2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.jbgui;
23 import java.awt.BorderLayout;
24 import java.awt.Color;
25 import java.awt.Component;
26 import java.awt.Dimension;
27 import java.awt.FlowLayout;
29 import java.awt.GridBagConstraints;
30 import java.awt.GridBagLayout;
31 import java.awt.GridLayout;
32 import java.awt.Insets;
33 import java.awt.Rectangle;
34 import java.awt.event.ActionEvent;
35 import java.awt.event.ActionListener;
36 import java.awt.event.FocusEvent;
37 import java.awt.event.KeyEvent;
38 import java.awt.event.KeyListener;
39 import java.awt.event.MouseAdapter;
40 import java.awt.event.MouseEvent;
41 import java.util.Arrays;
42 import java.util.List;
44 import javax.swing.AbstractCellEditor;
45 import javax.swing.BorderFactory;
46 import javax.swing.ButtonGroup;
47 import javax.swing.DefaultListCellRenderer;
48 import javax.swing.JButton;
49 import javax.swing.JCheckBox;
50 import javax.swing.JComboBox;
51 import javax.swing.JFileChooser;
52 import javax.swing.JLabel;
53 import javax.swing.JPanel;
54 import javax.swing.JPasswordField;
55 import javax.swing.JRadioButton;
56 import javax.swing.JScrollPane;
57 import javax.swing.JSpinner;
58 import javax.swing.JTabbedPane;
59 import javax.swing.JTable;
60 import javax.swing.JTextArea;
61 import javax.swing.JTextField;
62 import javax.swing.ListSelectionModel;
63 import javax.swing.SpinnerModel;
64 import javax.swing.SpinnerNumberModel;
65 import javax.swing.SwingConstants;
66 import javax.swing.border.Border;
67 import javax.swing.border.EmptyBorder;
68 import javax.swing.border.EtchedBorder;
69 import javax.swing.border.TitledBorder;
70 import javax.swing.event.ChangeEvent;
71 import javax.swing.event.ChangeListener;
72 import javax.swing.event.DocumentEvent;
73 import javax.swing.event.DocumentListener;
74 import javax.swing.table.TableCellEditor;
75 import javax.swing.table.TableCellRenderer;
77 import jalview.bin.Cache;
78 import jalview.fts.core.FTSDataColumnPreferences;
79 import jalview.fts.core.FTSDataColumnPreferences.PreferenceSource;
80 import jalview.fts.service.pdb.PDBFTSRestClient;
81 import jalview.gui.Desktop;
82 import jalview.gui.JalviewBooleanRadioButtons;
83 import jalview.gui.JvOptionPane;
84 import jalview.gui.JvSwingUtils;
85 import jalview.gui.StructureViewer.ViewerType;
86 import jalview.io.BackupFilenameParts;
87 import jalview.io.BackupFiles;
88 import jalview.io.BackupFilesPresetEntry;
89 import jalview.io.IntKeyStringValueEntry;
90 import jalview.util.MessageManager;
91 import jalview.util.Platform;
94 * Base class for the Preferences panel.
99 public class GPreferences extends JPanel
101 private static final Font LABEL_FONT = JvSwingUtils.getLabelFont();
103 private static final Font LABEL_FONT_ITALIC = JvSwingUtils
104 .getLabelFont(false, true);
106 private static final Font LABEL_FONT_BOLD = JvSwingUtils
107 .getLabelFont(true, false);
110 * Visual tab components
112 protected JCheckBox fullScreen = new JCheckBox();
114 protected JCheckBox openoverv = new JCheckBox();
116 protected JCheckBox seqLimit = new JCheckBox();
118 protected JCheckBox rightAlign = new JCheckBox();
120 protected JComboBox<String> fontSizeCB = new JComboBox<>();
122 protected JComboBox<String> fontStyleCB = new JComboBox<>();
124 protected JComboBox<String> fontNameCB = new JComboBox<>();
126 protected JCheckBox showOccupancy = new JCheckBox();
128 protected JCheckBox showUnconserved = new JCheckBox();
130 protected JCheckBox idItalics = new JCheckBox();
132 protected JCheckBox smoothFont = new JCheckBox();
134 protected JCheckBox scaleProteinToCdna = new JCheckBox();
136 protected JComboBox<String> gapSymbolCB = new JComboBox<>();
138 protected JCheckBox wrap = new JCheckBox();
140 protected JComboBox<String> sortby = new JComboBox<>();
142 protected JComboBox<String> sortAnnBy = new JComboBox<>();
144 protected JComboBox<String> sortAutocalc = new JComboBox<>();
146 protected JCheckBox startupCheckbox = new JCheckBox();
148 protected JTextField startupFileTextfield = new JTextField();
150 // below are in the 'second column'
151 protected JCheckBox annotations = new JCheckBox();
153 protected JCheckBox quality = new JCheckBox();
155 protected JCheckBox conservation = new JCheckBox();
157 protected JCheckBox identity = new JCheckBox();
159 protected JCheckBox showGroupConsensus = new JCheckBox();
161 protected JCheckBox showGroupConservation = new JCheckBox();
163 protected JCheckBox showConsensHistogram = new JCheckBox();
165 protected JCheckBox showConsensLogo = new JCheckBox();
167 protected JCheckBox showDbRefTooltip = new JCheckBox();
169 protected JCheckBox showNpTooltip = new JCheckBox();
172 * Structure tab and components
174 protected JPanel structureTab;
176 protected JCheckBox structFromPdb = new JCheckBox();
178 protected JCheckBox useRnaView = new JCheckBox();
180 protected JCheckBox addSecondaryStructure = new JCheckBox();
182 protected JCheckBox addTempFactor = new JCheckBox();
184 protected JComboBox<String> structViewer = new JComboBox<>();
186 protected JLabel structureViewerPathLabel;
188 protected JTextField structureViewerPath = new JTextField();
190 protected ButtonGroup mappingMethod = new ButtonGroup();
192 protected JRadioButton siftsMapping = new JRadioButton();
194 protected JRadioButton nwMapping = new JRadioButton();
197 * Colours tab components
199 protected JPanel minColour = new JPanel();
201 protected JPanel maxColour = new JPanel();
203 protected JComboBox<String> protColour = new JComboBox<>();
205 protected JComboBox<String> nucColour = new JComboBox<>();
208 * Overview tab components
210 protected JPanel gapColour = new JPanel();
212 protected JPanel hiddenColour = new JPanel();
214 protected JCheckBox useLegacyGap;
216 protected JCheckBox showHiddenAtStart;
218 protected JLabel gapLabel;
221 * Connections tab components
223 protected JPanel connectTab;
225 protected JTable linkUrlTable = new JTable();
227 protected JButton editLink = new JButton();
229 protected JButton deleteLink = new JButton();
231 protected JTextField filterTB = new JTextField();
233 protected JButton doReset = new JButton();
235 protected JButton userOnly = new JButton();
237 protected JLabel httpLabel = new JLabel();
239 protected JLabel httpsLabel = new JLabel();
241 protected JLabel portLabel = new JLabel();
243 protected JLabel serverLabel = new JLabel();
245 protected JLabel portLabel2 = new JLabel();
247 protected JLabel serverLabel2 = new JLabel();
249 protected JLabel proxyAuthUsernameLabel = new JLabel();
251 protected JLabel proxyAuthPasswordLabel = new JLabel();
253 protected JLabel passwordNotStoredLabel = new JLabel();
255 protected JTextField proxyServerHttpTB = new JTextField();
257 protected JTextField proxyPortHttpTB = new JTextField();
259 protected JTextField proxyServerHttpsTB = new JTextField();
261 protected JTextField proxyPortHttpsTB = new JTextField();
263 protected JCheckBox proxyAuth = new JCheckBox();
265 protected JTextField proxyAuthUsernameTB = new JTextField();
267 protected JPasswordField proxyAuthPasswordPB = new JPasswordField();
269 protected JTextField defaultBrowser = new JTextField();
271 protected ButtonGroup proxyType = new ButtonGroup();
273 protected JRadioButton noProxy = new JRadioButton();
275 protected JRadioButton systemProxy = new JRadioButton();
277 protected JRadioButton customProxy = new JRadioButton();
279 protected JButton applyProxyButton = new JButton();
281 protected JCheckBox usagestats = new JCheckBox();
283 protected JCheckBox questionnaire = new JCheckBox();
285 protected JCheckBox versioncheck = new JCheckBox();
288 * Output tab components
290 protected JComboBox<Object> epsRendering = new JComboBox<>();
292 protected JComboBox<Object> htmlRendering = new JComboBox<>();
294 protected JComboBox<Object> svgRendering = new JComboBox<>();
296 protected JLabel userIdWidthlabel = new JLabel();
298 protected JCheckBox autoIdWidth = new JCheckBox();
300 protected JTextField userIdWidth = new JTextField();
302 protected JCheckBox blcjv = new JCheckBox();
304 protected JCheckBox pileupjv = new JCheckBox();
306 protected JCheckBox clustaljv = new JCheckBox();
308 protected JCheckBox msfjv = new JCheckBox();
310 protected JCheckBox fastajv = new JCheckBox();
312 protected JCheckBox pfamjv = new JCheckBox();
314 protected JCheckBox pirjv = new JCheckBox();
316 protected JCheckBox modellerOutput = new JCheckBox();
318 protected JCheckBox embbedBioJSON = new JCheckBox();
321 * Editing tab components
323 protected JCheckBox autoCalculateConsCheck = new JCheckBox();
325 protected JCheckBox padGaps = new JCheckBox();
327 protected JCheckBox sortByTree = new JCheckBox();
332 protected JPanel wsTab = new JPanel();
335 * Backups tab components
336 * a lot of these are member variables instead of local variables only so that they
337 * can be enabled/disabled easily in one go
340 protected JCheckBox enableBackupFiles = new JCheckBox();
342 protected JPanel presetsPanel = new JPanel();
344 protected JLabel presetsComboLabel = new JLabel();
346 protected JCheckBox customiseCheckbox = new JCheckBox();
348 protected JButton revertButton = new JButton();
350 protected JComboBox<Object> backupfilesPresetsCombo = new JComboBox<>();
352 private int backupfilesPresetsComboLastSelected = 0;
354 protected JPanel suffixPanel = new JPanel();
356 protected JPanel keepfilesPanel = new JPanel();
358 protected JPanel exampleFilesPanel = new JPanel();
360 protected JTextField suffixTemplate = new JTextField(null, 8);
362 protected JLabel suffixTemplateLabel = new JLabel();
364 protected JLabel suffixDigitsLabel = new JLabel();
366 protected JSpinner suffixDigitsSpinner = new JSpinner();
368 protected JalviewBooleanRadioButtons suffixReverse = new JalviewBooleanRadioButtons();
370 protected JalviewBooleanRadioButtons backupfilesKeepAll = new JalviewBooleanRadioButtons();
372 public JSpinner backupfilesRollMaxSpinner = new JSpinner();
374 protected JLabel oldBackupFilesLabel = new JLabel();
376 protected JalviewBooleanRadioButtons backupfilesConfirmDelete = new JalviewBooleanRadioButtons();
378 protected JTextArea backupfilesExampleLabel = new JTextArea();
380 private final JTabbedPane tabbedPane = new JTabbedPane();
382 private JLabel messageLabel = new JLabel("", JLabel.CENTER);
385 * Creates a new GPreferences object.
387 public GPreferences()
392 } catch (Exception ex)
394 ex.printStackTrace();
399 * Construct the panel and its tabbed sub-panels.
403 private void jbInit() throws Exception
405 // final JTabbedPane tabbedPane = new JTabbedPane();
406 this.setLayout(new BorderLayout());
408 // message label at top
409 this.add(messageLabel, BorderLayout.NORTH);
411 JPanel okCancelPanel = initOkCancelPanel();
412 this.add(tabbedPane, BorderLayout.CENTER);
413 this.add(okCancelPanel, BorderLayout.SOUTH);
415 tabbedPane.add(initVisualTab(),
416 MessageManager.getString("label.visual"));
418 tabbedPane.add(initColoursTab(),
419 MessageManager.getString("label.colours"));
421 tabbedPane.add(initOverviewTab(),
422 MessageManager.getString("label.overview"));
424 tabbedPane.add(initStructureTab(),
425 MessageManager.getString("label.structure"));
427 tabbedPane.add(initConnectionsTab(),
428 MessageManager.getString("label.connections"));
430 if (!Platform.isJS())
432 tabbedPane.add(initBackupsTab(),
433 MessageManager.getString("label.backups"));
436 tabbedPane.add(initLinksTab(),
437 MessageManager.getString("label.urllinks"));
439 tabbedPane.add(initOutputTab(),
440 MessageManager.getString("label.output"));
442 tabbedPane.add(initEditingTab(),
443 MessageManager.getString("label.editing"));
446 * See WsPreferences for the real work of configuring this tab.
448 if (!Platform.isJS())
450 wsTab.setLayout(new BorderLayout());
451 tabbedPane.add(wsTab, MessageManager.getString("label.web_services"));
455 * Handler to validate a tab before leaving it - currently only for
457 * Adding a clearMessage() so messages are cleared when changing tabs.
459 tabbedPane.addChangeListener(new ChangeListener()
461 private Component lastTab;
464 public void stateChanged(ChangeEvent e)
466 if (lastTab == structureTab
467 && tabbedPane.getSelectedComponent() != structureTab)
469 if (!validateStructure())
471 tabbedPane.setSelectedComponent(structureTab);
475 lastTab = tabbedPane.getSelectedComponent();
483 public void setMessage(String message)
487 messageLabel.setText(message);
488 messageLabel.setFont(LABEL_FONT_BOLD);
489 messageLabel.setForeground(Color.RED.darker());
490 messageLabel.revalidate();
491 messageLabel.repaint();
493 // note message not cleared if message is null. call clearMessage()
499 public void clearMessage()
501 // only repaint if message exists
502 if (messageLabel.getText() != null
503 && messageLabel.getText().length() > 0)
505 messageLabel.setText("");
506 messageLabel.revalidate();
507 messageLabel.repaint();
513 public final static int CONNECTIONS_TAB = 5;
515 public void selectTab(int selectTab)
517 // select a given tab - currently only for Connections
520 case CONNECTIONS_TAB:
521 tabbedPane.setSelectedComponent(connectTab);
528 * Initialises the Editing tabbed panel.
532 private JPanel initEditingTab()
534 JPanel editingTab = new JPanel();
535 editingTab.setLayout(null);
536 autoCalculateConsCheck.setFont(LABEL_FONT);
537 autoCalculateConsCheck.setText(
538 MessageManager.getString("label.autocalculate_consensus"));
539 autoCalculateConsCheck.setBounds(new Rectangle(21, 52, 209, 23));
540 padGaps.setFont(LABEL_FONT);
542 MessageManager.getString("label.pad_gaps_when_editing"));
543 padGaps.setBounds(new Rectangle(22, 94, 168, 23));
544 sortByTree.setFont(LABEL_FONT);
546 .setText(MessageManager.getString("label.sort_with_new_tree"));
547 sortByTree.setToolTipText(MessageManager.getString(
548 "label.any_trees_calculated_or_loaded_alignment_automatically_sort"));
549 sortByTree.setBounds(new Rectangle(22, 136, 168, 23));
550 editingTab.add(autoCalculateConsCheck);
551 editingTab.add(padGaps);
552 editingTab.add(sortByTree);
557 * Initialises the Output tab
561 private JPanel initOutputTab()
563 JPanel outputTab = new JPanel();
564 outputTab.setLayout(null);
566 JLabel epsLabel = new JLabel(
567 MessageManager.formatMessage("label.rendering_style", "EPS"));
568 epsLabel.setFont(LABEL_FONT);
569 epsLabel.setHorizontalAlignment(SwingConstants.RIGHT);
570 epsLabel.setBounds(new Rectangle(9, 31, 160, 24));
571 epsRendering.setFont(LABEL_FONT);
572 epsRendering.setBounds(new Rectangle(174, 34, 187, 21));
573 JLabel htmlLabel = new JLabel(
574 MessageManager.formatMessage("label.rendering_style", "HTML"));
575 htmlLabel.setFont(LABEL_FONT);
576 htmlLabel.setHorizontalAlignment(SwingConstants.RIGHT);
577 htmlLabel.setBounds(new Rectangle(9, 55, 160, 24));
578 htmlRendering.setFont(LABEL_FONT);
579 htmlRendering.setBounds(new Rectangle(174, 58, 187, 21));
580 JLabel svgLabel = new JLabel(
581 MessageManager.formatMessage("label.rendering_style", "SVG"));
582 svgLabel.setFont(LABEL_FONT);
583 svgLabel.setHorizontalAlignment(SwingConstants.RIGHT);
584 svgLabel.setBounds(new Rectangle(9, 79, 160, 24));
585 svgRendering.setFont(LABEL_FONT);
586 svgRendering.setBounds(new Rectangle(174, 82, 187, 21));
588 JLabel jLabel1 = new JLabel();
589 jLabel1.setFont(LABEL_FONT);
590 jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
591 jLabel1.setText(MessageManager.getString("label.append_start_end"));
592 jLabel1.setFont(LABEL_FONT);
594 fastajv.setFont(LABEL_FONT);
595 fastajv.setHorizontalAlignment(SwingConstants.LEFT);
596 clustaljv.setText(MessageManager.getString("label.clustal") + " ");
597 blcjv.setText(MessageManager.getString("label.blc") + " ");
598 fastajv.setText(MessageManager.getString("label.fasta") + " ");
599 msfjv.setText(MessageManager.getString("label.msf") + " ");
600 pfamjv.setText(MessageManager.getString("label.pfam") + " ");
601 pileupjv.setText(MessageManager.getString("label.pileup") + " ");
602 msfjv.setFont(LABEL_FONT);
603 msfjv.setHorizontalAlignment(SwingConstants.LEFT);
604 pirjv.setText(MessageManager.getString("label.pir") + " ");
605 JPanel jPanel11 = new JPanel();
606 jPanel11.setFont(LABEL_FONT);
607 TitledBorder titledBorder2 = new TitledBorder(
608 MessageManager.getString("label.file_output"));
609 jPanel11.setBorder(titledBorder2);
610 jPanel11.setBounds(new Rectangle(30, 120, 196, 182));
611 GridLayout gridLayout3 = new GridLayout();
612 jPanel11.setLayout(gridLayout3);
613 gridLayout3.setRows(8);
614 blcjv.setFont(LABEL_FONT);
615 blcjv.setHorizontalAlignment(SwingConstants.LEFT);
616 clustaljv.setFont(LABEL_FONT);
617 clustaljv.setHorizontalAlignment(SwingConstants.LEFT);
618 pfamjv.setFont(LABEL_FONT);
619 pfamjv.setHorizontalAlignment(SwingConstants.LEFT);
620 pileupjv.setFont(LABEL_FONT);
621 pileupjv.setHorizontalAlignment(SwingConstants.LEFT);
622 pirjv.setFont(LABEL_FONT);
623 pirjv.setHorizontalAlignment(SwingConstants.LEFT);
624 autoIdWidth.setFont(LABEL_FONT);
626 MessageManager.getString("label.automatically_set_id_width"));
627 autoIdWidth.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager
628 .getString("label.adjusts_width_generated_eps_png")));
629 autoIdWidth.setBounds(new Rectangle(228, 144, 320, 23));
630 autoIdWidth.addActionListener(new ActionListener()
634 public void actionPerformed(ActionEvent e)
636 autoIdWidth_actionPerformed();
639 userIdWidthlabel.setFont(LABEL_FONT);
640 userIdWidthlabel.setText(
641 MessageManager.getString("label.figure_id_column_width"));
642 userIdWidth.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager
643 .getString("label.manually_specify_width_left_column")));
644 userIdWidthlabel.setToolTipText(
645 JvSwingUtils.wrapTooltip(true, MessageManager.getString(
646 "label.manually_specify_width_left_column")));
647 userIdWidthlabel.setBounds(new Rectangle(236, 168, 320, 23));
648 userIdWidth.setFont(JvSwingUtils.getTextAreaFont());
649 userIdWidth.setText("");
650 userIdWidth.setBounds(new Rectangle(232, 192, 84, 23));
651 userIdWidth.addActionListener(new ActionListener()
655 public void actionPerformed(ActionEvent e)
657 userIdWidth_actionPerformed();
660 modellerOutput.setFont(LABEL_FONT);
662 .setText(MessageManager.getString("label.use_modeller_output"));
663 modellerOutput.setBounds(new Rectangle(228, 274, 320, 23));
664 embbedBioJSON.setFont(LABEL_FONT);
665 embbedBioJSON.setText(MessageManager.getString("label.embbed_biojson"));
666 embbedBioJSON.setBounds(new Rectangle(228, 248, 250, 23));
668 jPanel11.add(jLabel1);
670 jPanel11.add(clustaljv);
671 jPanel11.add(fastajv);
673 jPanel11.add(pfamjv);
674 jPanel11.add(pileupjv);
676 outputTab.add(autoIdWidth);
677 outputTab.add(userIdWidth);
678 outputTab.add(userIdWidthlabel);
679 outputTab.add(modellerOutput);
680 if (!Platform.isJS())
683 * JalviewJS doesn't support Lineart option or SVG output
685 outputTab.add(embbedBioJSON);
686 outputTab.add(epsLabel);
687 outputTab.add(epsRendering);
688 outputTab.add(htmlLabel);
689 outputTab.add(htmlRendering);
690 outputTab.add(svgLabel);
691 outputTab.add(svgRendering);
693 outputTab.add(jPanel11);
698 * Initialises the Connections tabbed panel.
702 private JPanel initConnectionsTab()
704 connectTab = new JPanel();
705 connectTab.setLayout(new GridBagLayout());
707 // Label for browser text box
708 JLabel browserLabel = new JLabel();
709 browserLabel.setFont(LABEL_FONT);
710 browserLabel.setHorizontalAlignment(SwingConstants.TRAILING);
711 browserLabel.setText(
712 MessageManager.getString("label.default_browser_unix"));
713 defaultBrowser.setFont(LABEL_FONT);
714 defaultBrowser.setText("");
715 final String tooltip = JvSwingUtils.wrapTooltip(true,
716 MessageManager.getString("label.double_click_to_browse"));
717 defaultBrowser.setToolTipText(tooltip);
718 defaultBrowser.addMouseListener(new MouseAdapter()
721 public void mouseClicked(MouseEvent e)
723 if (e.getClickCount() > 1)
725 defaultBrowser_mouseClicked(e);
730 JPanel proxyPanel = initConnTabProxyPanel();
731 initConnTabCheckboxes();
733 // Add default Browser text box
734 connectTab.add(browserLabel,
735 new GridBagConstraints(0, 0, 1, 1, 0.0, 0.0,
736 GridBagConstraints.WEST, GridBagConstraints.NONE,
737 new Insets(10, 0, 5, 5), 5, 1));
738 defaultBrowser.setFont(LABEL_FONT);
739 defaultBrowser.setText("");
741 connectTab.add(defaultBrowser, new GridBagConstraints(1, 0, 1, 1, 1.0,
742 0.0, GridBagConstraints.CENTER, GridBagConstraints.HORIZONTAL,
743 new Insets(10, 0, 5, 10), 30, 1));
745 // Add proxy server panel
746 connectTab.add(proxyPanel, new GridBagConstraints(0, 1, 2, 1, 1.0, 0.0,
747 GridBagConstraints.CENTER, GridBagConstraints.HORIZONTAL,
748 new Insets(10, 0, 5, 12), 4, 10));
750 // Add usage stats, version check and questionnaire checkboxes
751 connectTab.add(usagestats,
752 new GridBagConstraints(0, 2, 1, 1, 1.0, 0.0,
753 GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
754 new Insets(0, 2, 5, 5), 70, 1));
755 connectTab.add(questionnaire,
756 new GridBagConstraints(1, 2, 1, 1, 1.0, 0.0,
757 GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
758 new Insets(0, 2, 5, 10), 70, 1));
759 connectTab.add(versioncheck,
760 new GridBagConstraints(0, 3, 1, 1, 1.0, 0.0,
761 GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
762 new Insets(0, 2, 5, 5), 70, 1));
764 versioncheck.setVisible(false);
766 // Add padding so the panel doesn't look ridiculous
767 JPanel spacePanel = new JPanel();
768 connectTab.add(spacePanel,
769 new GridBagConstraints(0, 4, 1, 1, 1.0, 1.0,
770 GridBagConstraints.WEST, GridBagConstraints.BOTH,
771 new Insets(0, 0, 0, 5), 70, 1));
777 * Initialises the Links tabbed panel.
781 private JPanel initLinksTab()
783 JPanel linkTab = new JPanel();
784 linkTab.setLayout(new GridBagLayout());
786 // Set up table for Url links
787 linkUrlTable.getTableHeader().setReorderingAllowed(false);
788 linkUrlTable.setFillsViewportHeight(true);
789 linkUrlTable.setAutoResizeMode(JTable.AUTO_RESIZE_ALL_COLUMNS);
790 linkUrlTable.setAutoCreateRowSorter(true);
791 linkUrlTable.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
793 // adjust row height so radio buttons actually fit
794 // don't do this in the renderer, it causes the awt thread to activate
796 JRadioButton temp = new JRadioButton();
797 linkUrlTable.setRowHeight(temp.getMinimumSize().height);
799 // Table in scrollpane so that the table is given a scrollbar
800 JScrollPane linkScrollPane = new JScrollPane(linkUrlTable);
801 linkScrollPane.setBorder(null);
803 // Panel for links functionality
804 JPanel linkPanel = new JPanel(new GridBagLayout());
805 linkPanel.setBorder(new TitledBorder(
806 MessageManager.getString("label.url_linkfrom_sequence_id")));
808 // Put the Url links panel together
810 // Buttons go at top right, resizing only resizes the blank space vertically
811 JPanel buttonPanel = initLinkTabUrlButtons();
812 GridBagConstraints linkConstraints1 = new GridBagConstraints();
813 linkConstraints1.insets = new Insets(0, 0, 5, 0);
814 linkConstraints1.gridx = 0;
815 linkConstraints1.gridy = 0;
816 linkConstraints1.weightx = 1.0;
817 linkConstraints1.fill = GridBagConstraints.HORIZONTAL;
818 linkTab.add(buttonPanel, linkConstraints1);
820 // Links table goes at top left, resizing resizes the table
821 GridBagConstraints linkConstraints2 = new GridBagConstraints();
822 linkConstraints2.insets = new Insets(0, 0, 5, 5);
823 linkConstraints2.gridx = 0;
824 linkConstraints2.gridy = 1;
825 linkConstraints2.weightx = 1.0;
826 linkConstraints2.weighty = 1.0;
827 linkConstraints2.fill = GridBagConstraints.BOTH;
828 linkTab.add(linkScrollPane, linkConstraints2);
830 // Filter box and buttons goes at bottom left, resizing resizes the text box
831 JPanel filterPanel = initLinkTabFilterPanel();
832 GridBagConstraints linkConstraints3 = new GridBagConstraints();
833 linkConstraints3.insets = new Insets(0, 0, 0, 5);
834 linkConstraints3.gridx = 0;
835 linkConstraints3.gridy = 2;
836 linkConstraints3.weightx = 1.0;
837 linkConstraints3.fill = GridBagConstraints.HORIZONTAL;
838 linkTab.add(filterPanel, linkConstraints3);
843 private JPanel initLinkTabFilterPanel()
845 // Filter textbox and reset button
846 JLabel filterLabel = new JLabel(
847 MessageManager.getString("label.filter"));
848 filterLabel.setFont(LABEL_FONT);
849 filterLabel.setHorizontalAlignment(SwingConstants.RIGHT);
850 filterLabel.setHorizontalTextPosition(SwingConstants.LEADING);
852 filterTB.setFont(LABEL_FONT);
853 filterTB.setText("");
855 doReset.setText(MessageManager.getString("action.showall"));
856 userOnly.setText(MessageManager.getString("action.customfilter"));
858 // Panel for filter functionality
859 JPanel filterPanel = new JPanel(new GridBagLayout());
860 filterPanel.setBorder(new TitledBorder("Filter"));
861 GridBagConstraints gbc = new GridBagConstraints();
864 gbc.fill = GridBagConstraints.NONE;
865 gbc.anchor = GridBagConstraints.WEST;
867 filterPanel.add(filterLabel, gbc);
869 GridBagConstraints gbc1 = new GridBagConstraints();
872 gbc1.fill = GridBagConstraints.HORIZONTAL;
873 gbc1.anchor = GridBagConstraints.WEST;
875 filterPanel.add(filterTB, gbc1);
877 GridBagConstraints gbc2 = new GridBagConstraints();
879 gbc2.fill = GridBagConstraints.NONE;
880 gbc2.anchor = GridBagConstraints.WEST;
881 filterPanel.add(doReset, gbc2);
883 GridBagConstraints gbc3 = new GridBagConstraints();
885 gbc3.fill = GridBagConstraints.NONE;
886 gbc3.anchor = GridBagConstraints.WEST;
887 filterPanel.add(userOnly, gbc3);
892 private JPanel initLinkTabUrlButtons()
894 // Buttons for new / edit / delete Url links
895 JButton newLink = new JButton();
896 newLink.setText(MessageManager.getString("action.new"));
898 editLink.setText(MessageManager.getString("action.edit"));
900 deleteLink.setText(MessageManager.getString("action.delete"));
902 // no current selection, so initially disable delete/edit buttons
903 editLink.setEnabled(false);
904 deleteLink.setEnabled(false);
906 newLink.addActionListener(new java.awt.event.ActionListener()
909 public void actionPerformed(ActionEvent e)
911 newLink_actionPerformed(e);
915 editLink.setText(MessageManager.getString("action.edit"));
916 editLink.addActionListener(new java.awt.event.ActionListener()
919 public void actionPerformed(ActionEvent e)
921 editLink_actionPerformed(e);
925 deleteLink.setText(MessageManager.getString("action.delete"));
926 deleteLink.addActionListener(new java.awt.event.ActionListener()
929 public void actionPerformed(ActionEvent e)
931 deleteLink_actionPerformed(e);
935 JPanel buttonPanel = new JPanel(new GridBagLayout());
936 buttonPanel.setBorder(new TitledBorder("Edit links"));
937 GridBagConstraints gbc = new GridBagConstraints();
940 gbc.fill = GridBagConstraints.NONE;
941 buttonPanel.add(newLink, gbc);
943 GridBagConstraints gbc1 = new GridBagConstraints();
946 gbc1.fill = GridBagConstraints.NONE;
947 buttonPanel.add(editLink, gbc1);
949 GridBagConstraints gbc2 = new GridBagConstraints();
952 gbc2.fill = GridBagConstraints.NONE;
953 buttonPanel.add(deleteLink, gbc2);
955 GridBagConstraints gbc3 = new GridBagConstraints();
958 gbc3.fill = GridBagConstraints.HORIZONTAL;
960 JPanel spacePanel = new JPanel();
961 spacePanel.setBorder(null);
962 buttonPanel.add(spacePanel, gbc3);
968 * Initialises the proxy server panel in the Connections tab
970 * @return the proxy server panel
972 private JPanel initConnTabProxyPanel()
974 // Label for server text box
975 serverLabel.setText(MessageManager.getString("label.host") + ": ");
976 serverLabel.setHorizontalAlignment(SwingConstants.RIGHT);
977 serverLabel.setFont(LABEL_FONT);
978 serverLabel2.setText(MessageManager.getString("label.host") + ": ");
979 serverLabel2.setHorizontalAlignment(SwingConstants.RIGHT);
980 serverLabel2.setFont(LABEL_FONT);
982 // Proxy server and port text boxes
983 proxyServerHttpTB.setFont(LABEL_FONT);
984 proxyServerHttpTB.setColumns(40);
985 proxyPortHttpTB.setFont(LABEL_FONT);
986 proxyPortHttpTB.setColumns(4);
987 proxyServerHttpsTB.setFont(LABEL_FONT);
988 proxyServerHttpsTB.setColumns(40);
989 proxyPortHttpsTB.setFont(LABEL_FONT);
990 proxyPortHttpsTB.setColumns(4);
991 proxyAuthUsernameTB.setFont(LABEL_FONT);
992 proxyAuthUsernameTB.setColumns(30);
993 proxyAuthPasswordPB.setFont(LABEL_FONT);
994 proxyAuthPasswordPB.setColumns(30);
995 proxyAuthPasswordPB.getDocument()
996 .addDocumentListener(new DocumentListener()
999 public void changedUpdate(DocumentEvent e)
1001 if (!proxyAuthPasswordPB.getBackground()
1002 .equals(Color.WHITE))
1003 proxyAuthPasswordPB.setBackground(Color.WHITE);
1007 public void insertUpdate(DocumentEvent e)
1009 if (!proxyAuthPasswordPB.getBackground()
1010 .equals(Color.WHITE))
1011 proxyAuthPasswordPB.setBackground(Color.WHITE);
1015 public void removeUpdate(DocumentEvent e)
1017 if (!proxyAuthPasswordPB.getBackground()
1018 .equals(Color.WHITE))
1019 proxyAuthPasswordPB.setBackground(Color.WHITE);
1024 // Label for Port text box
1025 portLabel.setFont(LABEL_FONT);
1026 portLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1027 portLabel.setText(MessageManager.getString("label.port") + ": ");
1028 portLabel2.setFont(LABEL_FONT);
1029 portLabel2.setHorizontalAlignment(SwingConstants.RIGHT);
1030 portLabel2.setText(MessageManager.getString("label.port") + ": ");
1032 httpLabel.setText("HTTP");
1033 httpLabel.setFont(LABEL_FONT_BOLD);
1034 httpLabel.setHorizontalAlignment(SwingConstants.LEFT);
1035 httpsLabel.setText("HTTPS");
1036 httpsLabel.setFont(LABEL_FONT_BOLD);
1037 httpsLabel.setHorizontalAlignment(SwingConstants.LEFT);
1039 proxyAuthUsernameLabel
1040 .setText(MessageManager.getString("label.username") + ": ");
1041 proxyAuthUsernameLabel.setFont(LABEL_FONT);
1042 proxyAuthUsernameLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1043 proxyAuthPasswordLabel
1044 .setText(MessageManager.getString("label.password") + ": ");
1045 proxyAuthPasswordLabel.setFont(LABEL_FONT);
1046 proxyAuthPasswordLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1047 passwordNotStoredLabel.setText(
1048 "(" + MessageManager.getString("label.not_stored") + ")");
1049 passwordNotStoredLabel.setFont(LABEL_FONT_ITALIC);
1050 passwordNotStoredLabel.setHorizontalAlignment(SwingConstants.LEFT);
1052 // Proxy type radio buttons
1053 noProxy.setFont(LABEL_FONT);
1054 noProxy.setHorizontalAlignment(SwingConstants.LEFT);
1055 noProxy.setText(MessageManager.getString("label.no_proxy"));
1056 systemProxy.setFont(LABEL_FONT);
1057 systemProxy.setHorizontalAlignment(SwingConstants.LEFT);
1058 systemProxy.setText(MessageManager.formatMessage("label.system_proxy",
1059 displayUserHostPort(Cache.startupProxyProperties[4],
1060 Cache.startupProxyProperties[0],
1061 Cache.startupProxyProperties[1]),
1062 displayUserHostPort(Cache.startupProxyProperties[6],
1063 Cache.startupProxyProperties[2],
1064 Cache.startupProxyProperties[3])));
1065 customProxy.setFont(LABEL_FONT);
1066 customProxy.setHorizontalAlignment(SwingConstants.LEFT);
1067 customProxy.setText(
1068 MessageManager.getString("label.use_proxy_server") + ":");
1069 ActionListener al = new ActionListener()
1072 public void actionPerformed(ActionEvent e)
1074 proxyType_actionPerformed();
1077 noProxy.addActionListener(al);
1078 systemProxy.addActionListener(al);
1079 customProxy.addActionListener(al);
1080 proxyType.add(noProxy);
1081 proxyType.add(systemProxy);
1082 proxyType.add(customProxy);
1084 proxyAuth.setFont(LABEL_FONT);
1085 proxyAuth.setHorizontalAlignment(SwingConstants.LEFT);
1086 proxyAuth.setText(MessageManager.getString("label.auth_required"));
1087 proxyAuth.addActionListener(new ActionListener()
1090 public void actionPerformed(ActionEvent e)
1092 proxyAuth_actionPerformed();
1096 setCustomProxyEnabled();
1098 // Make proxy server panel
1099 JPanel proxyPanel = new JPanel();
1100 TitledBorder titledBorder1 = new TitledBorder(
1101 MessageManager.getString("label.proxy_servers"));
1102 proxyPanel.setBorder(titledBorder1);
1103 proxyPanel.setLayout(new GridBagLayout());
1104 GridBagConstraints gbc = new GridBagConstraints();
1105 gbc.fill = GridBagConstraints.HORIZONTAL;
1108 GridBagConstraints c = new GridBagConstraints();
1109 // Proxy type radio buttons (3)
1110 JPanel ptPanel = new JPanel();
1111 ptPanel.setLayout(new GridBagLayout());
1116 c.fill = GridBagConstraints.HORIZONTAL;
1117 ptPanel.add(noProxy, c);
1119 ptPanel.add(systemProxy, c);
1121 ptPanel.add(customProxy, c);
1124 proxyPanel.add(ptPanel, gbc);
1126 // host and port text boxes
1127 JPanel hpPanel = new JPanel();
1128 hpPanel.setLayout(new GridBagLayout());
1129 // HTTP host port row
1134 c.anchor = GridBagConstraints.LINE_START;
1135 hpPanel.add(httpLabel, c);
1139 c.anchor = GridBagConstraints.LINE_END;
1140 hpPanel.add(serverLabel, c);
1144 c.anchor = GridBagConstraints.LINE_START;
1145 hpPanel.add(proxyServerHttpTB, c);
1149 c.anchor = GridBagConstraints.LINE_END;
1150 hpPanel.add(portLabel, c);
1154 c.anchor = GridBagConstraints.LINE_START;
1155 hpPanel.add(proxyPortHttpTB, c);
1157 // HTTPS host port row
1162 c.anchor = GridBagConstraints.LINE_START;
1163 hpPanel.add(httpsLabel, c);
1166 c.anchor = GridBagConstraints.LINE_END;
1167 hpPanel.add(serverLabel2, c);
1170 c.anchor = GridBagConstraints.LINE_START;
1171 hpPanel.add(proxyServerHttpsTB, c);
1174 c.anchor = GridBagConstraints.LINE_END;
1175 hpPanel.add(portLabel2, c);
1178 c.anchor = GridBagConstraints.LINE_START;
1179 hpPanel.add(proxyPortHttpsTB, c);
1182 proxyPanel.add(hpPanel, gbc);
1184 // Require authentication checkbox
1186 proxyPanel.add(proxyAuth, gbc);
1188 // username and password
1189 JPanel upPanel = new JPanel();
1190 upPanel.setLayout(new GridBagLayout());
1196 c.anchor = GridBagConstraints.LINE_END;
1197 upPanel.add(proxyAuthUsernameLabel, c);
1201 c.anchor = GridBagConstraints.LINE_START;
1202 upPanel.add(proxyAuthUsernameTB, c);
1208 c.anchor = GridBagConstraints.LINE_END;
1209 upPanel.add(proxyAuthPasswordLabel, c);
1213 c.anchor = GridBagConstraints.LINE_START;
1214 upPanel.add(proxyAuthPasswordPB, c);
1218 c.anchor = GridBagConstraints.LINE_START;
1219 upPanel.add(passwordNotStoredLabel, c);
1222 proxyPanel.add(upPanel, gbc);
1224 applyProxyButton.setText(MessageManager.getString("action.apply"));
1225 applyProxyButton.addActionListener(new ActionListener()
1228 public void actionPerformed(ActionEvent e)
1230 saveProxySettings();
1234 gbc.fill = GridBagConstraints.NONE;
1235 gbc.anchor = GridBagConstraints.LINE_END;
1236 proxyPanel.add(applyProxyButton, gbc);
1241 public void proxyAuthPasswordFocus()
1243 proxyAuthPasswordPB.grabFocus();
1244 proxyAuthPasswordPB.setBackground(Color.PINK);
1247 public void saveProxySettings()
1249 // overridden in Preferences
1252 private String displayUserHostPort(String user, String host, String port)
1254 boolean hostBlank = (host == null || host.isEmpty());
1255 boolean portBlank = (port == null || port.isEmpty());
1256 if (hostBlank && portBlank)
1258 return MessageManager.getString("label.none");
1261 StringBuilder sb = new StringBuilder();
1264 sb.append(user.isEmpty() || user.indexOf(" ") > -1 ? '"' + user + '"'
1268 sb.append(hostBlank ? "" : host);
1274 return sb.toString();
1278 * Initialises the checkboxes in the Connections tab
1280 private void initConnTabCheckboxes()
1282 // Usage stats checkbox label
1284 MessageManager.getString("label.send_usage_statistics"));
1285 usagestats.setFont(LABEL_FONT);
1286 usagestats.setHorizontalAlignment(SwingConstants.RIGHT);
1287 usagestats.setHorizontalTextPosition(SwingConstants.LEADING);
1289 // Questionnaire checkbox label
1290 questionnaire.setText(
1291 MessageManager.getString("label.check_for_questionnaires"));
1292 questionnaire.setFont(LABEL_FONT);
1293 questionnaire.setHorizontalAlignment(SwingConstants.RIGHT);
1294 questionnaire.setHorizontalTextPosition(SwingConstants.LEADING);
1296 // Check for latest version checkbox label
1297 versioncheck.setText(
1298 MessageManager.getString("label.check_for_latest_version"));
1299 versioncheck.setFont(LABEL_FONT);
1300 versioncheck.setHorizontalAlignment(SwingConstants.RIGHT);
1301 versioncheck.setHorizontalTextPosition(SwingConstants.LEADING);
1305 * Initialises the parent panel which contains the tabbed sections.
1309 private JPanel initOkCancelPanel()
1311 JButton ok = new JButton();
1312 ok.setText(MessageManager.getString("action.ok"));
1313 ok.addActionListener(new ActionListener()
1316 public void actionPerformed(ActionEvent e)
1318 ok_actionPerformed(e);
1321 JButton cancel = new JButton();
1322 cancel.setText(MessageManager.getString("action.cancel"));
1323 cancel.addActionListener(new ActionListener()
1326 public void actionPerformed(ActionEvent e)
1328 cancel_actionPerformed(e);
1331 JPanel okCancelPanel = new JPanel();
1332 okCancelPanel.add(ok);
1333 okCancelPanel.add(cancel);
1334 return okCancelPanel;
1338 * Initialises the Colours tabbed panel.
1342 private JPanel initColoursTab()
1344 JPanel coloursTab = new JPanel();
1345 coloursTab.setBorder(new TitledBorder(
1346 MessageManager.getString("action.open_new_alignment")));
1347 coloursTab.setLayout(new FlowLayout());
1348 JLabel mincolourLabel = new JLabel();
1349 mincolourLabel.setFont(LABEL_FONT);
1350 mincolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1351 mincolourLabel.setText(MessageManager.getString("label.min_colour"));
1352 minColour.setFont(LABEL_FONT);
1353 minColour.setBorder(BorderFactory.createEtchedBorder());
1354 minColour.setPreferredSize(new Dimension(40, 20));
1355 minColour.addMouseListener(new MouseAdapter()
1358 public void mousePressed(MouseEvent e)
1360 minColour_actionPerformed(minColour);
1363 JLabel maxcolourLabel = new JLabel();
1364 maxcolourLabel.setFont(LABEL_FONT);
1365 maxcolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1366 maxcolourLabel.setText(MessageManager.getString("label.max_colour"));
1367 maxColour.setFont(LABEL_FONT);
1368 maxColour.setBorder(BorderFactory.createEtchedBorder());
1369 maxColour.setPreferredSize(new Dimension(40, 20));
1370 maxColour.addMouseListener(new MouseAdapter()
1373 public void mousePressed(MouseEvent e)
1375 maxColour_actionPerformed(maxColour);
1379 protColour.setFont(LABEL_FONT);
1380 protColour.setBounds(new Rectangle(172, 225, 155, 21));
1381 JLabel protColourLabel = new JLabel();
1382 protColourLabel.setFont(LABEL_FONT);
1383 protColourLabel.setHorizontalAlignment(SwingConstants.LEFT);
1384 protColourLabel.setText(
1385 MessageManager.getString("label.prot_alignment_colour") + " ");
1386 JvSwingUtils.addtoLayout(coloursTab,
1388 .getString("label.default_colour_scheme_for_alignment"),
1389 protColourLabel, protColour);
1391 nucColour.setFont(LABEL_FONT);
1392 nucColour.setBounds(new Rectangle(172, 240, 155, 21));
1393 JLabel nucColourLabel = new JLabel();
1394 nucColourLabel.setFont(LABEL_FONT);
1395 nucColourLabel.setHorizontalAlignment(SwingConstants.LEFT);
1396 nucColourLabel.setText(
1397 MessageManager.getString("label.nuc_alignment_colour") + " ");
1398 JvSwingUtils.addtoLayout(coloursTab,
1400 .getString("label.default_colour_scheme_for_alignment"),
1401 nucColourLabel, nucColour);
1403 JPanel annotationShding = new JPanel();
1404 annotationShding.setBorder(new TitledBorder(
1405 MessageManager.getString("label.annotation_shading_default")));
1406 annotationShding.setLayout(new GridLayout(1, 2));
1407 JvSwingUtils.addtoLayout(annotationShding,
1408 MessageManager.getString(
1409 "label.default_minimum_colour_annotation_shading"),
1410 mincolourLabel, minColour);
1411 JvSwingUtils.addtoLayout(annotationShding,
1412 MessageManager.getString(
1413 "label.default_maximum_colour_annotation_shading"),
1414 maxcolourLabel, maxColour);
1415 coloursTab.add(annotationShding); // , FlowLayout.LEFT);
1420 * Initialises the Overview tabbed panel.
1424 private JPanel initOverviewTab()
1426 JPanel overviewPanel = new JPanel();
1427 overviewPanel.setBorder(new TitledBorder(
1428 MessageManager.getString("label.overview_settings")));
1430 gapColour.setFont(LABEL_FONT);
1431 // fixing the border colours stops apparent colour bleed from the panel
1432 gapColour.setBorder(
1433 BorderFactory.createEtchedBorder(Color.white, Color.lightGray));
1434 gapColour.setPreferredSize(new Dimension(40, 20));
1435 gapColour.addMouseListener(new MouseAdapter()
1438 public void mousePressed(MouseEvent e)
1440 gapColour_actionPerformed(gapColour);
1444 hiddenColour.setFont(LABEL_FONT);
1445 // fixing the border colours stops apparent colour bleed from the panel
1446 hiddenColour.setBorder(
1447 BorderFactory.createEtchedBorder(Color.white, Color.lightGray));
1448 hiddenColour.setPreferredSize(new Dimension(40, 20));
1449 hiddenColour.addMouseListener(new MouseAdapter()
1452 public void mousePressed(MouseEvent e)
1454 hiddenColour_actionPerformed(hiddenColour);
1458 useLegacyGap = new JCheckBox(
1459 MessageManager.getString("label.ov_legacy_gap"));
1460 useLegacyGap.setFont(LABEL_FONT);
1461 useLegacyGap.setHorizontalAlignment(SwingConstants.LEFT);
1462 useLegacyGap.setVerticalTextPosition(SwingConstants.TOP);
1463 gapLabel = new JLabel(MessageManager.getString("label.gap_colour"));
1464 gapLabel.setFont(LABEL_FONT);
1465 gapLabel.setHorizontalAlignment(SwingConstants.LEFT);
1466 gapLabel.setVerticalTextPosition(SwingConstants.TOP);
1467 showHiddenAtStart = new JCheckBox(
1468 MessageManager.getString("label.ov_show_hide_default"));
1469 showHiddenAtStart.setFont(LABEL_FONT);
1470 showHiddenAtStart.setHorizontalAlignment(SwingConstants.LEFT);
1471 showHiddenAtStart.setVerticalTextPosition(SwingConstants.TOP);
1472 JLabel hiddenLabel = new JLabel(
1473 MessageManager.getString("label.hidden_colour"));
1474 hiddenLabel.setFont(LABEL_FONT);
1475 hiddenLabel.setHorizontalAlignment(SwingConstants.LEFT);
1476 hiddenLabel.setVerticalTextPosition(SwingConstants.TOP);
1478 useLegacyGap.addActionListener(new ActionListener()
1481 public void actionPerformed(ActionEvent e)
1483 useLegacyGaps_actionPerformed(e);
1487 overviewPanel.setLayout(new GridBagLayout());
1488 GridBagConstraints c1 = new GridBagConstraints();
1490 c1.fill = GridBagConstraints.HORIZONTAL;
1495 c1.anchor = GridBagConstraints.FIRST_LINE_START;
1496 overviewPanel.add(useLegacyGap, c1);
1498 GridBagConstraints c2 = new GridBagConstraints();
1499 c2.fill = GridBagConstraints.HORIZONTAL;
1502 c2.insets = new Insets(0, 15, 0, 10);
1503 overviewPanel.add(gapLabel, c2);
1505 GridBagConstraints c3 = new GridBagConstraints();
1506 c3.fill = GridBagConstraints.HORIZONTAL;
1509 c3.insets = new Insets(0, 0, 0, 15);
1510 overviewPanel.add(gapColour, c3);
1512 GridBagConstraints c4 = new GridBagConstraints();
1513 c4.fill = GridBagConstraints.HORIZONTAL;
1517 overviewPanel.add(showHiddenAtStart, c4);
1519 GridBagConstraints c5 = new GridBagConstraints();
1520 c5.fill = GridBagConstraints.HORIZONTAL;
1523 c5.insets = new Insets(0, 15, 0, 10);
1524 overviewPanel.add(hiddenLabel, c5);
1526 GridBagConstraints c6 = new GridBagConstraints();
1527 c6.fill = GridBagConstraints.HORIZONTAL;
1530 c6.insets = new Insets(0, 0, 0, 15);
1531 overviewPanel.add(hiddenColour, c6);
1533 JButton resetButton = new JButton(
1534 MessageManager.getString("label.reset_to_defaults"));
1536 resetButton.addActionListener(new ActionListener()
1539 public void actionPerformed(ActionEvent e)
1541 resetOvDefaults_actionPerformed(e);
1545 GridBagConstraints c7 = new GridBagConstraints();
1546 c7.fill = GridBagConstraints.NONE;
1549 c7.insets = new Insets(10, 0, 0, 0);
1550 c7.anchor = GridBagConstraints.WEST;
1551 overviewPanel.add(resetButton, c7);
1553 // Add padding so the panel doesn't look ridiculous
1554 JPanel spacePanel = new JPanel();
1555 overviewPanel.add(spacePanel,
1556 new GridBagConstraints(0, 3, 1, 1, 1.0, 1.0,
1557 GridBagConstraints.WEST, GridBagConstraints.BOTH,
1558 new Insets(0, 0, 0, 5), 0, 0));
1560 return overviewPanel;
1564 * Initialises the Structure tabbed panel.
1568 private JPanel initStructureTab()
1570 structureTab = new JPanel();
1572 structureTab.setBorder(new TitledBorder(
1573 MessageManager.getString("label.structure_options")));
1574 structureTab.setLayout(null);
1575 final int width = 420;
1576 final int height = 22;
1577 final int lineSpacing = 25;
1580 structFromPdb.setFont(LABEL_FONT);
1582 .setText(MessageManager.getString("label.struct_from_pdb"));
1583 structFromPdb.setBounds(new Rectangle(5, ypos, width, height));
1584 structFromPdb.addActionListener(new ActionListener()
1587 public void actionPerformed(ActionEvent e)
1589 boolean selected = structFromPdb.isSelected();
1590 // enable other options only when the first is checked
1591 useRnaView.setEnabled(selected);
1592 addSecondaryStructure.setEnabled(selected);
1593 addTempFactor.setEnabled(selected);
1596 structureTab.add(structFromPdb);
1598 // indent checkboxes that are conditional on the first one
1599 ypos += lineSpacing;
1600 useRnaView.setFont(LABEL_FONT);
1601 useRnaView.setText(MessageManager.getString("label.use_rnaview"));
1602 useRnaView.setBounds(new Rectangle(25, ypos, width, height));
1603 structureTab.add(useRnaView);
1605 ypos += lineSpacing;
1606 addSecondaryStructure.setFont(LABEL_FONT);
1607 addSecondaryStructure
1608 .setText(MessageManager.getString("label.autoadd_secstr"));
1609 addSecondaryStructure.setBounds(new Rectangle(25, ypos, width, height));
1610 structureTab.add(addSecondaryStructure);
1612 ypos += lineSpacing;
1613 addTempFactor.setFont(LABEL_FONT);
1614 addTempFactor.setText(MessageManager.getString("label.autoadd_temp"));
1615 addTempFactor.setBounds(new Rectangle(25, ypos, width, height));
1616 structureTab.add(addTempFactor);
1618 ypos += lineSpacing;
1619 JLabel viewerLabel = new JLabel();
1620 viewerLabel.setFont(LABEL_FONT);
1621 viewerLabel.setHorizontalAlignment(SwingConstants.LEFT);
1622 viewerLabel.setText(MessageManager.getString("label.structure_viewer"));
1623 viewerLabel.setBounds(new Rectangle(10, ypos, 220, height));
1624 structureTab.add(viewerLabel);
1627 * add all external viewers as options here - check
1628 * when selected whether the program is installed
1630 structViewer.setFont(LABEL_FONT);
1631 structViewer.setBounds(new Rectangle(190, ypos, 120, height));
1632 structViewer.addItem(ViewerType.JMOL.name());
1633 structViewer.addItem(ViewerType.CHIMERA.name());
1634 structViewer.addItem(ViewerType.CHIMERAX.name());
1635 structViewer.addItem(ViewerType.PYMOL.name());
1636 structViewer.addActionListener(new ActionListener()
1639 public void actionPerformed(ActionEvent e)
1641 structureViewer_actionPerformed(
1642 (String) structViewer.getSelectedItem());
1645 structureTab.add(structViewer);
1647 ypos += lineSpacing;
1648 structureViewerPathLabel = new JLabel();
1649 structureViewerPathLabel.setFont(LABEL_FONT);// new Font("SansSerif", 0, 11));
1650 structureViewerPathLabel.setHorizontalAlignment(SwingConstants.LEFT);
1651 structureViewerPathLabel.setText(MessageManager
1652 .formatMessage("label.viewer_path", "Chimera(X)"));
1653 structureViewerPathLabel.setBounds(new Rectangle(10, ypos, 170, height));
1654 structureViewerPathLabel.setEnabled(false);
1655 structureTab.add(structureViewerPathLabel);
1657 structureViewerPath.setFont(LABEL_FONT);
1658 structureViewerPath.setText("");
1659 structureViewerPath.setEnabled(false);
1660 final String tooltip = JvSwingUtils.wrapTooltip(true,
1661 MessageManager.getString("label.viewer_path_tip"));
1662 structureViewerPath.setToolTipText(tooltip);
1663 structureViewerPath.setBounds(new Rectangle(190, ypos, 290, height));
1664 structureViewerPath.addMouseListener(new MouseAdapter()
1667 public void mouseClicked(MouseEvent e)
1669 if (structureViewerPath.isEnabled() && e.getClickCount() == 2)
1671 String chosen = openFileChooser();
1674 structureViewerPath.setText(chosen);
1679 structureTab.add(structureViewerPath);
1681 ypos += lineSpacing;
1682 nwMapping.setFont(LABEL_FONT);
1683 nwMapping.setText(MessageManager.getString("label.nw_mapping"));
1684 siftsMapping.setFont(LABEL_FONT);
1685 siftsMapping.setText(MessageManager.getString("label.sifts_mapping"));
1686 mappingMethod.add(nwMapping);
1687 mappingMethod.add(siftsMapping);
1688 JPanel mappingPanel = new JPanel();
1689 mappingPanel.setFont(LABEL_FONT);
1690 TitledBorder mmTitledBorder = new TitledBorder(
1691 MessageManager.getString("label.mapping_method"));
1692 mmTitledBorder.setTitleFont(LABEL_FONT);
1693 mappingPanel.setBorder(mmTitledBorder);
1694 mappingPanel.setBounds(new Rectangle(10, ypos, 472, 45));
1695 // GridLayout mappingLayout = new GridLayout();
1696 mappingPanel.setLayout(new GridLayout());
1697 mappingPanel.add(nwMapping);
1698 mappingPanel.add(siftsMapping);
1699 structureTab.add(mappingPanel);
1701 ypos += lineSpacing;
1702 ypos += lineSpacing;
1703 FTSDataColumnPreferences docFieldPref = new FTSDataColumnPreferences(
1704 PreferenceSource.PREFERENCES, PDBFTSRestClient.getInstance());
1705 docFieldPref.setBounds(new Rectangle(10, ypos, 470, 120));
1706 structureTab.add(docFieldPref);
1709 * hide Chimera options in JalviewJS
1711 if (Platform.isJS())
1713 structureViewerPathLabel.setVisible(false);
1714 structureViewerPath.setVisible(false);
1715 viewerLabel.setVisible(false);
1716 structViewer.setVisible(false);
1719 return structureTab;
1723 * Action on choosing a structure viewer from combobox options.
1725 * @param selectedItem
1727 protected void structureViewer_actionPerformed(String selectedItem)
1732 * Show a dialog for the user to choose a file. Returns the chosen path, or
1737 protected String openFileChooser()
1739 String choice = null;
1740 JFileChooser chooser = new JFileChooser();
1742 // chooser.setFileView(new JalviewFileView());
1743 chooser.setDialogTitle(
1744 MessageManager.getString("label.open_local_file"));
1745 chooser.setToolTipText(MessageManager.getString("action.open"));
1747 int value = chooser.showOpenDialog(this);
1749 if (value == JFileChooser.APPROVE_OPTION)
1751 choice = chooser.getSelectedFile().getPath();
1757 * Validate the structure tab preferences; if invalid, set focus on this tab.
1761 protected boolean validateStructure(FocusEvent e)
1763 if (!validateStructure())
1765 e.getComponent().requestFocusInWindow();
1771 protected boolean validateStructure()
1777 * Initialises the Visual tabbed panel.
1781 private JPanel initVisualTab()
1783 JPanel visualTab = new JPanel();
1784 visualTab.setBorder(new TitledBorder(
1785 MessageManager.getString("action.open_new_alignment")));
1786 visualTab.setLayout(null);
1787 fullScreen.setFont(LABEL_FONT);
1788 fullScreen.setHorizontalAlignment(SwingConstants.RIGHT);
1789 fullScreen.setHorizontalTextPosition(SwingConstants.LEFT);
1790 fullScreen.setText(MessageManager.getString("label.maximize_window"));
1791 quality.setEnabled(false);
1792 quality.setFont(LABEL_FONT);
1793 quality.setHorizontalAlignment(SwingConstants.RIGHT);
1794 quality.setHorizontalTextPosition(SwingConstants.LEFT);
1795 quality.setSelected(true);
1796 quality.setText(MessageManager.getString("label.quality"));
1797 conservation.setEnabled(false);
1798 conservation.setFont(LABEL_FONT);
1799 conservation.setHorizontalAlignment(SwingConstants.RIGHT);
1800 conservation.setHorizontalTextPosition(SwingConstants.LEFT);
1801 conservation.setSelected(true);
1802 conservation.setText(MessageManager.getString("label.conservation"));
1803 identity.setEnabled(false);
1804 identity.setFont(LABEL_FONT);
1805 identity.setHorizontalAlignment(SwingConstants.RIGHT);
1806 identity.setHorizontalTextPosition(SwingConstants.LEFT);
1807 identity.setSelected(true);
1808 identity.setText(MessageManager.getString("label.consensus"));
1809 showOccupancy.setFont(LABEL_FONT);
1810 showOccupancy.setEnabled(false);
1811 showOccupancy.setHorizontalAlignment(SwingConstants.RIGHT);
1812 showOccupancy.setHorizontalTextPosition(SwingConstants.LEFT);
1813 showOccupancy.setSelected(true);
1814 showOccupancy.setText(MessageManager.getString("label.occupancy"));
1816 JLabel showGroupbits = new JLabel();
1817 showGroupbits.setFont(LABEL_FONT);
1818 showGroupbits.setHorizontalAlignment(SwingConstants.RIGHT);
1819 showGroupbits.setHorizontalTextPosition(SwingConstants.LEFT);
1821 .setText(MessageManager.getString("action.show_group") + ":");
1822 JLabel showConsensbits = new JLabel();
1823 showConsensbits.setFont(LABEL_FONT);
1824 showConsensbits.setHorizontalAlignment(SwingConstants.RIGHT);
1825 showConsensbits.setHorizontalTextPosition(SwingConstants.LEFT);
1827 .setText(MessageManager.getString("label.consensus") + ":");
1828 showConsensHistogram.setEnabled(false);
1829 showConsensHistogram.setFont(LABEL_FONT);
1830 showConsensHistogram.setHorizontalAlignment(SwingConstants.RIGHT);
1831 showConsensHistogram.setHorizontalTextPosition(SwingConstants.LEFT);
1832 showConsensHistogram.setSelected(true);
1833 showConsensHistogram
1834 .setText(MessageManager.getString("label.histogram"));
1835 showConsensLogo.setEnabled(false);
1836 showConsensLogo.setFont(LABEL_FONT);
1837 showConsensLogo.setHorizontalAlignment(SwingConstants.RIGHT);
1838 showConsensLogo.setHorizontalTextPosition(SwingConstants.LEFT);
1839 showConsensLogo.setSelected(true);
1840 showConsensLogo.setText(MessageManager.getString("label.logo"));
1841 showGroupConsensus.setEnabled(false);
1842 showGroupConsensus.setFont(LABEL_FONT);
1843 showGroupConsensus.setHorizontalAlignment(SwingConstants.RIGHT);
1844 showGroupConsensus.setHorizontalTextPosition(SwingConstants.LEFT);
1845 showGroupConsensus.setSelected(true);
1846 showGroupConsensus.setText(MessageManager.getString("label.consensus"));
1847 showGroupConservation.setEnabled(false);
1848 showGroupConservation.setFont(LABEL_FONT);
1849 showGroupConservation.setHorizontalAlignment(SwingConstants.RIGHT);
1850 showGroupConservation.setHorizontalTextPosition(SwingConstants.LEFT);
1851 showGroupConservation.setSelected(true);
1852 showGroupConservation
1853 .setText(MessageManager.getString("label.conservation"));
1854 showNpTooltip.setEnabled(true);
1855 showNpTooltip.setFont(LABEL_FONT);
1856 showNpTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
1857 showNpTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
1858 showNpTooltip.setSelected(true);
1859 showNpTooltip.setText(
1860 MessageManager.getString("label.non_positional_features"));
1861 showDbRefTooltip.setEnabled(true);
1862 showDbRefTooltip.setFont(LABEL_FONT);
1863 showDbRefTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
1864 showDbRefTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
1865 showDbRefTooltip.setSelected(true);
1867 .setText(MessageManager.getString("label.database_references"));
1868 annotations.setFont(LABEL_FONT);
1869 annotations.setHorizontalAlignment(SwingConstants.RIGHT);
1870 annotations.setHorizontalTextPosition(SwingConstants.LEFT);
1871 annotations.setSelected(true);
1872 annotations.setText(MessageManager.getString("label.show_annotations"));
1873 // annotations.setBounds(new Rectangle(169, 12, 200, 23));
1874 annotations.addActionListener(new ActionListener()
1877 public void actionPerformed(ActionEvent e)
1879 annotations_actionPerformed(e);
1882 identity.addActionListener(new ActionListener()
1885 public void actionPerformed(ActionEvent e)
1887 annotations_actionPerformed(e);
1890 showGroupConsensus.addActionListener(new ActionListener()
1893 public void actionPerformed(ActionEvent e)
1895 annotations_actionPerformed(e);
1898 showUnconserved.setFont(LABEL_FONT);
1899 showUnconserved.setHorizontalAlignment(SwingConstants.RIGHT);
1900 showUnconserved.setHorizontalTextPosition(SwingConstants.LEFT);
1901 showUnconserved.setSelected(true);
1903 .setText(MessageManager.getString("action.show_unconserved"));
1904 showUnconserved.addActionListener(new ActionListener()
1907 public void actionPerformed(ActionEvent e)
1909 showunconserved_actionPerformed(e);
1913 // TODO these are not yet added to / action from Preferences
1914 // JCheckBox shareSelections = new JCheckBox();
1915 // shareSelections.setFont(verdana11);
1916 // shareSelections.setHorizontalAlignment(SwingConstants.RIGHT);
1917 // shareSelections.setHorizontalTextPosition(SwingConstants.LEFT);
1918 // shareSelections.setSelected(true);
1919 // shareSelections.setText(MessageManager
1920 // .getString("label.share_selection_across_views"));
1921 // JCheckBox followHighlight = new JCheckBox();
1922 // followHighlight.setFont(verdana11);
1923 // followHighlight.setHorizontalAlignment(SwingConstants.RIGHT);
1924 // followHighlight.setHorizontalTextPosition(SwingConstants.LEFT);
1925 // // showUnconserved.setBounds(new Rectangle(169, 40, 200, 23));
1926 // followHighlight.setSelected(true);
1927 // followHighlight.setText(MessageManager
1928 // .getString("label.scroll_highlighted_regions"));
1930 seqLimit.setFont(LABEL_FONT);
1931 seqLimit.setHorizontalAlignment(SwingConstants.RIGHT);
1932 seqLimit.setHorizontalTextPosition(SwingConstants.LEFT);
1933 seqLimit.setText(MessageManager.getString("label.full_sequence_id"));
1934 smoothFont.setFont(LABEL_FONT);
1935 smoothFont.setHorizontalAlignment(SwingConstants.RIGHT);
1936 smoothFont.setHorizontalTextPosition(SwingConstants.LEADING);
1937 smoothFont.setText(MessageManager.getString("label.smooth_font"));
1938 scaleProteinToCdna.setFont(LABEL_FONT);
1939 scaleProteinToCdna.setHorizontalAlignment(SwingConstants.RIGHT);
1940 scaleProteinToCdna.setHorizontalTextPosition(SwingConstants.LEADING);
1941 scaleProteinToCdna.setText(
1942 MessageManager.getString("label.scale_protein_to_cdna"));
1943 scaleProteinToCdna.setToolTipText(
1944 MessageManager.getString("label.scale_protein_to_cdna_tip"));
1945 JLabel gapLabel = new JLabel();
1946 gapLabel.setFont(LABEL_FONT);
1947 gapLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1948 gapLabel.setText(MessageManager.getString("label.gap_symbol") + " ");
1949 JLabel fontLabel = new JLabel();
1950 fontLabel.setFont(LABEL_FONT);
1951 fontLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1952 fontLabel.setText(MessageManager.getString("label.font"));
1953 fontSizeCB.setFont(LABEL_FONT);
1954 fontSizeCB.setBounds(new Rectangle(320, 112, 65, 23));
1955 fontStyleCB.setFont(LABEL_FONT);
1956 fontStyleCB.setBounds(new Rectangle(382, 112, 80, 23));
1957 fontNameCB.setFont(LABEL_FONT);
1958 fontNameCB.setBounds(new Rectangle(172, 112, 147, 23));
1959 gapSymbolCB.setFont(LABEL_FONT);
1960 gapSymbolCB.setBounds(new Rectangle(172, 215, 69, 23));
1961 DefaultListCellRenderer dlcr = new DefaultListCellRenderer();
1962 dlcr.setHorizontalAlignment(DefaultListCellRenderer.CENTER);
1963 gapSymbolCB.setRenderer(dlcr);
1965 startupCheckbox.setText(MessageManager.getString("action.open_file"));
1966 startupCheckbox.setFont(LABEL_FONT);
1967 startupCheckbox.setHorizontalAlignment(SwingConstants.RIGHT);
1968 startupCheckbox.setHorizontalTextPosition(SwingConstants.LEFT);
1969 startupCheckbox.setSelected(true);
1970 startupFileTextfield.setFont(LABEL_FONT);
1971 startupFileTextfield.setBounds(new Rectangle(172, 310, 330, 20));
1972 final String tooltip = JvSwingUtils.wrapTooltip(true,
1973 MessageManager.getString("label.double_click_to_browse"));
1974 startupFileTextfield.setToolTipText(tooltip);
1975 startupFileTextfield.addMouseListener(new MouseAdapter()
1978 public void mouseClicked(MouseEvent e)
1980 if (e.getClickCount() > 1)
1982 startupFileTextfield_mouseClicked();
1987 sortby.setFont(LABEL_FONT);
1988 sortby.setBounds(new Rectangle(172, 260, 155, 21));
1989 JLabel sortLabel = new JLabel();
1990 sortLabel.setFont(LABEL_FONT);
1991 sortLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1992 sortLabel.setText(MessageManager.getString("label.sort_by"));
1993 sortAnnBy.setFont(LABEL_FONT);
1994 sortAnnBy.setBounds(new Rectangle(172, 285, 110, 21));
1995 JLabel sortAnnLabel = new JLabel();
1996 sortAnnLabel.setFont(LABEL_FONT);
1997 sortAnnLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1998 sortAnnLabel.setText(MessageManager.getString("label.sort_ann_by"));
1999 sortAutocalc.setFont(LABEL_FONT);
2000 sortAutocalc.setBounds(new Rectangle(290, 285, 165, 21));
2002 JPanel annsettingsPanel = new JPanel();
2003 annsettingsPanel.setBounds(new Rectangle(173, 13, 320, 96));
2004 annsettingsPanel.setLayout(new FlowLayout(FlowLayout.LEFT, 0, 0));
2005 annsettingsPanel.setBorder(new EtchedBorder());
2006 visualTab.add(annsettingsPanel);
2007 Border jb = new EmptyBorder(1, 1, 4, 5);
2008 annotations.setBorder(jb);
2009 showOccupancy.setBorder(jb);
2010 quality.setBorder(jb);
2011 conservation.setBorder(jb);
2012 identity.setBorder(jb);
2013 showConsensbits.setBorder(jb);
2014 showGroupbits.setBorder(jb);
2015 showGroupConsensus.setBorder(jb);
2016 showGroupConservation.setBorder(jb);
2017 showConsensHistogram.setBorder(jb);
2018 showConsensLogo.setBorder(jb);
2020 JPanel autoAnnotSettings = new JPanel();
2021 annsettingsPanel.add(autoAnnotSettings);
2022 autoAnnotSettings.setLayout(new GridLayout(0, 2));
2023 autoAnnotSettings.add(annotations);
2024 autoAnnotSettings.add(quality);
2025 // second row of autoannotation box
2026 autoAnnotSettings = new JPanel();
2027 annsettingsPanel.add(autoAnnotSettings);
2029 autoAnnotSettings.setLayout(new GridLayout(0, 3));
2030 autoAnnotSettings.add(conservation);
2031 autoAnnotSettings.add(identity);
2032 autoAnnotSettings.add(showOccupancy);
2033 autoAnnotSettings.add(showGroupbits);
2034 autoAnnotSettings.add(showGroupConservation);
2035 autoAnnotSettings.add(showGroupConsensus);
2036 autoAnnotSettings.add(showConsensbits);
2037 autoAnnotSettings.add(showConsensHistogram);
2038 autoAnnotSettings.add(showConsensLogo);
2040 JPanel tooltipSettings = new JPanel();
2041 tooltipSettings.setBorder(new TitledBorder(
2042 MessageManager.getString("label.sequence_id_tooltip")));
2043 tooltipSettings.setBounds(173, 140, 220, 62);
2044 tooltipSettings.setLayout(new GridLayout(2, 1));
2045 tooltipSettings.add(showDbRefTooltip);
2046 tooltipSettings.add(showNpTooltip);
2047 visualTab.add(tooltipSettings);
2049 wrap.setFont(LABEL_FONT);
2050 wrap.setHorizontalAlignment(SwingConstants.TRAILING);
2051 wrap.setHorizontalTextPosition(SwingConstants.LEADING);
2052 wrap.setText(MessageManager.getString("label.wrap_alignment"));
2053 rightAlign.setFont(LABEL_FONT);
2054 rightAlign.setForeground(Color.black);
2055 rightAlign.setHorizontalAlignment(SwingConstants.RIGHT);
2056 rightAlign.setHorizontalTextPosition(SwingConstants.LEFT);
2057 rightAlign.setText(MessageManager.getString("label.right_align_ids"));
2058 idItalics.setFont(LABEL_FONT_ITALIC);
2059 idItalics.setHorizontalAlignment(SwingConstants.RIGHT);
2060 idItalics.setHorizontalTextPosition(SwingConstants.LEADING);
2062 MessageManager.getString("label.sequence_name_italics"));
2063 openoverv.setFont(LABEL_FONT);
2064 openoverv.setActionCommand(
2065 MessageManager.getString("label.open_overview"));
2066 openoverv.setHorizontalAlignment(SwingConstants.RIGHT);
2067 openoverv.setHorizontalTextPosition(SwingConstants.LEFT);
2068 openoverv.setText(MessageManager.getString("label.open_overview"));
2069 JPanel jPanel2 = new JPanel();
2070 jPanel2.setBounds(new Rectangle(7, 17, 158, 310));
2071 jPanel2.setLayout(new GridLayout(14, 1));
2072 jPanel2.add(fullScreen);
2073 jPanel2.add(openoverv);
2074 jPanel2.add(seqLimit);
2075 jPanel2.add(rightAlign);
2076 jPanel2.add(fontLabel);
2077 jPanel2.add(showUnconserved);
2078 jPanel2.add(idItalics);
2079 jPanel2.add(smoothFont);
2080 jPanel2.add(scaleProteinToCdna);
2081 jPanel2.add(gapLabel);
2083 jPanel2.add(sortLabel);
2084 jPanel2.add(sortAnnLabel);
2085 jPanel2.add(startupCheckbox);
2086 visualTab.add(jPanel2);
2087 visualTab.add(startupFileTextfield);
2088 visualTab.add(sortby);
2089 visualTab.add(sortAnnBy);
2090 visualTab.add(sortAutocalc);
2091 visualTab.add(gapSymbolCB);
2092 visualTab.add(fontNameCB);
2093 visualTab.add(fontSizeCB);
2094 visualTab.add(fontStyleCB);
2096 if (Platform.isJS())
2098 startupCheckbox.setVisible(false);
2099 startupFileTextfield.setVisible(false);
2106 * Load the saved Backups options EXCEPT "Enabled" and "Scheme"
2109 protected void loadLastSavedBackupsOptions()
2111 BackupFilesPresetEntry savedPreset = BackupFilesPresetEntry
2112 .getSavedBackupEntry();
2114 .setSelected(Cache.getDefault(BackupFiles.ENABLED, !Platform.isJS()));
2116 BackupFilesPresetEntry backupfilesCustomEntry = BackupFilesPresetEntry
2117 .createBackupFilesPresetEntry(Cache
2118 .getDefault(BackupFilesPresetEntry.CUSTOMCONFIG, null));
2119 if (backupfilesCustomEntry == null)
2121 backupfilesCustomEntry = BackupFilesPresetEntry.backupfilesPresetEntriesValues
2122 .get(BackupFilesPresetEntry.BACKUPFILESSCHEMEDEFAULT);
2124 BackupFilesPresetEntry.backupfilesPresetEntriesValues.put(
2125 BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM,
2126 backupfilesCustomEntry);
2128 setComboIntStringKey(backupfilesPresetsCombo,
2129 Cache.getDefault(BackupFiles.NS + "_PRESET",
2130 BackupFilesPresetEntry.BACKUPFILESSCHEMEDEFAULT));
2132 backupsSetOptions(savedPreset);
2134 backupsOptionsSetEnabled();
2135 updateBackupFilesExampleLabel();
2138 private boolean warnAboutSuffixReverseChange()
2140 BackupFilesPresetEntry bfpe = BackupFilesPresetEntry
2141 .getSavedBackupEntry();
2142 boolean savedSuffixReverse = bfpe.reverse;
2143 int savedSuffixDigits = bfpe.digits;
2144 String savedSuffixTemplate = bfpe.suffix;
2146 boolean nowSuffixReverse = suffixReverse.isSelected();
2147 int nowSuffixDigits = getSpinnerInt(suffixDigitsSpinner, 3);
2148 String nowSuffixTemplate = suffixTemplate.getText();
2149 return nowSuffixReverse != savedSuffixReverse
2150 && nowSuffixDigits == savedSuffixDigits
2151 && nowSuffixTemplate != null
2152 && nowSuffixTemplate.equals(savedSuffixTemplate);
2156 * Initialises the Backups tabbed panel.
2160 private JPanel initBackupsTab()
2162 JPanel backupsTab = new JPanel();
2163 backupsTab.setBorder(new TitledBorder(
2164 MessageManager.getString("label.backup_files")));
2165 backupsTab.setLayout(new GridBagLayout());
2167 GridBagConstraints gbc = new GridBagConstraints();
2170 gbc.anchor = GridBagConstraints.FIRST_LINE_START;
2171 gbc.fill = GridBagConstraints.NONE;
2173 initBackupsTabPresetsPanel();
2174 initBackupsTabSuffixPanel();
2175 initBackupsTabKeepFilesPanel();
2176 initBackupsTabFilenameExamplesPanel();
2178 enableBackupFiles.setFont(LABEL_FONT_BOLD);
2180 .setText(MessageManager.getString("label.enable_backupfiles"));
2181 enableBackupFiles.addActionListener(new ActionListener()
2184 public void actionPerformed(ActionEvent e)
2186 // enable other options only when the first is checked
2187 backupsOptionsSetEnabled();
2192 // enable checkbox 1 col
2196 gbc.gridy = 0; // row 0
2197 backupsTab.add(enableBackupFiles, gbc);
2199 // summary of scheme box (over two rows)
2203 gbc.anchor = GridBagConstraints.FIRST_LINE_END;
2204 gbc.fill = GridBagConstraints.BOTH;
2205 backupsTab.add(exampleFilesPanel, gbc);
2207 gbc.anchor = GridBagConstraints.FIRST_LINE_START;
2208 gbc.fill = GridBagConstraints.NONE;
2210 // fill empty space on right
2213 backupsTab.add(new JPanel(), gbc);
2218 gbc.gridy++; // row 1
2219 backupsTab.add(presetsPanel, gbc);
2221 // now using whole row
2226 gbc.gridy++; // row 2
2227 backupsTab.add(keepfilesPanel, gbc);
2229 // filename strategy box
2230 gbc.gridy++; // row 3
2231 backupsTab.add(suffixPanel, gbc);
2234 gbc.gridy++; // row 4
2236 backupsTab.add(new JPanel(), gbc);
2238 backupsOptionsSetEnabled();
2242 private JPanel initBackupsTabPresetsPanel()
2245 String title = MessageManager.getString("label.schemes");
2247 presetsPanel.setLayout(new GridBagLayout());
2249 GridBagConstraints gbc = new GridBagConstraints();
2252 gbc.anchor = GridBagConstraints.BASELINE_LEADING;
2253 gbc.fill = GridBagConstraints.NONE;
2261 presetsComboLabel = new JLabel(title + ":");
2262 presetsPanel.add(presetsComboLabel, gbc);
2264 List<Object> entries = Arrays
2265 .asList((Object[]) BackupFilesPresetEntry.backupfilesPresetEntries);
2266 List<String> tooltips = Arrays.asList(
2267 BackupFilesPresetEntry.backupfilesPresetEntryDescriptions);
2268 backupfilesPresetsCombo = JvSwingUtils.buildComboWithTooltips(entries,
2271 for (int i = 0; i < BackupFilesPresetEntry.backupfilesPresetEntries.length; i++)
2273 backupfilesPresetsCombo
2274 .addItem(BackupFilesPresetEntry.backupfilesPresetEntries[i]);
2278 backupfilesPresetsCombo.addActionListener(new ActionListener()
2281 public void actionPerformed(ActionEvent e)
2283 int key = getComboIntStringKey(backupfilesPresetsCombo);
2284 if (!customiseCheckbox.isSelected())
2286 backupfilesPresetsComboLastSelected = key;
2288 if (key == BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM)
2290 if (customiseCheckbox.isSelected())
2292 // got here by clicking on customiseCheckbox so don't change the values
2293 backupfilesCustomOptionsSetEnabled();
2297 backupsTabUpdatePresets();
2298 backupfilesCustomOptionsSetEnabled();
2303 customiseCheckbox.setSelected(false);
2304 backupsTabUpdatePresets();
2305 backupfilesCustomOptionsSetEnabled();
2310 // dropdown list of preset schemes
2312 presetsPanel.add(backupfilesPresetsCombo, gbc);
2314 revertButton.setText(MessageManager.getString("label.cancel_changes"));
2315 revertButton.setToolTipText(
2316 MessageManager.getString("label.cancel_changes_description"));
2317 revertButton.addActionListener(new ActionListener()
2320 public void actionPerformed(ActionEvent e)
2323 BackupFilesPresetEntry.backupfilesPresetEntriesValues.get(
2324 BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM));
2325 backupfilesCustomOptionsSetEnabled();
2329 revertButton.setFont(LABEL_FONT);
2331 customiseCheckbox.setFont(LABEL_FONT);
2332 customiseCheckbox.setText(MessageManager.getString("label.customise"));
2333 customiseCheckbox.addActionListener(new ActionListener()
2336 public void actionPerformed(ActionEvent e)
2338 int currently = getComboIntStringKey(backupfilesPresetsCombo);
2339 if (customiseCheckbox.isSelected())
2341 backupfilesPresetsComboLastSelected = currently;
2342 setComboIntStringKey(backupfilesPresetsCombo,
2343 BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM);
2347 setComboIntStringKey(backupfilesPresetsCombo,
2348 backupfilesPresetsComboLastSelected);
2351 backupfilesCustomOptionsSetEnabled();
2354 customiseCheckbox.setToolTipText(
2355 MessageManager.getString("label.customise_description"));
2357 // customise checkbox
2360 presetsPanel.add(customiseCheckbox, gbc);
2362 // "Cancel changes" button (aligned with combo box above)
2364 presetsPanel.add(revertButton, gbc);
2366 return presetsPanel;
2369 private JPanel initBackupsTabFilenameExamplesPanel()
2371 String title = MessageManager
2372 .getString("label.scheme_examples");
2373 TitledBorder tb = new TitledBorder(title);
2374 exampleFilesPanel.setBorder(tb);
2375 exampleFilesPanel.setLayout(new GridBagLayout());
2378 backupfilesExampleLabel.setEditable(false);
2379 backupfilesExampleLabel
2380 .setBackground(exampleFilesPanel.getBackground());
2382 updateBackupFilesExampleLabel();
2384 GridBagConstraints gbc = new GridBagConstraints();
2387 gbc.fill = GridBagConstraints.NONE;
2388 gbc.anchor = GridBagConstraints.FIRST_LINE_START;
2390 exampleFilesPanel.add(backupfilesExampleLabel, gbc);
2391 return exampleFilesPanel;
2394 private void backupsTabUpdatePresets()
2396 IntKeyStringValueEntry entry = (IntKeyStringValueEntry) backupfilesPresetsCombo
2399 String value = entry.v;
2401 if (BackupFilesPresetEntry.backupfilesPresetEntriesValues
2405 BackupFilesPresetEntry.backupfilesPresetEntriesValues
2411 "Preset '" + value + "' [key:" + key + "] not implemented");
2414 // Custom options will now be enabled when the customiseCheckbox is checked
2415 // (performed above)
2416 // backupfilesCustomOptionsSetEnabled();
2417 updateBackupFilesExampleLabel();
2420 protected int getComboIntStringKey(
2421 JComboBox<Object> backupfilesPresetsCombo2)
2423 IntKeyStringValueEntry e;
2426 e = (IntKeyStringValueEntry) backupfilesPresetsCombo2
2428 } catch (Exception ex)
2431 "Problem casting Combo entry to IntKeyStringValueEntry.");
2434 return e != null ? e.k : 0;
2437 protected void setComboIntStringKey(
2438 JComboBox<Object> backupfilesPresetsCombo2,
2441 for (int i = 0; i < backupfilesPresetsCombo2.getItemCount(); i++)
2443 IntKeyStringValueEntry e;
2446 e = (IntKeyStringValueEntry) backupfilesPresetsCombo2.getItemAt(i);
2447 } catch (Exception ex)
2450 "Problem casting Combo entry to IntKeyStringValueEntry. Skipping item. ");
2455 backupfilesPresetsCombo2.setSelectedIndex(i);
2459 // backupsTabUpdatePresets();
2462 private JPanel initBackupsTabSuffixPanel()
2464 suffixPanel.setBorder(new TitledBorder(
2465 MessageManager.getString("label.backup_filename_strategy")));
2466 suffixPanel.setLayout(new GridBagLayout());
2469 .setText(MessageManager.getString("label.append_to_filename"));
2470 suffixTemplateLabel.setHorizontalAlignment(SwingConstants.LEFT);
2471 suffixTemplateLabel.setFont(LABEL_FONT);
2473 final String tooltip = JvSwingUtils.wrapTooltip(true,
2474 MessageManager.getString("label.append_to_filename_tooltip"));
2475 suffixTemplate.setToolTipText(tooltip);
2476 suffixTemplate.addActionListener(new ActionListener()
2479 public void actionPerformed(ActionEvent e)
2481 updateBackupFilesExampleLabel();
2482 backupfilesCustomOptionsSetEnabled();
2483 backupfilesRevertButtonSetEnabled(true);
2487 suffixTemplate.addKeyListener(new KeyListener()
2490 public void keyReleased(KeyEvent e)
2492 updateBackupFilesExampleLabel();
2493 backupfilesCustomOptionsSetEnabled();
2494 backupfilesRevertButtonSetEnabled(true);
2498 public void keyPressed(KeyEvent e)
2502 // disable use of ':' or '/' or '\'
2504 public void keyTyped(KeyEvent e)
2506 char c = e.getKeyChar();
2507 if (c == ':' || c == '/' || c == '\\')
2509 // don't process ':' or '/' or '\'
2518 .setText(MessageManager.getString("label.index_digits"));
2519 suffixDigitsLabel.setHorizontalAlignment(SwingConstants.LEFT);
2520 suffixDigitsLabel.setFont(LABEL_FONT);
2521 ChangeListener c = new ChangeListener()
2524 public void stateChanged(ChangeEvent e)
2526 backupfilesRevertButtonSetEnabled(true);
2527 updateBackupFilesExampleLabel();
2531 setIntegerSpinner(suffixDigitsSpinner, BackupFilesPresetEntry.DIGITSMIN,
2532 BackupFilesPresetEntry.DIGITSMAX, 3, c);
2534 suffixReverse.setLabels(MessageManager.getString("label.reverse_roll"),
2535 MessageManager.getString("label.increment_index"));
2536 suffixReverse.addActionListener(new ActionListener()
2539 public void actionPerformed(ActionEvent e)
2541 boolean okay = true;
2542 if (warnAboutSuffixReverseChange())
2545 okay = confirmSuffixReverseChange();
2549 backupfilesRevertButtonSetEnabled(true);
2550 updateBackupFilesExampleLabel();
2554 boolean savedSuffixReverse = BackupFilesPresetEntry
2555 .getSavedBackupEntry().reverse;
2556 suffixReverse.setSelected(savedSuffixReverse);
2561 GridBagConstraints sgbc = new GridBagConstraints();
2563 // first row (template text box)
2564 sgbc.anchor = GridBagConstraints.WEST;
2568 sgbc.gridheight = 1;
2571 sgbc.fill = GridBagConstraints.NONE;
2572 suffixPanel.add(suffixTemplateLabel, sgbc);
2575 sgbc.fill = GridBagConstraints.HORIZONTAL;
2576 suffixPanel.add(suffixTemplate, sgbc);
2578 // second row (number of digits spinner)
2582 sgbc.fill = GridBagConstraints.NONE;
2583 suffixPanel.add(suffixDigitsLabel, sgbc);
2586 sgbc.fill = GridBagConstraints.HORIZONTAL;
2587 suffixPanel.add(suffixDigitsSpinner, sgbc);
2589 // third row (forward order radio selection)
2592 sgbc.gridwidth = GridBagConstraints.REMAINDER;
2593 sgbc.fill = GridBagConstraints.HORIZONTAL;
2594 suffixPanel.add(suffixReverse.getFalseButton(), sgbc);
2596 // fourth row (reverse order radio selection)
2598 suffixPanel.add(suffixReverse.getTrueButton(), sgbc);
2602 private boolean confirmSuffixReverseChange()
2604 boolean ret = false;
2605 String warningMessage = MessageManager
2606 .getString("label.warning_confirm_change_reverse");
2607 int confirm = JvOptionPane.showConfirmDialog(Desktop.desktop,
2609 MessageManager.getString("label.change_increment_decrement"),
2610 JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE);
2612 ret = (confirm == JvOptionPane.YES_OPTION);
2616 private JPanel initBackupsTabKeepFilesPanel()
2618 keepfilesPanel.setBorder(
2619 new TitledBorder(MessageManager.getString("label.keep_files")));
2620 keepfilesPanel.setLayout(new GridBagLayout());
2622 backupfilesKeepAll.setLabels(
2623 MessageManager.getString("label.keep_all_backup_files"),
2624 MessageManager.getString(
2625 "label.keep_only_this_number_of_backup_files"));
2626 backupfilesKeepAll.addTrueActionListener(new ActionListener()
2629 public void actionPerformed(ActionEvent e)
2631 backupfilesRevertButtonSetEnabled(true);
2632 updateBackupFilesExampleLabel();
2635 backupfilesKeepAll.addActionListener(new ActionListener()
2638 public void actionPerformed(ActionEvent e)
2640 backupfilesRevertButtonSetEnabled(true);
2641 keepRollMaxOptionsEnabled();
2642 updateBackupFilesExampleLabel();
2646 ChangeListener c = new ChangeListener()
2649 public void stateChanged(ChangeEvent e)
2651 backupfilesRevertButtonSetEnabled(true);
2652 updateBackupFilesExampleLabel();
2656 setIntegerSpinner(backupfilesRollMaxSpinner,
2657 BackupFilesPresetEntry.ROLLMAXMIN,
2658 BackupFilesPresetEntry.ROLLMAXMAX, 4, true, c);
2660 backupfilesConfirmDelete.setLabels(
2661 MessageManager.getString("label.always_ask"),
2662 MessageManager.getString("label.auto_delete"));
2663 backupfilesConfirmDelete.addActionListener(new ActionListener()
2666 public void actionPerformed(ActionEvent e)
2668 backupfilesRevertButtonSetEnabled(true);
2671 // update the enabled section
2672 keepRollMaxOptionsEnabled();
2674 GridBagConstraints kgbc = new GridBagConstraints();
2676 // first row (template text box)
2677 kgbc.anchor = GridBagConstraints.WEST;
2680 kgbc.gridwidth = GridBagConstraints.REMAINDER;
2681 kgbc.gridheight = 1;
2684 kgbc.fill = GridBagConstraints.HORIZONTAL;
2685 keepfilesPanel.add(backupfilesKeepAll.getTrueButton(), kgbc);
2691 kgbc.gridwidth = GridBagConstraints.RELATIVE;
2692 keepfilesPanel.add(backupfilesKeepAll.getFalseButton(), kgbc);
2695 kgbc.gridwidth = GridBagConstraints.REMAINDER;
2696 keepfilesPanel.add(backupfilesRollMaxSpinner, kgbc);
2698 // third row (indented)
2700 kgbc.insets = new Insets(0, 20, 0, 0);
2703 kgbc.gridwidth = GridBagConstraints.REMAINDER;
2704 kgbc.fill = GridBagConstraints.HORIZONTAL;
2707 JPanel jp = new JPanel();
2708 jp.setLayout(new FlowLayout());
2710 .setText(MessageManager
2711 .getString("label.autodelete_old_backup_files"));
2712 oldBackupFilesLabel.setFont(LABEL_FONT);
2713 oldBackupFilesLabel.setHorizontalAlignment(SwingConstants.LEFT);
2714 jp.add(oldBackupFilesLabel);
2715 jp.add(backupfilesConfirmDelete.getTrueButton());
2716 jp.add(backupfilesConfirmDelete.getFalseButton());
2717 keepfilesPanel.add(jp, kgbc);
2719 return keepfilesPanel;
2722 protected void updateBackupFilesExampleLabel()
2724 int exampleindex = 12;
2725 String base = MessageManager.getString("label.filename") + ".fa";
2726 if (base == null || base.length() == 0)
2728 base = "file_name.fa";
2731 boolean reverse = suffixReverse.isSelected();
2732 boolean keepAll = backupfilesKeepAll.isSelected();
2734 String suffix = suffixTemplate.getText();
2737 backupfilesExampleLabel.setFont(LABEL_FONT_ITALIC);
2738 if (suffix == null || suffix.length() == 0)
2740 backupfilesExampleLabel
2741 .setText(MessageManager.getString("label.no_backup_files"));
2742 backupfilesExampleLabel.setFont(LABEL_FONT_BOLD);
2746 rollMax = getSpinnerInt(backupfilesRollMaxSpinner, 4);
2747 rollMax = rollMax < 1 ? 1 : rollMax;
2749 if (suffix.indexOf(BackupFiles.NUM_PLACEHOLDER) == -1)
2754 digits = getSpinnerInt(suffixDigitsSpinner, 3);
2755 digits = digits < 1 ? 1 : digits;
2757 int lowersurround = 2;
2758 int uppersurround = 0;
2759 StringBuilder exampleSB = new StringBuilder();
2760 boolean firstLine = true;
2766 int max = keepAll ? exampleindex : rollMax;
2767 for (int index = min; index <= max; index++)
2769 if (index == min + lowersurround && index < max - uppersurround - 1)
2771 exampleSB.append("\n...");
2774 else if (index > min + lowersurround && index < max - uppersurround)
2786 exampleSB.append("\n");
2789 exampleSB.append(BackupFilenameParts.getBackupFilename(index,
2790 base, suffix, digits));
2793 // no extra text needed
2795 else if (index == min)
2797 String newest = MessageManager.getString("label.braced_newest");
2798 if (newest != null && newest.length() > 0)
2800 exampleSB.append(" " + newest);
2803 else if (index == max)
2805 String oldest = MessageManager.getString("label.braced_oldest");
2806 if (oldest != null && oldest.length() > 0)
2808 exampleSB.append(" " + oldest);
2817 int min = (keepAll || exampleindex - rollMax < 0) ? 1
2818 : exampleindex - rollMax + 1;
2819 int max = exampleindex;
2821 for (int index = min; index <= max; index++)
2824 if (index == min + lowersurround && index < max - uppersurround - 1)
2826 exampleSB.append("\n...");
2829 else if (index > min + lowersurround && index < max - uppersurround)
2841 exampleSB.append("\n");
2844 exampleSB.append(BackupFilenameParts.getBackupFilename(index,
2845 base, suffix, digits));
2848 // no extra text needed
2850 else if (index == min)
2852 String oldest = MessageManager.getString("label.braced_oldest");
2853 if (oldest != null && oldest.length() > 0)
2855 exampleSB.append(" " + oldest);
2858 else if (index == max)
2860 String newest = MessageManager.getString("label.braced_newest");
2861 if (newest != null && newest.length() > 0)
2863 exampleSB.append(" " + newest);
2871 // add some extra empty lines to pad out the example files box. ugh, please tell
2872 // me how to do this better
2873 int remainingLines = lowersurround + uppersurround + 1 - lineNumber;
2874 if (remainingLines > 0)
2876 for (int i = 0; i < remainingLines; i++)
2878 exampleSB.append("\n ");
2883 backupfilesExampleLabel.setText(exampleSB.toString());
2886 protected void setIntegerSpinner(JSpinner s, int min, int max, int def,
2887 boolean useExistingVal, ChangeListener c)
2894 i = ((Integer) s.getValue()).intValue();
2895 } catch (Exception e)
2898 "Exception casting the initial value of s.getValue()");
2902 setIntegerSpinner(s, min, max, i, c);
2905 protected void setIntegerSpinner(JSpinner s, int min, int max, int def,
2908 // integer spinner for number of digits
2917 SpinnerModel sModel = new SpinnerNumberModel(def, min, max, 1);
2920 s.addChangeListener(c);
2924 protected static int getSpinnerInt(JSpinner s, int def)
2930 i = (Integer) s.getValue();
2931 } catch (Exception e)
2933 Cache.log.error("Failed casting (Integer) JSpinner s.getValue()");
2938 private void keepRollMaxOptionsEnabled()
2940 boolean enabled = backupfilesKeepAll.isEnabled()
2941 && !backupfilesKeepAll.isSelected();
2942 oldBackupFilesLabel.setEnabled(enabled);
2943 backupfilesRollMaxSpinner.setEnabled(enabled);
2944 backupfilesConfirmDelete.setEnabled(enabled);
2947 private void backupfilesKeepAllSetEnabled(boolean tryEnabled)
2949 boolean enabled = tryEnabled && enableBackupFiles.isSelected()
2950 && customiseCheckbox.isSelected()
2951 && suffixTemplate.getText()
2952 .indexOf(BackupFiles.NUM_PLACEHOLDER) > -1;
2953 keepfilesPanel.setEnabled(enabled);
2954 backupfilesKeepAll.setEnabled(enabled);
2955 oldBackupFilesLabel.setEnabled(enabled);
2956 keepRollMaxOptionsEnabled();
2959 private void backupfilesSuffixTemplateDigitsSetEnabled()
2961 boolean enabled = suffixTemplate.isEnabled() && suffixTemplate.getText()
2962 .indexOf(BackupFiles.NUM_PLACEHOLDER) > -1;
2963 suffixDigitsLabel.setEnabled(enabled);
2964 suffixDigitsSpinner.setEnabled(enabled);
2965 suffixReverse.setEnabled(enabled);
2968 private void backupfilesSuffixTemplateSetEnabled(boolean tryEnabled)
2970 boolean enabled = tryEnabled && enableBackupFiles.isSelected()
2971 && customiseCheckbox.isSelected();
2972 suffixPanel.setEnabled(enabled);
2973 suffixTemplateLabel.setEnabled(enabled);
2974 suffixTemplate.setEnabled(enabled);
2975 backupfilesSuffixTemplateDigitsSetEnabled();
2978 private void backupfilesRevertButtonSetEnabled(boolean tryEnabled)
2980 boolean enabled = tryEnabled && enableBackupFiles.isSelected()
2981 && customiseCheckbox.isSelected() && backupfilesCustomChanged();
2982 revertButton.setEnabled(enabled);
2985 private boolean backupfilesCustomChanged()
2987 BackupFilesPresetEntry custom = BackupFilesPresetEntry.backupfilesPresetEntriesValues
2988 .get(BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM);
2989 BackupFilesPresetEntry current = getBackupfilesCurrentEntry();
2990 return !custom.equals(current);
2993 protected BackupFilesPresetEntry getBackupfilesCurrentEntry()
2995 String suffix = suffixTemplate.getText();
2996 int digits = getSpinnerInt(suffixDigitsSpinner, 3);
2997 boolean reverse = suffixReverse.isSelected();
2998 boolean keepAll = backupfilesKeepAll.isSelected();
2999 int rollMax = getSpinnerInt(backupfilesRollMaxSpinner, 3);
3000 boolean confirmDelete = backupfilesConfirmDelete.isSelected();
3002 BackupFilesPresetEntry bfpe = new BackupFilesPresetEntry(suffix, digits,
3003 reverse, keepAll, rollMax, confirmDelete);
3008 protected void backupfilesCustomOptionsSetEnabled()
3010 boolean enabled = customiseCheckbox.isSelected();
3012 backupfilesRevertButtonSetEnabled(enabled);
3013 backupfilesSuffixTemplateSetEnabled(enabled);
3014 backupfilesKeepAllSetEnabled(enabled);
3017 private void backupfilesSummarySetEnabled()
3019 boolean enabled = enableBackupFiles.isSelected();
3020 backupfilesExampleLabel.setEnabled(enabled);
3021 exampleFilesPanel.setEnabled(enabled);
3024 private void backupfilesPresetsSetEnabled()
3026 boolean enabled = enableBackupFiles.isSelected();
3027 presetsPanel.setEnabled(enabled);
3028 presetsComboLabel.setEnabled(enabled);
3029 backupfilesPresetsCombo.setEnabled(enabled);
3030 customiseCheckbox.setEnabled(enabled);
3031 revertButton.setEnabled(enabled);
3034 protected void backupsOptionsSetEnabled()
3036 backupfilesPresetsSetEnabled();
3037 backupfilesSummarySetEnabled();
3038 backupfilesCustomOptionsSetEnabled();
3041 protected void backupsSetOptions(String suffix, int digits,
3042 boolean reverse, boolean keepAll, int rollMax,
3043 boolean confirmDelete)
3045 suffixTemplate.setText(suffix);
3046 suffixDigitsSpinner.setValue(digits);
3047 suffixReverse.setSelected(reverse);
3048 backupfilesKeepAll.setSelected(keepAll);
3049 backupfilesRollMaxSpinner.setValue(rollMax);
3050 backupfilesConfirmDelete.setSelected(confirmDelete);
3053 protected void backupsSetOptions(BackupFilesPresetEntry p)
3055 backupsSetOptions(p.suffix, p.digits, p.reverse, p.keepAll, p.rollMax,
3059 protected void autoIdWidth_actionPerformed()
3061 // TODO Auto-generated method stub
3065 protected void userIdWidth_actionPerformed()
3067 // TODO Auto-generated method stub
3071 protected void maxColour_actionPerformed(JPanel panel)
3075 protected void minColour_actionPerformed(JPanel panel)
3079 protected void gapColour_actionPerformed(JPanel panel)
3083 protected void hiddenColour_actionPerformed(JPanel panel)
3087 protected void showunconserved_actionPerformed(ActionEvent e)
3089 // TODO Auto-generated method stub
3093 protected void useLegacyGaps_actionPerformed(ActionEvent e)
3097 protected void resetOvDefaults_actionPerformed(ActionEvent e)
3107 public void ok_actionPerformed(ActionEvent e)
3117 public void cancel_actionPerformed(ActionEvent e)
3127 public void annotations_actionPerformed(ActionEvent e)
3134 public void startupFileTextfield_mouseClicked()
3138 public void newLink_actionPerformed(ActionEvent e)
3143 public void editLink_actionPerformed(ActionEvent e)
3148 public void deleteLink_actionPerformed(ActionEvent e)
3153 public void defaultBrowser_mouseClicked(MouseEvent e)
3158 public void linkURLList_keyTyped(KeyEvent e)
3163 public void setProxyAuthEnabled()
3165 boolean enabled = proxyAuth.isSelected() && proxyAuth.isEnabled();
3166 proxyAuthUsernameLabel.setEnabled(enabled);
3167 proxyAuthPasswordLabel.setEnabled(enabled);
3168 passwordNotStoredLabel.setEnabled(enabled);
3169 proxyAuthUsernameTB.setEnabled(enabled);
3170 proxyAuthPasswordPB.setEnabled(enabled);
3173 public void setCustomProxyEnabled()
3175 boolean enabled = customProxy.isSelected();
3176 portLabel.setEnabled(enabled);
3177 serverLabel.setEnabled(enabled);
3178 portLabel2.setEnabled(enabled);
3179 serverLabel2.setEnabled(enabled);
3180 httpLabel.setEnabled(enabled);
3181 httpsLabel.setEnabled(enabled);
3182 proxyServerHttpTB.setEnabled(enabled);
3183 proxyPortHttpTB.setEnabled(enabled);
3184 proxyServerHttpsTB.setEnabled(enabled);
3185 proxyPortHttpsTB.setEnabled(enabled);
3186 proxyAuth.setEnabled(enabled);
3187 setProxyAuthEnabled();
3190 public void proxyType_actionPerformed()
3192 setCustomProxyEnabled();
3195 public void proxyAuth_actionPerformed()
3197 setProxyAuthEnabled();
3201 * Customer renderer for JTable: supports column of radio buttons
3203 public class RadioButtonRenderer extends JRadioButton
3204 implements TableCellRenderer
3206 public RadioButtonRenderer()
3208 setHorizontalAlignment(CENTER);
3209 setToolTipText(MessageManager.getString("label.urltooltip"));
3213 public Component getTableCellRendererComponent(JTable table,
3214 Object value, boolean isSelected, boolean hasFocus, int row,
3217 setSelected((boolean) value);
3219 // set colours to match rest of table
3222 setBackground(table.getSelectionBackground());
3223 setForeground(table.getSelectionForeground());
3227 setBackground(table.getBackground());
3228 setForeground(table.getForeground());
3235 * Customer cell editor for JTable: supports column of radio buttons in
3236 * conjunction with renderer
3238 public class RadioButtonEditor extends AbstractCellEditor
3239 implements TableCellEditor
3241 private JRadioButton button = new JRadioButton();
3243 public RadioButtonEditor()
3245 button.setHorizontalAlignment(SwingConstants.CENTER);
3246 this.button.addActionListener(new ActionListener()
3249 public void actionPerformed(ActionEvent e)
3251 fireEditingStopped();
3257 public Component getTableCellEditorComponent(JTable table, Object value,
3258 boolean isSelected, int row, int column)
3260 button.setSelected((boolean) value);
3265 public Object getCellEditorValue()
3267 return button.isSelected();