWidthlabel .setToolTipText(JvSwingUtils.wrapTooltip(MessageManager.getString("label.manually_specify_width_left_column"))); userIdWidthlabel.setBounds(new Rectangle(236, 120, 168, 23)); userIdWidth.setFont(JvSwingUtils.getTextAreaFont()); userIdWidth.setText(""); userIdWidth.setBounds(new Rectangle(232, 144, 84, 23)); userIdWidth.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { userIdWidth_actionPerformed(); } }); modellerOutput.setFont(JvSwingUtils.getLabelFont()); modellerOutput.setText(MessageManager .getString("label.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(MessageManager.getString("label.wrap_alignment")); rightAlign.setFont(JvSwingUtils.getLabelFont()); rightAlign.setForeground(Color.black); rightAlign.setHorizontalAlignment(SwingConstants.RIGHT); rightAlign.setHorizontalTextPosition(SwingConstants.LEFT); rightAlign.setText(MessageManager.getString("label.right_align_ids")); idItalics.setFont(JvSwingUtils.getLabelFont()); idItalics.setHorizontalAlignment(SwingConstants.RIGHT); idItalics.setHorizontalTextPosition(SwingConstants.LEADING); idItalics.setText(MessageManager .getString("label.sequence_name_italics")); openoverv.setFont(JvSwingUtils.getLabelFont()); openoverv.setActionCommand(MessageManager .getString("label.open_overview")); openoverv.setHorizontalAlignment(SwingConstants.RIGHT); openoverv.setHorizontalTextPosition(SwingConstants.LEFT); openoverv.setText(MessageManager.getString(("label.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(MessageManager .getString("label.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, MessageManager .getString("label.default_colour_scheme_for_alignment"), colourLabel, colour); JPanel annotationShding = new JPanel(); annotationShding.setBorder(new TitledBorder(MessageManager .getString("label.annotation_shading_default"))); annotationShding.setLayout(new GridLayout(1, 2)); JvSwingUtils.addtoLayout(annotationShding, MessageManager .getString("label.default_minimum_colour_annotation_shading"), mincolourLabel, minColour); JvSwingUtils.addtoLayout(annotationShding, MessageManager .getString("label.default_maximum_colour_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, MessageManager.getString("label.visual")); tabbedPane.add(visual2Tab, MessageManager.getString("label.colours")); tabbedPane.add(connectTab, MessageManager.getString("label.connections")); tabbedPane.add(exportTab, MessageManager.getString("label.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(autoIdWidth); exportTab.add(userIdWidth); exportTab.add(userIdWidthlabel); exportTab.add(modellerOutput); tabbedPane.add(calcTab, MessageManager.getString("label.editing")); calcTab.add(autoCalculateConsCheck); calcTab.add(padGaps); calcTab.add(sortByTree); tabbedPane .add(dasPanel, MessageManager.getString("label.das_settings")); tabbedPane.add(wsPanel, MessageManager.getString("label.web_services")); exportTab.add(epsLabel); exportTab.add(epsRendering); exportTab.add(jPanel11); } protected void autoIdWidth_actionPerformed() { // TODO Auto-generated method stub } protected void userIdWidth_actionPerformed() { // TODO Auto-generated method stub } 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()); } }