X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGPreferences.java;h=c132e49d01a17384a65f19d1d118881a9bdb7ceb;hb=682ebcd21b2123786463a3f56cc6f7c17f361bae;hp=4f4afb0037ee32febb6ea67dbfd198b6dd6e454c;hpb=2526066acdc3faf3a178e50672c78e428287e9ef;p=jalview.git diff --git a/src/jalview/jbgui/GPreferences.java b/src/jalview/jbgui/GPreferences.java index 4f4afb0..c132e49 100755 --- a/src/jalview/jbgui/GPreferences.java +++ b/src/jalview/jbgui/GPreferences.java @@ -20,9 +20,19 @@ */ package jalview.jbgui; +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.jbgui.PDBDocFieldPreferences.PreferenceSource; +import jalview.io.BackupFilenameParts; +import jalview.io.BackupFiles; +import jalview.io.BackupFilesPresetEntry; +import jalview.io.IntKeyStringValueEntry; import jalview.util.MessageManager; import java.awt.BorderLayout; @@ -40,22 +50,30 @@ 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 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.JList; 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; @@ -63,8 +81,8 @@ import javax.swing.border.EtchedBorder; import javax.swing.border.TitledBorder; import javax.swing.event.ChangeEvent; import javax.swing.event.ChangeListener; -import javax.swing.event.ListSelectionEvent; -import javax.swing.event.ListSelectionListener; +import javax.swing.table.TableCellEditor; +import javax.swing.table.TableCellRenderer; /** * Base class for the Preferences panel. @@ -79,6 +97,9 @@ public class GPreferences extends JPanel 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 */ @@ -90,11 +111,13 @@ public class GPreferences extends JPanel protected JCheckBox rightAlign = new JCheckBox(); - protected JComboBox fontSizeCB = new JComboBox(); + protected JComboBox fontSizeCB = new JComboBox<>(); + + protected JComboBox fontStyleCB = new JComboBox<>(); - protected JComboBox fontStyleCB = new JComboBox(); + protected JComboBox fontNameCB = new JComboBox<>(); - protected JComboBox fontNameCB = new JComboBox(); + protected JCheckBox showOccupancy = new JCheckBox(); protected JCheckBox showUnconserved = new JCheckBox(); @@ -104,15 +127,15 @@ public class GPreferences extends JPanel protected JCheckBox scaleProteinToCdna = new JCheckBox(); - protected JComboBox gapSymbolCB = new JComboBox(); + protected JComboBox gapSymbolCB = new JComboBox<>(); protected JCheckBox wrap = new JCheckBox(); - protected JComboBox sortby = new JComboBox(); + protected JComboBox sortby = new JComboBox<>(); - protected JComboBox sortAnnBy = new JComboBox(); + protected JComboBox sortAnnBy = new JComboBox<>(); - protected JComboBox sortAutocalc = new JComboBox(); + protected JComboBox sortAutocalc = new JComboBox<>(); protected JCheckBox startupCheckbox = new JCheckBox(); @@ -152,10 +175,15 @@ public class GPreferences extends JPanel protected JCheckBox addTempFactor = new JCheckBox(); - protected JComboBox structViewer = new JComboBox(); + protected JComboBox structViewer = new JComboBox<>(); protected JTextField chimeraPath = new JTextField(); + protected ButtonGroup mappingMethod = new ButtonGroup(); + + protected JRadioButton siftsMapping = new JRadioButton(); + + protected JRadioButton nwMapping = new JRadioButton(); /* * Colours tab components @@ -164,14 +192,41 @@ public class GPreferences extends JPanel protected JPanel maxColour = new JPanel(); - protected JComboBox protColour = new JComboBox(); + 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 JComboBox nucColour = new JComboBox(); + protected JCheckBox showHiddenAtStart; + + protected JLabel gapLabel; /* * Connections tab components */ - protected JList linkURLList = new JList(); + 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(); @@ -179,8 +234,6 @@ public class GPreferences extends JPanel protected JTextField defaultBrowser = new JTextField(); - protected JList linkNameList = new JList(); - protected JCheckBox useProxy = new JCheckBox(); protected JCheckBox usagestats = new JCheckBox(); @@ -192,7 +245,7 @@ public class GPreferences extends JPanel /* * Output tab components */ - protected JComboBox epsRendering = new JComboBox(); + protected JComboBox epsRendering = new JComboBox<>(); protected JLabel userIdWidthlabel = new JLabel(); @@ -228,14 +281,55 @@ public class GPreferences extends JPanel protected JCheckBox sortByTree = new JCheckBox(); /* - * DAS Settings tab + * Web Services tab */ - protected JPanel dasTab = new JPanel(); + protected JPanel wsTab = new JPanel(); /* - * Web Services tab + * 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 JPanel wsTab = new JPanel(); + + 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. @@ -270,22 +364,26 @@ public class GPreferences extends JPanel 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(initOutputTab(), MessageManager.getString("label.output")); + tabbedPane.add(initBackupsTab(), + MessageManager.getString("label.backups")); - tabbedPane.add(initEditingTab(), MessageManager.getString("label.editing")); + tabbedPane.add(initLinksTab(), + MessageManager.getString("label.urllinks")); - /* - * See DasSourceBrowser for the real work of configuring this tab. - */ - dasTab.setLayout(new BorderLayout()); - tabbedPane - .add(dasTab, MessageManager.getString("label.das_settings")); + tabbedPane.add(initOutputTab(), + MessageManager.getString("label.output")); + + tabbedPane.add(initEditingTab(), + MessageManager.getString("label.editing")); /* * See WsPreferences for the real work of configuring this tab. @@ -329,18 +427,18 @@ public class GPreferences extends JPanel JPanel editingTab = new JPanel(); editingTab.setLayout(null); autoCalculateConsCheck.setFont(LABEL_FONT); - autoCalculateConsCheck.setText(MessageManager - .getString("label.autocalculate_consensus")); + 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.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.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); @@ -400,10 +498,10 @@ public class GPreferences extends JPanel 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.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() { @@ -415,12 +513,13 @@ public class GPreferences extends JPanel } }); 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.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(""); @@ -435,8 +534,8 @@ public class GPreferences extends JPanel } }); modellerOutput.setFont(LABEL_FONT); - modellerOutput.setText(MessageManager - .getString("label.use_modeller_output")); + 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")); @@ -470,173 +569,355 @@ public class GPreferences extends JPanel { JPanel connectTab = new JPanel(); connectTab.setLayout(new GridBagLayout()); - JLabel serverLabel = new JLabel(); - serverLabel.setText(MessageManager.getString("label.address")); - serverLabel.setHorizontalAlignment(SwingConstants.RIGHT); - serverLabel.setFont(LABEL_FONT); - proxyServerTB.setFont(LABEL_FONT); - proxyPortTB.setFont(LABEL_FONT); - JLabel portLabel = new JLabel(); - portLabel.setFont(LABEL_FONT); - portLabel.setHorizontalAlignment(SwingConstants.RIGHT); - portLabel.setText(MessageManager.getString("label.port")); + + // Label for browser text box JLabel browserLabel = new JLabel(); - browserLabel.setFont(new java.awt.Font("SansSerif", 0, 11)); + browserLabel.setFont(LABEL_FONT); browserLabel.setHorizontalAlignment(SwingConstants.TRAILING); - browserLabel.setText(MessageManager - .getString("label.default_browser_unix")); + browserLabel.setText( + MessageManager.getString("label.default_browser_unix")); defaultBrowser.setFont(LABEL_FONT); defaultBrowser.setText(""); - usagestats.setText(MessageManager - .getString("label.send_usage_statistics")); - usagestats.setFont(LABEL_FONT); - usagestats.setHorizontalAlignment(SwingConstants.RIGHT); - usagestats.setHorizontalTextPosition(SwingConstants.LEADING); - questionnaire.setText(MessageManager - .getString("label.check_for_questionnaires")); - questionnaire.setFont(LABEL_FONT); - questionnaire.setHorizontalAlignment(SwingConstants.RIGHT); - questionnaire.setHorizontalTextPosition(SwingConstants.LEADING); - versioncheck.setText(MessageManager - .getString("label.check_for_latest_version")); - versioncheck.setFont(LABEL_FONT); - versioncheck.setHorizontalAlignment(SwingConstants.RIGHT); - versioncheck.setHorizontalTextPosition(SwingConstants.LEADING); + 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)); + + // 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); } }); - JButton editLink = new JButton(); + editLink.setText(MessageManager.getString("action.edit")); editLink.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { editLink_actionPerformed(e); } }); - JButton deleteLink = new JButton(); + deleteLink.setText(MessageManager.getString("action.delete")); deleteLink.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { deleteLink_actionPerformed(e); } }); - linkURLList.addListSelectionListener(new ListSelectionListener() - { - public void valueChanged(ListSelectionEvent e) - { - int index = linkURLList.getSelectedIndex(); - linkNameList.setSelectedIndex(index); - } - }); + 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; + } - linkNameList.addListSelectionListener(new ListSelectionListener() - { - public void valueChanged(ListSelectionEvent e) - { - int index = linkNameList.getSelectedIndex(); - linkURLList.setSelectedIndex(index); - } - }); + /** + * 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); - JScrollPane linkScrollPane = new JScrollPane(); - linkScrollPane.setBorder(null); - JPanel linkPanel = new JPanel(); - linkPanel.setBorder(new TitledBorder(MessageManager - .getString("label.url_linkfrom_sequence_id"))); - linkPanel.setLayout(new BorderLayout()); - GridLayout gridLayout1 = new GridLayout(); - JPanel editLinkButtons = new JPanel(); - editLinkButtons.setLayout(gridLayout1); - gridLayout1.setRows(3); - linkNameList.setFont(LABEL_FONT); - linkNameList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION); - BorderLayout borderLayout3 = new BorderLayout(); - JPanel linkPanel2 = new JPanel(); - linkPanel2.setLayout(borderLayout3); - linkURLList.setFont(LABEL_FONT); - linkURLList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION); + // Proxy server and port text boxes + proxyServerTB.setFont(LABEL_FONT); + proxyPortTB.setFont(LABEL_FONT); - defaultBrowser.addMouseListener(new MouseAdapter() - { - public void mouseClicked(MouseEvent e) - { - if (e.getClickCount() > 1) - { - defaultBrowser_mouseClicked(e); - } - } - }); + // 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(); } }); - 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); - JPanel jPanel1 = new JPanel(); + + // Make proxy server panel + JPanel proxyPanel = new JPanel(); TitledBorder titledBorder1 = new TitledBorder( MessageManager.getString("label.proxy_server")); - jPanel1.setBorder(titledBorder1); - jPanel1.setLayout(new GridBagLayout()); - 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(useProxy, new GridBagConstraints(0, 0, 2, 1, 0.0, 0.0, - GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0, - 2, 5, 185), 2, -4)); - 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)); - return connectTab; + 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); } /** @@ -650,6 +931,7 @@ public class GPreferences extends JPanel ok.setText(MessageManager.getString("action.ok")); ok.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { ok_actionPerformed(e); @@ -659,6 +941,7 @@ public class GPreferences extends JPanel cancel.setText(MessageManager.getString("action.cancel")); cancel.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { cancel_actionPerformed(e); @@ -678,8 +961,8 @@ public class GPreferences extends JPanel private JPanel initColoursTab() { JPanel coloursTab = new JPanel(); - coloursTab.setBorder(new TitledBorder(MessageManager - .getString("action.open_new_alignment"))); + coloursTab.setBorder(new TitledBorder( + MessageManager.getString("action.open_new_alignment"))); coloursTab.setLayout(new FlowLayout()); JLabel mincolourLabel = new JLabel(); mincolourLabel.setFont(LABEL_FONT); @@ -690,6 +973,7 @@ public class GPreferences extends JPanel minColour.setPreferredSize(new Dimension(40, 20)); minColour.addMouseListener(new MouseAdapter() { + @Override public void mousePressed(MouseEvent e) { minColour_actionPerformed(minColour); @@ -704,6 +988,7 @@ public class GPreferences extends JPanel maxColour.setPreferredSize(new Dimension(40, 20)); maxColour.addMouseListener(new MouseAdapter() { + @Override public void mousePressed(MouseEvent e) { maxColour_actionPerformed(maxColour); @@ -715,10 +1000,11 @@ public class GPreferences extends JPanel 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.setText( + MessageManager.getString("label.prot_alignment_colour") + " "); + JvSwingUtils.addtoLayout(coloursTab, + MessageManager + .getString("label.default_colour_scheme_for_alignment"), protColourLabel, protColour); nucColour.setFont(LABEL_FONT); @@ -726,28 +1012,174 @@ public class GPreferences extends JPanel 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.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.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"), + JvSwingUtils.addtoLayout(annotationShding, + MessageManager.getString( + "label.default_minimum_colour_annotation_shading"), mincolourLabel, minColour); - JvSwingUtils.addtoLayout(annotationShding, MessageManager - .getString("label.default_maximum_colour_annotation_shading"), + 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 @@ -756,16 +1188,17 @@ public class GPreferences extends JPanel { structureTab = new JPanel(); - structureTab.setBorder(new TitledBorder(MessageManager - .getString("label.structure_options"))); + structureTab.setBorder(new TitledBorder( + MessageManager.getString("label.structure_options"))); structureTab.setLayout(null); final int width = 400; final int height = 22; final int lineSpacing = 25; - int ypos = 30; + int ypos = 15; structFromPdb.setFont(LABEL_FONT); - structFromPdb.setText(MessageManager.getString("label.struct_from_pdb")); + structFromPdb + .setText(MessageManager.getString("label.struct_from_pdb")); structFromPdb.setBounds(new Rectangle(5, ypos, width, height)); structFromPdb.addActionListener(new ActionListener() { @@ -790,8 +1223,8 @@ public class GPreferences extends JPanel ypos += lineSpacing; addSecondaryStructure.setFont(LABEL_FONT); - addSecondaryStructure.setText(MessageManager - .getString("label.autoadd_secstr")); + addSecondaryStructure + .setText(MessageManager.getString("label.autoadd_secstr")); addSecondaryStructure.setBounds(new Rectangle(25, ypos, width, height)); structureTab.add(addSecondaryStructure); @@ -818,8 +1251,8 @@ public class GPreferences extends JPanel @Override public void actionPerformed(ActionEvent e) { - structureViewer_actionPerformed((String) structViewer - .getSelectedItem()); + structureViewer_actionPerformed( + (String) structViewer.getSelectedItem()); } }); structureTab.add(structViewer); @@ -829,14 +1262,14 @@ public class GPreferences extends JPanel pathLabel.setFont(new java.awt.Font("SansSerif", 0, 11)); pathLabel.setHorizontalAlignment(SwingConstants.LEFT); pathLabel.setText(MessageManager.getString("label.chimera_path")); - final String tooltip = JvSwingUtils.wrapTooltip(true, - MessageManager.getString("label.chimera_path_tip")); - pathLabel.setToolTipText(tooltip); pathLabel.setBounds(new Rectangle(10, ypos, 140, height)); structureTab.add(pathLabel); chimeraPath.setFont(LABEL_FONT); chimeraPath.setText(""); + final String tooltip = JvSwingUtils.wrapTooltip(true, + MessageManager.getString("label.chimera_path_tip")); + chimeraPath.setToolTipText(tooltip); chimeraPath.setBounds(new Rectangle(160, ypos, 300, height)); chimeraPath.addMouseListener(new MouseAdapter() { @@ -856,22 +1289,35 @@ public class GPreferences extends JPanel structureTab.add(chimeraPath); ypos += lineSpacing; - // scrl_pdbDocFieldConfig.setPreferredSize(new Dimension(450, 100)); - // scrl_pdbDocFieldConfig - // .setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_NEVER); - // scrl_pdbDocFieldConfig.setBounds(); - PDBDocFieldPreferences docFieldPref = new PDBDocFieldPreferences( - PreferenceSource.PREFERENCES); - docFieldPref.setBounds(new Rectangle(10, ypos + 5, 450, 120)); - structureTab.add(docFieldPref); - - + 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, 452, 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, 450, 120)); + structureTab.add(docFieldPref); return structureTab; } - /** * Action on choosing a structure viewer from combobox options. * @@ -893,8 +1339,8 @@ public class GPreferences extends JPanel JFileChooser chooser = new JFileChooser(); // chooser.setFileView(new JalviewFileView()); - chooser.setDialogTitle(MessageManager - .getString("label.open_local_file")); + chooser.setDialogTitle( + MessageManager.getString("label.open_local_file")); chooser.setToolTipText(MessageManager.getString("action.open")); int value = chooser.showOpenDialog(this); @@ -934,8 +1380,8 @@ public class GPreferences extends JPanel private JPanel initVisualTab() { JPanel visualTab = new JPanel(); - visualTab.setBorder(new TitledBorder(MessageManager - .getString("action.open_new_alignment"))); + visualTab.setBorder(new TitledBorder( + MessageManager.getString("action.open_new_alignment"))); visualTab.setLayout(null); fullScreen.setFont(LABEL_FONT); fullScreen.setHorizontalAlignment(SwingConstants.RIGHT); @@ -959,25 +1405,32 @@ public class GPreferences extends JPanel 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") - + ":"); + 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") - + ":"); + 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")); + showConsensHistogram + .setText(MessageManager.getString("label.histogram")); showConsensLogo.setEnabled(false); showConsensLogo.setFont(LABEL_FONT); showConsensLogo.setHorizontalAlignment(SwingConstants.RIGHT); @@ -995,30 +1448,31 @@ public class GPreferences extends JPanel showGroupConservation.setHorizontalAlignment(SwingConstants.RIGHT); showGroupConservation.setHorizontalTextPosition(SwingConstants.LEFT); showGroupConservation.setSelected(true); - showGroupConservation.setText(MessageManager - .getString("label.conservation")); + 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")); + 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")); + showDbRefTooltip + .setText(MessageManager.getString("label.database_references")); annotations.setFont(LABEL_FONT); annotations.setHorizontalAlignment(SwingConstants.RIGHT); - annotations.setHorizontalTextPosition(SwingConstants.LEADING); + annotations.setHorizontalTextPosition(SwingConstants.LEFT); annotations.setSelected(true); annotations.setText(MessageManager.getString("label.show_annotations")); - annotations.setBounds(new Rectangle(169, 12, 200, 23)); + // annotations.setBounds(new Rectangle(169, 12, 200, 23)); annotations.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { annotations_actionPerformed(e); @@ -1026,6 +1480,7 @@ public class GPreferences extends JPanel }); identity.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { annotations_actionPerformed(e); @@ -1033,6 +1488,7 @@ public class GPreferences extends JPanel }); showGroupConsensus.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { annotations_actionPerformed(e); @@ -1042,10 +1498,11 @@ public class GPreferences extends JPanel showUnconserved.setHorizontalAlignment(SwingConstants.RIGHT); showUnconserved.setHorizontalTextPosition(SwingConstants.LEFT); showUnconserved.setSelected(true); - showUnconserved.setText(MessageManager - .getString("action.show_unconserved")); + showUnconserved + .setText(MessageManager.getString("action.show_unconserved")); showUnconserved.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { showunconserved_actionPerformed(e); @@ -1080,10 +1537,10 @@ public class GPreferences extends JPanel 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")); + 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); @@ -1111,8 +1568,12 @@ public class GPreferences extends JPanel 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) @@ -1121,7 +1582,7 @@ public class GPreferences extends JPanel } } }); - + sortby.setFont(LABEL_FONT); sortby.setBounds(new Rectangle(172, 260, 155, 21)); JLabel sortLabel = new JLabel(); @@ -1138,11 +1599,13 @@ public class GPreferences extends JPanel sortAutocalc.setBounds(new Rectangle(290, 285, 165, 21)); JPanel annsettingsPanel = new JPanel(); - annsettingsPanel.setBounds(new Rectangle(173, 34, 320, 75)); + 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); @@ -1154,11 +1617,18 @@ public class GPreferences extends JPanel showConsensLogo.setBorder(jb); JPanel autoAnnotSettings = new JPanel(); - autoAnnotSettings.setLayout(new GridLayout(3, 3)); 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); @@ -1167,8 +1637,8 @@ public class GPreferences extends JPanel autoAnnotSettings.add(showConsensLogo); JPanel tooltipSettings = new JPanel(); - tooltipSettings.setBorder(new TitledBorder(MessageManager - .getString("label.sequence_id_tooltip"))); + 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); @@ -1187,14 +1657,14 @@ public class GPreferences extends JPanel idItalics.setFont(LABEL_FONT_ITALIC); idItalics.setHorizontalAlignment(SwingConstants.RIGHT); idItalics.setHorizontalTextPosition(SwingConstants.LEADING); - idItalics.setText(MessageManager - .getString("label.sequence_name_italics")); + idItalics.setText( + MessageManager.getString("label.sequence_name_italics")); openoverv.setFont(LABEL_FONT); - openoverv.setActionCommand(MessageManager - .getString("label.open_overview")); + openoverv.setActionCommand( + MessageManager.getString("label.open_overview")); openoverv.setHorizontalAlignment(SwingConstants.RIGHT); openoverv.setHorizontalTextPosition(SwingConstants.LEFT); - openoverv.setText(MessageManager.getString(("label.open_overview"))); + 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)); @@ -1213,7 +1683,6 @@ public class GPreferences extends JPanel jPanel2.add(sortAnnLabel); jPanel2.add(startupCheckbox); visualTab.add(jPanel2); - visualTab.add(annotations); visualTab.add(startupFileTextfield); visualTab.add(sortby); visualTab.add(sortAnnBy); @@ -1225,46 +1694,993 @@ public class GPreferences extends JPanel return visualTab; } - protected void autoIdWidth_actionPerformed() - { - // TODO Auto-generated method stub - - } + /** + * Load the saved Backups options EXCEPT "Enabled" and "Scheme" + */ - protected void userIdWidth_actionPerformed() + protected void loadLastSavedBackupsOptions() { - // TODO Auto-generated method stub + 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)); + // backupsTabUpdatePresets(); - protected void maxColour_actionPerformed(JPanel panel) - { + System.out + .println("LOADLASTSAVEDBACKUPSOPTIONS SETTING BACKUPS OPTIONS"); + backupsSetOptions(savedPreset); + + backupsOptionsSetEnabled(); + updateBackupFilesExampleLabel(); } - protected void minColour_actionPerformed(JPanel panel) + private void setBackupfilesCustomPreset() { + if (customiseCheckbox.isSelected() && getComboIntStringKey( + backupfilesPresetsCombo) == BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM) + { + BackupFilesPresetEntry.backupfilesPresetEntriesValues + .put(BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM, + getBackupfilesCurrentEntry()); + } } - protected void showunconserved_actionPerformed(ActionEvent e) + private boolean warnAboutSuffixReverseChange() { - // TODO Auto-generated method stub - + 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); } /** - * DOCUMENT ME! + * Initialises the Backups tabbed panel. * - * @param e - * DOCUMENT ME! + * @return */ - public void ok_actionPerformed(ActionEvent e) + private JPanel initBackupsTab() { - } - - /** - * DOCUMENT ME! - * - * @param e + 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); + + // gbc.anchor = GridBagConstraints.NORTHWEST; + // 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"); + // TitledBorder tb = new TitledBorder(new EmptyBorder(0, 0, 0, 0), title); + // TitledBorder tb = new TitledBorder(title); + // tb.setTitleFont(LABEL_FONT); + // presetsPanel.setBorder(tb); + + 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); + + 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.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(); + } + }); + + // 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.summary_of_backups_scheme"); + 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.getKey(); + String value = entry.getValue(); + + if (BackupFilesPresetEntry.backupfilesPresetEntriesValues + .containsKey(key)) + { + backupsSetOptions( + BackupFilesPresetEntry.backupfilesPresetEntriesValues + .get(key)); + } + else + { + System.out.println( + "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 c) + { + IntKeyStringValueEntry e = (IntKeyStringValueEntry) c.getSelectedItem(); + return e != null ? e.getKey() : 0; + } + + protected void setComboIntStringKey(JComboBox c, + int key) + { + for (int i = 0; i < c.getItemCount(); i++) + { + IntKeyStringValueEntry e = c.getItemAt(i); + if (e.getKey() == key) + { + c.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) + { + int count = 300; + 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; + /* + keepfilesPanel.add(backupfilesConfirmDelete.getTrueButton(), kgbc); + + // fourth row (indented) + kgbc.gridy = 3; + keepfilesPanel.add(backupfilesConfirmDelete.getFalseButton(), kgbc); + */ + + 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; + 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..."); + } + else if (index > min + lowersurround && index < max - uppersurround) + { + // nothing + } + else + { + if (firstLine) + { + firstLine = false; + } + else + { + exampleSB.append("\n"); + } + 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..."); + } + else if (index > min + lowersurround && index < max - uppersurround) + { + // nothing + } + else + { + if (firstLine) + { + firstLine = false; + } + else + { + exampleSB.append("\n"); + } + 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); + } + } + } + } + + } + + 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.parseInt((String) s.getValue()); + } catch (Exception e) + { + System.out.println( + "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; + } + 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) + { + System.out.println("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() + { + // int scheme = getComboIntStringKey(backupfilesPresetsCombo); + // boolean enabled = scheme == BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM && + // enableBackupFiles.isSelected(); + boolean enabled = customiseCheckbox.isSelected(); + //boolean enabled = customiseCheckbox.isSelected() && enableBackupFiles.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) @@ -1315,8 +2731,83 @@ public class GPreferences extends JPanel public void useProxy_actionPerformed() { - proxyServerTB.setEnabled(useProxy.isSelected()); - proxyPortTB.setEnabled(useProxy.isSelected()); + 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(); + } + + } } +