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 jalview.bin.Cache;
24 import jalview.fts.core.FTSDataColumnPreferences;
25 import jalview.fts.core.FTSDataColumnPreferences.PreferenceSource;
26 import jalview.fts.service.pdb.PDBFTSRestClient;
27 import jalview.gui.Desktop;
28 import jalview.gui.JalviewBooleanRadioButtons;
29 import jalview.gui.JvOptionPane;
30 import jalview.gui.JvSwingUtils;
31 import jalview.gui.StructureViewer.ViewerType;
32 import jalview.io.BackupFilenameParts;
33 import jalview.io.BackupFiles;
34 import jalview.io.BackupFilesPresetEntry;
35 import jalview.io.IntKeyStringValueEntry;
36 import jalview.util.MessageManager;
38 import java.awt.BorderLayout;
39 import java.awt.Color;
40 import java.awt.Component;
41 import java.awt.Dimension;
42 import java.awt.FlowLayout;
44 import java.awt.GridBagConstraints;
45 import java.awt.GridBagLayout;
46 import java.awt.GridLayout;
47 import java.awt.Insets;
48 import java.awt.Rectangle;
49 import java.awt.event.ActionEvent;
50 import java.awt.event.ActionListener;
51 import java.awt.event.FocusEvent;
52 import java.awt.event.KeyEvent;
53 import java.awt.event.KeyListener;
54 import java.awt.event.MouseAdapter;
55 import java.awt.event.MouseEvent;
56 import java.util.Arrays;
57 import java.util.List;
59 import javax.swing.AbstractCellEditor;
60 import javax.swing.BorderFactory;
61 import javax.swing.ButtonGroup;
62 import javax.swing.DefaultListCellRenderer;
63 import javax.swing.JButton;
64 import javax.swing.JCheckBox;
65 import javax.swing.JComboBox;
66 import javax.swing.JFileChooser;
67 import javax.swing.JLabel;
68 import javax.swing.JPanel;
69 import javax.swing.JRadioButton;
70 import javax.swing.JScrollPane;
71 import javax.swing.JSpinner;
72 import javax.swing.JTabbedPane;
73 import javax.swing.JTable;
74 import javax.swing.JTextArea;
75 import javax.swing.JTextField;
76 import javax.swing.ListSelectionModel;
77 import javax.swing.SpinnerModel;
78 import javax.swing.SpinnerNumberModel;
79 import javax.swing.SwingConstants;
80 import javax.swing.border.Border;
81 import javax.swing.border.EmptyBorder;
82 import javax.swing.border.EtchedBorder;
83 import javax.swing.border.TitledBorder;
84 import javax.swing.event.ChangeEvent;
85 import javax.swing.event.ChangeListener;
86 import javax.swing.table.TableCellEditor;
87 import javax.swing.table.TableCellRenderer;
90 * Base class for the Preferences panel.
95 public class GPreferences extends JPanel
97 private static final Font LABEL_FONT = JvSwingUtils.getLabelFont();
99 private static final Font LABEL_FONT_ITALIC = JvSwingUtils
100 .getLabelFont(false, true);
102 private static final Font LABEL_FONT_BOLD = JvSwingUtils
103 .getLabelFont(true, false);
106 * Visual tab components
108 protected JCheckBox fullScreen = new JCheckBox();
110 protected JCheckBox openoverv = new JCheckBox();
112 protected JCheckBox seqLimit = new JCheckBox();
114 protected JCheckBox rightAlign = new JCheckBox();
116 protected JComboBox<String> fontSizeCB = new JComboBox<>();
118 protected JComboBox<String> fontStyleCB = new JComboBox<>();
120 protected JComboBox<String> fontNameCB = new JComboBox<>();
122 protected JCheckBox showOccupancy = new JCheckBox();
124 protected JCheckBox showUnconserved = new JCheckBox();
126 protected JCheckBox idItalics = new JCheckBox();
128 protected JCheckBox smoothFont = new JCheckBox();
130 protected JCheckBox scaleProteinToCdna = new JCheckBox();
132 protected JComboBox<String> gapSymbolCB = new JComboBox<>();
134 protected JCheckBox wrap = new JCheckBox();
136 protected JComboBox<String> sortby = new JComboBox<>();
138 protected JComboBox<String> sortAnnBy = new JComboBox<>();
140 protected JComboBox<String> sortAutocalc = new JComboBox<>();
142 protected JCheckBox startupCheckbox = new JCheckBox();
144 protected JTextField startupFileTextfield = new JTextField();
146 // below are in the 'second column'
147 protected JCheckBox annotations = new JCheckBox();
149 protected JCheckBox quality = new JCheckBox();
151 protected JCheckBox conservation = new JCheckBox();
153 protected JCheckBox identity = new JCheckBox();
155 protected JCheckBox showGroupConsensus = new JCheckBox();
157 protected JCheckBox showGroupConservation = new JCheckBox();
159 protected JCheckBox showConsensHistogram = new JCheckBox();
161 protected JCheckBox showConsensLogo = new JCheckBox();
163 protected JCheckBox showDbRefTooltip = new JCheckBox();
165 protected JCheckBox showNpTooltip = new JCheckBox();
168 * Structure tab and components
170 protected JPanel structureTab;
172 protected JCheckBox structFromPdb = new JCheckBox();
174 protected JCheckBox useRnaView = new JCheckBox();
176 protected JCheckBox addSecondaryStructure = new JCheckBox();
178 protected JCheckBox addTempFactor = new JCheckBox();
180 protected JComboBox<String> structViewer = new JComboBox<>();
182 protected JTextField chimeraPath = new JTextField();
184 protected ButtonGroup mappingMethod = new ButtonGroup();
186 protected JRadioButton siftsMapping = new JRadioButton();
188 protected JRadioButton nwMapping = new JRadioButton();
191 * Colours tab components
193 protected JPanel minColour = new JPanel();
195 protected JPanel maxColour = new JPanel();
197 protected JComboBox<String> protColour = new JComboBox<>();
199 protected JComboBox<String> nucColour = new JComboBox<>();
202 * Overview tab components
204 protected JPanel gapColour = new JPanel();
206 protected JPanel hiddenColour = new JPanel();
208 protected JCheckBox useLegacyGap;
210 protected JCheckBox showHiddenAtStart;
212 protected JLabel gapLabel;
215 * Connections tab components
217 protected JTable linkUrlTable = new JTable();
219 protected JButton editLink = new JButton();
221 protected JButton deleteLink = new JButton();
223 protected JTextField filterTB = new JTextField();
225 protected JButton doReset = new JButton();
227 protected JButton userOnly = new JButton();
229 protected JLabel portLabel = new JLabel();
231 protected JLabel serverLabel = new JLabel();
233 protected JTextField proxyServerTB = new JTextField();
235 protected JTextField proxyPortTB = new JTextField();
237 protected JTextField defaultBrowser = new JTextField();
239 protected JCheckBox useProxy = new JCheckBox();
241 protected JCheckBox usagestats = new JCheckBox();
243 protected JCheckBox questionnaire = new JCheckBox();
245 protected JCheckBox versioncheck = new JCheckBox();
248 * Output tab components
250 protected JComboBox<Object> epsRendering = new JComboBox<>();
252 protected JLabel userIdWidthlabel = new JLabel();
254 protected JCheckBox autoIdWidth = new JCheckBox();
256 protected JTextField userIdWidth = new JTextField();
258 protected JCheckBox blcjv = new JCheckBox();
260 protected JCheckBox pileupjv = new JCheckBox();
262 protected JCheckBox clustaljv = new JCheckBox();
264 protected JCheckBox msfjv = new JCheckBox();
266 protected JCheckBox fastajv = new JCheckBox();
268 protected JCheckBox pfamjv = new JCheckBox();
270 protected JCheckBox pirjv = new JCheckBox();
272 protected JCheckBox modellerOutput = new JCheckBox();
274 protected JCheckBox embbedBioJSON = new JCheckBox();
277 * Editing tab components
279 protected JCheckBox autoCalculateConsCheck = new JCheckBox();
281 protected JCheckBox padGaps = new JCheckBox();
283 protected JCheckBox sortByTree = new JCheckBox();
288 protected JPanel wsTab = new JPanel();
291 * Backups tab components
292 * a lot of these are member variables instead of local variables only so that they
293 * can be enabled/disabled easily in one go
296 protected JCheckBox enableBackupFiles = new JCheckBox();
298 protected JPanel presetsPanel = new JPanel();
300 protected JLabel presetsComboLabel = new JLabel();
302 protected JCheckBox customiseCheckbox = new JCheckBox();
304 protected JButton revertButton = new JButton();
306 protected JComboBox<Object> backupfilesPresetsCombo = new JComboBox<>();
308 private int backupfilesPresetsComboLastSelected = 0;
310 protected JPanel suffixPanel = new JPanel();
312 protected JPanel keepfilesPanel = new JPanel();
314 protected JPanel exampleFilesPanel = new JPanel();
316 protected JTextField suffixTemplate = new JTextField(null, 8);
318 protected JLabel suffixTemplateLabel = new JLabel();
320 protected JLabel suffixDigitsLabel = new JLabel();
322 protected JSpinner suffixDigitsSpinner = new JSpinner();
324 protected JalviewBooleanRadioButtons suffixReverse = new JalviewBooleanRadioButtons();
326 protected JalviewBooleanRadioButtons backupfilesKeepAll = new JalviewBooleanRadioButtons();
328 public JSpinner backupfilesRollMaxSpinner = new JSpinner();
330 protected JLabel oldBackupFilesLabel = new JLabel();
332 protected JalviewBooleanRadioButtons backupfilesConfirmDelete = new JalviewBooleanRadioButtons();
334 protected JTextArea backupfilesExampleLabel = new JTextArea();
337 * Creates a new GPreferences object.
339 public GPreferences()
344 } catch (Exception ex)
346 ex.printStackTrace();
351 * Construct the panel and its tabbed sub-panels.
355 private void jbInit() throws Exception
357 final JTabbedPane tabbedPane = new JTabbedPane();
358 this.setLayout(new BorderLayout());
359 JPanel okCancelPanel = initOkCancelPanel();
360 this.add(tabbedPane, BorderLayout.CENTER);
361 this.add(okCancelPanel, BorderLayout.SOUTH);
363 tabbedPane.add(initVisualTab(),
364 MessageManager.getString("label.visual"));
366 tabbedPane.add(initColoursTab(),
367 MessageManager.getString("label.colours"));
369 tabbedPane.add(initOverviewTab(),
370 MessageManager.getString("label.overview"));
372 tabbedPane.add(initStructureTab(),
373 MessageManager.getString("label.structure"));
375 tabbedPane.add(initConnectionsTab(),
376 MessageManager.getString("label.connections"));
378 tabbedPane.add(initBackupsTab(),
379 MessageManager.getString("label.backups"));
381 tabbedPane.add(initLinksTab(),
382 MessageManager.getString("label.urllinks"));
384 tabbedPane.add(initOutputTab(),
385 MessageManager.getString("label.output"));
387 tabbedPane.add(initEditingTab(),
388 MessageManager.getString("label.editing"));
391 * See WsPreferences for the real work of configuring this tab.
393 wsTab.setLayout(new BorderLayout());
394 tabbedPane.add(wsTab, MessageManager.getString("label.web_services"));
397 * Handler to validate a tab before leaving it - currently only for
400 tabbedPane.addChangeListener(new ChangeListener()
402 private Component lastTab;
405 public void stateChanged(ChangeEvent e)
407 if (lastTab == structureTab
408 && tabbedPane.getSelectedComponent() != structureTab)
410 if (!validateStructure())
412 tabbedPane.setSelectedComponent(structureTab);
416 lastTab = tabbedPane.getSelectedComponent();
423 * Initialises the Editing tabbed panel.
427 private JPanel initEditingTab()
429 JPanel editingTab = new JPanel();
430 editingTab.setLayout(null);
431 autoCalculateConsCheck.setFont(LABEL_FONT);
432 autoCalculateConsCheck.setText(
433 MessageManager.getString("label.autocalculate_consensus"));
434 autoCalculateConsCheck.setBounds(new Rectangle(21, 52, 209, 23));
435 padGaps.setFont(LABEL_FONT);
437 MessageManager.getString("label.pad_gaps_when_editing"));
438 padGaps.setBounds(new Rectangle(22, 94, 168, 23));
439 sortByTree.setFont(LABEL_FONT);
441 .setText(MessageManager.getString("label.sort_with_new_tree"));
442 sortByTree.setToolTipText(MessageManager.getString(
443 "label.any_trees_calculated_or_loaded_alignment_automatically_sort"));
444 sortByTree.setBounds(new Rectangle(22, 136, 168, 23));
445 editingTab.add(autoCalculateConsCheck);
446 editingTab.add(padGaps);
447 editingTab.add(sortByTree);
452 * Initialises the Output tabbed panel.
456 private JPanel initOutputTab()
458 JPanel outputTab = new JPanel();
459 outputTab.setLayout(null);
460 JLabel epsLabel = new JLabel();
461 epsLabel.setFont(LABEL_FONT);
462 epsLabel.setHorizontalAlignment(SwingConstants.RIGHT);
463 epsLabel.setText(MessageManager.getString("label.eps_rendering_style"));
464 epsLabel.setBounds(new Rectangle(9, 31, 140, 24));
465 epsRendering.setFont(LABEL_FONT);
466 epsRendering.setBounds(new Rectangle(154, 34, 187, 21));
467 JLabel jLabel1 = new JLabel();
468 jLabel1.setFont(LABEL_FONT);
469 jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
470 jLabel1.setText(MessageManager.getString("label.append_start_end"));
471 jLabel1.setFont(LABEL_FONT);
472 fastajv.setFont(LABEL_FONT);
473 fastajv.setHorizontalAlignment(SwingConstants.LEFT);
474 clustaljv.setText(MessageManager.getString("label.clustal") + " ");
475 blcjv.setText(MessageManager.getString("label.blc") + " ");
476 fastajv.setText(MessageManager.getString("label.fasta") + " ");
477 msfjv.setText(MessageManager.getString("label.msf") + " ");
478 pfamjv.setText(MessageManager.getString("label.pfam") + " ");
479 pileupjv.setText(MessageManager.getString("label.pileup") + " ");
480 msfjv.setFont(LABEL_FONT);
481 msfjv.setHorizontalAlignment(SwingConstants.LEFT);
482 pirjv.setText(MessageManager.getString("label.pir") + " ");
483 JPanel jPanel11 = new JPanel();
484 jPanel11.setFont(LABEL_FONT);
485 TitledBorder titledBorder2 = new TitledBorder(
486 MessageManager.getString("label.file_output"));
487 jPanel11.setBorder(titledBorder2);
488 jPanel11.setBounds(new Rectangle(30, 72, 196, 182));
489 GridLayout gridLayout3 = new GridLayout();
490 jPanel11.setLayout(gridLayout3);
491 gridLayout3.setRows(8);
492 blcjv.setFont(LABEL_FONT);
493 blcjv.setHorizontalAlignment(SwingConstants.LEFT);
494 clustaljv.setFont(LABEL_FONT);
495 clustaljv.setHorizontalAlignment(SwingConstants.LEFT);
496 pfamjv.setFont(LABEL_FONT);
497 pfamjv.setHorizontalAlignment(SwingConstants.LEFT);
498 pileupjv.setFont(LABEL_FONT);
499 pileupjv.setHorizontalAlignment(SwingConstants.LEFT);
500 pirjv.setFont(LABEL_FONT);
501 pirjv.setHorizontalAlignment(SwingConstants.LEFT);
502 autoIdWidth.setFont(LABEL_FONT);
504 MessageManager.getString("label.automatically_set_id_width"));
505 autoIdWidth.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager
506 .getString("label.adjusts_width_generated_eps_png")));
507 autoIdWidth.setBounds(new Rectangle(228, 96, 188, 23));
508 autoIdWidth.addActionListener(new ActionListener()
512 public void actionPerformed(ActionEvent e)
514 autoIdWidth_actionPerformed();
517 userIdWidthlabel.setFont(LABEL_FONT);
518 userIdWidthlabel.setText(
519 MessageManager.getString("label.figure_id_column_width"));
520 userIdWidth.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager
521 .getString("label.manually_specify_width_left_column")));
522 userIdWidthlabel.setToolTipText(
523 JvSwingUtils.wrapTooltip(true, MessageManager.getString(
524 "label.manually_specify_width_left_column")));
525 userIdWidthlabel.setBounds(new Rectangle(236, 120, 168, 23));
526 userIdWidth.setFont(JvSwingUtils.getTextAreaFont());
527 userIdWidth.setText("");
528 userIdWidth.setBounds(new Rectangle(232, 144, 84, 23));
529 userIdWidth.addActionListener(new ActionListener()
533 public void actionPerformed(ActionEvent e)
535 userIdWidth_actionPerformed();
538 modellerOutput.setFont(LABEL_FONT);
540 .setText(MessageManager.getString("label.use_modeller_output"));
541 modellerOutput.setBounds(new Rectangle(228, 226, 168, 23));
542 embbedBioJSON.setFont(LABEL_FONT);
543 embbedBioJSON.setText(MessageManager.getString("label.embbed_biojson"));
544 embbedBioJSON.setBounds(new Rectangle(228, 200, 250, 23));
546 jPanel11.add(jLabel1);
548 jPanel11.add(clustaljv);
549 jPanel11.add(fastajv);
551 jPanel11.add(pfamjv);
552 jPanel11.add(pileupjv);
554 outputTab.add(autoIdWidth);
555 outputTab.add(userIdWidth);
556 outputTab.add(userIdWidthlabel);
557 outputTab.add(modellerOutput);
558 outputTab.add(embbedBioJSON);
559 outputTab.add(epsLabel);
560 outputTab.add(epsRendering);
561 outputTab.add(jPanel11);
566 * Initialises the Connections tabbed panel.
570 private JPanel initConnectionsTab()
572 JPanel connectTab = new JPanel();
573 connectTab.setLayout(new GridBagLayout());
575 // Label for browser text box
576 JLabel browserLabel = new JLabel();
577 browserLabel.setFont(LABEL_FONT);
578 browserLabel.setHorizontalAlignment(SwingConstants.TRAILING);
579 browserLabel.setText(
580 MessageManager.getString("label.default_browser_unix"));
581 defaultBrowser.setFont(LABEL_FONT);
582 defaultBrowser.setText("");
583 final String tooltip = JvSwingUtils.wrapTooltip(true,
584 MessageManager.getString("label.double_click_to_browse"));
585 defaultBrowser.setToolTipText(tooltip);
586 defaultBrowser.addMouseListener(new MouseAdapter()
589 public void mouseClicked(MouseEvent e)
591 if (e.getClickCount() > 1)
593 defaultBrowser_mouseClicked(e);
598 JPanel proxyPanel = initConnTabProxyPanel();
599 initConnTabCheckboxes();
601 // Add default Browser text box
602 connectTab.add(browserLabel,
603 new GridBagConstraints(0, 0, 1, 1, 0.0, 0.0,
604 GridBagConstraints.WEST, GridBagConstraints.NONE,
605 new Insets(10, 0, 5, 5), 5, 1));
606 defaultBrowser.setFont(LABEL_FONT);
607 defaultBrowser.setText("");
609 connectTab.add(defaultBrowser, new GridBagConstraints(1, 0, 1, 1, 1.0,
610 0.0, GridBagConstraints.CENTER, GridBagConstraints.HORIZONTAL,
611 new Insets(10, 0, 5, 10), 30, 1));
613 // Add proxy server panel
614 connectTab.add(proxyPanel, new GridBagConstraints(0, 1, 2, 1, 1.0, 0.0,
615 GridBagConstraints.CENTER, GridBagConstraints.HORIZONTAL,
616 new Insets(10, 0, 5, 12), 4, 10));
618 // Add usage stats, version check and questionnaire checkboxes
619 connectTab.add(usagestats,
620 new GridBagConstraints(0, 2, 1, 1, 1.0, 0.0,
621 GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
622 new Insets(0, 2, 5, 5), 70, 1));
623 connectTab.add(questionnaire,
624 new GridBagConstraints(1, 2, 1, 1, 1.0, 0.0,
625 GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
626 new Insets(0, 2, 5, 10), 70, 1));
627 connectTab.add(versioncheck,
628 new GridBagConstraints(0, 3, 1, 1, 1.0, 0.0,
629 GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
630 new Insets(0, 2, 5, 5), 70, 1));
632 // Add padding so the panel doesn't look ridiculous
633 JPanel spacePanel = new JPanel();
634 connectTab.add(spacePanel,
635 new GridBagConstraints(0, 4, 1, 1, 1.0, 1.0,
636 GridBagConstraints.WEST, GridBagConstraints.BOTH,
637 new Insets(0, 0, 0, 5), 70, 1));
643 * Initialises the Links tabbed panel.
647 private JPanel initLinksTab()
649 JPanel linkTab = new JPanel();
650 linkTab.setLayout(new GridBagLayout());
652 // Set up table for Url links
653 linkUrlTable.getTableHeader().setReorderingAllowed(false);
654 linkUrlTable.setFillsViewportHeight(true);
655 linkUrlTable.setAutoResizeMode(JTable.AUTO_RESIZE_ALL_COLUMNS);
656 linkUrlTable.setAutoCreateRowSorter(true);
657 linkUrlTable.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
659 // adjust row height so radio buttons actually fit
660 // don't do this in the renderer, it causes the awt thread to activate
662 JRadioButton temp = new JRadioButton();
663 linkUrlTable.setRowHeight(temp.getMinimumSize().height);
665 // Table in scrollpane so that the table is given a scrollbar
666 JScrollPane linkScrollPane = new JScrollPane(linkUrlTable);
667 linkScrollPane.setBorder(null);
669 // Panel for links functionality
670 JPanel linkPanel = new JPanel(new GridBagLayout());
671 linkPanel.setBorder(new TitledBorder(
672 MessageManager.getString("label.url_linkfrom_sequence_id")));
674 // Put the Url links panel together
676 // Buttons go at top right, resizing only resizes the blank space vertically
677 JPanel buttonPanel = initLinkTabUrlButtons();
678 GridBagConstraints linkConstraints1 = new GridBagConstraints();
679 linkConstraints1.insets = new Insets(0, 0, 5, 0);
680 linkConstraints1.gridx = 0;
681 linkConstraints1.gridy = 0;
682 linkConstraints1.weightx = 1.0;
683 linkConstraints1.fill = GridBagConstraints.HORIZONTAL;
684 linkTab.add(buttonPanel, linkConstraints1);
686 // Links table goes at top left, resizing resizes the table
687 GridBagConstraints linkConstraints2 = new GridBagConstraints();
688 linkConstraints2.insets = new Insets(0, 0, 5, 5);
689 linkConstraints2.gridx = 0;
690 linkConstraints2.gridy = 1;
691 linkConstraints2.weightx = 1.0;
692 linkConstraints2.weighty = 1.0;
693 linkConstraints2.fill = GridBagConstraints.BOTH;
694 linkTab.add(linkScrollPane, linkConstraints2);
696 // Filter box and buttons goes at bottom left, resizing resizes the text box
697 JPanel filterPanel = initLinkTabFilterPanel();
698 GridBagConstraints linkConstraints3 = new GridBagConstraints();
699 linkConstraints3.insets = new Insets(0, 0, 0, 5);
700 linkConstraints3.gridx = 0;
701 linkConstraints3.gridy = 2;
702 linkConstraints3.weightx = 1.0;
703 linkConstraints3.fill = GridBagConstraints.HORIZONTAL;
704 linkTab.add(filterPanel, linkConstraints3);
709 private JPanel initLinkTabFilterPanel()
711 // Filter textbox and reset button
712 JLabel filterLabel = new JLabel(
713 MessageManager.getString("label.filter"));
714 filterLabel.setFont(LABEL_FONT);
715 filterLabel.setHorizontalAlignment(SwingConstants.RIGHT);
716 filterLabel.setHorizontalTextPosition(SwingConstants.LEADING);
718 filterTB.setFont(LABEL_FONT);
719 filterTB.setText("");
721 doReset.setText(MessageManager.getString("action.showall"));
722 userOnly.setText(MessageManager.getString("action.customfilter"));
724 // Panel for filter functionality
725 JPanel filterPanel = new JPanel(new GridBagLayout());
726 filterPanel.setBorder(new TitledBorder("Filter"));
727 GridBagConstraints gbc = new GridBagConstraints();
730 gbc.fill = GridBagConstraints.NONE;
731 gbc.anchor = GridBagConstraints.WEST;
733 filterPanel.add(filterLabel, gbc);
735 GridBagConstraints gbc1 = new GridBagConstraints();
738 gbc1.fill = GridBagConstraints.HORIZONTAL;
739 gbc1.anchor = GridBagConstraints.WEST;
741 filterPanel.add(filterTB, gbc1);
743 GridBagConstraints gbc2 = new GridBagConstraints();
745 gbc2.fill = GridBagConstraints.NONE;
746 gbc2.anchor = GridBagConstraints.WEST;
747 filterPanel.add(doReset, gbc2);
749 GridBagConstraints gbc3 = new GridBagConstraints();
751 gbc3.fill = GridBagConstraints.NONE;
752 gbc3.anchor = GridBagConstraints.WEST;
753 filterPanel.add(userOnly, gbc3);
758 private JPanel initLinkTabUrlButtons()
760 // Buttons for new / edit / delete Url links
761 JButton newLink = new JButton();
762 newLink.setText(MessageManager.getString("action.new"));
764 editLink.setText(MessageManager.getString("action.edit"));
766 deleteLink.setText(MessageManager.getString("action.delete"));
768 // no current selection, so initially disable delete/edit buttons
769 editLink.setEnabled(false);
770 deleteLink.setEnabled(false);
772 newLink.addActionListener(new java.awt.event.ActionListener()
775 public void actionPerformed(ActionEvent e)
777 newLink_actionPerformed(e);
781 editLink.setText(MessageManager.getString("action.edit"));
782 editLink.addActionListener(new java.awt.event.ActionListener()
785 public void actionPerformed(ActionEvent e)
787 editLink_actionPerformed(e);
791 deleteLink.setText(MessageManager.getString("action.delete"));
792 deleteLink.addActionListener(new java.awt.event.ActionListener()
795 public void actionPerformed(ActionEvent e)
797 deleteLink_actionPerformed(e);
801 JPanel buttonPanel = new JPanel(new GridBagLayout());
802 buttonPanel.setBorder(new TitledBorder("Edit links"));
803 GridBagConstraints gbc = new GridBagConstraints();
806 gbc.fill = GridBagConstraints.NONE;
807 buttonPanel.add(newLink, gbc);
809 GridBagConstraints gbc1 = new GridBagConstraints();
812 gbc1.fill = GridBagConstraints.NONE;
813 buttonPanel.add(editLink, gbc1);
815 GridBagConstraints gbc2 = new GridBagConstraints();
818 gbc2.fill = GridBagConstraints.NONE;
819 buttonPanel.add(deleteLink, gbc2);
821 GridBagConstraints gbc3 = new GridBagConstraints();
824 gbc3.fill = GridBagConstraints.HORIZONTAL;
826 JPanel spacePanel = new JPanel();
827 spacePanel.setBorder(null);
828 buttonPanel.add(spacePanel, gbc3);
834 * Initialises the proxy server panel in the Connections tab
836 * @return the proxy server panel
838 private JPanel initConnTabProxyPanel()
840 // Label for server text box
841 serverLabel.setText(MessageManager.getString("label.address"));
842 serverLabel.setHorizontalAlignment(SwingConstants.RIGHT);
843 serverLabel.setFont(LABEL_FONT);
845 // Proxy server and port text boxes
846 proxyServerTB.setFont(LABEL_FONT);
847 proxyPortTB.setFont(LABEL_FONT);
849 // Label for Port text box
850 portLabel.setFont(LABEL_FONT);
851 portLabel.setHorizontalAlignment(SwingConstants.RIGHT);
852 portLabel.setText(MessageManager.getString("label.port"));
854 // Use proxy server checkbox
855 useProxy.setFont(LABEL_FONT);
856 useProxy.setHorizontalAlignment(SwingConstants.RIGHT);
857 useProxy.setHorizontalTextPosition(SwingConstants.LEADING);
858 useProxy.setText(MessageManager.getString("label.use_proxy_server"));
859 useProxy.addActionListener(new ActionListener()
862 public void actionPerformed(ActionEvent e)
864 useProxy_actionPerformed();
868 // Make proxy server panel
869 JPanel proxyPanel = new JPanel();
870 TitledBorder titledBorder1 = new TitledBorder(
871 MessageManager.getString("label.proxy_server"));
872 proxyPanel.setBorder(titledBorder1);
873 proxyPanel.setLayout(new GridBagLayout());
874 proxyPanel.add(serverLabel,
875 new GridBagConstraints(0, 1, 1, 1, 0.0, 0.0,
876 GridBagConstraints.WEST, GridBagConstraints.NONE,
877 new Insets(0, 2, 2, 0), 5, 0));
878 proxyPanel.add(portLabel,
879 new GridBagConstraints(2, 1, 1, 1, 0.0, 0.0,
880 GridBagConstraints.WEST, GridBagConstraints.NONE,
881 new Insets(0, 0, 2, 0), 11, 0));
882 proxyPanel.add(useProxy,
883 new GridBagConstraints(0, 0, 2, 1, 0.0, 0.0,
884 GridBagConstraints.WEST, GridBagConstraints.NONE,
885 new Insets(0, 2, 5, 185), 2, -4));
886 proxyPanel.add(proxyPortTB,
887 new GridBagConstraints(3, 1, 1, 1, 1.0, 0.0,
888 GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
889 new Insets(0, 2, 2, 2), 54, 1));
890 proxyPanel.add(proxyServerTB,
891 new GridBagConstraints(1, 1, 1, 1, 1.0, 0.0,
892 GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
893 new Insets(0, 2, 2, 0), 263, 1));
899 * Initialises the checkboxes in the Connections tab
901 private void initConnTabCheckboxes()
903 // Usage stats checkbox label
905 MessageManager.getString("label.send_usage_statistics"));
906 usagestats.setFont(LABEL_FONT);
907 usagestats.setHorizontalAlignment(SwingConstants.RIGHT);
908 usagestats.setHorizontalTextPosition(SwingConstants.LEADING);
910 // Questionnaire checkbox label
911 questionnaire.setText(
912 MessageManager.getString("label.check_for_questionnaires"));
913 questionnaire.setFont(LABEL_FONT);
914 questionnaire.setHorizontalAlignment(SwingConstants.RIGHT);
915 questionnaire.setHorizontalTextPosition(SwingConstants.LEADING);
917 // Check for latest version checkbox label
918 versioncheck.setText(
919 MessageManager.getString("label.check_for_latest_version"));
920 versioncheck.setFont(LABEL_FONT);
921 versioncheck.setHorizontalAlignment(SwingConstants.RIGHT);
922 versioncheck.setHorizontalTextPosition(SwingConstants.LEADING);
926 * Initialises the parent panel which contains the tabbed sections.
930 private JPanel initOkCancelPanel()
932 JButton ok = new JButton();
933 ok.setText(MessageManager.getString("action.ok"));
934 ok.addActionListener(new ActionListener()
937 public void actionPerformed(ActionEvent e)
939 ok_actionPerformed(e);
942 JButton cancel = new JButton();
943 cancel.setText(MessageManager.getString("action.cancel"));
944 cancel.addActionListener(new ActionListener()
947 public void actionPerformed(ActionEvent e)
949 cancel_actionPerformed(e);
952 JPanel okCancelPanel = new JPanel();
953 okCancelPanel.add(ok);
954 okCancelPanel.add(cancel);
955 return okCancelPanel;
959 * Initialises the Colours tabbed panel.
963 private JPanel initColoursTab()
965 JPanel coloursTab = new JPanel();
966 coloursTab.setBorder(new TitledBorder(
967 MessageManager.getString("action.open_new_alignment")));
968 coloursTab.setLayout(new FlowLayout());
969 JLabel mincolourLabel = new JLabel();
970 mincolourLabel.setFont(LABEL_FONT);
971 mincolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
972 mincolourLabel.setText(MessageManager.getString("label.min_colour"));
973 minColour.setFont(LABEL_FONT);
974 minColour.setBorder(BorderFactory.createEtchedBorder());
975 minColour.setPreferredSize(new Dimension(40, 20));
976 minColour.addMouseListener(new MouseAdapter()
979 public void mousePressed(MouseEvent e)
981 minColour_actionPerformed(minColour);
984 JLabel maxcolourLabel = new JLabel();
985 maxcolourLabel.setFont(LABEL_FONT);
986 maxcolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
987 maxcolourLabel.setText(MessageManager.getString("label.max_colour"));
988 maxColour.setFont(LABEL_FONT);
989 maxColour.setBorder(BorderFactory.createEtchedBorder());
990 maxColour.setPreferredSize(new Dimension(40, 20));
991 maxColour.addMouseListener(new MouseAdapter()
994 public void mousePressed(MouseEvent e)
996 maxColour_actionPerformed(maxColour);
1000 protColour.setFont(LABEL_FONT);
1001 protColour.setBounds(new Rectangle(172, 225, 155, 21));
1002 JLabel protColourLabel = new JLabel();
1003 protColourLabel.setFont(LABEL_FONT);
1004 protColourLabel.setHorizontalAlignment(SwingConstants.LEFT);
1005 protColourLabel.setText(
1006 MessageManager.getString("label.prot_alignment_colour") + " ");
1007 JvSwingUtils.addtoLayout(coloursTab,
1009 .getString("label.default_colour_scheme_for_alignment"),
1010 protColourLabel, protColour);
1012 nucColour.setFont(LABEL_FONT);
1013 nucColour.setBounds(new Rectangle(172, 240, 155, 21));
1014 JLabel nucColourLabel = new JLabel();
1015 nucColourLabel.setFont(LABEL_FONT);
1016 nucColourLabel.setHorizontalAlignment(SwingConstants.LEFT);
1017 nucColourLabel.setText(
1018 MessageManager.getString("label.nuc_alignment_colour") + " ");
1019 JvSwingUtils.addtoLayout(coloursTab,
1021 .getString("label.default_colour_scheme_for_alignment"),
1022 nucColourLabel, nucColour);
1024 JPanel annotationShding = new JPanel();
1025 annotationShding.setBorder(new TitledBorder(
1026 MessageManager.getString("label.annotation_shading_default")));
1027 annotationShding.setLayout(new GridLayout(1, 2));
1028 JvSwingUtils.addtoLayout(annotationShding,
1029 MessageManager.getString(
1030 "label.default_minimum_colour_annotation_shading"),
1031 mincolourLabel, minColour);
1032 JvSwingUtils.addtoLayout(annotationShding,
1033 MessageManager.getString(
1034 "label.default_maximum_colour_annotation_shading"),
1035 maxcolourLabel, maxColour);
1036 coloursTab.add(annotationShding); // , FlowLayout.LEFT);
1041 * Initialises the Overview tabbed panel.
1045 private JPanel initOverviewTab()
1047 JPanel overviewPanel = new JPanel();
1048 overviewPanel.setBorder(new TitledBorder(
1049 MessageManager.getString("label.overview_settings")));
1051 gapColour.setFont(LABEL_FONT);
1052 // fixing the border colours stops apparent colour bleed from the panel
1053 gapColour.setBorder(
1054 BorderFactory.createEtchedBorder(Color.white, Color.lightGray));
1055 gapColour.setPreferredSize(new Dimension(40, 20));
1056 gapColour.addMouseListener(new MouseAdapter()
1059 public void mousePressed(MouseEvent e)
1061 gapColour_actionPerformed(gapColour);
1065 hiddenColour.setFont(LABEL_FONT);
1066 // fixing the border colours stops apparent colour bleed from the panel
1067 hiddenColour.setBorder(
1068 BorderFactory.createEtchedBorder(Color.white, Color.lightGray));
1069 hiddenColour.setPreferredSize(new Dimension(40, 20));
1070 hiddenColour.addMouseListener(new MouseAdapter()
1073 public void mousePressed(MouseEvent e)
1075 hiddenColour_actionPerformed(hiddenColour);
1079 useLegacyGap = new JCheckBox(
1080 MessageManager.getString("label.ov_legacy_gap"));
1081 useLegacyGap.setFont(LABEL_FONT);
1082 useLegacyGap.setHorizontalAlignment(SwingConstants.LEFT);
1083 useLegacyGap.setVerticalTextPosition(SwingConstants.TOP);
1084 gapLabel = new JLabel(MessageManager.getString("label.gap_colour"));
1085 gapLabel.setFont(LABEL_FONT);
1086 gapLabel.setHorizontalAlignment(SwingConstants.LEFT);
1087 gapLabel.setVerticalTextPosition(SwingConstants.TOP);
1088 showHiddenAtStart = new JCheckBox(
1089 MessageManager.getString("label.ov_show_hide_default"));
1090 showHiddenAtStart.setFont(LABEL_FONT);
1091 showHiddenAtStart.setHorizontalAlignment(SwingConstants.LEFT);
1092 showHiddenAtStart.setVerticalTextPosition(SwingConstants.TOP);
1093 JLabel hiddenLabel = new JLabel(
1094 MessageManager.getString("label.hidden_colour"));
1095 hiddenLabel.setFont(LABEL_FONT);
1096 hiddenLabel.setHorizontalAlignment(SwingConstants.LEFT);
1097 hiddenLabel.setVerticalTextPosition(SwingConstants.TOP);
1099 useLegacyGap.addActionListener(new ActionListener()
1102 public void actionPerformed(ActionEvent e)
1104 useLegacyGaps_actionPerformed(e);
1108 overviewPanel.setLayout(new GridBagLayout());
1109 GridBagConstraints c1 = new GridBagConstraints();
1111 c1.fill = GridBagConstraints.HORIZONTAL;
1116 c1.anchor = GridBagConstraints.FIRST_LINE_START;
1117 overviewPanel.add(useLegacyGap, c1);
1119 GridBagConstraints c2 = new GridBagConstraints();
1120 c2.fill = GridBagConstraints.HORIZONTAL;
1123 c2.insets = new Insets(0, 15, 0, 10);
1124 overviewPanel.add(gapLabel, c2);
1126 GridBagConstraints c3 = new GridBagConstraints();
1127 c3.fill = GridBagConstraints.HORIZONTAL;
1130 c3.insets = new Insets(0, 0, 0, 15);
1131 overviewPanel.add(gapColour, c3);
1133 GridBagConstraints c4 = new GridBagConstraints();
1134 c4.fill = GridBagConstraints.HORIZONTAL;
1138 overviewPanel.add(showHiddenAtStart, c4);
1140 GridBagConstraints c5 = new GridBagConstraints();
1141 c5.fill = GridBagConstraints.HORIZONTAL;
1144 c5.insets = new Insets(0, 15, 0, 10);
1145 overviewPanel.add(hiddenLabel, c5);
1147 GridBagConstraints c6 = new GridBagConstraints();
1148 c6.fill = GridBagConstraints.HORIZONTAL;
1151 c6.insets = new Insets(0, 0, 0, 15);
1152 overviewPanel.add(hiddenColour, c6);
1154 JButton resetButton = new JButton(
1155 MessageManager.getString("label.reset_to_defaults"));
1157 resetButton.addActionListener(new ActionListener()
1160 public void actionPerformed(ActionEvent e)
1162 resetOvDefaults_actionPerformed(e);
1166 GridBagConstraints c7 = new GridBagConstraints();
1167 c7.fill = GridBagConstraints.NONE;
1170 c7.insets = new Insets(10, 0, 0, 0);
1171 c7.anchor = GridBagConstraints.WEST;
1172 overviewPanel.add(resetButton, c7);
1174 // Add padding so the panel doesn't look ridiculous
1175 JPanel spacePanel = new JPanel();
1176 overviewPanel.add(spacePanel,
1177 new GridBagConstraints(0, 3, 1, 1, 1.0, 1.0,
1178 GridBagConstraints.WEST, GridBagConstraints.BOTH,
1179 new Insets(0, 0, 0, 5), 0, 0));
1181 return overviewPanel;
1185 * Initialises the Structure tabbed panel.
1189 private JPanel initStructureTab()
1191 structureTab = new JPanel();
1193 structureTab.setBorder(new TitledBorder(
1194 MessageManager.getString("label.structure_options")));
1195 structureTab.setLayout(null);
1196 final int width = 400;
1197 final int height = 22;
1198 final int lineSpacing = 25;
1201 structFromPdb.setFont(LABEL_FONT);
1203 .setText(MessageManager.getString("label.struct_from_pdb"));
1204 structFromPdb.setBounds(new Rectangle(5, ypos, width, height));
1205 structFromPdb.addActionListener(new ActionListener()
1208 public void actionPerformed(ActionEvent e)
1210 boolean selected = structFromPdb.isSelected();
1211 // enable other options only when the first is checked
1212 useRnaView.setEnabled(selected);
1213 addSecondaryStructure.setEnabled(selected);
1214 addTempFactor.setEnabled(selected);
1217 structureTab.add(structFromPdb);
1219 // indent checkboxes that are conditional on the first one
1220 ypos += lineSpacing;
1221 useRnaView.setFont(LABEL_FONT);
1222 useRnaView.setText(MessageManager.getString("label.use_rnaview"));
1223 useRnaView.setBounds(new Rectangle(25, ypos, width, height));
1224 structureTab.add(useRnaView);
1226 ypos += lineSpacing;
1227 addSecondaryStructure.setFont(LABEL_FONT);
1228 addSecondaryStructure
1229 .setText(MessageManager.getString("label.autoadd_secstr"));
1230 addSecondaryStructure.setBounds(new Rectangle(25, ypos, width, height));
1231 structureTab.add(addSecondaryStructure);
1233 ypos += lineSpacing;
1234 addTempFactor.setFont(LABEL_FONT);
1235 addTempFactor.setText(MessageManager.getString("label.autoadd_temp"));
1236 addTempFactor.setBounds(new Rectangle(25, ypos, width, height));
1237 structureTab.add(addTempFactor);
1239 ypos += lineSpacing;
1240 JLabel viewerLabel = new JLabel();
1241 viewerLabel.setFont(LABEL_FONT);
1242 viewerLabel.setHorizontalAlignment(SwingConstants.LEFT);
1243 viewerLabel.setText(MessageManager.getString("label.structure_viewer"));
1244 viewerLabel.setBounds(new Rectangle(10, ypos, 200, height));
1245 structureTab.add(viewerLabel);
1247 structViewer.setFont(LABEL_FONT);
1248 structViewer.setBounds(new Rectangle(160, ypos, 120, height));
1249 structViewer.addItem(ViewerType.JMOL.name());
1250 structViewer.addItem(ViewerType.CHIMERA.name());
1251 structViewer.addActionListener(new ActionListener()
1254 public void actionPerformed(ActionEvent e)
1256 structureViewer_actionPerformed(
1257 (String) structViewer.getSelectedItem());
1260 structureTab.add(structViewer);
1262 ypos += lineSpacing;
1263 JLabel pathLabel = new JLabel();
1264 pathLabel.setFont(new java.awt.Font("SansSerif", 0, 11));
1265 pathLabel.setHorizontalAlignment(SwingConstants.LEFT);
1266 pathLabel.setText(MessageManager.getString("label.chimera_path"));
1267 pathLabel.setBounds(new Rectangle(10, ypos, 140, height));
1268 structureTab.add(pathLabel);
1270 chimeraPath.setFont(LABEL_FONT);
1271 chimeraPath.setText("");
1272 final String tooltip = JvSwingUtils.wrapTooltip(true,
1273 MessageManager.getString("label.chimera_path_tip"));
1274 chimeraPath.setToolTipText(tooltip);
1275 chimeraPath.setBounds(new Rectangle(160, ypos, 300, height));
1276 chimeraPath.addMouseListener(new MouseAdapter()
1279 public void mouseClicked(MouseEvent e)
1281 if (e.getClickCount() == 2)
1283 String chosen = openFileChooser();
1286 chimeraPath.setText(chosen);
1291 structureTab.add(chimeraPath);
1293 ypos += lineSpacing;
1294 nwMapping.setFont(LABEL_FONT);
1295 nwMapping.setText(MessageManager.getString("label.nw_mapping"));
1296 siftsMapping.setFont(LABEL_FONT);
1297 siftsMapping.setText(MessageManager.getString("label.sifts_mapping"));
1298 mappingMethod.add(nwMapping);
1299 mappingMethod.add(siftsMapping);
1300 JPanel mappingPanel = new JPanel();
1301 mappingPanel.setFont(LABEL_FONT);
1302 TitledBorder mmTitledBorder = new TitledBorder(
1303 MessageManager.getString("label.mapping_method"));
1304 mmTitledBorder.setTitleFont(LABEL_FONT);
1305 mappingPanel.setBorder(mmTitledBorder);
1306 mappingPanel.setBounds(new Rectangle(10, ypos, 452, 45));
1307 // GridLayout mappingLayout = new GridLayout();
1308 mappingPanel.setLayout(new GridLayout());
1309 mappingPanel.add(nwMapping);
1310 mappingPanel.add(siftsMapping);
1311 structureTab.add(mappingPanel);
1313 ypos += lineSpacing;
1314 ypos += lineSpacing;
1315 FTSDataColumnPreferences docFieldPref = new FTSDataColumnPreferences(
1316 PreferenceSource.PREFERENCES, PDBFTSRestClient.getInstance());
1317 docFieldPref.setBounds(new Rectangle(10, ypos, 450, 120));
1318 structureTab.add(docFieldPref);
1320 return structureTab;
1324 * Action on choosing a structure viewer from combobox options.
1326 * @param selectedItem
1328 protected void structureViewer_actionPerformed(String selectedItem)
1333 * Show a dialog for the user to choose a file. Returns the chosen path, or
1338 protected String openFileChooser()
1340 String choice = null;
1341 JFileChooser chooser = new JFileChooser();
1343 // chooser.setFileView(new JalviewFileView());
1344 chooser.setDialogTitle(
1345 MessageManager.getString("label.open_local_file"));
1346 chooser.setToolTipText(MessageManager.getString("action.open"));
1348 int value = chooser.showOpenDialog(this);
1350 if (value == JFileChooser.APPROVE_OPTION)
1352 choice = chooser.getSelectedFile().getPath();
1358 * Validate the structure tab preferences; if invalid, set focus on this tab.
1362 protected boolean validateStructure(FocusEvent e)
1364 if (!validateStructure())
1366 e.getComponent().requestFocusInWindow();
1372 protected boolean validateStructure()
1378 * Initialises the Visual tabbed panel.
1382 private JPanel initVisualTab()
1384 JPanel visualTab = new JPanel();
1385 visualTab.setBorder(new TitledBorder(
1386 MessageManager.getString("action.open_new_alignment")));
1387 visualTab.setLayout(null);
1388 fullScreen.setFont(LABEL_FONT);
1389 fullScreen.setHorizontalAlignment(SwingConstants.RIGHT);
1390 fullScreen.setHorizontalTextPosition(SwingConstants.LEFT);
1391 fullScreen.setText(MessageManager.getString("label.maximize_window"));
1392 quality.setEnabled(false);
1393 quality.setFont(LABEL_FONT);
1394 quality.setHorizontalAlignment(SwingConstants.RIGHT);
1395 quality.setHorizontalTextPosition(SwingConstants.LEFT);
1396 quality.setSelected(true);
1397 quality.setText(MessageManager.getString("label.quality"));
1398 conservation.setEnabled(false);
1399 conservation.setFont(LABEL_FONT);
1400 conservation.setHorizontalAlignment(SwingConstants.RIGHT);
1401 conservation.setHorizontalTextPosition(SwingConstants.LEFT);
1402 conservation.setSelected(true);
1403 conservation.setText(MessageManager.getString("label.conservation"));
1404 identity.setEnabled(false);
1405 identity.setFont(LABEL_FONT);
1406 identity.setHorizontalAlignment(SwingConstants.RIGHT);
1407 identity.setHorizontalTextPosition(SwingConstants.LEFT);
1408 identity.setSelected(true);
1409 identity.setText(MessageManager.getString("label.consensus"));
1410 showOccupancy.setFont(LABEL_FONT);
1411 showOccupancy.setEnabled(false);
1412 showOccupancy.setHorizontalAlignment(SwingConstants.RIGHT);
1413 showOccupancy.setHorizontalTextPosition(SwingConstants.LEFT);
1414 showOccupancy.setSelected(true);
1415 showOccupancy.setText(MessageManager.getString("label.occupancy"));
1417 JLabel showGroupbits = new JLabel();
1418 showGroupbits.setFont(LABEL_FONT);
1419 showGroupbits.setHorizontalAlignment(SwingConstants.RIGHT);
1420 showGroupbits.setHorizontalTextPosition(SwingConstants.LEFT);
1422 .setText(MessageManager.getString("action.show_group") + ":");
1423 JLabel showConsensbits = new JLabel();
1424 showConsensbits.setFont(LABEL_FONT);
1425 showConsensbits.setHorizontalAlignment(SwingConstants.RIGHT);
1426 showConsensbits.setHorizontalTextPosition(SwingConstants.LEFT);
1428 .setText(MessageManager.getString("label.consensus") + ":");
1429 showConsensHistogram.setEnabled(false);
1430 showConsensHistogram.setFont(LABEL_FONT);
1431 showConsensHistogram.setHorizontalAlignment(SwingConstants.RIGHT);
1432 showConsensHistogram.setHorizontalTextPosition(SwingConstants.LEFT);
1433 showConsensHistogram.setSelected(true);
1434 showConsensHistogram
1435 .setText(MessageManager.getString("label.histogram"));
1436 showConsensLogo.setEnabled(false);
1437 showConsensLogo.setFont(LABEL_FONT);
1438 showConsensLogo.setHorizontalAlignment(SwingConstants.RIGHT);
1439 showConsensLogo.setHorizontalTextPosition(SwingConstants.LEFT);
1440 showConsensLogo.setSelected(true);
1441 showConsensLogo.setText(MessageManager.getString("label.logo"));
1442 showGroupConsensus.setEnabled(false);
1443 showGroupConsensus.setFont(LABEL_FONT);
1444 showGroupConsensus.setHorizontalAlignment(SwingConstants.RIGHT);
1445 showGroupConsensus.setHorizontalTextPosition(SwingConstants.LEFT);
1446 showGroupConsensus.setSelected(true);
1447 showGroupConsensus.setText(MessageManager.getString("label.consensus"));
1448 showGroupConservation.setEnabled(false);
1449 showGroupConservation.setFont(LABEL_FONT);
1450 showGroupConservation.setHorizontalAlignment(SwingConstants.RIGHT);
1451 showGroupConservation.setHorizontalTextPosition(SwingConstants.LEFT);
1452 showGroupConservation.setSelected(true);
1453 showGroupConservation
1454 .setText(MessageManager.getString("label.conservation"));
1455 showNpTooltip.setEnabled(true);
1456 showNpTooltip.setFont(LABEL_FONT);
1457 showNpTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
1458 showNpTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
1459 showNpTooltip.setSelected(true);
1460 showNpTooltip.setText(
1461 MessageManager.getString("label.non_positional_features"));
1462 showDbRefTooltip.setEnabled(true);
1463 showDbRefTooltip.setFont(LABEL_FONT);
1464 showDbRefTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
1465 showDbRefTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
1466 showDbRefTooltip.setSelected(true);
1468 .setText(MessageManager.getString("label.database_references"));
1469 annotations.setFont(LABEL_FONT);
1470 annotations.setHorizontalAlignment(SwingConstants.RIGHT);
1471 annotations.setHorizontalTextPosition(SwingConstants.LEFT);
1472 annotations.setSelected(true);
1473 annotations.setText(MessageManager.getString("label.show_annotations"));
1474 // annotations.setBounds(new Rectangle(169, 12, 200, 23));
1475 annotations.addActionListener(new ActionListener()
1478 public void actionPerformed(ActionEvent e)
1480 annotations_actionPerformed(e);
1483 identity.addActionListener(new ActionListener()
1486 public void actionPerformed(ActionEvent e)
1488 annotations_actionPerformed(e);
1491 showGroupConsensus.addActionListener(new ActionListener()
1494 public void actionPerformed(ActionEvent e)
1496 annotations_actionPerformed(e);
1499 showUnconserved.setFont(LABEL_FONT);
1500 showUnconserved.setHorizontalAlignment(SwingConstants.RIGHT);
1501 showUnconserved.setHorizontalTextPosition(SwingConstants.LEFT);
1502 showUnconserved.setSelected(true);
1504 .setText(MessageManager.getString("action.show_unconserved"));
1505 showUnconserved.addActionListener(new ActionListener()
1508 public void actionPerformed(ActionEvent e)
1510 showunconserved_actionPerformed(e);
1514 // TODO these are not yet added to / action from Preferences
1515 // JCheckBox shareSelections = new JCheckBox();
1516 // shareSelections.setFont(verdana11);
1517 // shareSelections.setHorizontalAlignment(SwingConstants.RIGHT);
1518 // shareSelections.setHorizontalTextPosition(SwingConstants.LEFT);
1519 // shareSelections.setSelected(true);
1520 // shareSelections.setText(MessageManager
1521 // .getString("label.share_selection_across_views"));
1522 // JCheckBox followHighlight = new JCheckBox();
1523 // followHighlight.setFont(verdana11);
1524 // followHighlight.setHorizontalAlignment(SwingConstants.RIGHT);
1525 // followHighlight.setHorizontalTextPosition(SwingConstants.LEFT);
1526 // // showUnconserved.setBounds(new Rectangle(169, 40, 200, 23));
1527 // followHighlight.setSelected(true);
1528 // followHighlight.setText(MessageManager
1529 // .getString("label.scroll_highlighted_regions"));
1531 seqLimit.setFont(LABEL_FONT);
1532 seqLimit.setHorizontalAlignment(SwingConstants.RIGHT);
1533 seqLimit.setHorizontalTextPosition(SwingConstants.LEFT);
1534 seqLimit.setText(MessageManager.getString("label.full_sequence_id"));
1535 smoothFont.setFont(LABEL_FONT);
1536 smoothFont.setHorizontalAlignment(SwingConstants.RIGHT);
1537 smoothFont.setHorizontalTextPosition(SwingConstants.LEADING);
1538 smoothFont.setText(MessageManager.getString("label.smooth_font"));
1539 scaleProteinToCdna.setFont(LABEL_FONT);
1540 scaleProteinToCdna.setHorizontalAlignment(SwingConstants.RIGHT);
1541 scaleProteinToCdna.setHorizontalTextPosition(SwingConstants.LEADING);
1542 scaleProteinToCdna.setText(
1543 MessageManager.getString("label.scale_protein_to_cdna"));
1544 scaleProteinToCdna.setToolTipText(
1545 MessageManager.getString("label.scale_protein_to_cdna_tip"));
1546 JLabel gapLabel = new JLabel();
1547 gapLabel.setFont(LABEL_FONT);
1548 gapLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1549 gapLabel.setText(MessageManager.getString("label.gap_symbol") + " ");
1550 JLabel fontLabel = new JLabel();
1551 fontLabel.setFont(LABEL_FONT);
1552 fontLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1553 fontLabel.setText(MessageManager.getString("label.font"));
1554 fontSizeCB.setFont(LABEL_FONT);
1555 fontSizeCB.setBounds(new Rectangle(320, 112, 65, 23));
1556 fontStyleCB.setFont(LABEL_FONT);
1557 fontStyleCB.setBounds(new Rectangle(382, 112, 80, 23));
1558 fontNameCB.setFont(LABEL_FONT);
1559 fontNameCB.setBounds(new Rectangle(172, 112, 147, 23));
1560 gapSymbolCB.setFont(LABEL_FONT);
1561 gapSymbolCB.setBounds(new Rectangle(172, 215, 69, 23));
1562 DefaultListCellRenderer dlcr = new DefaultListCellRenderer();
1563 dlcr.setHorizontalAlignment(DefaultListCellRenderer.CENTER);
1564 gapSymbolCB.setRenderer(dlcr);
1566 startupCheckbox.setText(MessageManager.getString("action.open_file"));
1567 startupCheckbox.setFont(LABEL_FONT);
1568 startupCheckbox.setHorizontalAlignment(SwingConstants.RIGHT);
1569 startupCheckbox.setHorizontalTextPosition(SwingConstants.LEFT);
1570 startupCheckbox.setSelected(true);
1571 startupFileTextfield.setFont(LABEL_FONT);
1572 startupFileTextfield.setBounds(new Rectangle(172, 310, 330, 20));
1573 final String tooltip = JvSwingUtils.wrapTooltip(true,
1574 MessageManager.getString("label.double_click_to_browse"));
1575 startupFileTextfield.setToolTipText(tooltip);
1576 startupFileTextfield.addMouseListener(new MouseAdapter()
1579 public void mouseClicked(MouseEvent e)
1581 if (e.getClickCount() > 1)
1583 startupFileTextfield_mouseClicked();
1588 sortby.setFont(LABEL_FONT);
1589 sortby.setBounds(new Rectangle(172, 260, 155, 21));
1590 JLabel sortLabel = new JLabel();
1591 sortLabel.setFont(LABEL_FONT);
1592 sortLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1593 sortLabel.setText(MessageManager.getString("label.sort_by"));
1594 sortAnnBy.setFont(LABEL_FONT);
1595 sortAnnBy.setBounds(new Rectangle(172, 285, 110, 21));
1596 JLabel sortAnnLabel = new JLabel();
1597 sortAnnLabel.setFont(LABEL_FONT);
1598 sortAnnLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1599 sortAnnLabel.setText(MessageManager.getString("label.sort_ann_by"));
1600 sortAutocalc.setFont(LABEL_FONT);
1601 sortAutocalc.setBounds(new Rectangle(290, 285, 165, 21));
1603 JPanel annsettingsPanel = new JPanel();
1604 annsettingsPanel.setBounds(new Rectangle(173, 13, 320, 96));
1605 annsettingsPanel.setLayout(new FlowLayout(FlowLayout.LEFT, 0, 0));
1606 annsettingsPanel.setBorder(new EtchedBorder());
1607 visualTab.add(annsettingsPanel);
1608 Border jb = new EmptyBorder(1, 1, 4, 5);
1609 annotations.setBorder(jb);
1610 showOccupancy.setBorder(jb);
1611 quality.setBorder(jb);
1612 conservation.setBorder(jb);
1613 identity.setBorder(jb);
1614 showConsensbits.setBorder(jb);
1615 showGroupbits.setBorder(jb);
1616 showGroupConsensus.setBorder(jb);
1617 showGroupConservation.setBorder(jb);
1618 showConsensHistogram.setBorder(jb);
1619 showConsensLogo.setBorder(jb);
1621 JPanel autoAnnotSettings = new JPanel();
1622 annsettingsPanel.add(autoAnnotSettings);
1623 autoAnnotSettings.setLayout(new GridLayout(0, 2));
1624 autoAnnotSettings.add(annotations);
1625 autoAnnotSettings.add(quality);
1626 // second row of autoannotation box
1627 autoAnnotSettings = new JPanel();
1628 annsettingsPanel.add(autoAnnotSettings);
1630 autoAnnotSettings.setLayout(new GridLayout(0, 3));
1631 autoAnnotSettings.add(conservation);
1632 autoAnnotSettings.add(identity);
1633 autoAnnotSettings.add(showOccupancy);
1634 autoAnnotSettings.add(showGroupbits);
1635 autoAnnotSettings.add(showGroupConservation);
1636 autoAnnotSettings.add(showGroupConsensus);
1637 autoAnnotSettings.add(showConsensbits);
1638 autoAnnotSettings.add(showConsensHistogram);
1639 autoAnnotSettings.add(showConsensLogo);
1641 JPanel tooltipSettings = new JPanel();
1642 tooltipSettings.setBorder(new TitledBorder(
1643 MessageManager.getString("label.sequence_id_tooltip")));
1644 tooltipSettings.setBounds(173, 140, 220, 62);
1645 tooltipSettings.setLayout(new GridLayout(2, 1));
1646 tooltipSettings.add(showDbRefTooltip);
1647 tooltipSettings.add(showNpTooltip);
1648 visualTab.add(tooltipSettings);
1650 wrap.setFont(LABEL_FONT);
1651 wrap.setHorizontalAlignment(SwingConstants.TRAILING);
1652 wrap.setHorizontalTextPosition(SwingConstants.LEADING);
1653 wrap.setText(MessageManager.getString("label.wrap_alignment"));
1654 rightAlign.setFont(LABEL_FONT);
1655 rightAlign.setForeground(Color.black);
1656 rightAlign.setHorizontalAlignment(SwingConstants.RIGHT);
1657 rightAlign.setHorizontalTextPosition(SwingConstants.LEFT);
1658 rightAlign.setText(MessageManager.getString("label.right_align_ids"));
1659 idItalics.setFont(LABEL_FONT_ITALIC);
1660 idItalics.setHorizontalAlignment(SwingConstants.RIGHT);
1661 idItalics.setHorizontalTextPosition(SwingConstants.LEADING);
1663 MessageManager.getString("label.sequence_name_italics"));
1664 openoverv.setFont(LABEL_FONT);
1665 openoverv.setActionCommand(
1666 MessageManager.getString("label.open_overview"));
1667 openoverv.setHorizontalAlignment(SwingConstants.RIGHT);
1668 openoverv.setHorizontalTextPosition(SwingConstants.LEFT);
1669 openoverv.setText(MessageManager.getString("label.open_overview"));
1670 JPanel jPanel2 = new JPanel();
1671 jPanel2.setBounds(new Rectangle(7, 17, 158, 310));
1672 jPanel2.setLayout(new GridLayout(14, 1));
1673 jPanel2.add(fullScreen);
1674 jPanel2.add(openoverv);
1675 jPanel2.add(seqLimit);
1676 jPanel2.add(rightAlign);
1677 jPanel2.add(fontLabel);
1678 jPanel2.add(showUnconserved);
1679 jPanel2.add(idItalics);
1680 jPanel2.add(smoothFont);
1681 jPanel2.add(scaleProteinToCdna);
1682 jPanel2.add(gapLabel);
1684 jPanel2.add(sortLabel);
1685 jPanel2.add(sortAnnLabel);
1686 jPanel2.add(startupCheckbox);
1687 visualTab.add(jPanel2);
1688 visualTab.add(startupFileTextfield);
1689 visualTab.add(sortby);
1690 visualTab.add(sortAnnBy);
1691 visualTab.add(sortAutocalc);
1692 visualTab.add(gapSymbolCB);
1693 visualTab.add(fontNameCB);
1694 visualTab.add(fontSizeCB);
1695 visualTab.add(fontStyleCB);
1700 * Load the saved Backups options EXCEPT "Enabled" and "Scheme"
1703 protected void loadLastSavedBackupsOptions()
1705 BackupFilesPresetEntry savedPreset = BackupFilesPresetEntry
1706 .getSavedBackupEntry();
1708 .setSelected(Cache.getDefault(BackupFiles.ENABLED, true));
1710 BackupFilesPresetEntry backupfilesCustomEntry = BackupFilesPresetEntry
1711 .createBackupFilesPresetEntry(Cache
1712 .getDefault(BackupFilesPresetEntry.CUSTOMCONFIG, null));
1713 if (backupfilesCustomEntry == null)
1715 backupfilesCustomEntry = BackupFilesPresetEntry.backupfilesPresetEntriesValues
1716 .get(BackupFilesPresetEntry.BACKUPFILESSCHEMEDEFAULT);
1718 BackupFilesPresetEntry.backupfilesPresetEntriesValues.put(
1719 BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM,
1720 backupfilesCustomEntry);
1722 setComboIntStringKey(backupfilesPresetsCombo,
1723 Cache.getDefault(BackupFiles.NS + "_PRESET",
1724 BackupFilesPresetEntry.BACKUPFILESSCHEMEDEFAULT));
1726 backupsSetOptions(savedPreset);
1728 backupsOptionsSetEnabled();
1729 updateBackupFilesExampleLabel();
1732 private boolean warnAboutSuffixReverseChange()
1734 BackupFilesPresetEntry bfpe = BackupFilesPresetEntry
1735 .getSavedBackupEntry();
1736 boolean savedSuffixReverse = bfpe.reverse;
1737 int savedSuffixDigits = bfpe.digits;
1738 String savedSuffixTemplate = bfpe.suffix;
1740 boolean nowSuffixReverse = suffixReverse.isSelected();
1741 int nowSuffixDigits = getSpinnerInt(suffixDigitsSpinner, 3);
1742 String nowSuffixTemplate = suffixTemplate.getText();
1743 return nowSuffixReverse != savedSuffixReverse
1744 && nowSuffixDigits == savedSuffixDigits
1745 && nowSuffixTemplate != null
1746 && nowSuffixTemplate.equals(savedSuffixTemplate);
1750 * Initialises the Backups tabbed panel.
1754 private JPanel initBackupsTab()
1756 JPanel backupsTab = new JPanel();
1757 backupsTab.setBorder(new TitledBorder(
1758 MessageManager.getString("label.backup_files")));
1759 backupsTab.setLayout(new GridBagLayout());
1761 GridBagConstraints gbc = new GridBagConstraints();
1764 gbc.anchor = GridBagConstraints.FIRST_LINE_START;
1765 gbc.fill = GridBagConstraints.NONE;
1767 initBackupsTabPresetsPanel();
1768 initBackupsTabSuffixPanel();
1769 initBackupsTabKeepFilesPanel();
1770 initBackupsTabFilenameExamplesPanel();
1772 enableBackupFiles.setFont(LABEL_FONT_BOLD);
1774 .setText(MessageManager.getString("label.enable_backupfiles"));
1775 enableBackupFiles.addActionListener(new ActionListener()
1778 public void actionPerformed(ActionEvent e)
1780 // enable other options only when the first is checked
1781 backupsOptionsSetEnabled();
1786 // enable checkbox 1 col
1790 gbc.gridy = 0; // row 0
1791 backupsTab.add(enableBackupFiles, gbc);
1793 // summary of scheme box (over two rows)
1797 gbc.anchor = GridBagConstraints.FIRST_LINE_END;
1798 gbc.fill = GridBagConstraints.BOTH;
1799 backupsTab.add(exampleFilesPanel, gbc);
1801 gbc.anchor = GridBagConstraints.FIRST_LINE_START;
1802 gbc.fill = GridBagConstraints.NONE;
1804 // fill empty space on right
1807 backupsTab.add(new JPanel(), gbc);
1812 gbc.gridy++; // row 1
1813 backupsTab.add(presetsPanel, gbc);
1815 // now using whole row
1820 gbc.gridy++; // row 2
1821 backupsTab.add(keepfilesPanel, gbc);
1823 // filename strategy box
1824 gbc.gridy++; // row 3
1825 backupsTab.add(suffixPanel, gbc);
1828 gbc.gridy++; // row 4
1830 backupsTab.add(new JPanel(), gbc);
1832 backupsOptionsSetEnabled();
1836 private JPanel initBackupsTabPresetsPanel()
1839 String title = MessageManager.getString("label.schemes");
1841 presetsPanel.setLayout(new GridBagLayout());
1843 GridBagConstraints gbc = new GridBagConstraints();
1846 gbc.anchor = GridBagConstraints.BASELINE_LEADING;
1847 gbc.fill = GridBagConstraints.NONE;
1855 presetsComboLabel = new JLabel(title + ":");
1856 presetsPanel.add(presetsComboLabel, gbc);
1858 List<Object> entries = Arrays
1859 .asList((Object[]) BackupFilesPresetEntry.backupfilesPresetEntries);
1860 List<String> tooltips = Arrays.asList(
1861 BackupFilesPresetEntry.backupfilesPresetEntryDescriptions);
1862 backupfilesPresetsCombo = JvSwingUtils.buildComboWithTooltips(entries,
1865 for (int i = 0; i < BackupFilesPresetEntry.backupfilesPresetEntries.length; i++)
1867 backupfilesPresetsCombo
1868 .addItem(BackupFilesPresetEntry.backupfilesPresetEntries[i]);
1872 backupfilesPresetsCombo.addActionListener(new ActionListener()
1875 public void actionPerformed(ActionEvent e)
1877 int key = getComboIntStringKey(backupfilesPresetsCombo);
1878 if (!customiseCheckbox.isSelected())
1880 backupfilesPresetsComboLastSelected = key;
1882 if (key == BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM)
1884 if (customiseCheckbox.isSelected())
1886 // got here by clicking on customiseCheckbox so don't change the values
1887 backupfilesCustomOptionsSetEnabled();
1891 backupsTabUpdatePresets();
1892 backupfilesCustomOptionsSetEnabled();
1897 customiseCheckbox.setSelected(false);
1898 backupsTabUpdatePresets();
1899 backupfilesCustomOptionsSetEnabled();
1904 // dropdown list of preset schemes
1906 presetsPanel.add(backupfilesPresetsCombo, gbc);
1908 revertButton.setText(MessageManager.getString("label.cancel_changes"));
1909 revertButton.setToolTipText(
1910 MessageManager.getString("label.cancel_changes_description"));
1911 revertButton.addActionListener(new ActionListener()
1914 public void actionPerformed(ActionEvent e)
1917 BackupFilesPresetEntry.backupfilesPresetEntriesValues.get(
1918 BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM));
1919 backupfilesCustomOptionsSetEnabled();
1923 revertButton.setFont(LABEL_FONT);
1925 customiseCheckbox.setFont(LABEL_FONT);
1926 customiseCheckbox.setText(MessageManager.getString("label.customise"));
1927 customiseCheckbox.addActionListener(new ActionListener()
1930 public void actionPerformed(ActionEvent e)
1932 int currently = getComboIntStringKey(backupfilesPresetsCombo);
1933 if (customiseCheckbox.isSelected())
1935 backupfilesPresetsComboLastSelected = currently;
1936 setComboIntStringKey(backupfilesPresetsCombo,
1937 BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM);
1941 setComboIntStringKey(backupfilesPresetsCombo,
1942 backupfilesPresetsComboLastSelected);
1945 backupfilesCustomOptionsSetEnabled();
1948 customiseCheckbox.setToolTipText(
1949 MessageManager.getString("label.customise_description"));
1951 // customise checkbox
1954 presetsPanel.add(customiseCheckbox, gbc);
1956 // "Cancel changes" button (aligned with combo box above)
1958 presetsPanel.add(revertButton, gbc);
1960 return presetsPanel;
1963 private JPanel initBackupsTabFilenameExamplesPanel()
1965 String title = MessageManager
1966 .getString("label.scheme_examples");
1967 TitledBorder tb = new TitledBorder(title);
1968 exampleFilesPanel.setBorder(tb);
1969 exampleFilesPanel.setLayout(new GridBagLayout());
1972 backupfilesExampleLabel.setEditable(false);
1973 backupfilesExampleLabel
1974 .setBackground(exampleFilesPanel.getBackground());
1976 updateBackupFilesExampleLabel();
1978 GridBagConstraints gbc = new GridBagConstraints();
1981 gbc.fill = GridBagConstraints.NONE;
1982 gbc.anchor = GridBagConstraints.FIRST_LINE_START;
1984 exampleFilesPanel.add(backupfilesExampleLabel, gbc);
1985 return exampleFilesPanel;
1988 private void backupsTabUpdatePresets()
1990 IntKeyStringValueEntry entry = (IntKeyStringValueEntry) backupfilesPresetsCombo
1993 String value = entry.v;
1995 if (BackupFilesPresetEntry.backupfilesPresetEntriesValues
1999 BackupFilesPresetEntry.backupfilesPresetEntriesValues
2005 "Preset '" + value + "' [key:" + key + "] not implemented");
2008 // Custom options will now be enabled when the customiseCheckbox is checked
2009 // (performed above)
2010 // backupfilesCustomOptionsSetEnabled();
2011 updateBackupFilesExampleLabel();
2014 protected int getComboIntStringKey(
2015 JComboBox<Object> backupfilesPresetsCombo2)
2017 IntKeyStringValueEntry e;
2020 e = (IntKeyStringValueEntry) backupfilesPresetsCombo2
2022 } catch (Exception ex)
2025 "Problem casting Combo entry to IntKeyStringValueEntry.");
2028 return e != null ? e.k : 0;
2031 protected void setComboIntStringKey(
2032 JComboBox<Object> backupfilesPresetsCombo2,
2035 for (int i = 0; i < backupfilesPresetsCombo2.getItemCount(); i++)
2037 IntKeyStringValueEntry e;
2040 e = (IntKeyStringValueEntry) backupfilesPresetsCombo2.getItemAt(i);
2041 } catch (Exception ex)
2044 "Problem casting Combo entry to IntKeyStringValueEntry. Skipping item. ");
2049 backupfilesPresetsCombo2.setSelectedIndex(i);
2053 // backupsTabUpdatePresets();
2056 private JPanel initBackupsTabSuffixPanel()
2058 suffixPanel.setBorder(new TitledBorder(
2059 MessageManager.getString("label.backup_filename_strategy")));
2060 suffixPanel.setLayout(new GridBagLayout());
2063 .setText(MessageManager.getString("label.append_to_filename"));
2064 suffixTemplateLabel.setHorizontalAlignment(SwingConstants.LEFT);
2065 suffixTemplateLabel.setFont(LABEL_FONT);
2067 final String tooltip = JvSwingUtils.wrapTooltip(true,
2068 MessageManager.getString("label.append_to_filename_tooltip"));
2069 suffixTemplate.setToolTipText(tooltip);
2070 suffixTemplate.addActionListener(new ActionListener()
2073 public void actionPerformed(ActionEvent e)
2075 updateBackupFilesExampleLabel();
2076 backupfilesCustomOptionsSetEnabled();
2077 backupfilesRevertButtonSetEnabled(true);
2081 suffixTemplate.addKeyListener(new KeyListener()
2084 public void keyReleased(KeyEvent e)
2086 updateBackupFilesExampleLabel();
2087 backupfilesCustomOptionsSetEnabled();
2088 backupfilesRevertButtonSetEnabled(true);
2092 public void keyPressed(KeyEvent e)
2096 // disable use of ':' or '/' or '\'
2098 public void keyTyped(KeyEvent e)
2100 char c = e.getKeyChar();
2101 if (c == ':' || c == '/' || c == '\\')
2103 // don't process ':' or '/' or '\'
2112 .setText(MessageManager.getString("label.index_digits"));
2113 suffixDigitsLabel.setHorizontalAlignment(SwingConstants.LEFT);
2114 suffixDigitsLabel.setFont(LABEL_FONT);
2115 ChangeListener c = new ChangeListener()
2118 public void stateChanged(ChangeEvent e)
2120 backupfilesRevertButtonSetEnabled(true);
2121 updateBackupFilesExampleLabel();
2125 setIntegerSpinner(suffixDigitsSpinner, BackupFilesPresetEntry.DIGITSMIN,
2126 BackupFilesPresetEntry.DIGITSMAX, 3, c);
2128 suffixReverse.setLabels(MessageManager.getString("label.reverse_roll"),
2129 MessageManager.getString("label.increment_index"));
2130 suffixReverse.addActionListener(new ActionListener()
2133 public void actionPerformed(ActionEvent e)
2135 boolean okay = true;
2136 if (warnAboutSuffixReverseChange())
2139 okay = confirmSuffixReverseChange();
2143 backupfilesRevertButtonSetEnabled(true);
2144 updateBackupFilesExampleLabel();
2148 boolean savedSuffixReverse = BackupFilesPresetEntry
2149 .getSavedBackupEntry().reverse;
2150 suffixReverse.setSelected(savedSuffixReverse);
2155 GridBagConstraints sgbc = new GridBagConstraints();
2157 // first row (template text box)
2158 sgbc.anchor = GridBagConstraints.WEST;
2162 sgbc.gridheight = 1;
2165 sgbc.fill = GridBagConstraints.NONE;
2166 suffixPanel.add(suffixTemplateLabel, sgbc);
2169 sgbc.fill = GridBagConstraints.HORIZONTAL;
2170 suffixPanel.add(suffixTemplate, sgbc);
2172 // second row (number of digits spinner)
2176 sgbc.fill = GridBagConstraints.NONE;
2177 suffixPanel.add(suffixDigitsLabel, sgbc);
2180 sgbc.fill = GridBagConstraints.HORIZONTAL;
2181 suffixPanel.add(suffixDigitsSpinner, sgbc);
2183 // third row (forward order radio selection)
2186 sgbc.gridwidth = GridBagConstraints.REMAINDER;
2187 sgbc.fill = GridBagConstraints.HORIZONTAL;
2188 suffixPanel.add(suffixReverse.getFalseButton(), sgbc);
2190 // fourth row (reverse order radio selection)
2192 suffixPanel.add(suffixReverse.getTrueButton(), sgbc);
2196 private boolean confirmSuffixReverseChange()
2198 boolean ret = false;
2199 String warningMessage = MessageManager
2200 .getString("label.warning_confirm_change_reverse");
2201 int confirm = JvOptionPane.showConfirmDialog(Desktop.desktop,
2203 MessageManager.getString("label.change_increment_decrement"),
2204 JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE);
2206 ret = (confirm == JvOptionPane.YES_OPTION);
2210 private JPanel initBackupsTabKeepFilesPanel()
2212 keepfilesPanel.setBorder(
2213 new TitledBorder(MessageManager.getString("label.keep_files")));
2214 keepfilesPanel.setLayout(new GridBagLayout());
2216 backupfilesKeepAll.setLabels(
2217 MessageManager.getString("label.keep_all_backup_files"),
2218 MessageManager.getString(
2219 "label.keep_only_this_number_of_backup_files"));
2220 backupfilesKeepAll.addTrueActionListener(new ActionListener()
2223 public void actionPerformed(ActionEvent e)
2225 backupfilesRevertButtonSetEnabled(true);
2226 updateBackupFilesExampleLabel();
2229 backupfilesKeepAll.addActionListener(new ActionListener()
2232 public void actionPerformed(ActionEvent e)
2234 backupfilesRevertButtonSetEnabled(true);
2235 keepRollMaxOptionsEnabled();
2236 updateBackupFilesExampleLabel();
2240 ChangeListener c = new ChangeListener()
2243 public void stateChanged(ChangeEvent e)
2245 backupfilesRevertButtonSetEnabled(true);
2246 updateBackupFilesExampleLabel();
2250 setIntegerSpinner(backupfilesRollMaxSpinner,
2251 BackupFilesPresetEntry.ROLLMAXMIN,
2252 BackupFilesPresetEntry.ROLLMAXMAX, 4, true, c);
2254 backupfilesConfirmDelete.setLabels(
2255 MessageManager.getString("label.always_ask"),
2256 MessageManager.getString("label.auto_delete"));
2257 backupfilesConfirmDelete.addActionListener(new ActionListener()
2260 public void actionPerformed(ActionEvent e)
2262 backupfilesRevertButtonSetEnabled(true);
2265 // update the enabled section
2266 keepRollMaxOptionsEnabled();
2268 GridBagConstraints kgbc = new GridBagConstraints();
2270 // first row (template text box)
2271 kgbc.anchor = GridBagConstraints.WEST;
2274 kgbc.gridwidth = GridBagConstraints.REMAINDER;
2275 kgbc.gridheight = 1;
2278 kgbc.fill = GridBagConstraints.HORIZONTAL;
2279 keepfilesPanel.add(backupfilesKeepAll.getTrueButton(), kgbc);
2285 kgbc.gridwidth = GridBagConstraints.RELATIVE;
2286 keepfilesPanel.add(backupfilesKeepAll.getFalseButton(), kgbc);
2289 kgbc.gridwidth = GridBagConstraints.REMAINDER;
2290 keepfilesPanel.add(backupfilesRollMaxSpinner, kgbc);
2292 // third row (indented)
2294 kgbc.insets = new Insets(0, 20, 0, 0);
2297 kgbc.gridwidth = GridBagConstraints.REMAINDER;
2298 kgbc.fill = GridBagConstraints.HORIZONTAL;
2301 JPanel jp = new JPanel();
2302 jp.setLayout(new FlowLayout());
2304 .setText(MessageManager
2305 .getString("label.autodelete_old_backup_files"));
2306 oldBackupFilesLabel.setFont(LABEL_FONT);
2307 oldBackupFilesLabel.setHorizontalAlignment(SwingConstants.LEFT);
2308 jp.add(oldBackupFilesLabel);
2309 jp.add(backupfilesConfirmDelete.getTrueButton());
2310 jp.add(backupfilesConfirmDelete.getFalseButton());
2311 keepfilesPanel.add(jp, kgbc);
2313 return keepfilesPanel;
2316 protected void updateBackupFilesExampleLabel()
2318 int exampleindex = 12;
2319 String base = MessageManager.getString("label.filename") + ".fa";
2320 if (base == null || base.length() == 0)
2322 base = "file_name.fa";
2325 boolean reverse = suffixReverse.isSelected();
2326 boolean keepAll = backupfilesKeepAll.isSelected();
2328 String suffix = suffixTemplate.getText();
2331 backupfilesExampleLabel.setFont(LABEL_FONT_ITALIC);
2332 if (suffix == null || suffix.length() == 0)
2334 backupfilesExampleLabel
2335 .setText(MessageManager.getString("label.no_backup_files"));
2336 backupfilesExampleLabel.setFont(LABEL_FONT_BOLD);
2340 rollMax = getSpinnerInt(backupfilesRollMaxSpinner, 4);
2341 rollMax = rollMax < 1 ? 1 : rollMax;
2343 if (suffix.indexOf(BackupFiles.NUM_PLACEHOLDER) == -1)
2348 digits = getSpinnerInt(suffixDigitsSpinner, 3);
2349 digits = digits < 1 ? 1 : digits;
2351 int lowersurround = 2;
2352 int uppersurround = 0;
2353 StringBuilder exampleSB = new StringBuilder();
2354 boolean firstLine = true;
2360 int max = keepAll ? exampleindex : rollMax;
2361 for (int index = min; index <= max; index++)
2363 if (index == min + lowersurround && index < max - uppersurround - 1)
2365 exampleSB.append("\n...");
2368 else if (index > min + lowersurround && index < max - uppersurround)
2380 exampleSB.append("\n");
2383 exampleSB.append(BackupFilenameParts.getBackupFilename(index,
2384 base, suffix, digits));
2387 // no extra text needed
2389 else if (index == min)
2391 String newest = MessageManager.getString("label.braced_newest");
2392 if (newest != null && newest.length() > 0)
2394 exampleSB.append(" " + newest);
2397 else if (index == max)
2399 String oldest = MessageManager.getString("label.braced_oldest");
2400 if (oldest != null && oldest.length() > 0)
2402 exampleSB.append(" " + oldest);
2411 int min = (keepAll || exampleindex - rollMax < 0) ? 1
2412 : exampleindex - rollMax + 1;
2413 int max = exampleindex;
2415 for (int index = min; index <= max; index++)
2418 if (index == min + lowersurround && index < max - uppersurround - 1)
2420 exampleSB.append("\n...");
2423 else if (index > min + lowersurround && index < max - uppersurround)
2435 exampleSB.append("\n");
2438 exampleSB.append(BackupFilenameParts.getBackupFilename(index,
2439 base, suffix, digits));
2442 // no extra text needed
2444 else if (index == min)
2446 String oldest = MessageManager.getString("label.braced_oldest");
2447 if (oldest != null && oldest.length() > 0)
2449 exampleSB.append(" " + oldest);
2452 else if (index == max)
2454 String newest = MessageManager.getString("label.braced_newest");
2455 if (newest != null && newest.length() > 0)
2457 exampleSB.append(" " + newest);
2465 // add some extra empty lines to pad out the example files box. ugh, please tell
2466 // me how to do this better
2467 int remainingLines = lowersurround + uppersurround + 1 - lineNumber;
2468 if (remainingLines > 0)
2470 for (int i = 0; i < remainingLines; i++)
2472 exampleSB.append("\n ");
2477 backupfilesExampleLabel.setText(exampleSB.toString());
2480 protected void setIntegerSpinner(JSpinner s, int min, int max, int def,
2481 boolean useExistingVal, ChangeListener c)
2488 i = Integer.parseInt((String) s.getValue());
2489 } catch (Exception e)
2492 "Exception casting the initial value of s.getValue()");
2496 setIntegerSpinner(s, min, max, i, c);
2499 protected void setIntegerSpinner(JSpinner s, int min, int max, int def,
2502 // integer spinner for number of digits
2507 SpinnerModel sModel = new SpinnerNumberModel(def, min, max, 1);
2510 s.addChangeListener(c);
2514 protected static int getSpinnerInt(JSpinner s, int def)
2520 i = (Integer) s.getValue();
2521 } catch (Exception e)
2523 Cache.log.error("Failed casting (Integer) JSpinner s.getValue()");
2528 private void keepRollMaxOptionsEnabled()
2530 boolean enabled = backupfilesKeepAll.isEnabled()
2531 && !backupfilesKeepAll.isSelected();
2532 oldBackupFilesLabel.setEnabled(enabled);
2533 backupfilesRollMaxSpinner.setEnabled(enabled);
2534 backupfilesConfirmDelete.setEnabled(enabled);
2537 private void backupfilesKeepAllSetEnabled(boolean tryEnabled)
2539 boolean enabled = tryEnabled && enableBackupFiles.isSelected()
2540 && customiseCheckbox.isSelected()
2541 && suffixTemplate.getText()
2542 .indexOf(BackupFiles.NUM_PLACEHOLDER) > -1;
2543 keepfilesPanel.setEnabled(enabled);
2544 backupfilesKeepAll.setEnabled(enabled);
2545 oldBackupFilesLabel.setEnabled(enabled);
2546 keepRollMaxOptionsEnabled();
2549 private void backupfilesSuffixTemplateDigitsSetEnabled()
2551 boolean enabled = suffixTemplate.isEnabled() && suffixTemplate.getText()
2552 .indexOf(BackupFiles.NUM_PLACEHOLDER) > -1;
2553 suffixDigitsLabel.setEnabled(enabled);
2554 suffixDigitsSpinner.setEnabled(enabled);
2555 suffixReverse.setEnabled(enabled);
2558 private void backupfilesSuffixTemplateSetEnabled(boolean tryEnabled)
2560 boolean enabled = tryEnabled && enableBackupFiles.isSelected()
2561 && customiseCheckbox.isSelected();
2562 suffixPanel.setEnabled(enabled);
2563 suffixTemplateLabel.setEnabled(enabled);
2564 suffixTemplate.setEnabled(enabled);
2565 backupfilesSuffixTemplateDigitsSetEnabled();
2568 private void backupfilesRevertButtonSetEnabled(boolean tryEnabled)
2570 boolean enabled = tryEnabled && enableBackupFiles.isSelected()
2571 && customiseCheckbox.isSelected() && backupfilesCustomChanged();
2572 revertButton.setEnabled(enabled);
2575 private boolean backupfilesCustomChanged()
2577 BackupFilesPresetEntry custom = BackupFilesPresetEntry.backupfilesPresetEntriesValues
2578 .get(BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM);
2579 BackupFilesPresetEntry current = getBackupfilesCurrentEntry();
2580 return !custom.equals(current);
2583 protected BackupFilesPresetEntry getBackupfilesCurrentEntry()
2585 String suffix = suffixTemplate.getText();
2586 int digits = getSpinnerInt(suffixDigitsSpinner, 3);
2587 boolean reverse = suffixReverse.isSelected();
2588 boolean keepAll = backupfilesKeepAll.isSelected();
2589 int rollMax = getSpinnerInt(backupfilesRollMaxSpinner, 3);
2590 boolean confirmDelete = backupfilesConfirmDelete.isSelected();
2592 BackupFilesPresetEntry bfpe = new BackupFilesPresetEntry(suffix, digits,
2593 reverse, keepAll, rollMax, confirmDelete);
2598 protected void backupfilesCustomOptionsSetEnabled()
2600 boolean enabled = customiseCheckbox.isSelected();
2602 backupfilesRevertButtonSetEnabled(enabled);
2603 backupfilesSuffixTemplateSetEnabled(enabled);
2604 backupfilesKeepAllSetEnabled(enabled);
2607 private void backupfilesSummarySetEnabled()
2609 boolean enabled = enableBackupFiles.isSelected();
2610 backupfilesExampleLabel.setEnabled(enabled);
2611 exampleFilesPanel.setEnabled(enabled);
2614 private void backupfilesPresetsSetEnabled()
2616 boolean enabled = enableBackupFiles.isSelected();
2617 presetsPanel.setEnabled(enabled);
2618 presetsComboLabel.setEnabled(enabled);
2619 backupfilesPresetsCombo.setEnabled(enabled);
2620 customiseCheckbox.setEnabled(enabled);
2621 revertButton.setEnabled(enabled);
2624 protected void backupsOptionsSetEnabled()
2626 backupfilesPresetsSetEnabled();
2627 backupfilesSummarySetEnabled();
2628 backupfilesCustomOptionsSetEnabled();
2631 protected void backupsSetOptions(String suffix, int digits,
2632 boolean reverse, boolean keepAll, int rollMax,
2633 boolean confirmDelete)
2635 suffixTemplate.setText(suffix);
2636 suffixDigitsSpinner.setValue(digits);
2637 suffixReverse.setSelected(reverse);
2638 backupfilesKeepAll.setSelected(keepAll);
2639 backupfilesRollMaxSpinner.setValue(rollMax);
2640 backupfilesConfirmDelete.setSelected(confirmDelete);
2643 protected void backupsSetOptions(BackupFilesPresetEntry p)
2645 backupsSetOptions(p.suffix, p.digits, p.reverse, p.keepAll, p.rollMax,
2649 protected void autoIdWidth_actionPerformed()
2651 // TODO Auto-generated method stub
2655 protected void userIdWidth_actionPerformed()
2657 // TODO Auto-generated method stub
2661 protected void maxColour_actionPerformed(JPanel panel)
2665 protected void minColour_actionPerformed(JPanel panel)
2669 protected void gapColour_actionPerformed(JPanel panel)
2673 protected void hiddenColour_actionPerformed(JPanel panel)
2677 protected void showunconserved_actionPerformed(ActionEvent e)
2679 // TODO Auto-generated method stub
2683 protected void useLegacyGaps_actionPerformed(ActionEvent e)
2687 protected void resetOvDefaults_actionPerformed(ActionEvent e)
2697 public void ok_actionPerformed(ActionEvent e)
2707 public void cancel_actionPerformed(ActionEvent e)
2717 public void annotations_actionPerformed(ActionEvent e)
2724 public void startupFileTextfield_mouseClicked()
2728 public void newLink_actionPerformed(ActionEvent e)
2733 public void editLink_actionPerformed(ActionEvent e)
2738 public void deleteLink_actionPerformed(ActionEvent e)
2743 public void defaultBrowser_mouseClicked(MouseEvent e)
2748 public void linkURLList_keyTyped(KeyEvent e)
2753 public void useProxy_actionPerformed()
2755 boolean enabled = useProxy.isSelected();
2756 portLabel.setEnabled(enabled);
2757 serverLabel.setEnabled(enabled);
2758 proxyServerTB.setEnabled(enabled);
2759 proxyPortTB.setEnabled(enabled);
2763 * Customer renderer for JTable: supports column of radio buttons
2765 public class RadioButtonRenderer extends JRadioButton
2766 implements TableCellRenderer
2768 public RadioButtonRenderer()
2770 setHorizontalAlignment(CENTER);
2771 setToolTipText(MessageManager.getString("label.urltooltip"));
2775 public Component getTableCellRendererComponent(JTable table,
2776 Object value, boolean isSelected, boolean hasFocus, int row,
2779 setSelected((boolean) value);
2781 // set colours to match rest of table
2784 setBackground(table.getSelectionBackground());
2785 setForeground(table.getSelectionForeground());
2789 setBackground(table.getBackground());
2790 setForeground(table.getForeground());
2797 * Customer cell editor for JTable: supports column of radio buttons in
2798 * conjunction with renderer
2800 public class RadioButtonEditor extends AbstractCellEditor
2801 implements TableCellEditor
2803 private JRadioButton button = new JRadioButton();
2805 public RadioButtonEditor()
2807 button.setHorizontalAlignment(SwingConstants.CENTER);
2808 this.button.addActionListener(new ActionListener()
2811 public void actionPerformed(ActionEvent e)
2813 fireEditingStopped();
2819 public Component getTableCellEditorComponent(JTable table, Object value,
2820 boolean isSelected, int row, int column)
2822 button.setSelected((boolean) value);
2827 public Object getCellEditorValue()
2829 return button.isSelected();