/* * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) * Copyright (C) $$Year-Rel$$ 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 java.awt.BorderLayout; import java.awt.Color; import java.awt.Component; import java.awt.Dimension; import java.awt.FlowLayout; import java.awt.Font; import java.awt.GridBagConstraints; import java.awt.GridBagLayout; import java.awt.GridLayout; import java.awt.Insets; import java.awt.Rectangle; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.awt.event.FocusEvent; import java.awt.event.KeyEvent; import java.awt.event.KeyListener; import java.awt.event.MouseAdapter; import java.awt.event.MouseEvent; import java.util.Arrays; import java.util.List; import javax.swing.AbstractCellEditor; import javax.swing.BorderFactory; import javax.swing.ButtonGroup; import javax.swing.DefaultListCellRenderer; import javax.swing.JButton; import javax.swing.JCheckBox; import javax.swing.JComboBox; import javax.swing.JFileChooser; import javax.swing.JLabel; import javax.swing.JPanel; import javax.swing.JRadioButton; import javax.swing.JScrollPane; import javax.swing.JSpinner; import javax.swing.JTabbedPane; import javax.swing.JTable; import javax.swing.JTextArea; import javax.swing.JTextField; import javax.swing.ListSelectionModel; import javax.swing.SpinnerModel; import javax.swing.SpinnerNumberModel; import javax.swing.SwingConstants; import javax.swing.border.Border; import javax.swing.border.EmptyBorder; import javax.swing.border.EtchedBorder; import javax.swing.border.TitledBorder; import javax.swing.event.ChangeEvent; import javax.swing.event.ChangeListener; import javax.swing.table.TableCellEditor; import javax.swing.table.TableCellRenderer; import jalview.bin.Cache; import jalview.fts.core.FTSDataColumnPreferences; import jalview.fts.core.FTSDataColumnPreferences.PreferenceSource; import jalview.fts.service.pdb.PDBFTSRestClient; import jalview.gui.Desktop; import jalview.gui.JalviewBooleanRadioButtons; import jalview.gui.JvOptionPane; import jalview.gui.JvSwingUtils; import jalview.gui.StructureViewer.ViewerType; import jalview.io.BackupFilenameParts; import jalview.io.BackupFiles; import jalview.io.BackupFilesPresetEntry; import jalview.io.IntKeyStringValueEntry; import jalview.util.MessageManager; /** * Base class for the Preferences panel. * * @author $author$ * @version $Revision$ */ public class GPreferences extends JPanel { private static final Font LABEL_FONT = JvSwingUtils.getLabelFont(); private static final Font LABEL_FONT_ITALIC = JvSwingUtils .getLabelFont(false, true); private static final Font LABEL_FONT_BOLD = JvSwingUtils .getLabelFont(true, false); /* * Visual tab components */ protected JCheckBox fullScreen = new JCheckBox(); protected JCheckBox openoverv = new JCheckBox(); protected JCheckBox seqLimit = new JCheckBox(); protected JCheckBox rightAlign = new JCheckBox(); protected JComboBox fontSizeCB = new JComboBox<>(); protected JComboBox fontStyleCB = new JComboBox<>(); protected JComboBox fontNameCB = new JComboBox<>(); protected JCheckBox showOccupancy = new JCheckBox(); protected JCheckBox showUnconserved = new JCheckBox(); protected JCheckBox idItalics = new JCheckBox(); protected JCheckBox smoothFont = new JCheckBox(); protected JCheckBox scaleProteinToCdna = new JCheckBox(); protected JComboBox gapSymbolCB = new JComboBox<>(); protected JCheckBox wrap = new JCheckBox(); protected JComboBox sortby = new JComboBox<>(); protected JComboBox sortAnnBy = new JComboBox<>(); protected JComboBox sortAutocalc = new JComboBox<>(); protected JCheckBox startupCheckbox = new JCheckBox(); protected JTextField startupFileTextfield = new JTextField(); // below are in the 'second column' protected JCheckBox annotations = new JCheckBox(); protected JCheckBox quality = new JCheckBox(); protected JCheckBox conservation = new JCheckBox(); protected JCheckBox identity = new JCheckBox(); protected JCheckBox showGroupConsensus = new JCheckBox(); protected JCheckBox showGroupConservation = new JCheckBox(); protected JCheckBox showConsensHistogram = new JCheckBox(); protected JCheckBox showConsensLogo = new JCheckBox(); protected JCheckBox showDbRefTooltip = new JCheckBox(); protected JCheckBox showNpTooltip = new JCheckBox(); /* * Structure tab and components */ protected JPanel structureTab; protected JCheckBox structFromPdb = new JCheckBox(); protected JCheckBox useRnaView = new JCheckBox(); protected JCheckBox addSecondaryStructure = new JCheckBox(); protected JCheckBox addTempFactor = new JCheckBox(); protected JComboBox structViewer = new JComboBox<>(); protected JLabel structureViewerPathLabel; protected JTextField structureViewerPath = new JTextField(); protected ButtonGroup mappingMethod = new ButtonGroup(); protected JRadioButton siftsMapping = new JRadioButton(); protected JRadioButton nwMapping = new JRadioButton(); /* * Colours tab components */ protected JPanel minColour = new JPanel(); protected JPanel maxColour = new JPanel(); protected JComboBox protColour = new JComboBox<>(); protected JComboBox nucColour = new JComboBox<>(); /* * Overview tab components */ protected JPanel gapColour = new JPanel(); protected JPanel hiddenColour = new JPanel(); protected JCheckBox useLegacyGap; protected JCheckBox showHiddenAtStart; protected JLabel gapLabel; /* * Connections tab components */ protected JTable linkUrlTable = new JTable(); protected JButton editLink = new JButton(); protected JButton deleteLink = new JButton(); protected JTextField filterTB = new JTextField(); protected JButton doReset = new JButton(); protected JButton userOnly = new JButton(); protected JLabel portLabel = new JLabel(); protected JLabel serverLabel = new JLabel(); protected JTextField proxyServerTB = new JTextField(); protected JTextField proxyPortTB = new JTextField(); protected JTextField defaultBrowser = new JTextField(); protected JCheckBox useProxy = new JCheckBox(); protected JCheckBox usagestats = new JCheckBox(); protected JCheckBox questionnaire = new JCheckBox(); protected JCheckBox versioncheck = new JCheckBox(); /* * Output tab components */ protected JComboBox epsRendering = new JComboBox<>(); protected JLabel userIdWidthlabel = new JLabel(); protected JCheckBox autoIdWidth = new JCheckBox(); protected JTextField userIdWidth = new JTextField(); 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(); protected JCheckBox pirjv = new JCheckBox(); protected JCheckBox modellerOutput = new JCheckBox(); protected JCheckBox embbedBioJSON = new JCheckBox(); /* * Editing tab components */ protected JCheckBox autoCalculateConsCheck = new JCheckBox(); protected JCheckBox padGaps = new JCheckBox(); protected JCheckBox sortByTree = new JCheckBox(); /* * Web Services tab */ protected JPanel wsTab = new JPanel(); /* * Backups tab components * a lot of these are member variables instead of local variables only so that they * can be enabled/disabled easily in one go */ protected JCheckBox enableBackupFiles = new JCheckBox(); protected JPanel presetsPanel = new JPanel(); protected JLabel presetsComboLabel = new JLabel(); protected JCheckBox customiseCheckbox = new JCheckBox(); protected JButton revertButton = new JButton(); protected JComboBox backupfilesPresetsCombo = new JComboBox<>(); private int backupfilesPresetsComboLastSelected = 0; protected JPanel suffixPanel = new JPanel(); protected JPanel keepfilesPanel = new JPanel(); protected JPanel exampleFilesPanel = new JPanel(); protected JTextField suffixTemplate = new JTextField(null, 8); protected JLabel suffixTemplateLabel = new JLabel(); protected JLabel suffixDigitsLabel = new JLabel(); protected JSpinner suffixDigitsSpinner = new JSpinner(); protected JalviewBooleanRadioButtons suffixReverse = new JalviewBooleanRadioButtons(); protected JalviewBooleanRadioButtons backupfilesKeepAll = new JalviewBooleanRadioButtons(); public JSpinner backupfilesRollMaxSpinner = new JSpinner(); protected JLabel oldBackupFilesLabel = new JLabel(); protected JalviewBooleanRadioButtons backupfilesConfirmDelete = new JalviewBooleanRadioButtons(); protected JTextArea backupfilesExampleLabel = new JTextArea(); /** * Creates a new GPreferences object. */ public GPreferences() { try { jbInit(); } catch (Exception ex) { ex.printStackTrace(); } } /** * Construct the panel and its tabbed sub-panels. * * @throws Exception */ private void jbInit() throws Exception { final JTabbedPane tabbedPane = new JTabbedPane(); this.setLayout(new BorderLayout()); JPanel okCancelPanel = initOkCancelPanel(); this.add(tabbedPane, BorderLayout.CENTER); this.add(okCancelPanel, BorderLayout.SOUTH); tabbedPane.add(initVisualTab(), MessageManager.getString("label.visual")); tabbedPane.add(initColoursTab(), MessageManager.getString("label.colours")); tabbedPane.add(initOverviewTab(), MessageManager.getString("label.overview")); tabbedPane.add(initStructureTab(), MessageManager.getString("label.structure")); tabbedPane.add(initConnectionsTab(), MessageManager.getString("label.connections")); tabbedPane.add(initBackupsTab(), MessageManager.getString("label.backups")); tabbedPane.add(initLinksTab(), MessageManager.getString("label.urllinks")); tabbedPane.add(initOutputTab(), MessageManager.getString("label.output")); tabbedPane.add(initEditingTab(), MessageManager.getString("label.editing")); /* * See WsPreferences for the real work of configuring this tab. */ wsTab.setLayout(new BorderLayout()); tabbedPane.add(wsTab, MessageManager.getString("label.web_services")); /* * Handler to validate a tab before leaving it - currently only for * Structure. */ tabbedPane.addChangeListener(new ChangeListener() { private Component lastTab; @Override public void stateChanged(ChangeEvent e) { if (lastTab == structureTab && tabbedPane.getSelectedComponent() != structureTab) { if (!validateStructure()) { tabbedPane.setSelectedComponent(structureTab); return; } } lastTab = tabbedPane.getSelectedComponent(); } }); } /** * Initialises the Editing tabbed panel. * * @return */ private JPanel initEditingTab() { JPanel editingTab = new JPanel(); editingTab.setLayout(null); autoCalculateConsCheck.setFont(LABEL_FONT); autoCalculateConsCheck.setText( MessageManager.getString("label.autocalculate_consensus")); autoCalculateConsCheck.setBounds(new Rectangle(21, 52, 209, 23)); padGaps.setFont(LABEL_FONT); padGaps.setText( MessageManager.getString("label.pad_gaps_when_editing")); padGaps.setBounds(new Rectangle(22, 94, 168, 23)); sortByTree.setFont(LABEL_FONT); 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)); editingTab.add(autoCalculateConsCheck); editingTab.add(padGaps); editingTab.add(sortByTree); return editingTab; } /** * Initialises the Output tabbed panel. * * @return */ private JPanel initOutputTab() { JPanel outputTab = new JPanel(); outputTab.setLayout(null); JLabel epsLabel = new JLabel(); epsLabel.setFont(LABEL_FONT); epsLabel.setHorizontalAlignment(SwingConstants.RIGHT); epsLabel.setText(MessageManager.getString("label.eps_rendering_style")); epsLabel.setBounds(new Rectangle(9, 31, 140, 24)); epsRendering.setFont(LABEL_FONT); epsRendering.setBounds(new Rectangle(154, 34, 187, 21)); JLabel jLabel1 = new JLabel(); jLabel1.setFont(LABEL_FONT); jLabel1.setHorizontalAlignment(SwingConstants.CENTER); jLabel1.setText(MessageManager.getString("label.append_start_end")); jLabel1.setFont(LABEL_FONT); fastajv.setFont(LABEL_FONT); 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(LABEL_FONT); msfjv.setHorizontalAlignment(SwingConstants.LEFT); pirjv.setText(MessageManager.getString("label.pir") + " "); JPanel jPanel11 = new JPanel(); jPanel11.setFont(LABEL_FONT); TitledBorder titledBorder2 = new TitledBorder( MessageManager.getString("label.file_output")); jPanel11.setBorder(titledBorder2); jPanel11.setBounds(new Rectangle(30, 72, 196, 182)); GridLayout gridLayout3 = new GridLayout(); jPanel11.setLayout(gridLayout3); gridLayout3.setRows(8); blcjv.setFont(LABEL_FONT); blcjv.setHorizontalAlignment(SwingConstants.LEFT); clustaljv.setFont(LABEL_FONT); clustaljv.setHorizontalAlignment(SwingConstants.LEFT); pfamjv.setFont(LABEL_FONT); pfamjv.setHorizontalAlignment(SwingConstants.LEFT); pileupjv.setFont(LABEL_FONT); pileupjv.setHorizontalAlignment(SwingConstants.LEFT); pirjv.setFont(LABEL_FONT); pirjv.setHorizontalAlignment(SwingConstants.LEFT); autoIdWidth.setFont(LABEL_FONT); autoIdWidth.setText( MessageManager.getString("label.automatically_set_id_width")); autoIdWidth.setToolTipText(JvSwingUtils.wrapTooltip(true, 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(LABEL_FONT); userIdWidthlabel.setText( MessageManager.getString("label.figure_id_column_width")); userIdWidth.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager .getString("label.manually_specify_width_left_column"))); userIdWidthlabel.setToolTipText( JvSwingUtils.wrapTooltip(true, 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(LABEL_FONT); modellerOutput .setText(MessageManager.getString("label.use_modeller_output")); modellerOutput.setBounds(new Rectangle(228, 226, 168, 23)); embbedBioJSON.setFont(LABEL_FONT); embbedBioJSON.setText(MessageManager.getString("label.embbed_biojson")); embbedBioJSON.setBounds(new Rectangle(228, 200, 250, 23)); jPanel11.add(jLabel1); jPanel11.add(blcjv); jPanel11.add(clustaljv); jPanel11.add(fastajv); jPanel11.add(msfjv); jPanel11.add(pfamjv); jPanel11.add(pileupjv); jPanel11.add(pirjv); outputTab.add(autoIdWidth); outputTab.add(userIdWidth); outputTab.add(userIdWidthlabel); outputTab.add(modellerOutput); outputTab.add(embbedBioJSON); outputTab.add(epsLabel); outputTab.add(epsRendering); outputTab.add(jPanel11); return outputTab; } /** * Initialises the Connections tabbed panel. * * @return */ private JPanel initConnectionsTab() { JPanel connectTab = new JPanel(); connectTab.setLayout(new GridBagLayout()); // Label for browser text box JLabel browserLabel = new JLabel(); browserLabel.setFont(LABEL_FONT); browserLabel.setHorizontalAlignment(SwingConstants.TRAILING); browserLabel.setText( MessageManager.getString("label.default_browser_unix")); defaultBrowser.setFont(LABEL_FONT); defaultBrowser.setText(""); final String tooltip = JvSwingUtils.wrapTooltip(true, MessageManager.getString("label.double_click_to_browse")); defaultBrowser.setToolTipText(tooltip); defaultBrowser.addMouseListener(new MouseAdapter() { @Override public void mouseClicked(MouseEvent e) { if (e.getClickCount() > 1) { defaultBrowser_mouseClicked(e); } } }); JPanel proxyPanel = initConnTabProxyPanel(); initConnTabCheckboxes(); // Add default Browser text box connectTab.add(browserLabel, new GridBagConstraints(0, 0, 1, 1, 0.0, 0.0, GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(10, 0, 5, 5), 5, 1)); defaultBrowser.setFont(LABEL_FONT); defaultBrowser.setText(""); connectTab.add(defaultBrowser, new GridBagConstraints(1, 0, 1, 1, 1.0, 0.0, GridBagConstraints.CENTER, GridBagConstraints.HORIZONTAL, new Insets(10, 0, 5, 10), 30, 1)); // Add proxy server panel connectTab.add(proxyPanel, new GridBagConstraints(0, 1, 2, 1, 1.0, 0.0, GridBagConstraints.CENTER, GridBagConstraints.HORIZONTAL, new Insets(10, 0, 5, 12), 4, 10)); // Add usage stats, version check and questionnaire checkboxes connectTab.add(usagestats, new GridBagConstraints(0, 2, 1, 1, 1.0, 0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL, new Insets(0, 2, 5, 5), 70, 1)); connectTab.add(questionnaire, new GridBagConstraints(1, 2, 1, 1, 1.0, 0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL, new Insets(0, 2, 5, 10), 70, 1)); connectTab.add(versioncheck, new GridBagConstraints(0, 3, 1, 1, 1.0, 0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL, new Insets(0, 2, 5, 5), 70, 1)); versioncheck.setVisible(false); // Add padding so the panel doesn't look ridiculous JPanel spacePanel = new JPanel(); connectTab.add(spacePanel, new GridBagConstraints(0, 4, 1, 1, 1.0, 1.0, GridBagConstraints.WEST, GridBagConstraints.BOTH, new Insets(0, 0, 0, 5), 70, 1)); return connectTab; } /** * Initialises the Links tabbed panel. * * @return */ private JPanel initLinksTab() { JPanel linkTab = new JPanel(); linkTab.setLayout(new GridBagLayout()); // Set up table for Url links linkUrlTable.getTableHeader().setReorderingAllowed(false); linkUrlTable.setFillsViewportHeight(true); linkUrlTable.setAutoResizeMode(JTable.AUTO_RESIZE_ALL_COLUMNS); linkUrlTable.setAutoCreateRowSorter(true); linkUrlTable.setSelectionMode(ListSelectionModel.SINGLE_SELECTION); // adjust row height so radio buttons actually fit // don't do this in the renderer, it causes the awt thread to activate // constantly JRadioButton temp = new JRadioButton(); linkUrlTable.setRowHeight(temp.getMinimumSize().height); // Table in scrollpane so that the table is given a scrollbar JScrollPane linkScrollPane = new JScrollPane(linkUrlTable); linkScrollPane.setBorder(null); // Panel for links functionality JPanel linkPanel = new JPanel(new GridBagLayout()); linkPanel.setBorder(new TitledBorder( MessageManager.getString("label.url_linkfrom_sequence_id"))); // Put the Url links panel together // Buttons go at top right, resizing only resizes the blank space vertically JPanel buttonPanel = initLinkTabUrlButtons(); GridBagConstraints linkConstraints1 = new GridBagConstraints(); linkConstraints1.insets = new Insets(0, 0, 5, 0); linkConstraints1.gridx = 0; linkConstraints1.gridy = 0; linkConstraints1.weightx = 1.0; linkConstraints1.fill = GridBagConstraints.HORIZONTAL; linkTab.add(buttonPanel, linkConstraints1); // Links table goes at top left, resizing resizes the table GridBagConstraints linkConstraints2 = new GridBagConstraints(); linkConstraints2.insets = new Insets(0, 0, 5, 5); linkConstraints2.gridx = 0; linkConstraints2.gridy = 1; linkConstraints2.weightx = 1.0; linkConstraints2.weighty = 1.0; linkConstraints2.fill = GridBagConstraints.BOTH; linkTab.add(linkScrollPane, linkConstraints2); // Filter box and buttons goes at bottom left, resizing resizes the text box JPanel filterPanel = initLinkTabFilterPanel(); GridBagConstraints linkConstraints3 = new GridBagConstraints(); linkConstraints3.insets = new Insets(0, 0, 0, 5); linkConstraints3.gridx = 0; linkConstraints3.gridy = 2; linkConstraints3.weightx = 1.0; linkConstraints3.fill = GridBagConstraints.HORIZONTAL; linkTab.add(filterPanel, linkConstraints3); return linkTab; } private JPanel initLinkTabFilterPanel() { // Filter textbox and reset button JLabel filterLabel = new JLabel( MessageManager.getString("label.filter")); filterLabel.setFont(LABEL_FONT); filterLabel.setHorizontalAlignment(SwingConstants.RIGHT); filterLabel.setHorizontalTextPosition(SwingConstants.LEADING); filterTB.setFont(LABEL_FONT); filterTB.setText(""); doReset.setText(MessageManager.getString("action.showall")); userOnly.setText(MessageManager.getString("action.customfilter")); // Panel for filter functionality JPanel filterPanel = new JPanel(new GridBagLayout()); filterPanel.setBorder(new TitledBorder("Filter")); GridBagConstraints gbc = new GridBagConstraints(); gbc.gridx = 0; gbc.gridy = 0; gbc.fill = GridBagConstraints.NONE; gbc.anchor = GridBagConstraints.WEST; filterPanel.add(filterLabel, gbc); GridBagConstraints gbc1 = new GridBagConstraints(); gbc1.gridx = 1; gbc1.gridwidth = 2; gbc1.fill = GridBagConstraints.HORIZONTAL; gbc1.anchor = GridBagConstraints.WEST; gbc1.weightx = 1.0; filterPanel.add(filterTB, gbc1); GridBagConstraints gbc2 = new GridBagConstraints(); gbc2.gridx = 3; gbc2.fill = GridBagConstraints.NONE; gbc2.anchor = GridBagConstraints.WEST; filterPanel.add(doReset, gbc2); GridBagConstraints gbc3 = new GridBagConstraints(); gbc3.gridx = 4; gbc3.fill = GridBagConstraints.NONE; gbc3.anchor = GridBagConstraints.WEST; filterPanel.add(userOnly, gbc3); return filterPanel; } private JPanel initLinkTabUrlButtons() { // Buttons for new / edit / delete Url links JButton newLink = new JButton(); newLink.setText(MessageManager.getString("action.new")); editLink.setText(MessageManager.getString("action.edit")); deleteLink.setText(MessageManager.getString("action.delete")); // no current selection, so initially disable delete/edit buttons editLink.setEnabled(false); deleteLink.setEnabled(false); newLink.addActionListener(new java.awt.event.ActionListener() { @Override public void actionPerformed(ActionEvent e) { newLink_actionPerformed(e); } }); editLink.setText(MessageManager.getString("action.edit")); editLink.addActionListener(new java.awt.event.ActionListener() { @Override public void actionPerformed(ActionEvent e) { editLink_actionPerformed(e); } }); deleteLink.setText(MessageManager.getString("action.delete")); deleteLink.addActionListener(new java.awt.event.ActionListener() { @Override public void actionPerformed(ActionEvent e) { deleteLink_actionPerformed(e); } }); JPanel buttonPanel = new JPanel(new GridBagLayout()); buttonPanel.setBorder(new TitledBorder("Edit links")); GridBagConstraints gbc = new GridBagConstraints(); gbc.gridx = 0; gbc.gridy = 0; gbc.fill = GridBagConstraints.NONE; buttonPanel.add(newLink, gbc); GridBagConstraints gbc1 = new GridBagConstraints(); gbc1.gridx = 1; gbc1.gridy = 0; gbc1.fill = GridBagConstraints.NONE; buttonPanel.add(editLink, gbc1); GridBagConstraints gbc2 = new GridBagConstraints(); gbc2.gridx = 2; gbc2.gridy = 0; gbc2.fill = GridBagConstraints.NONE; buttonPanel.add(deleteLink, gbc2); GridBagConstraints gbc3 = new GridBagConstraints(); gbc3.gridx = 3; gbc3.gridy = 0; gbc3.fill = GridBagConstraints.HORIZONTAL; gbc3.weightx = 1.0; JPanel spacePanel = new JPanel(); spacePanel.setBorder(null); buttonPanel.add(spacePanel, gbc3); return buttonPanel; } /** * Initialises the proxy server panel in the Connections tab * * @return the proxy server panel */ private JPanel initConnTabProxyPanel() { // Label for server text box serverLabel.setText(MessageManager.getString("label.address")); serverLabel.setHorizontalAlignment(SwingConstants.RIGHT); serverLabel.setFont(LABEL_FONT); // Proxy server and port text boxes proxyServerTB.setFont(LABEL_FONT); proxyPortTB.setFont(LABEL_FONT); // Label for Port text box portLabel.setFont(LABEL_FONT); portLabel.setHorizontalAlignment(SwingConstants.RIGHT); portLabel.setText(MessageManager.getString("label.port")); // Use proxy server checkbox useProxy.setFont(LABEL_FONT); useProxy.setHorizontalAlignment(SwingConstants.RIGHT); useProxy.setHorizontalTextPosition(SwingConstants.LEADING); useProxy.setText(MessageManager.getString("label.use_proxy_server")); useProxy.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { useProxy_actionPerformed(); } }); // Make proxy server panel JPanel proxyPanel = new JPanel(); TitledBorder titledBorder1 = new TitledBorder( MessageManager.getString("label.proxy_server")); proxyPanel.setBorder(titledBorder1); proxyPanel.setLayout(new GridBagLayout()); proxyPanel.add(serverLabel, new GridBagConstraints(0, 1, 1, 1, 0.0, 0.0, GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0, 2, 2, 0), 5, 0)); proxyPanel.add(portLabel, new GridBagConstraints(2, 1, 1, 1, 0.0, 0.0, GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0, 0, 2, 0), 11, 0)); proxyPanel.add(useProxy, new GridBagConstraints(0, 0, 2, 1, 0.0, 0.0, GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0, 2, 5, 185), 2, -4)); proxyPanel.add(proxyPortTB, new GridBagConstraints(3, 1, 1, 1, 1.0, 0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL, new Insets(0, 2, 2, 2), 54, 1)); proxyPanel.add(proxyServerTB, new GridBagConstraints(1, 1, 1, 1, 1.0, 0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL, new Insets(0, 2, 2, 0), 263, 1)); return proxyPanel; } /** * Initialises the checkboxes in the Connections tab */ private void initConnTabCheckboxes() { // Usage stats checkbox label usagestats.setText( MessageManager.getString("label.send_usage_statistics")); usagestats.setFont(LABEL_FONT); usagestats.setHorizontalAlignment(SwingConstants.RIGHT); usagestats.setHorizontalTextPosition(SwingConstants.LEADING); // Questionnaire checkbox label questionnaire.setText( MessageManager.getString("label.check_for_questionnaires")); questionnaire.setFont(LABEL_FONT); questionnaire.setHorizontalAlignment(SwingConstants.RIGHT); questionnaire.setHorizontalTextPosition(SwingConstants.LEADING); // Check for latest version checkbox label versioncheck.setText( MessageManager.getString("label.check_for_latest_version")); versioncheck.setFont(LABEL_FONT); versioncheck.setHorizontalAlignment(SwingConstants.RIGHT); versioncheck.setHorizontalTextPosition(SwingConstants.LEADING); } /** * Initialises the parent panel which contains the tabbed sections. * * @return */ private JPanel initOkCancelPanel() { JButton ok = new JButton(); ok.setText(MessageManager.getString("action.ok")); ok.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { ok_actionPerformed(e); } }); JButton cancel = new JButton(); cancel.setText(MessageManager.getString("action.cancel")); cancel.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { cancel_actionPerformed(e); } }); JPanel okCancelPanel = new JPanel(); okCancelPanel.add(ok); okCancelPanel.add(cancel); return okCancelPanel; } /** * Initialises the Colours tabbed panel. * * @return */ private JPanel initColoursTab() { JPanel coloursTab = new JPanel(); coloursTab.setBorder(new TitledBorder( MessageManager.getString("action.open_new_alignment"))); coloursTab.setLayout(new FlowLayout()); JLabel mincolourLabel = new JLabel(); mincolourLabel.setFont(LABEL_FONT); mincolourLabel.setHorizontalAlignment(SwingConstants.RIGHT); mincolourLabel.setText(MessageManager.getString("label.min_colour")); minColour.setFont(LABEL_FONT); minColour.setBorder(BorderFactory.createEtchedBorder()); minColour.setPreferredSize(new Dimension(40, 20)); minColour.addMouseListener(new MouseAdapter() { @Override public void mousePressed(MouseEvent e) { minColour_actionPerformed(minColour); } }); JLabel maxcolourLabel = new JLabel(); maxcolourLabel.setFont(LABEL_FONT); maxcolourLabel.setHorizontalAlignment(SwingConstants.RIGHT); maxcolourLabel.setText(MessageManager.getString("label.max_colour")); maxColour.setFont(LABEL_FONT); maxColour.setBorder(BorderFactory.createEtchedBorder()); maxColour.setPreferredSize(new Dimension(40, 20)); maxColour.addMouseListener(new MouseAdapter() { @Override public void mousePressed(MouseEvent e) { maxColour_actionPerformed(maxColour); } }); protColour.setFont(LABEL_FONT); protColour.setBounds(new Rectangle(172, 225, 155, 21)); JLabel protColourLabel = new JLabel(); protColourLabel.setFont(LABEL_FONT); protColourLabel.setHorizontalAlignment(SwingConstants.LEFT); protColourLabel.setText( MessageManager.getString("label.prot_alignment_colour") + " "); JvSwingUtils.addtoLayout(coloursTab, MessageManager .getString("label.default_colour_scheme_for_alignment"), protColourLabel, protColour); nucColour.setFont(LABEL_FONT); nucColour.setBounds(new Rectangle(172, 240, 155, 21)); JLabel nucColourLabel = new JLabel(); nucColourLabel.setFont(LABEL_FONT); nucColourLabel.setHorizontalAlignment(SwingConstants.LEFT); nucColourLabel.setText( MessageManager.getString("label.nuc_alignment_colour") + " "); JvSwingUtils.addtoLayout(coloursTab, MessageManager .getString("label.default_colour_scheme_for_alignment"), nucColourLabel, nucColour); 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); coloursTab.add(annotationShding); // , FlowLayout.LEFT); return coloursTab; } /** * Initialises the Overview tabbed panel. * * @return */ private JPanel initOverviewTab() { JPanel overviewPanel = new JPanel(); overviewPanel.setBorder(new TitledBorder( MessageManager.getString("label.overview_settings"))); gapColour.setFont(LABEL_FONT); // fixing the border colours stops apparent colour bleed from the panel gapColour.setBorder( BorderFactory.createEtchedBorder(Color.white, Color.lightGray)); gapColour.setPreferredSize(new Dimension(40, 20)); gapColour.addMouseListener(new MouseAdapter() { @Override public void mousePressed(MouseEvent e) { gapColour_actionPerformed(gapColour); } }); hiddenColour.setFont(LABEL_FONT); // fixing the border colours stops apparent colour bleed from the panel hiddenColour.setBorder( BorderFactory.createEtchedBorder(Color.white, Color.lightGray)); hiddenColour.setPreferredSize(new Dimension(40, 20)); hiddenColour.addMouseListener(new MouseAdapter() { @Override public void mousePressed(MouseEvent e) { hiddenColour_actionPerformed(hiddenColour); } }); useLegacyGap = new JCheckBox( MessageManager.getString("label.ov_legacy_gap")); useLegacyGap.setFont(LABEL_FONT); useLegacyGap.setHorizontalAlignment(SwingConstants.LEFT); useLegacyGap.setVerticalTextPosition(SwingConstants.TOP); gapLabel = new JLabel(MessageManager.getString("label.gap_colour")); gapLabel.setFont(LABEL_FONT); gapLabel.setHorizontalAlignment(SwingConstants.LEFT); gapLabel.setVerticalTextPosition(SwingConstants.TOP); showHiddenAtStart = new JCheckBox( MessageManager.getString("label.ov_show_hide_default")); showHiddenAtStart.setFont(LABEL_FONT); showHiddenAtStart.setHorizontalAlignment(SwingConstants.LEFT); showHiddenAtStart.setVerticalTextPosition(SwingConstants.TOP); JLabel hiddenLabel = new JLabel( MessageManager.getString("label.hidden_colour")); hiddenLabel.setFont(LABEL_FONT); hiddenLabel.setHorizontalAlignment(SwingConstants.LEFT); hiddenLabel.setVerticalTextPosition(SwingConstants.TOP); useLegacyGap.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { useLegacyGaps_actionPerformed(e); } }); overviewPanel.setLayout(new GridBagLayout()); GridBagConstraints c1 = new GridBagConstraints(); c1.fill = GridBagConstraints.HORIZONTAL; c1.gridx = 0; c1.gridy = 0; c1.weightx = 1; c1.ipady = 20; c1.anchor = GridBagConstraints.FIRST_LINE_START; overviewPanel.add(useLegacyGap, c1); GridBagConstraints c2 = new GridBagConstraints(); c2.fill = GridBagConstraints.HORIZONTAL; c2.gridx = 1; c2.gridy = 0; c2.insets = new Insets(0, 15, 0, 10); overviewPanel.add(gapLabel, c2); GridBagConstraints c3 = new GridBagConstraints(); c3.fill = GridBagConstraints.HORIZONTAL; c3.gridx = 2; c3.gridy = 0; c3.insets = new Insets(0, 0, 0, 15); overviewPanel.add(gapColour, c3); GridBagConstraints c4 = new GridBagConstraints(); c4.fill = GridBagConstraints.HORIZONTAL; c4.gridx = 0; c4.gridy = 1; c4.weightx = 1; overviewPanel.add(showHiddenAtStart, c4); GridBagConstraints c5 = new GridBagConstraints(); c5.fill = GridBagConstraints.HORIZONTAL; c5.gridx = 1; c5.gridy = 1; c5.insets = new Insets(0, 15, 0, 10); overviewPanel.add(hiddenLabel, c5); GridBagConstraints c6 = new GridBagConstraints(); c6.fill = GridBagConstraints.HORIZONTAL; c6.gridx = 2; c6.gridy = 1; c6.insets = new Insets(0, 0, 0, 15); overviewPanel.add(hiddenColour, c6); JButton resetButton = new JButton( MessageManager.getString("label.reset_to_defaults")); resetButton.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { resetOvDefaults_actionPerformed(e); } }); GridBagConstraints c7 = new GridBagConstraints(); c7.fill = GridBagConstraints.NONE; c7.gridx = 0; c7.gridy = 2; c7.insets = new Insets(10, 0, 0, 0); c7.anchor = GridBagConstraints.WEST; overviewPanel.add(resetButton, c7); // Add padding so the panel doesn't look ridiculous JPanel spacePanel = new JPanel(); overviewPanel.add(spacePanel, new GridBagConstraints(0, 3, 1, 1, 1.0, 1.0, GridBagConstraints.WEST, GridBagConstraints.BOTH, new Insets(0, 0, 0, 5), 0, 0)); return overviewPanel; } /** * Initialises the Structure tabbed panel. * * @return */ private JPanel initStructureTab() { structureTab = new JPanel(); structureTab.setBorder(new TitledBorder( MessageManager.getString("label.structure_options"))); structureTab.setLayout(null); final int width = 420; final int height = 22; final int lineSpacing = 25; int ypos = 15; structFromPdb.setFont(LABEL_FONT); structFromPdb .setText(MessageManager.getString("label.struct_from_pdb")); structFromPdb.setBounds(new Rectangle(5, ypos, width, height)); structFromPdb.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { boolean selected = structFromPdb.isSelected(); // enable other options only when the first is checked useRnaView.setEnabled(selected); addSecondaryStructure.setEnabled(selected); addTempFactor.setEnabled(selected); } }); structureTab.add(structFromPdb); // indent checkboxes that are conditional on the first one ypos += lineSpacing; useRnaView.setFont(LABEL_FONT); useRnaView.setText(MessageManager.getString("label.use_rnaview")); useRnaView.setBounds(new Rectangle(25, ypos, width, height)); structureTab.add(useRnaView); ypos += lineSpacing; addSecondaryStructure.setFont(LABEL_FONT); addSecondaryStructure .setText(MessageManager.getString("label.autoadd_secstr")); addSecondaryStructure.setBounds(new Rectangle(25, ypos, width, height)); structureTab.add(addSecondaryStructure); ypos += lineSpacing; addTempFactor.setFont(LABEL_FONT); addTempFactor.setText(MessageManager.getString("label.autoadd_temp")); addTempFactor.setBounds(new Rectangle(25, ypos, width, height)); structureTab.add(addTempFactor); ypos += lineSpacing; JLabel viewerLabel = new JLabel(); viewerLabel.setFont(LABEL_FONT); viewerLabel.setHorizontalAlignment(SwingConstants.LEFT); viewerLabel.setText(MessageManager.getString("label.structure_viewer")); viewerLabel.setBounds(new Rectangle(10, ypos, 220, height)); structureTab.add(viewerLabel); /* * add all external viewers as options here - check * when selected whether the program is installed */ structViewer.setFont(LABEL_FONT); structViewer.setBounds(new Rectangle(190, ypos, 120, height)); structViewer.addItem(ViewerType.JMOL.name()); structViewer.addItem(ViewerType.CHIMERA.name()); structViewer.addItem(ViewerType.CHIMERAX.name()); structViewer.addItem(ViewerType.PYMOL.name()); structViewer.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { structureViewer_actionPerformed( (String) structViewer.getSelectedItem()); } }); structureTab.add(structViewer); ypos += lineSpacing; structureViewerPathLabel = new JLabel(); structureViewerPathLabel.setFont(LABEL_FONT);// new Font("SansSerif", 0, 11)); structureViewerPathLabel.setHorizontalAlignment(SwingConstants.LEFT); structureViewerPathLabel.setText(MessageManager .formatMessage("label.viewer_path", "Chimera(X)")); structureViewerPathLabel.setBounds(new Rectangle(10, ypos, 170, height)); structureViewerPathLabel.setEnabled(false); structureTab.add(structureViewerPathLabel); structureViewerPath.setFont(LABEL_FONT); structureViewerPath.setText(""); structureViewerPath.setEnabled(false); final String tooltip = JvSwingUtils.wrapTooltip(true, MessageManager.getString("label.viewer_path_tip")); structureViewerPath.setToolTipText(tooltip); structureViewerPath.setBounds(new Rectangle(190, ypos, 290, height)); structureViewerPath.addMouseListener(new MouseAdapter() { @Override public void mouseClicked(MouseEvent e) { if (structureViewerPath.isEnabled() && e.getClickCount() == 2) { String chosen = openFileChooser(); if (chosen != null) { structureViewerPath.setText(chosen); } } } }); structureTab.add(structureViewerPath); ypos += lineSpacing; nwMapping.setFont(LABEL_FONT); nwMapping.setText(MessageManager.getString("label.nw_mapping")); siftsMapping.setFont(LABEL_FONT); siftsMapping.setText(MessageManager.getString("label.sifts_mapping")); mappingMethod.add(nwMapping); mappingMethod.add(siftsMapping); JPanel mappingPanel = new JPanel(); mappingPanel.setFont(LABEL_FONT); TitledBorder mmTitledBorder = new TitledBorder( MessageManager.getString("label.mapping_method")); mmTitledBorder.setTitleFont(LABEL_FONT); mappingPanel.setBorder(mmTitledBorder); mappingPanel.setBounds(new Rectangle(10, ypos, 472, 45)); // GridLayout mappingLayout = new GridLayout(); mappingPanel.setLayout(new GridLayout()); mappingPanel.add(nwMapping); mappingPanel.add(siftsMapping); structureTab.add(mappingPanel); ypos += lineSpacing; ypos += lineSpacing; FTSDataColumnPreferences docFieldPref = new FTSDataColumnPreferences( PreferenceSource.PREFERENCES, PDBFTSRestClient.getInstance()); docFieldPref.setBounds(new Rectangle(10, ypos, 470, 120)); structureTab.add(docFieldPref); return structureTab; } /** * Action on choosing a structure viewer from combobox options. * * @param selectedItem */ protected void structureViewer_actionPerformed(String selectedItem) { } /** * Show a dialog for the user to choose a file. Returns the chosen path, or * null on Cancel. * * @return */ protected String openFileChooser() { String choice = null; JFileChooser chooser = new JFileChooser(); // chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle( MessageManager.getString("label.open_local_file")); chooser.setToolTipText(MessageManager.getString("action.open")); int value = chooser.showOpenDialog(this); if (value == JFileChooser.APPROVE_OPTION) { choice = chooser.getSelectedFile().getPath(); } return choice; } /** * Validate the structure tab preferences; if invalid, set focus on this tab. * * @param e */ protected boolean validateStructure(FocusEvent e) { if (!validateStructure()) { e.getComponent().requestFocusInWindow(); return false; } return true; } protected boolean validateStructure() { return false; } /** * Initialises the Visual tabbed panel. * * @return */ private JPanel initVisualTab() { JPanel visualTab = new JPanel(); visualTab.setBorder(new TitledBorder( MessageManager.getString("action.open_new_alignment"))); visualTab.setLayout(null); fullScreen.setFont(LABEL_FONT); fullScreen.setHorizontalAlignment(SwingConstants.RIGHT); fullScreen.setHorizontalTextPosition(SwingConstants.LEFT); fullScreen.setText(MessageManager.getString("label.maximize_window")); quality.setEnabled(false); quality.setFont(LABEL_FONT); quality.setHorizontalAlignment(SwingConstants.RIGHT); quality.setHorizontalTextPosition(SwingConstants.LEFT); quality.setSelected(true); quality.setText(MessageManager.getString("label.quality")); conservation.setEnabled(false); conservation.setFont(LABEL_FONT); conservation.setHorizontalAlignment(SwingConstants.RIGHT); conservation.setHorizontalTextPosition(SwingConstants.LEFT); conservation.setSelected(true); conservation.setText(MessageManager.getString("label.conservation")); identity.setEnabled(false); identity.setFont(LABEL_FONT); identity.setHorizontalAlignment(SwingConstants.RIGHT); identity.setHorizontalTextPosition(SwingConstants.LEFT); identity.setSelected(true); identity.setText(MessageManager.getString("label.consensus")); showOccupancy.setFont(LABEL_FONT); showOccupancy.setEnabled(false); showOccupancy.setHorizontalAlignment(SwingConstants.RIGHT); showOccupancy.setHorizontalTextPosition(SwingConstants.LEFT); showOccupancy.setSelected(true); showOccupancy.setText(MessageManager.getString("label.occupancy")); JLabel showGroupbits = new JLabel(); showGroupbits.setFont(LABEL_FONT); showGroupbits.setHorizontalAlignment(SwingConstants.RIGHT); showGroupbits.setHorizontalTextPosition(SwingConstants.LEFT); showGroupbits .setText(MessageManager.getString("action.show_group") + ":"); JLabel showConsensbits = new JLabel(); showConsensbits.setFont(LABEL_FONT); showConsensbits.setHorizontalAlignment(SwingConstants.RIGHT); showConsensbits.setHorizontalTextPosition(SwingConstants.LEFT); showConsensbits .setText(MessageManager.getString("label.consensus") + ":"); showConsensHistogram.setEnabled(false); showConsensHistogram.setFont(LABEL_FONT); showConsensHistogram.setHorizontalAlignment(SwingConstants.RIGHT); showConsensHistogram.setHorizontalTextPosition(SwingConstants.LEFT); showConsensHistogram.setSelected(true); showConsensHistogram .setText(MessageManager.getString("label.histogram")); showConsensLogo.setEnabled(false); showConsensLogo.setFont(LABEL_FONT); showConsensLogo.setHorizontalAlignment(SwingConstants.RIGHT); showConsensLogo.setHorizontalTextPosition(SwingConstants.LEFT); showConsensLogo.setSelected(true); showConsensLogo.setText(MessageManager.getString("label.logo")); showGroupConsensus.setEnabled(false); showGroupConsensus.setFont(LABEL_FONT); showGroupConsensus.setHorizontalAlignment(SwingConstants.RIGHT); showGroupConsensus.setHorizontalTextPosition(SwingConstants.LEFT); showGroupConsensus.setSelected(true); showGroupConsensus.setText(MessageManager.getString("label.consensus")); showGroupConservation.setEnabled(false); showGroupConservation.setFont(LABEL_FONT); showGroupConservation.setHorizontalAlignment(SwingConstants.RIGHT); showGroupConservation.setHorizontalTextPosition(SwingConstants.LEFT); showGroupConservation.setSelected(true); showGroupConservation .setText(MessageManager.getString("label.conservation")); showNpTooltip.setEnabled(true); showNpTooltip.setFont(LABEL_FONT); showNpTooltip.setHorizontalAlignment(SwingConstants.RIGHT); showNpTooltip.setHorizontalTextPosition(SwingConstants.LEFT); showNpTooltip.setSelected(true); showNpTooltip.setText( MessageManager.getString("label.non_positional_features")); showDbRefTooltip.setEnabled(true); showDbRefTooltip.setFont(LABEL_FONT); showDbRefTooltip.setHorizontalAlignment(SwingConstants.RIGHT); showDbRefTooltip.setHorizontalTextPosition(SwingConstants.LEFT); showDbRefTooltip.setSelected(true); showDbRefTooltip .setText(MessageManager.getString("label.database_references")); annotations.setFont(LABEL_FONT); annotations.setHorizontalAlignment(SwingConstants.RIGHT); annotations.setHorizontalTextPosition(SwingConstants.LEFT); annotations.setSelected(true); annotations.setText(MessageManager.getString("label.show_annotations")); // annotations.setBounds(new Rectangle(169, 12, 200, 23)); annotations.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { annotations_actionPerformed(e); } }); identity.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { annotations_actionPerformed(e); } }); showGroupConsensus.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { annotations_actionPerformed(e); } }); showUnconserved.setFont(LABEL_FONT); showUnconserved.setHorizontalAlignment(SwingConstants.RIGHT); showUnconserved.setHorizontalTextPosition(SwingConstants.LEFT); showUnconserved.setSelected(true); showUnconserved .setText(MessageManager.getString("action.show_unconserved")); showUnconserved.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { showunconserved_actionPerformed(e); } }); // TODO these are not yet added to / action from Preferences // JCheckBox shareSelections = new JCheckBox(); // shareSelections.setFont(verdana11); // shareSelections.setHorizontalAlignment(SwingConstants.RIGHT); // shareSelections.setHorizontalTextPosition(SwingConstants.LEFT); // shareSelections.setSelected(true); // shareSelections.setText(MessageManager // .getString("label.share_selection_across_views")); // JCheckBox followHighlight = new JCheckBox(); // 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")); seqLimit.setFont(LABEL_FONT); seqLimit.setHorizontalAlignment(SwingConstants.RIGHT); seqLimit.setHorizontalTextPosition(SwingConstants.LEFT); seqLimit.setText(MessageManager.getString("label.full_sequence_id")); smoothFont.setFont(LABEL_FONT); smoothFont.setHorizontalAlignment(SwingConstants.RIGHT); smoothFont.setHorizontalTextPosition(SwingConstants.LEADING); smoothFont.setText(MessageManager.getString("label.smooth_font")); scaleProteinToCdna.setFont(LABEL_FONT); scaleProteinToCdna.setHorizontalAlignment(SwingConstants.RIGHT); scaleProteinToCdna.setHorizontalTextPosition(SwingConstants.LEADING); scaleProteinToCdna.setText( MessageManager.getString("label.scale_protein_to_cdna")); scaleProteinToCdna.setToolTipText( MessageManager.getString("label.scale_protein_to_cdna_tip")); JLabel gapLabel = new JLabel(); gapLabel.setFont(LABEL_FONT); gapLabel.setHorizontalAlignment(SwingConstants.RIGHT); gapLabel.setText(MessageManager.getString("label.gap_symbol") + " "); JLabel fontLabel = new JLabel(); fontLabel.setFont(LABEL_FONT); fontLabel.setHorizontalAlignment(SwingConstants.RIGHT); fontLabel.setText(MessageManager.getString("label.font")); fontSizeCB.setFont(LABEL_FONT); fontSizeCB.setBounds(new Rectangle(320, 112, 65, 23)); fontStyleCB.setFont(LABEL_FONT); fontStyleCB.setBounds(new Rectangle(382, 112, 80, 23)); fontNameCB.setFont(LABEL_FONT); fontNameCB.setBounds(new Rectangle(172, 112, 147, 23)); gapSymbolCB.setFont(LABEL_FONT); gapSymbolCB.setBounds(new Rectangle(172, 215, 69, 23)); DefaultListCellRenderer dlcr = new DefaultListCellRenderer(); dlcr.setHorizontalAlignment(DefaultListCellRenderer.CENTER); gapSymbolCB.setRenderer(dlcr); startupCheckbox.setText(MessageManager.getString("action.open_file")); startupCheckbox.setFont(LABEL_FONT); startupCheckbox.setHorizontalAlignment(SwingConstants.RIGHT); startupCheckbox.setHorizontalTextPosition(SwingConstants.LEFT); startupCheckbox.setSelected(true); startupFileTextfield.setFont(LABEL_FONT); startupFileTextfield.setBounds(new Rectangle(172, 310, 330, 20)); final String tooltip = JvSwingUtils.wrapTooltip(true, MessageManager.getString("label.double_click_to_browse")); startupFileTextfield.setToolTipText(tooltip); startupFileTextfield.addMouseListener(new MouseAdapter() { @Override public void mouseClicked(MouseEvent e) { if (e.getClickCount() > 1) { startupFileTextfield_mouseClicked(); } } }); sortby.setFont(LABEL_FONT); sortby.setBounds(new Rectangle(172, 260, 155, 21)); JLabel sortLabel = new JLabel(); sortLabel.setFont(LABEL_FONT); sortLabel.setHorizontalAlignment(SwingConstants.RIGHT); sortLabel.setText(MessageManager.getString("label.sort_by")); sortAnnBy.setFont(LABEL_FONT); sortAnnBy.setBounds(new Rectangle(172, 285, 110, 21)); JLabel sortAnnLabel = new JLabel(); sortAnnLabel.setFont(LABEL_FONT); sortAnnLabel.setHorizontalAlignment(SwingConstants.RIGHT); sortAnnLabel.setText(MessageManager.getString("label.sort_ann_by")); sortAutocalc.setFont(LABEL_FONT); sortAutocalc.setBounds(new Rectangle(290, 285, 165, 21)); JPanel annsettingsPanel = new JPanel(); annsettingsPanel.setBounds(new Rectangle(173, 13, 320, 96)); annsettingsPanel.setLayout(new FlowLayout(FlowLayout.LEFT, 0, 0)); annsettingsPanel.setBorder(new EtchedBorder()); visualTab.add(annsettingsPanel); Border jb = new EmptyBorder(1, 1, 4, 5); annotations.setBorder(jb); showOccupancy.setBorder(jb); 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); JPanel autoAnnotSettings = new JPanel(); annsettingsPanel.add(autoAnnotSettings); autoAnnotSettings.setLayout(new GridLayout(0, 2)); autoAnnotSettings.add(annotations); autoAnnotSettings.add(quality); // second row of autoannotation box autoAnnotSettings = new JPanel(); annsettingsPanel.add(autoAnnotSettings); autoAnnotSettings.setLayout(new GridLayout(0, 3)); autoAnnotSettings.add(conservation); autoAnnotSettings.add(identity); autoAnnotSettings.add(showOccupancy); autoAnnotSettings.add(showGroupbits); autoAnnotSettings.add(showGroupConservation); autoAnnotSettings.add(showGroupConsensus); autoAnnotSettings.add(showConsensbits); autoAnnotSettings.add(showConsensHistogram); autoAnnotSettings.add(showConsensLogo); JPanel tooltipSettings = new JPanel(); tooltipSettings.setBorder(new TitledBorder( MessageManager.getString("label.sequence_id_tooltip"))); tooltipSettings.setBounds(173, 140, 220, 62); tooltipSettings.setLayout(new GridLayout(2, 1)); tooltipSettings.add(showDbRefTooltip); tooltipSettings.add(showNpTooltip); visualTab.add(tooltipSettings); wrap.setFont(LABEL_FONT); wrap.setHorizontalAlignment(SwingConstants.TRAILING); wrap.setHorizontalTextPosition(SwingConstants.LEADING); wrap.setText(MessageManager.getString("label.wrap_alignment")); rightAlign.setFont(LABEL_FONT); rightAlign.setForeground(Color.black); rightAlign.setHorizontalAlignment(SwingConstants.RIGHT); rightAlign.setHorizontalTextPosition(SwingConstants.LEFT); rightAlign.setText(MessageManager.getString("label.right_align_ids")); idItalics.setFont(LABEL_FONT_ITALIC); idItalics.setHorizontalAlignment(SwingConstants.RIGHT); idItalics.setHorizontalTextPosition(SwingConstants.LEADING); idItalics.setText( MessageManager.getString("label.sequence_name_italics")); openoverv.setFont(LABEL_FONT); openoverv.setActionCommand( MessageManager.getString("label.open_overview")); openoverv.setHorizontalAlignment(SwingConstants.RIGHT); openoverv.setHorizontalTextPosition(SwingConstants.LEFT); openoverv.setText(MessageManager.getString("label.open_overview")); JPanel jPanel2 = new JPanel(); jPanel2.setBounds(new Rectangle(7, 17, 158, 310)); jPanel2.setLayout(new GridLayout(14, 1)); 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(scaleProteinToCdna); jPanel2.add(gapLabel); jPanel2.add(wrap); jPanel2.add(sortLabel); jPanel2.add(sortAnnLabel); jPanel2.add(startupCheckbox); visualTab.add(jPanel2); visualTab.add(startupFileTextfield); visualTab.add(sortby); visualTab.add(sortAnnBy); visualTab.add(sortAutocalc); visualTab.add(gapSymbolCB); visualTab.add(fontNameCB); visualTab.add(fontSizeCB); visualTab.add(fontStyleCB); return visualTab; } /** * Load the saved Backups options EXCEPT "Enabled" and "Scheme" */ protected void loadLastSavedBackupsOptions() { BackupFilesPresetEntry savedPreset = BackupFilesPresetEntry .getSavedBackupEntry(); enableBackupFiles .setSelected(Cache.getDefault(BackupFiles.ENABLED, true)); BackupFilesPresetEntry backupfilesCustomEntry = BackupFilesPresetEntry .createBackupFilesPresetEntry(Cache .getDefault(BackupFilesPresetEntry.CUSTOMCONFIG, null)); if (backupfilesCustomEntry == null) { backupfilesCustomEntry = BackupFilesPresetEntry.backupfilesPresetEntriesValues .get(BackupFilesPresetEntry.BACKUPFILESSCHEMEDEFAULT); } BackupFilesPresetEntry.backupfilesPresetEntriesValues.put( BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM, backupfilesCustomEntry); setComboIntStringKey(backupfilesPresetsCombo, Cache.getDefault(BackupFiles.NS + "_PRESET", BackupFilesPresetEntry.BACKUPFILESSCHEMEDEFAULT)); backupsSetOptions(savedPreset); backupsOptionsSetEnabled(); updateBackupFilesExampleLabel(); } private boolean warnAboutSuffixReverseChange() { BackupFilesPresetEntry bfpe = BackupFilesPresetEntry .getSavedBackupEntry(); boolean savedSuffixReverse = bfpe.reverse; int savedSuffixDigits = bfpe.digits; String savedSuffixTemplate = bfpe.suffix; boolean nowSuffixReverse = suffixReverse.isSelected(); int nowSuffixDigits = getSpinnerInt(suffixDigitsSpinner, 3); String nowSuffixTemplate = suffixTemplate.getText(); return nowSuffixReverse != savedSuffixReverse && nowSuffixDigits == savedSuffixDigits && nowSuffixTemplate != null && nowSuffixTemplate.equals(savedSuffixTemplate); } /** * Initialises the Backups tabbed panel. * * @return */ private JPanel initBackupsTab() { JPanel backupsTab = new JPanel(); backupsTab.setBorder(new TitledBorder( MessageManager.getString("label.backup_files"))); backupsTab.setLayout(new GridBagLayout()); GridBagConstraints gbc = new GridBagConstraints(); gbc.weightx = 0.0; gbc.weighty = 0.0; gbc.anchor = GridBagConstraints.FIRST_LINE_START; gbc.fill = GridBagConstraints.NONE; initBackupsTabPresetsPanel(); initBackupsTabSuffixPanel(); initBackupsTabKeepFilesPanel(); initBackupsTabFilenameExamplesPanel(); enableBackupFiles.setFont(LABEL_FONT_BOLD); enableBackupFiles .setText(MessageManager.getString("label.enable_backupfiles")); enableBackupFiles.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { // enable other options only when the first is checked backupsOptionsSetEnabled(); } }); // enable checkbox 1 col gbc.gridwidth = 1; gbc.gridheight = 1; gbc.gridx = 0; gbc.gridy = 0; // row 0 backupsTab.add(enableBackupFiles, gbc); // summary of scheme box (over two rows) gbc.gridx = 1; gbc.weightx = 0.0; gbc.gridheight = 2; gbc.anchor = GridBagConstraints.FIRST_LINE_END; gbc.fill = GridBagConstraints.BOTH; backupsTab.add(exampleFilesPanel, gbc); gbc.gridheight = 1; gbc.anchor = GridBagConstraints.FIRST_LINE_START; gbc.fill = GridBagConstraints.NONE; // fill empty space on right gbc.gridx++; gbc.weightx = 1.0; backupsTab.add(new JPanel(), gbc); // schemes box gbc.weightx = 0.0; gbc.gridx = 0; gbc.gridy++; // row 1 backupsTab.add(presetsPanel, gbc); // now using whole row gbc.gridwidth = 2; gbc.gridheight = 1; // keep files box gbc.gridx = 0; gbc.gridy++; // row 2 backupsTab.add(keepfilesPanel, gbc); // filename strategy box gbc.gridy++; // row 3 backupsTab.add(suffixPanel, gbc); // fill empty space gbc.gridy++; // row 4 gbc.weighty = 1.0; backupsTab.add(new JPanel(), gbc); backupsOptionsSetEnabled(); return backupsTab; } private JPanel initBackupsTabPresetsPanel() { String title = MessageManager.getString("label.schemes"); presetsPanel.setLayout(new GridBagLayout()); GridBagConstraints gbc = new GridBagConstraints(); gbc.weightx = 0.0; gbc.weighty = 0.0; gbc.anchor = GridBagConstraints.BASELINE_LEADING; gbc.fill = GridBagConstraints.NONE; gbc.gridwidth = 1; gbc.gridheight = 1; // "Scheme: " gbc.gridx = 0; gbc.gridy = 0; presetsComboLabel = new JLabel(title + ":"); presetsPanel.add(presetsComboLabel, gbc); List entries = Arrays .asList((Object[]) BackupFilesPresetEntry.backupfilesPresetEntries); List tooltips = Arrays.asList( BackupFilesPresetEntry.backupfilesPresetEntryDescriptions); backupfilesPresetsCombo = JvSwingUtils.buildComboWithTooltips(entries, tooltips); /* for (int i = 0; i < BackupFilesPresetEntry.backupfilesPresetEntries.length; i++) { backupfilesPresetsCombo .addItem(BackupFilesPresetEntry.backupfilesPresetEntries[i]); } */ backupfilesPresetsCombo.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { int key = getComboIntStringKey(backupfilesPresetsCombo); if (!customiseCheckbox.isSelected()) { backupfilesPresetsComboLastSelected = key; } if (key == BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM) { if (customiseCheckbox.isSelected()) { // got here by clicking on customiseCheckbox so don't change the values backupfilesCustomOptionsSetEnabled(); } else { backupsTabUpdatePresets(); backupfilesCustomOptionsSetEnabled(); } } else { customiseCheckbox.setSelected(false); backupsTabUpdatePresets(); backupfilesCustomOptionsSetEnabled(); } } }); // dropdown list of preset schemes gbc.gridx = 1; presetsPanel.add(backupfilesPresetsCombo, gbc); revertButton.setText(MessageManager.getString("label.cancel_changes")); revertButton.setToolTipText( MessageManager.getString("label.cancel_changes_description")); revertButton.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { backupsSetOptions( BackupFilesPresetEntry.backupfilesPresetEntriesValues.get( BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM)); backupfilesCustomOptionsSetEnabled(); } }); revertButton.setFont(LABEL_FONT); customiseCheckbox.setFont(LABEL_FONT); customiseCheckbox.setText(MessageManager.getString("label.customise")); customiseCheckbox.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { int currently = getComboIntStringKey(backupfilesPresetsCombo); if (customiseCheckbox.isSelected()) { backupfilesPresetsComboLastSelected = currently; setComboIntStringKey(backupfilesPresetsCombo, BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM); } else { setComboIntStringKey(backupfilesPresetsCombo, backupfilesPresetsComboLastSelected); } backupfilesCustomOptionsSetEnabled(); } }); customiseCheckbox.setToolTipText( MessageManager.getString("label.customise_description")); // customise checkbox gbc.gridx = 0; gbc.gridy++; presetsPanel.add(customiseCheckbox, gbc); // "Cancel changes" button (aligned with combo box above) gbc.gridx = 1; presetsPanel.add(revertButton, gbc); return presetsPanel; } private JPanel initBackupsTabFilenameExamplesPanel() { String title = MessageManager .getString("label.scheme_examples"); TitledBorder tb = new TitledBorder(title); exampleFilesPanel.setBorder(tb); exampleFilesPanel.setLayout(new GridBagLayout()); backupfilesExampleLabel.setEditable(false); backupfilesExampleLabel .setBackground(exampleFilesPanel.getBackground()); updateBackupFilesExampleLabel(); GridBagConstraints gbc = new GridBagConstraints(); gbc.weightx = 1.0; gbc.weighty = 1.0; gbc.fill = GridBagConstraints.NONE; gbc.anchor = GridBagConstraints.FIRST_LINE_START; exampleFilesPanel.add(backupfilesExampleLabel, gbc); return exampleFilesPanel; } private void backupsTabUpdatePresets() { IntKeyStringValueEntry entry = (IntKeyStringValueEntry) backupfilesPresetsCombo .getSelectedItem(); int key = entry.k; String value = entry.v; if (BackupFilesPresetEntry.backupfilesPresetEntriesValues .containsKey(key)) { backupsSetOptions( BackupFilesPresetEntry.backupfilesPresetEntriesValues .get(key)); } else { Cache.log.error( "Preset '" + value + "' [key:" + key + "] not implemented"); } // Custom options will now be enabled when the customiseCheckbox is checked // (performed above) // backupfilesCustomOptionsSetEnabled(); updateBackupFilesExampleLabel(); } protected int getComboIntStringKey( JComboBox backupfilesPresetsCombo2) { IntKeyStringValueEntry e; try { e = (IntKeyStringValueEntry) backupfilesPresetsCombo2 .getSelectedItem(); } catch (Exception ex) { Cache.log.error( "Problem casting Combo entry to IntKeyStringValueEntry."); e = null; } return e != null ? e.k : 0; } protected void setComboIntStringKey( JComboBox backupfilesPresetsCombo2, int key) { for (int i = 0; i < backupfilesPresetsCombo2.getItemCount(); i++) { IntKeyStringValueEntry e; try { e = (IntKeyStringValueEntry) backupfilesPresetsCombo2.getItemAt(i); } catch (Exception ex) { Cache.log.error( "Problem casting Combo entry to IntKeyStringValueEntry. Skipping item. "); continue; } if (e.k == key) { backupfilesPresetsCombo2.setSelectedIndex(i); break; } } // backupsTabUpdatePresets(); } private JPanel initBackupsTabSuffixPanel() { suffixPanel.setBorder(new TitledBorder( MessageManager.getString("label.backup_filename_strategy"))); suffixPanel.setLayout(new GridBagLayout()); suffixTemplateLabel .setText(MessageManager.getString("label.append_to_filename")); suffixTemplateLabel.setHorizontalAlignment(SwingConstants.LEFT); suffixTemplateLabel.setFont(LABEL_FONT); final String tooltip = JvSwingUtils.wrapTooltip(true, MessageManager.getString("label.append_to_filename_tooltip")); suffixTemplate.setToolTipText(tooltip); suffixTemplate.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { updateBackupFilesExampleLabel(); backupfilesCustomOptionsSetEnabled(); backupfilesRevertButtonSetEnabled(true); } }); suffixTemplate.addKeyListener(new KeyListener() { @Override public void keyReleased(KeyEvent e) { updateBackupFilesExampleLabel(); backupfilesCustomOptionsSetEnabled(); backupfilesRevertButtonSetEnabled(true); } @Override public void keyPressed(KeyEvent e) { } // disable use of ':' or '/' or '\' @Override public void keyTyped(KeyEvent e) { char c = e.getKeyChar(); if (c == ':' || c == '/' || c == '\\') { // don't process ':' or '/' or '\' e.consume(); } } }); // digits spinner suffixDigitsLabel .setText(MessageManager.getString("label.index_digits")); suffixDigitsLabel.setHorizontalAlignment(SwingConstants.LEFT); suffixDigitsLabel.setFont(LABEL_FONT); ChangeListener c = new ChangeListener() { @Override public void stateChanged(ChangeEvent e) { backupfilesRevertButtonSetEnabled(true); updateBackupFilesExampleLabel(); } }; setIntegerSpinner(suffixDigitsSpinner, BackupFilesPresetEntry.DIGITSMIN, BackupFilesPresetEntry.DIGITSMAX, 3, c); suffixReverse.setLabels(MessageManager.getString("label.reverse_roll"), MessageManager.getString("label.increment_index")); suffixReverse.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { boolean okay = true; if (warnAboutSuffixReverseChange()) { // Warning popup okay = confirmSuffixReverseChange(); } if (okay) { backupfilesRevertButtonSetEnabled(true); updateBackupFilesExampleLabel(); } else { boolean savedSuffixReverse = BackupFilesPresetEntry .getSavedBackupEntry().reverse; suffixReverse.setSelected(savedSuffixReverse); } } }); GridBagConstraints sgbc = new GridBagConstraints(); // first row (template text box) sgbc.anchor = GridBagConstraints.WEST; sgbc.gridx = 0; sgbc.gridy = 0; sgbc.gridwidth = 1; sgbc.gridheight = 1; sgbc.weightx = 1.0; sgbc.weighty = 0.0; sgbc.fill = GridBagConstraints.NONE; suffixPanel.add(suffixTemplateLabel, sgbc); sgbc.gridx = 1; sgbc.fill = GridBagConstraints.HORIZONTAL; suffixPanel.add(suffixTemplate, sgbc); // second row (number of digits spinner) sgbc.gridy = 1; sgbc.gridx = 0; sgbc.fill = GridBagConstraints.NONE; suffixPanel.add(suffixDigitsLabel, sgbc); sgbc.gridx = 1; sgbc.fill = GridBagConstraints.HORIZONTAL; suffixPanel.add(suffixDigitsSpinner, sgbc); // third row (forward order radio selection) sgbc.gridx = 0; sgbc.gridy = 2; sgbc.gridwidth = GridBagConstraints.REMAINDER; sgbc.fill = GridBagConstraints.HORIZONTAL; suffixPanel.add(suffixReverse.getFalseButton(), sgbc); // fourth row (reverse order radio selection) sgbc.gridy = 3; suffixPanel.add(suffixReverse.getTrueButton(), sgbc); return suffixPanel; } private boolean confirmSuffixReverseChange() { boolean ret = false; String warningMessage = MessageManager .getString("label.warning_confirm_change_reverse"); int confirm = JvOptionPane.showConfirmDialog(Desktop.desktop, warningMessage, MessageManager.getString("label.change_increment_decrement"), JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE); ret = (confirm == JvOptionPane.YES_OPTION); return ret; } private JPanel initBackupsTabKeepFilesPanel() { keepfilesPanel.setBorder( new TitledBorder(MessageManager.getString("label.keep_files"))); keepfilesPanel.setLayout(new GridBagLayout()); backupfilesKeepAll.setLabels( MessageManager.getString("label.keep_all_backup_files"), MessageManager.getString( "label.keep_only_this_number_of_backup_files")); backupfilesKeepAll.addTrueActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { backupfilesRevertButtonSetEnabled(true); updateBackupFilesExampleLabel(); } }); backupfilesKeepAll.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { backupfilesRevertButtonSetEnabled(true); keepRollMaxOptionsEnabled(); updateBackupFilesExampleLabel(); } }); ChangeListener c = new ChangeListener() { @Override public void stateChanged(ChangeEvent e) { backupfilesRevertButtonSetEnabled(true); updateBackupFilesExampleLabel(); } }; setIntegerSpinner(backupfilesRollMaxSpinner, BackupFilesPresetEntry.ROLLMAXMIN, BackupFilesPresetEntry.ROLLMAXMAX, 4, true, c); backupfilesConfirmDelete.setLabels( MessageManager.getString("label.always_ask"), MessageManager.getString("label.auto_delete")); backupfilesConfirmDelete.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { backupfilesRevertButtonSetEnabled(true); } }); // update the enabled section keepRollMaxOptionsEnabled(); GridBagConstraints kgbc = new GridBagConstraints(); // first row (template text box) kgbc.anchor = GridBagConstraints.WEST; kgbc.gridx = 0; kgbc.gridy = 0; kgbc.gridwidth = GridBagConstraints.REMAINDER; kgbc.gridheight = 1; kgbc.weightx = 1.0; kgbc.weighty = 0.0; kgbc.fill = GridBagConstraints.HORIZONTAL; keepfilesPanel.add(backupfilesKeepAll.getTrueButton(), kgbc); // second row kgbc.gridy = 1; kgbc.gridx = 0; kgbc.gridwidth = GridBagConstraints.RELATIVE; keepfilesPanel.add(backupfilesKeepAll.getFalseButton(), kgbc); kgbc.gridx = 1; kgbc.gridwidth = GridBagConstraints.REMAINDER; keepfilesPanel.add(backupfilesRollMaxSpinner, kgbc); // third row (indented) kgbc.gridy = 2; kgbc.insets = new Insets(0, 20, 0, 0); kgbc.gridx = 0; kgbc.gridwidth = GridBagConstraints.REMAINDER; kgbc.fill = GridBagConstraints.HORIZONTAL; kgbc.weightx = 1.0; JPanel jp = new JPanel(); jp.setLayout(new FlowLayout()); oldBackupFilesLabel .setText(MessageManager .getString("label.autodelete_old_backup_files")); oldBackupFilesLabel.setFont(LABEL_FONT); oldBackupFilesLabel.setHorizontalAlignment(SwingConstants.LEFT); jp.add(oldBackupFilesLabel); jp.add(backupfilesConfirmDelete.getTrueButton()); jp.add(backupfilesConfirmDelete.getFalseButton()); keepfilesPanel.add(jp, kgbc); return keepfilesPanel; } protected void updateBackupFilesExampleLabel() { int exampleindex = 12; String base = MessageManager.getString("label.filename") + ".fa"; if (base == null || base.length() == 0) { base = "file_name.fa"; } boolean reverse = suffixReverse.isSelected(); boolean keepAll = backupfilesKeepAll.isSelected(); int rollMax = 4; String suffix = suffixTemplate.getText(); int digits = 3; backupfilesExampleLabel.setFont(LABEL_FONT_ITALIC); if (suffix == null || suffix.length() == 0) { backupfilesExampleLabel .setText(MessageManager.getString("label.no_backup_files")); backupfilesExampleLabel.setFont(LABEL_FONT_BOLD); return; } rollMax = getSpinnerInt(backupfilesRollMaxSpinner, 4); rollMax = rollMax < 1 ? 1 : rollMax; if (suffix.indexOf(BackupFiles.NUM_PLACEHOLDER) == -1) { rollMax = 1; } digits = getSpinnerInt(suffixDigitsSpinner, 3); digits = digits < 1 ? 1 : digits; int lowersurround = 2; int uppersurround = 0; StringBuilder exampleSB = new StringBuilder(); boolean firstLine = true; int lineNumber = 0; if (reverse) { int min = 1; int max = keepAll ? exampleindex : rollMax; for (int index = min; index <= max; index++) { if (index == min + lowersurround && index < max - uppersurround - 1) { exampleSB.append("\n..."); lineNumber++; } else if (index > min + lowersurround && index < max - uppersurround) { // nothing } else { if (firstLine) { firstLine = false; } else { exampleSB.append("\n"); lineNumber++; } exampleSB.append(BackupFilenameParts.getBackupFilename(index, base, suffix, digits)); if (min == max) { // no extra text needed } else if (index == min) { String newest = MessageManager.getString("label.braced_newest"); if (newest != null && newest.length() > 0) { exampleSB.append(" " + newest); } } else if (index == max) { String oldest = MessageManager.getString("label.braced_oldest"); if (oldest != null && oldest.length() > 0) { exampleSB.append(" " + oldest); } } } } } else { int min = (keepAll || exampleindex - rollMax < 0) ? 1 : exampleindex - rollMax + 1; int max = exampleindex; for (int index = min; index <= max; index++) { if (index == min + lowersurround && index < max - uppersurround - 1) { exampleSB.append("\n..."); lineNumber++; } else if (index > min + lowersurround && index < max - uppersurround) { // nothing } else { if (firstLine) { firstLine = false; } else { exampleSB.append("\n"); lineNumber++; } exampleSB.append(BackupFilenameParts.getBackupFilename(index, base, suffix, digits)); if (min == max) { // no extra text needed } else if (index == min) { String oldest = MessageManager.getString("label.braced_oldest"); if (oldest != null && oldest.length() > 0) { exampleSB.append(" " + oldest); } } else if (index == max) { String newest = MessageManager.getString("label.braced_newest"); if (newest != null && newest.length() > 0) { exampleSB.append(" " + newest); } } } } } // add some extra empty lines to pad out the example files box. ugh, please tell // me how to do this better int remainingLines = lowersurround + uppersurround + 1 - lineNumber; if (remainingLines > 0) { for (int i = 0; i < remainingLines; i++) { exampleSB.append("\n "); lineNumber++; } } backupfilesExampleLabel.setText(exampleSB.toString()); } protected void setIntegerSpinner(JSpinner s, int min, int max, int def, boolean useExistingVal, ChangeListener c) { int i = def; if (useExistingVal) { try { i = ((Integer) s.getValue()).intValue(); } catch (Exception e) { Cache.log.error( "Exception casting the initial value of s.getValue()"); } } setIntegerSpinner(s, min, max, i, c); } protected void setIntegerSpinner(JSpinner s, int min, int max, int def, ChangeListener c) { // integer spinner for number of digits if (def > max) { max = def; } if (def < min) { def = min; } SpinnerModel sModel = new SpinnerNumberModel(def, min, max, 1); s.setModel(sModel); s.addChangeListener(c); } protected static int getSpinnerInt(JSpinner s, int def) { int i = def; try { s.commitEdit(); i = (Integer) s.getValue(); } catch (Exception e) { Cache.log.error("Failed casting (Integer) JSpinner s.getValue()"); } return i; } private void keepRollMaxOptionsEnabled() { boolean enabled = backupfilesKeepAll.isEnabled() && !backupfilesKeepAll.isSelected(); oldBackupFilesLabel.setEnabled(enabled); backupfilesRollMaxSpinner.setEnabled(enabled); backupfilesConfirmDelete.setEnabled(enabled); } private void backupfilesKeepAllSetEnabled(boolean tryEnabled) { boolean enabled = tryEnabled && enableBackupFiles.isSelected() && customiseCheckbox.isSelected() && suffixTemplate.getText() .indexOf(BackupFiles.NUM_PLACEHOLDER) > -1; keepfilesPanel.setEnabled(enabled); backupfilesKeepAll.setEnabled(enabled); oldBackupFilesLabel.setEnabled(enabled); keepRollMaxOptionsEnabled(); } private void backupfilesSuffixTemplateDigitsSetEnabled() { boolean enabled = suffixTemplate.isEnabled() && suffixTemplate.getText() .indexOf(BackupFiles.NUM_PLACEHOLDER) > -1; suffixDigitsLabel.setEnabled(enabled); suffixDigitsSpinner.setEnabled(enabled); suffixReverse.setEnabled(enabled); } private void backupfilesSuffixTemplateSetEnabled(boolean tryEnabled) { boolean enabled = tryEnabled && enableBackupFiles.isSelected() && customiseCheckbox.isSelected(); suffixPanel.setEnabled(enabled); suffixTemplateLabel.setEnabled(enabled); suffixTemplate.setEnabled(enabled); backupfilesSuffixTemplateDigitsSetEnabled(); } private void backupfilesRevertButtonSetEnabled(boolean tryEnabled) { boolean enabled = tryEnabled && enableBackupFiles.isSelected() && customiseCheckbox.isSelected() && backupfilesCustomChanged(); revertButton.setEnabled(enabled); } private boolean backupfilesCustomChanged() { BackupFilesPresetEntry custom = BackupFilesPresetEntry.backupfilesPresetEntriesValues .get(BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM); BackupFilesPresetEntry current = getBackupfilesCurrentEntry(); return !custom.equals(current); } protected BackupFilesPresetEntry getBackupfilesCurrentEntry() { String suffix = suffixTemplate.getText(); int digits = getSpinnerInt(suffixDigitsSpinner, 3); boolean reverse = suffixReverse.isSelected(); boolean keepAll = backupfilesKeepAll.isSelected(); int rollMax = getSpinnerInt(backupfilesRollMaxSpinner, 3); boolean confirmDelete = backupfilesConfirmDelete.isSelected(); BackupFilesPresetEntry bfpe = new BackupFilesPresetEntry(suffix, digits, reverse, keepAll, rollMax, confirmDelete); return bfpe; } protected void backupfilesCustomOptionsSetEnabled() { boolean enabled = customiseCheckbox.isSelected(); backupfilesRevertButtonSetEnabled(enabled); backupfilesSuffixTemplateSetEnabled(enabled); backupfilesKeepAllSetEnabled(enabled); } private void backupfilesSummarySetEnabled() { boolean enabled = enableBackupFiles.isSelected(); backupfilesExampleLabel.setEnabled(enabled); exampleFilesPanel.setEnabled(enabled); } private void backupfilesPresetsSetEnabled() { boolean enabled = enableBackupFiles.isSelected(); presetsPanel.setEnabled(enabled); presetsComboLabel.setEnabled(enabled); backupfilesPresetsCombo.setEnabled(enabled); customiseCheckbox.setEnabled(enabled); revertButton.setEnabled(enabled); } protected void backupsOptionsSetEnabled() { backupfilesPresetsSetEnabled(); backupfilesSummarySetEnabled(); backupfilesCustomOptionsSetEnabled(); } protected void backupsSetOptions(String suffix, int digits, boolean reverse, boolean keepAll, int rollMax, boolean confirmDelete) { suffixTemplate.setText(suffix); suffixDigitsSpinner.setValue(digits); suffixReverse.setSelected(reverse); backupfilesKeepAll.setSelected(keepAll); backupfilesRollMaxSpinner.setValue(rollMax); backupfilesConfirmDelete.setSelected(confirmDelete); } protected void backupsSetOptions(BackupFilesPresetEntry p) { backupsSetOptions(p.suffix, p.digits, p.reverse, p.keepAll, p.rollMax, p.confirmDelete); } protected void autoIdWidth_actionPerformed() { // TODO Auto-generated method stub } protected void userIdWidth_actionPerformed() { // TODO Auto-generated method stub } protected void maxColour_actionPerformed(JPanel panel) { } protected void minColour_actionPerformed(JPanel panel) { } protected void gapColour_actionPerformed(JPanel panel) { } protected void hiddenColour_actionPerformed(JPanel panel) { } protected void showunconserved_actionPerformed(ActionEvent e) { // TODO Auto-generated method stub } protected void useLegacyGaps_actionPerformed(ActionEvent e) { } protected void resetOvDefaults_actionPerformed(ActionEvent e) { } /** * 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() { boolean enabled = useProxy.isSelected(); portLabel.setEnabled(enabled); serverLabel.setEnabled(enabled); proxyServerTB.setEnabled(enabled); proxyPortTB.setEnabled(enabled); } /** * Customer renderer for JTable: supports column of radio buttons */ public class RadioButtonRenderer extends JRadioButton implements TableCellRenderer { public RadioButtonRenderer() { setHorizontalAlignment(CENTER); setToolTipText(MessageManager.getString("label.urltooltip")); } @Override public Component getTableCellRendererComponent(JTable table, Object value, boolean isSelected, boolean hasFocus, int row, int column) { setSelected((boolean) value); // set colours to match rest of table if (isSelected) { setBackground(table.getSelectionBackground()); setForeground(table.getSelectionForeground()); } else { setBackground(table.getBackground()); setForeground(table.getForeground()); } return this; } } /** * Customer cell editor for JTable: supports column of radio buttons in * conjunction with renderer */ public class RadioButtonEditor extends AbstractCellEditor implements TableCellEditor { private JRadioButton button = new JRadioButton(); public RadioButtonEditor() { button.setHorizontalAlignment(SwingConstants.CENTER); this.button.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { fireEditingStopped(); } }); } @Override public Component getTableCellEditorComponent(JTable table, Object value, boolean isSelected, int row, int column) { button.setSelected((boolean) value); return button; } @Override public Object getCellEditorValue() { return button.isSelected(); } } }