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 versioncheck.setVisible(false);
634 // Add padding so the panel doesn't look ridiculous
635 JPanel spacePanel = new JPanel();
636 connectTab.add(spacePanel,
637 new GridBagConstraints(0, 4, 1, 1, 1.0, 1.0,
638 GridBagConstraints.WEST, GridBagConstraints.BOTH,
639 new Insets(0, 0, 0, 5), 70, 1));
645 * Initialises the Links tabbed panel.
649 private JPanel initLinksTab()
651 JPanel linkTab = new JPanel();
652 linkTab.setLayout(new GridBagLayout());
654 // Set up table for Url links
655 linkUrlTable.getTableHeader().setReorderingAllowed(false);
656 linkUrlTable.setFillsViewportHeight(true);
657 linkUrlTable.setAutoResizeMode(JTable.AUTO_RESIZE_ALL_COLUMNS);
658 linkUrlTable.setAutoCreateRowSorter(true);
659 linkUrlTable.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
661 // adjust row height so radio buttons actually fit
662 // don't do this in the renderer, it causes the awt thread to activate
664 JRadioButton temp = new JRadioButton();
665 linkUrlTable.setRowHeight(temp.getMinimumSize().height);
667 // Table in scrollpane so that the table is given a scrollbar
668 JScrollPane linkScrollPane = new JScrollPane(linkUrlTable);
669 linkScrollPane.setBorder(null);
671 // Panel for links functionality
672 JPanel linkPanel = new JPanel(new GridBagLayout());
673 linkPanel.setBorder(new TitledBorder(
674 MessageManager.getString("label.url_linkfrom_sequence_id")));
676 // Put the Url links panel together
678 // Buttons go at top right, resizing only resizes the blank space vertically
679 JPanel buttonPanel = initLinkTabUrlButtons();
680 GridBagConstraints linkConstraints1 = new GridBagConstraints();
681 linkConstraints1.insets = new Insets(0, 0, 5, 0);
682 linkConstraints1.gridx = 0;
683 linkConstraints1.gridy = 0;
684 linkConstraints1.weightx = 1.0;
685 linkConstraints1.fill = GridBagConstraints.HORIZONTAL;
686 linkTab.add(buttonPanel, linkConstraints1);
688 // Links table goes at top left, resizing resizes the table
689 GridBagConstraints linkConstraints2 = new GridBagConstraints();
690 linkConstraints2.insets = new Insets(0, 0, 5, 5);
691 linkConstraints2.gridx = 0;
692 linkConstraints2.gridy = 1;
693 linkConstraints2.weightx = 1.0;
694 linkConstraints2.weighty = 1.0;
695 linkConstraints2.fill = GridBagConstraints.BOTH;
696 linkTab.add(linkScrollPane, linkConstraints2);
698 // Filter box and buttons goes at bottom left, resizing resizes the text box
699 JPanel filterPanel = initLinkTabFilterPanel();
700 GridBagConstraints linkConstraints3 = new GridBagConstraints();
701 linkConstraints3.insets = new Insets(0, 0, 0, 5);
702 linkConstraints3.gridx = 0;
703 linkConstraints3.gridy = 2;
704 linkConstraints3.weightx = 1.0;
705 linkConstraints3.fill = GridBagConstraints.HORIZONTAL;
706 linkTab.add(filterPanel, linkConstraints3);
711 private JPanel initLinkTabFilterPanel()
713 // Filter textbox and reset button
714 JLabel filterLabel = new JLabel(
715 MessageManager.getString("label.filter"));
716 filterLabel.setFont(LABEL_FONT);
717 filterLabel.setHorizontalAlignment(SwingConstants.RIGHT);
718 filterLabel.setHorizontalTextPosition(SwingConstants.LEADING);
720 filterTB.setFont(LABEL_FONT);
721 filterTB.setText("");
723 doReset.setText(MessageManager.getString("action.showall"));
724 userOnly.setText(MessageManager.getString("action.customfilter"));
726 // Panel for filter functionality
727 JPanel filterPanel = new JPanel(new GridBagLayout());
728 filterPanel.setBorder(new TitledBorder("Filter"));
729 GridBagConstraints gbc = new GridBagConstraints();
732 gbc.fill = GridBagConstraints.NONE;
733 gbc.anchor = GridBagConstraints.WEST;
735 filterPanel.add(filterLabel, gbc);
737 GridBagConstraints gbc1 = new GridBagConstraints();
740 gbc1.fill = GridBagConstraints.HORIZONTAL;
741 gbc1.anchor = GridBagConstraints.WEST;
743 filterPanel.add(filterTB, gbc1);
745 GridBagConstraints gbc2 = new GridBagConstraints();
747 gbc2.fill = GridBagConstraints.NONE;
748 gbc2.anchor = GridBagConstraints.WEST;
749 filterPanel.add(doReset, gbc2);
751 GridBagConstraints gbc3 = new GridBagConstraints();
753 gbc3.fill = GridBagConstraints.NONE;
754 gbc3.anchor = GridBagConstraints.WEST;
755 filterPanel.add(userOnly, gbc3);
760 private JPanel initLinkTabUrlButtons()
762 // Buttons for new / edit / delete Url links
763 JButton newLink = new JButton();
764 newLink.setText(MessageManager.getString("action.new"));
766 editLink.setText(MessageManager.getString("action.edit"));
768 deleteLink.setText(MessageManager.getString("action.delete"));
770 // no current selection, so initially disable delete/edit buttons
771 editLink.setEnabled(false);
772 deleteLink.setEnabled(false);
774 newLink.addActionListener(new java.awt.event.ActionListener()
777 public void actionPerformed(ActionEvent e)
779 newLink_actionPerformed(e);
783 editLink.setText(MessageManager.getString("action.edit"));
784 editLink.addActionListener(new java.awt.event.ActionListener()
787 public void actionPerformed(ActionEvent e)
789 editLink_actionPerformed(e);
793 deleteLink.setText(MessageManager.getString("action.delete"));
794 deleteLink.addActionListener(new java.awt.event.ActionListener()
797 public void actionPerformed(ActionEvent e)
799 deleteLink_actionPerformed(e);
803 JPanel buttonPanel = new JPanel(new GridBagLayout());
804 buttonPanel.setBorder(new TitledBorder("Edit links"));
805 GridBagConstraints gbc = new GridBagConstraints();
808 gbc.fill = GridBagConstraints.NONE;
809 buttonPanel.add(newLink, gbc);
811 GridBagConstraints gbc1 = new GridBagConstraints();
814 gbc1.fill = GridBagConstraints.NONE;
815 buttonPanel.add(editLink, gbc1);
817 GridBagConstraints gbc2 = new GridBagConstraints();
820 gbc2.fill = GridBagConstraints.NONE;
821 buttonPanel.add(deleteLink, gbc2);
823 GridBagConstraints gbc3 = new GridBagConstraints();
826 gbc3.fill = GridBagConstraints.HORIZONTAL;
828 JPanel spacePanel = new JPanel();
829 spacePanel.setBorder(null);
830 buttonPanel.add(spacePanel, gbc3);
836 * Initialises the proxy server panel in the Connections tab
838 * @return the proxy server panel
840 private JPanel initConnTabProxyPanel()
842 // Label for server text box
843 serverLabel.setText(MessageManager.getString("label.address"));
844 serverLabel.setHorizontalAlignment(SwingConstants.RIGHT);
845 serverLabel.setFont(LABEL_FONT);
847 // Proxy server and port text boxes
848 proxyServerTB.setFont(LABEL_FONT);
849 proxyPortTB.setFont(LABEL_FONT);
851 // Label for Port text box
852 portLabel.setFont(LABEL_FONT);
853 portLabel.setHorizontalAlignment(SwingConstants.RIGHT);
854 portLabel.setText(MessageManager.getString("label.port"));
856 // Use proxy server checkbox
857 useProxy.setFont(LABEL_FONT);
858 useProxy.setHorizontalAlignment(SwingConstants.RIGHT);
859 useProxy.setHorizontalTextPosition(SwingConstants.LEADING);
860 useProxy.setText(MessageManager.getString("label.use_proxy_server"));
861 useProxy.addActionListener(new ActionListener()
864 public void actionPerformed(ActionEvent e)
866 useProxy_actionPerformed();
870 // Make proxy server panel
871 JPanel proxyPanel = new JPanel();
872 TitledBorder titledBorder1 = new TitledBorder(
873 MessageManager.getString("label.proxy_server"));
874 proxyPanel.setBorder(titledBorder1);
875 proxyPanel.setLayout(new GridBagLayout());
876 proxyPanel.add(serverLabel,
877 new GridBagConstraints(0, 1, 1, 1, 0.0, 0.0,
878 GridBagConstraints.WEST, GridBagConstraints.NONE,
879 new Insets(0, 2, 2, 0), 5, 0));
880 proxyPanel.add(portLabel,
881 new GridBagConstraints(2, 1, 1, 1, 0.0, 0.0,
882 GridBagConstraints.WEST, GridBagConstraints.NONE,
883 new Insets(0, 0, 2, 0), 11, 0));
884 proxyPanel.add(useProxy,
885 new GridBagConstraints(0, 0, 2, 1, 0.0, 0.0,
886 GridBagConstraints.WEST, GridBagConstraints.NONE,
887 new Insets(0, 2, 5, 185), 2, -4));
888 proxyPanel.add(proxyPortTB,
889 new GridBagConstraints(3, 1, 1, 1, 1.0, 0.0,
890 GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
891 new Insets(0, 2, 2, 2), 54, 1));
892 proxyPanel.add(proxyServerTB,
893 new GridBagConstraints(1, 1, 1, 1, 1.0, 0.0,
894 GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
895 new Insets(0, 2, 2, 0), 263, 1));
901 * Initialises the checkboxes in the Connections tab
903 private void initConnTabCheckboxes()
905 // Usage stats checkbox label
907 MessageManager.getString("label.send_usage_statistics"));
908 usagestats.setFont(LABEL_FONT);
909 usagestats.setHorizontalAlignment(SwingConstants.RIGHT);
910 usagestats.setHorizontalTextPosition(SwingConstants.LEADING);
912 // Questionnaire checkbox label
913 questionnaire.setText(
914 MessageManager.getString("label.check_for_questionnaires"));
915 questionnaire.setFont(LABEL_FONT);
916 questionnaire.setHorizontalAlignment(SwingConstants.RIGHT);
917 questionnaire.setHorizontalTextPosition(SwingConstants.LEADING);
919 // Check for latest version checkbox label
920 versioncheck.setText(
921 MessageManager.getString("label.check_for_latest_version"));
922 versioncheck.setFont(LABEL_FONT);
923 versioncheck.setHorizontalAlignment(SwingConstants.RIGHT);
924 versioncheck.setHorizontalTextPosition(SwingConstants.LEADING);
928 * Initialises the parent panel which contains the tabbed sections.
932 private JPanel initOkCancelPanel()
934 JButton ok = new JButton();
935 ok.setText(MessageManager.getString("action.ok"));
936 ok.addActionListener(new ActionListener()
939 public void actionPerformed(ActionEvent e)
941 ok_actionPerformed(e);
944 JButton cancel = new JButton();
945 cancel.setText(MessageManager.getString("action.cancel"));
946 cancel.addActionListener(new ActionListener()
949 public void actionPerformed(ActionEvent e)
951 cancel_actionPerformed(e);
954 JPanel okCancelPanel = new JPanel();
955 okCancelPanel.add(ok);
956 okCancelPanel.add(cancel);
957 return okCancelPanel;
961 * Initialises the Colours tabbed panel.
965 private JPanel initColoursTab()
967 JPanel coloursTab = new JPanel();
968 coloursTab.setBorder(new TitledBorder(
969 MessageManager.getString("action.open_new_alignment")));
970 coloursTab.setLayout(new FlowLayout());
971 JLabel mincolourLabel = new JLabel();
972 mincolourLabel.setFont(LABEL_FONT);
973 mincolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
974 mincolourLabel.setText(MessageManager.getString("label.min_colour"));
975 minColour.setFont(LABEL_FONT);
976 minColour.setBorder(BorderFactory.createEtchedBorder());
977 minColour.setPreferredSize(new Dimension(40, 20));
978 minColour.addMouseListener(new MouseAdapter()
981 public void mousePressed(MouseEvent e)
983 minColour_actionPerformed(minColour);
986 JLabel maxcolourLabel = new JLabel();
987 maxcolourLabel.setFont(LABEL_FONT);
988 maxcolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
989 maxcolourLabel.setText(MessageManager.getString("label.max_colour"));
990 maxColour.setFont(LABEL_FONT);
991 maxColour.setBorder(BorderFactory.createEtchedBorder());
992 maxColour.setPreferredSize(new Dimension(40, 20));
993 maxColour.addMouseListener(new MouseAdapter()
996 public void mousePressed(MouseEvent e)
998 maxColour_actionPerformed(maxColour);
1002 protColour.setFont(LABEL_FONT);
1003 protColour.setBounds(new Rectangle(172, 225, 155, 21));
1004 JLabel protColourLabel = new JLabel();
1005 protColourLabel.setFont(LABEL_FONT);
1006 protColourLabel.setHorizontalAlignment(SwingConstants.LEFT);
1007 protColourLabel.setText(
1008 MessageManager.getString("label.prot_alignment_colour") + " ");
1009 JvSwingUtils.addtoLayout(coloursTab,
1011 .getString("label.default_colour_scheme_for_alignment"),
1012 protColourLabel, protColour);
1014 nucColour.setFont(LABEL_FONT);
1015 nucColour.setBounds(new Rectangle(172, 240, 155, 21));
1016 JLabel nucColourLabel = new JLabel();
1017 nucColourLabel.setFont(LABEL_FONT);
1018 nucColourLabel.setHorizontalAlignment(SwingConstants.LEFT);
1019 nucColourLabel.setText(
1020 MessageManager.getString("label.nuc_alignment_colour") + " ");
1021 JvSwingUtils.addtoLayout(coloursTab,
1023 .getString("label.default_colour_scheme_for_alignment"),
1024 nucColourLabel, nucColour);
1026 JPanel annotationShding = new JPanel();
1027 annotationShding.setBorder(new TitledBorder(
1028 MessageManager.getString("label.annotation_shading_default")));
1029 annotationShding.setLayout(new GridLayout(1, 2));
1030 JvSwingUtils.addtoLayout(annotationShding,
1031 MessageManager.getString(
1032 "label.default_minimum_colour_annotation_shading"),
1033 mincolourLabel, minColour);
1034 JvSwingUtils.addtoLayout(annotationShding,
1035 MessageManager.getString(
1036 "label.default_maximum_colour_annotation_shading"),
1037 maxcolourLabel, maxColour);
1038 coloursTab.add(annotationShding); // , FlowLayout.LEFT);
1043 * Initialises the Overview tabbed panel.
1047 private JPanel initOverviewTab()
1049 JPanel overviewPanel = new JPanel();
1050 overviewPanel.setBorder(new TitledBorder(
1051 MessageManager.getString("label.overview_settings")));
1053 gapColour.setFont(LABEL_FONT);
1054 // fixing the border colours stops apparent colour bleed from the panel
1055 gapColour.setBorder(
1056 BorderFactory.createEtchedBorder(Color.white, Color.lightGray));
1057 gapColour.setPreferredSize(new Dimension(40, 20));
1058 gapColour.addMouseListener(new MouseAdapter()
1061 public void mousePressed(MouseEvent e)
1063 gapColour_actionPerformed(gapColour);
1067 hiddenColour.setFont(LABEL_FONT);
1068 // fixing the border colours stops apparent colour bleed from the panel
1069 hiddenColour.setBorder(
1070 BorderFactory.createEtchedBorder(Color.white, Color.lightGray));
1071 hiddenColour.setPreferredSize(new Dimension(40, 20));
1072 hiddenColour.addMouseListener(new MouseAdapter()
1075 public void mousePressed(MouseEvent e)
1077 hiddenColour_actionPerformed(hiddenColour);
1081 useLegacyGap = new JCheckBox(
1082 MessageManager.getString("label.ov_legacy_gap"));
1083 useLegacyGap.setFont(LABEL_FONT);
1084 useLegacyGap.setHorizontalAlignment(SwingConstants.LEFT);
1085 useLegacyGap.setVerticalTextPosition(SwingConstants.TOP);
1086 gapLabel = new JLabel(MessageManager.getString("label.gap_colour"));
1087 gapLabel.setFont(LABEL_FONT);
1088 gapLabel.setHorizontalAlignment(SwingConstants.LEFT);
1089 gapLabel.setVerticalTextPosition(SwingConstants.TOP);
1090 showHiddenAtStart = new JCheckBox(
1091 MessageManager.getString("label.ov_show_hide_default"));
1092 showHiddenAtStart.setFont(LABEL_FONT);
1093 showHiddenAtStart.setHorizontalAlignment(SwingConstants.LEFT);
1094 showHiddenAtStart.setVerticalTextPosition(SwingConstants.TOP);
1095 JLabel hiddenLabel = new JLabel(
1096 MessageManager.getString("label.hidden_colour"));
1097 hiddenLabel.setFont(LABEL_FONT);
1098 hiddenLabel.setHorizontalAlignment(SwingConstants.LEFT);
1099 hiddenLabel.setVerticalTextPosition(SwingConstants.TOP);
1101 useLegacyGap.addActionListener(new ActionListener()
1104 public void actionPerformed(ActionEvent e)
1106 useLegacyGaps_actionPerformed(e);
1110 overviewPanel.setLayout(new GridBagLayout());
1111 GridBagConstraints c1 = new GridBagConstraints();
1113 c1.fill = GridBagConstraints.HORIZONTAL;
1118 c1.anchor = GridBagConstraints.FIRST_LINE_START;
1119 overviewPanel.add(useLegacyGap, c1);
1121 GridBagConstraints c2 = new GridBagConstraints();
1122 c2.fill = GridBagConstraints.HORIZONTAL;
1125 c2.insets = new Insets(0, 15, 0, 10);
1126 overviewPanel.add(gapLabel, c2);
1128 GridBagConstraints c3 = new GridBagConstraints();
1129 c3.fill = GridBagConstraints.HORIZONTAL;
1132 c3.insets = new Insets(0, 0, 0, 15);
1133 overviewPanel.add(gapColour, c3);
1135 GridBagConstraints c4 = new GridBagConstraints();
1136 c4.fill = GridBagConstraints.HORIZONTAL;
1140 overviewPanel.add(showHiddenAtStart, c4);
1142 GridBagConstraints c5 = new GridBagConstraints();
1143 c5.fill = GridBagConstraints.HORIZONTAL;
1146 c5.insets = new Insets(0, 15, 0, 10);
1147 overviewPanel.add(hiddenLabel, c5);
1149 GridBagConstraints c6 = new GridBagConstraints();
1150 c6.fill = GridBagConstraints.HORIZONTAL;
1153 c6.insets = new Insets(0, 0, 0, 15);
1154 overviewPanel.add(hiddenColour, c6);
1156 JButton resetButton = new JButton(
1157 MessageManager.getString("label.reset_to_defaults"));
1159 resetButton.addActionListener(new ActionListener()
1162 public void actionPerformed(ActionEvent e)
1164 resetOvDefaults_actionPerformed(e);
1168 GridBagConstraints c7 = new GridBagConstraints();
1169 c7.fill = GridBagConstraints.NONE;
1172 c7.insets = new Insets(10, 0, 0, 0);
1173 c7.anchor = GridBagConstraints.WEST;
1174 overviewPanel.add(resetButton, c7);
1176 // Add padding so the panel doesn't look ridiculous
1177 JPanel spacePanel = new JPanel();
1178 overviewPanel.add(spacePanel,
1179 new GridBagConstraints(0, 3, 1, 1, 1.0, 1.0,
1180 GridBagConstraints.WEST, GridBagConstraints.BOTH,
1181 new Insets(0, 0, 0, 5), 0, 0));
1183 return overviewPanel;
1187 * Initialises the Structure tabbed panel.
1191 private JPanel initStructureTab()
1193 structureTab = new JPanel();
1195 structureTab.setBorder(new TitledBorder(
1196 MessageManager.getString("label.structure_options")));
1197 structureTab.setLayout(null);
1198 final int width = 400;
1199 final int height = 22;
1200 final int lineSpacing = 25;
1203 structFromPdb.setFont(LABEL_FONT);
1205 .setText(MessageManager.getString("label.struct_from_pdb"));
1206 structFromPdb.setBounds(new Rectangle(5, ypos, width, height));
1207 structFromPdb.addActionListener(new ActionListener()
1210 public void actionPerformed(ActionEvent e)
1212 boolean selected = structFromPdb.isSelected();
1213 // enable other options only when the first is checked
1214 useRnaView.setEnabled(selected);
1215 addSecondaryStructure.setEnabled(selected);
1216 addTempFactor.setEnabled(selected);
1219 structureTab.add(structFromPdb);
1221 // indent checkboxes that are conditional on the first one
1222 ypos += lineSpacing;
1223 useRnaView.setFont(LABEL_FONT);
1224 useRnaView.setText(MessageManager.getString("label.use_rnaview"));
1225 useRnaView.setBounds(new Rectangle(25, ypos, width, height));
1226 structureTab.add(useRnaView);
1228 ypos += lineSpacing;
1229 addSecondaryStructure.setFont(LABEL_FONT);
1230 addSecondaryStructure
1231 .setText(MessageManager.getString("label.autoadd_secstr"));
1232 addSecondaryStructure.setBounds(new Rectangle(25, ypos, width, height));
1233 structureTab.add(addSecondaryStructure);
1235 ypos += lineSpacing;
1236 addTempFactor.setFont(LABEL_FONT);
1237 addTempFactor.setText(MessageManager.getString("label.autoadd_temp"));
1238 addTempFactor.setBounds(new Rectangle(25, ypos, width, height));
1239 structureTab.add(addTempFactor);
1241 ypos += lineSpacing;
1242 JLabel viewerLabel = new JLabel();
1243 viewerLabel.setFont(LABEL_FONT);
1244 viewerLabel.setHorizontalAlignment(SwingConstants.LEFT);
1245 viewerLabel.setText(MessageManager.getString("label.structure_viewer"));
1246 viewerLabel.setBounds(new Rectangle(10, ypos, 200, height));
1247 structureTab.add(viewerLabel);
1249 structViewer.setFont(LABEL_FONT);
1250 structViewer.setBounds(new Rectangle(160, ypos, 120, height));
1251 structViewer.addItem(ViewerType.JMOL.name());
1252 structViewer.addItem(ViewerType.CHIMERA.name());
1253 structViewer.addActionListener(new ActionListener()
1256 public void actionPerformed(ActionEvent e)
1258 structureViewer_actionPerformed(
1259 (String) structViewer.getSelectedItem());
1262 structureTab.add(structViewer);
1264 ypos += lineSpacing;
1265 JLabel pathLabel = new JLabel();
1266 pathLabel.setFont(new java.awt.Font("SansSerif", 0, 11));
1267 pathLabel.setHorizontalAlignment(SwingConstants.LEFT);
1268 pathLabel.setText(MessageManager.getString("label.chimera_path"));
1269 pathLabel.setBounds(new Rectangle(10, ypos, 140, height));
1270 structureTab.add(pathLabel);
1272 chimeraPath.setFont(LABEL_FONT);
1273 chimeraPath.setText("");
1274 final String tooltip = JvSwingUtils.wrapTooltip(true,
1275 MessageManager.getString("label.chimera_path_tip"));
1276 chimeraPath.setToolTipText(tooltip);
1277 chimeraPath.setBounds(new Rectangle(160, ypos, 300, height));
1278 chimeraPath.addMouseListener(new MouseAdapter()
1281 public void mouseClicked(MouseEvent e)
1283 if (e.getClickCount() == 2)
1285 String chosen = openFileChooser();
1288 chimeraPath.setText(chosen);
1293 structureTab.add(chimeraPath);
1295 ypos += lineSpacing;
1296 nwMapping.setFont(LABEL_FONT);
1297 nwMapping.setText(MessageManager.getString("label.nw_mapping"));
1298 siftsMapping.setFont(LABEL_FONT);
1299 siftsMapping.setText(MessageManager.getString("label.sifts_mapping"));
1300 mappingMethod.add(nwMapping);
1301 mappingMethod.add(siftsMapping);
1302 JPanel mappingPanel = new JPanel();
1303 mappingPanel.setFont(LABEL_FONT);
1304 TitledBorder mmTitledBorder = new TitledBorder(
1305 MessageManager.getString("label.mapping_method"));
1306 mmTitledBorder.setTitleFont(LABEL_FONT);
1307 mappingPanel.setBorder(mmTitledBorder);
1308 mappingPanel.setBounds(new Rectangle(10, ypos, 452, 45));
1309 // GridLayout mappingLayout = new GridLayout();
1310 mappingPanel.setLayout(new GridLayout());
1311 mappingPanel.add(nwMapping);
1312 mappingPanel.add(siftsMapping);
1313 structureTab.add(mappingPanel);
1315 ypos += lineSpacing;
1316 ypos += lineSpacing;
1317 FTSDataColumnPreferences docFieldPref = new FTSDataColumnPreferences(
1318 PreferenceSource.PREFERENCES, PDBFTSRestClient.getInstance());
1319 docFieldPref.setBounds(new Rectangle(10, ypos, 450, 120));
1320 structureTab.add(docFieldPref);
1322 return structureTab;
1326 * Action on choosing a structure viewer from combobox options.
1328 * @param selectedItem
1330 protected void structureViewer_actionPerformed(String selectedItem)
1335 * Show a dialog for the user to choose a file. Returns the chosen path, or
1340 protected String openFileChooser()
1342 String choice = null;
1343 JFileChooser chooser = new JFileChooser();
1345 // chooser.setFileView(new JalviewFileView());
1346 chooser.setDialogTitle(
1347 MessageManager.getString("label.open_local_file"));
1348 chooser.setToolTipText(MessageManager.getString("action.open"));
1350 int value = chooser.showOpenDialog(this);
1352 if (value == JFileChooser.APPROVE_OPTION)
1354 choice = chooser.getSelectedFile().getPath();
1360 * Validate the structure tab preferences; if invalid, set focus on this tab.
1364 protected boolean validateStructure(FocusEvent e)
1366 if (!validateStructure())
1368 e.getComponent().requestFocusInWindow();
1374 protected boolean validateStructure()
1380 * Initialises the Visual tabbed panel.
1384 private JPanel initVisualTab()
1386 JPanel visualTab = new JPanel();
1387 visualTab.setBorder(new TitledBorder(
1388 MessageManager.getString("action.open_new_alignment")));
1389 visualTab.setLayout(null);
1390 fullScreen.setFont(LABEL_FONT);
1391 fullScreen.setHorizontalAlignment(SwingConstants.RIGHT);
1392 fullScreen.setHorizontalTextPosition(SwingConstants.LEFT);
1393 fullScreen.setText(MessageManager.getString("label.maximize_window"));
1394 quality.setEnabled(false);
1395 quality.setFont(LABEL_FONT);
1396 quality.setHorizontalAlignment(SwingConstants.RIGHT);
1397 quality.setHorizontalTextPosition(SwingConstants.LEFT);
1398 quality.setSelected(true);
1399 quality.setText(MessageManager.getString("label.quality"));
1400 conservation.setEnabled(false);
1401 conservation.setFont(LABEL_FONT);
1402 conservation.setHorizontalAlignment(SwingConstants.RIGHT);
1403 conservation.setHorizontalTextPosition(SwingConstants.LEFT);
1404 conservation.setSelected(true);
1405 conservation.setText(MessageManager.getString("label.conservation"));
1406 identity.setEnabled(false);
1407 identity.setFont(LABEL_FONT);
1408 identity.setHorizontalAlignment(SwingConstants.RIGHT);
1409 identity.setHorizontalTextPosition(SwingConstants.LEFT);
1410 identity.setSelected(true);
1411 identity.setText(MessageManager.getString("label.consensus"));
1412 showOccupancy.setFont(LABEL_FONT);
1413 showOccupancy.setEnabled(false);
1414 showOccupancy.setHorizontalAlignment(SwingConstants.RIGHT);
1415 showOccupancy.setHorizontalTextPosition(SwingConstants.LEFT);
1416 showOccupancy.setSelected(true);
1417 showOccupancy.setText(MessageManager.getString("label.occupancy"));
1419 JLabel showGroupbits = new JLabel();
1420 showGroupbits.setFont(LABEL_FONT);
1421 showGroupbits.setHorizontalAlignment(SwingConstants.RIGHT);
1422 showGroupbits.setHorizontalTextPosition(SwingConstants.LEFT);
1424 .setText(MessageManager.getString("action.show_group") + ":");
1425 JLabel showConsensbits = new JLabel();
1426 showConsensbits.setFont(LABEL_FONT);
1427 showConsensbits.setHorizontalAlignment(SwingConstants.RIGHT);
1428 showConsensbits.setHorizontalTextPosition(SwingConstants.LEFT);
1430 .setText(MessageManager.getString("label.consensus") + ":");
1431 showConsensHistogram.setEnabled(false);
1432 showConsensHistogram.setFont(LABEL_FONT);
1433 showConsensHistogram.setHorizontalAlignment(SwingConstants.RIGHT);
1434 showConsensHistogram.setHorizontalTextPosition(SwingConstants.LEFT);
1435 showConsensHistogram.setSelected(true);
1436 showConsensHistogram
1437 .setText(MessageManager.getString("label.histogram"));
1438 showConsensLogo.setEnabled(false);
1439 showConsensLogo.setFont(LABEL_FONT);
1440 showConsensLogo.setHorizontalAlignment(SwingConstants.RIGHT);
1441 showConsensLogo.setHorizontalTextPosition(SwingConstants.LEFT);
1442 showConsensLogo.setSelected(true);
1443 showConsensLogo.setText(MessageManager.getString("label.logo"));
1444 showGroupConsensus.setEnabled(false);
1445 showGroupConsensus.setFont(LABEL_FONT);
1446 showGroupConsensus.setHorizontalAlignment(SwingConstants.RIGHT);
1447 showGroupConsensus.setHorizontalTextPosition(SwingConstants.LEFT);
1448 showGroupConsensus.setSelected(true);
1449 showGroupConsensus.setText(MessageManager.getString("label.consensus"));
1450 showGroupConservation.setEnabled(false);
1451 showGroupConservation.setFont(LABEL_FONT);
1452 showGroupConservation.setHorizontalAlignment(SwingConstants.RIGHT);
1453 showGroupConservation.setHorizontalTextPosition(SwingConstants.LEFT);
1454 showGroupConservation.setSelected(true);
1455 showGroupConservation
1456 .setText(MessageManager.getString("label.conservation"));
1457 showNpTooltip.setEnabled(true);
1458 showNpTooltip.setFont(LABEL_FONT);
1459 showNpTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
1460 showNpTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
1461 showNpTooltip.setSelected(true);
1462 showNpTooltip.setText(
1463 MessageManager.getString("label.non_positional_features"));
1464 showDbRefTooltip.setEnabled(true);
1465 showDbRefTooltip.setFont(LABEL_FONT);
1466 showDbRefTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
1467 showDbRefTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
1468 showDbRefTooltip.setSelected(true);
1470 .setText(MessageManager.getString("label.database_references"));
1471 annotations.setFont(LABEL_FONT);
1472 annotations.setHorizontalAlignment(SwingConstants.RIGHT);
1473 annotations.setHorizontalTextPosition(SwingConstants.LEFT);
1474 annotations.setSelected(true);
1475 annotations.setText(MessageManager.getString("label.show_annotations"));
1476 // annotations.setBounds(new Rectangle(169, 12, 200, 23));
1477 annotations.addActionListener(new ActionListener()
1480 public void actionPerformed(ActionEvent e)
1482 annotations_actionPerformed(e);
1485 identity.addActionListener(new ActionListener()
1488 public void actionPerformed(ActionEvent e)
1490 annotations_actionPerformed(e);
1493 showGroupConsensus.addActionListener(new ActionListener()
1496 public void actionPerformed(ActionEvent e)
1498 annotations_actionPerformed(e);
1501 showUnconserved.setFont(LABEL_FONT);
1502 showUnconserved.setHorizontalAlignment(SwingConstants.RIGHT);
1503 showUnconserved.setHorizontalTextPosition(SwingConstants.LEFT);
1504 showUnconserved.setSelected(true);
1506 .setText(MessageManager.getString("action.show_unconserved"));
1507 showUnconserved.addActionListener(new ActionListener()
1510 public void actionPerformed(ActionEvent e)
1512 showunconserved_actionPerformed(e);
1516 // TODO these are not yet added to / action from Preferences
1517 // JCheckBox shareSelections = new JCheckBox();
1518 // shareSelections.setFont(verdana11);
1519 // shareSelections.setHorizontalAlignment(SwingConstants.RIGHT);
1520 // shareSelections.setHorizontalTextPosition(SwingConstants.LEFT);
1521 // shareSelections.setSelected(true);
1522 // shareSelections.setText(MessageManager
1523 // .getString("label.share_selection_across_views"));
1524 // JCheckBox followHighlight = new JCheckBox();
1525 // followHighlight.setFont(verdana11);
1526 // followHighlight.setHorizontalAlignment(SwingConstants.RIGHT);
1527 // followHighlight.setHorizontalTextPosition(SwingConstants.LEFT);
1528 // // showUnconserved.setBounds(new Rectangle(169, 40, 200, 23));
1529 // followHighlight.setSelected(true);
1530 // followHighlight.setText(MessageManager
1531 // .getString("label.scroll_highlighted_regions"));
1533 seqLimit.setFont(LABEL_FONT);
1534 seqLimit.setHorizontalAlignment(SwingConstants.RIGHT);
1535 seqLimit.setHorizontalTextPosition(SwingConstants.LEFT);
1536 seqLimit.setText(MessageManager.getString("label.full_sequence_id"));
1537 smoothFont.setFont(LABEL_FONT);
1538 smoothFont.setHorizontalAlignment(SwingConstants.RIGHT);
1539 smoothFont.setHorizontalTextPosition(SwingConstants.LEADING);
1540 smoothFont.setText(MessageManager.getString("label.smooth_font"));
1541 scaleProteinToCdna.setFont(LABEL_FONT);
1542 scaleProteinToCdna.setHorizontalAlignment(SwingConstants.RIGHT);
1543 scaleProteinToCdna.setHorizontalTextPosition(SwingConstants.LEADING);
1544 scaleProteinToCdna.setText(
1545 MessageManager.getString("label.scale_protein_to_cdna"));
1546 scaleProteinToCdna.setToolTipText(
1547 MessageManager.getString("label.scale_protein_to_cdna_tip"));
1548 JLabel gapLabel = new JLabel();
1549 gapLabel.setFont(LABEL_FONT);
1550 gapLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1551 gapLabel.setText(MessageManager.getString("label.gap_symbol") + " ");
1552 JLabel fontLabel = new JLabel();
1553 fontLabel.setFont(LABEL_FONT);
1554 fontLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1555 fontLabel.setText(MessageManager.getString("label.font"));
1556 fontSizeCB.setFont(LABEL_FONT);
1557 fontSizeCB.setBounds(new Rectangle(320, 112, 65, 23));
1558 fontStyleCB.setFont(LABEL_FONT);
1559 fontStyleCB.setBounds(new Rectangle(382, 112, 80, 23));
1560 fontNameCB.setFont(LABEL_FONT);
1561 fontNameCB.setBounds(new Rectangle(172, 112, 147, 23));
1562 gapSymbolCB.setFont(LABEL_FONT);
1563 gapSymbolCB.setBounds(new Rectangle(172, 215, 69, 23));
1564 DefaultListCellRenderer dlcr = new DefaultListCellRenderer();
1565 dlcr.setHorizontalAlignment(DefaultListCellRenderer.CENTER);
1566 gapSymbolCB.setRenderer(dlcr);
1568 startupCheckbox.setText(MessageManager.getString("action.open_file"));
1569 startupCheckbox.setFont(LABEL_FONT);
1570 startupCheckbox.setHorizontalAlignment(SwingConstants.RIGHT);
1571 startupCheckbox.setHorizontalTextPosition(SwingConstants.LEFT);
1572 startupCheckbox.setSelected(true);
1573 startupFileTextfield.setFont(LABEL_FONT);
1574 startupFileTextfield.setBounds(new Rectangle(172, 310, 330, 20));
1575 final String tooltip = JvSwingUtils.wrapTooltip(true,
1576 MessageManager.getString("label.double_click_to_browse"));
1577 startupFileTextfield.setToolTipText(tooltip);
1578 startupFileTextfield.addMouseListener(new MouseAdapter()
1581 public void mouseClicked(MouseEvent e)
1583 if (e.getClickCount() > 1)
1585 startupFileTextfield_mouseClicked();
1590 sortby.setFont(LABEL_FONT);
1591 sortby.setBounds(new Rectangle(172, 260, 155, 21));
1592 JLabel sortLabel = new JLabel();
1593 sortLabel.setFont(LABEL_FONT);
1594 sortLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1595 sortLabel.setText(MessageManager.getString("label.sort_by"));
1596 sortAnnBy.setFont(LABEL_FONT);
1597 sortAnnBy.setBounds(new Rectangle(172, 285, 110, 21));
1598 JLabel sortAnnLabel = new JLabel();
1599 sortAnnLabel.setFont(LABEL_FONT);
1600 sortAnnLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1601 sortAnnLabel.setText(MessageManager.getString("label.sort_ann_by"));
1602 sortAutocalc.setFont(LABEL_FONT);
1603 sortAutocalc.setBounds(new Rectangle(290, 285, 165, 21));
1605 JPanel annsettingsPanel = new JPanel();
1606 annsettingsPanel.setBounds(new Rectangle(173, 13, 320, 96));
1607 annsettingsPanel.setLayout(new FlowLayout(FlowLayout.LEFT, 0, 0));
1608 annsettingsPanel.setBorder(new EtchedBorder());
1609 visualTab.add(annsettingsPanel);
1610 Border jb = new EmptyBorder(1, 1, 4, 5);
1611 annotations.setBorder(jb);
1612 showOccupancy.setBorder(jb);
1613 quality.setBorder(jb);
1614 conservation.setBorder(jb);
1615 identity.setBorder(jb);
1616 showConsensbits.setBorder(jb);
1617 showGroupbits.setBorder(jb);
1618 showGroupConsensus.setBorder(jb);
1619 showGroupConservation.setBorder(jb);
1620 showConsensHistogram.setBorder(jb);
1621 showConsensLogo.setBorder(jb);
1623 JPanel autoAnnotSettings = new JPanel();
1624 annsettingsPanel.add(autoAnnotSettings);
1625 autoAnnotSettings.setLayout(new GridLayout(0, 2));
1626 autoAnnotSettings.add(annotations);
1627 autoAnnotSettings.add(quality);
1628 // second row of autoannotation box
1629 autoAnnotSettings = new JPanel();
1630 annsettingsPanel.add(autoAnnotSettings);
1632 autoAnnotSettings.setLayout(new GridLayout(0, 3));
1633 autoAnnotSettings.add(conservation);
1634 autoAnnotSettings.add(identity);
1635 autoAnnotSettings.add(showOccupancy);
1636 autoAnnotSettings.add(showGroupbits);
1637 autoAnnotSettings.add(showGroupConservation);
1638 autoAnnotSettings.add(showGroupConsensus);
1639 autoAnnotSettings.add(showConsensbits);
1640 autoAnnotSettings.add(showConsensHistogram);
1641 autoAnnotSettings.add(showConsensLogo);
1643 JPanel tooltipSettings = new JPanel();
1644 tooltipSettings.setBorder(new TitledBorder(
1645 MessageManager.getString("label.sequence_id_tooltip")));
1646 tooltipSettings.setBounds(173, 140, 220, 62);
1647 tooltipSettings.setLayout(new GridLayout(2, 1));
1648 tooltipSettings.add(showDbRefTooltip);
1649 tooltipSettings.add(showNpTooltip);
1650 visualTab.add(tooltipSettings);
1652 wrap.setFont(LABEL_FONT);
1653 wrap.setHorizontalAlignment(SwingConstants.TRAILING);
1654 wrap.setHorizontalTextPosition(SwingConstants.LEADING);
1655 wrap.setText(MessageManager.getString("label.wrap_alignment"));
1656 rightAlign.setFont(LABEL_FONT);
1657 rightAlign.setForeground(Color.black);
1658 rightAlign.setHorizontalAlignment(SwingConstants.RIGHT);
1659 rightAlign.setHorizontalTextPosition(SwingConstants.LEFT);
1660 rightAlign.setText(MessageManager.getString("label.right_align_ids"));
1661 idItalics.setFont(LABEL_FONT_ITALIC);
1662 idItalics.setHorizontalAlignment(SwingConstants.RIGHT);
1663 idItalics.setHorizontalTextPosition(SwingConstants.LEADING);
1665 MessageManager.getString("label.sequence_name_italics"));
1666 openoverv.setFont(LABEL_FONT);
1667 openoverv.setActionCommand(
1668 MessageManager.getString("label.open_overview"));
1669 openoverv.setHorizontalAlignment(SwingConstants.RIGHT);
1670 openoverv.setHorizontalTextPosition(SwingConstants.LEFT);
1671 openoverv.setText(MessageManager.getString("label.open_overview"));
1672 JPanel jPanel2 = new JPanel();
1673 jPanel2.setBounds(new Rectangle(7, 17, 158, 310));
1674 jPanel2.setLayout(new GridLayout(14, 1));
1675 jPanel2.add(fullScreen);
1676 jPanel2.add(openoverv);
1677 jPanel2.add(seqLimit);
1678 jPanel2.add(rightAlign);
1679 jPanel2.add(fontLabel);
1680 jPanel2.add(showUnconserved);
1681 jPanel2.add(idItalics);
1682 jPanel2.add(smoothFont);
1683 jPanel2.add(scaleProteinToCdna);
1684 jPanel2.add(gapLabel);
1686 jPanel2.add(sortLabel);
1687 jPanel2.add(sortAnnLabel);
1688 jPanel2.add(startupCheckbox);
1689 visualTab.add(jPanel2);
1690 visualTab.add(startupFileTextfield);
1691 visualTab.add(sortby);
1692 visualTab.add(sortAnnBy);
1693 visualTab.add(sortAutocalc);
1694 visualTab.add(gapSymbolCB);
1695 visualTab.add(fontNameCB);
1696 visualTab.add(fontSizeCB);
1697 visualTab.add(fontStyleCB);
1702 * Load the saved Backups options EXCEPT "Enabled" and "Scheme"
1705 protected void loadLastSavedBackupsOptions()
1707 BackupFilesPresetEntry savedPreset = BackupFilesPresetEntry
1708 .getSavedBackupEntry();
1710 .setSelected(Cache.getDefault(BackupFiles.ENABLED, true));
1712 BackupFilesPresetEntry backupfilesCustomEntry = BackupFilesPresetEntry
1713 .createBackupFilesPresetEntry(Cache
1714 .getDefault(BackupFilesPresetEntry.CUSTOMCONFIG, null));
1715 if (backupfilesCustomEntry == null)
1717 backupfilesCustomEntry = BackupFilesPresetEntry.backupfilesPresetEntriesValues
1718 .get(BackupFilesPresetEntry.BACKUPFILESSCHEMEDEFAULT);
1720 BackupFilesPresetEntry.backupfilesPresetEntriesValues.put(
1721 BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM,
1722 backupfilesCustomEntry);
1724 setComboIntStringKey(backupfilesPresetsCombo,
1725 Cache.getDefault(BackupFiles.NS + "_PRESET",
1726 BackupFilesPresetEntry.BACKUPFILESSCHEMEDEFAULT));
1728 backupsSetOptions(savedPreset);
1730 backupsOptionsSetEnabled();
1731 updateBackupFilesExampleLabel();
1734 private boolean warnAboutSuffixReverseChange()
1736 BackupFilesPresetEntry bfpe = BackupFilesPresetEntry
1737 .getSavedBackupEntry();
1738 boolean savedSuffixReverse = bfpe.reverse;
1739 int savedSuffixDigits = bfpe.digits;
1740 String savedSuffixTemplate = bfpe.suffix;
1742 boolean nowSuffixReverse = suffixReverse.isSelected();
1743 int nowSuffixDigits = getSpinnerInt(suffixDigitsSpinner, 3);
1744 String nowSuffixTemplate = suffixTemplate.getText();
1745 return nowSuffixReverse != savedSuffixReverse
1746 && nowSuffixDigits == savedSuffixDigits
1747 && nowSuffixTemplate != null
1748 && nowSuffixTemplate.equals(savedSuffixTemplate);
1752 * Initialises the Backups tabbed panel.
1756 private JPanel initBackupsTab()
1758 JPanel backupsTab = new JPanel();
1759 backupsTab.setBorder(new TitledBorder(
1760 MessageManager.getString("label.backup_files")));
1761 backupsTab.setLayout(new GridBagLayout());
1763 GridBagConstraints gbc = new GridBagConstraints();
1766 gbc.anchor = GridBagConstraints.FIRST_LINE_START;
1767 gbc.fill = GridBagConstraints.NONE;
1769 initBackupsTabPresetsPanel();
1770 initBackupsTabSuffixPanel();
1771 initBackupsTabKeepFilesPanel();
1772 initBackupsTabFilenameExamplesPanel();
1774 enableBackupFiles.setFont(LABEL_FONT_BOLD);
1776 .setText(MessageManager.getString("label.enable_backupfiles"));
1777 enableBackupFiles.addActionListener(new ActionListener()
1780 public void actionPerformed(ActionEvent e)
1782 // enable other options only when the first is checked
1783 backupsOptionsSetEnabled();
1788 // enable checkbox 1 col
1792 gbc.gridy = 0; // row 0
1793 backupsTab.add(enableBackupFiles, gbc);
1795 // summary of scheme box (over two rows)
1799 gbc.anchor = GridBagConstraints.FIRST_LINE_END;
1800 gbc.fill = GridBagConstraints.BOTH;
1801 backupsTab.add(exampleFilesPanel, gbc);
1803 gbc.anchor = GridBagConstraints.FIRST_LINE_START;
1804 gbc.fill = GridBagConstraints.NONE;
1806 // fill empty space on right
1809 backupsTab.add(new JPanel(), gbc);
1814 gbc.gridy++; // row 1
1815 backupsTab.add(presetsPanel, gbc);
1817 // now using whole row
1822 gbc.gridy++; // row 2
1823 backupsTab.add(keepfilesPanel, gbc);
1825 // filename strategy box
1826 gbc.gridy++; // row 3
1827 backupsTab.add(suffixPanel, gbc);
1830 gbc.gridy++; // row 4
1832 backupsTab.add(new JPanel(), gbc);
1834 backupsOptionsSetEnabled();
1838 private JPanel initBackupsTabPresetsPanel()
1841 String title = MessageManager.getString("label.schemes");
1843 presetsPanel.setLayout(new GridBagLayout());
1845 GridBagConstraints gbc = new GridBagConstraints();
1848 gbc.anchor = GridBagConstraints.BASELINE_LEADING;
1849 gbc.fill = GridBagConstraints.NONE;
1857 presetsComboLabel = new JLabel(title + ":");
1858 presetsPanel.add(presetsComboLabel, gbc);
1860 List<Object> entries = Arrays
1861 .asList((Object[]) BackupFilesPresetEntry.backupfilesPresetEntries);
1862 List<String> tooltips = Arrays.asList(
1863 BackupFilesPresetEntry.backupfilesPresetEntryDescriptions);
1864 backupfilesPresetsCombo = JvSwingUtils.buildComboWithTooltips(entries,
1867 for (int i = 0; i < BackupFilesPresetEntry.backupfilesPresetEntries.length; i++)
1869 backupfilesPresetsCombo
1870 .addItem(BackupFilesPresetEntry.backupfilesPresetEntries[i]);
1874 backupfilesPresetsCombo.addActionListener(new ActionListener()
1877 public void actionPerformed(ActionEvent e)
1879 int key = getComboIntStringKey(backupfilesPresetsCombo);
1880 if (!customiseCheckbox.isSelected())
1882 backupfilesPresetsComboLastSelected = key;
1884 if (key == BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM)
1886 if (customiseCheckbox.isSelected())
1888 // got here by clicking on customiseCheckbox so don't change the values
1889 backupfilesCustomOptionsSetEnabled();
1893 backupsTabUpdatePresets();
1894 backupfilesCustomOptionsSetEnabled();
1899 customiseCheckbox.setSelected(false);
1900 backupsTabUpdatePresets();
1901 backupfilesCustomOptionsSetEnabled();
1906 // dropdown list of preset schemes
1908 presetsPanel.add(backupfilesPresetsCombo, gbc);
1910 revertButton.setText(MessageManager.getString("label.cancel_changes"));
1911 revertButton.setToolTipText(
1912 MessageManager.getString("label.cancel_changes_description"));
1913 revertButton.addActionListener(new ActionListener()
1916 public void actionPerformed(ActionEvent e)
1919 BackupFilesPresetEntry.backupfilesPresetEntriesValues.get(
1920 BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM));
1921 backupfilesCustomOptionsSetEnabled();
1925 revertButton.setFont(LABEL_FONT);
1927 customiseCheckbox.setFont(LABEL_FONT);
1928 customiseCheckbox.setText(MessageManager.getString("label.customise"));
1929 customiseCheckbox.addActionListener(new ActionListener()
1932 public void actionPerformed(ActionEvent e)
1934 int currently = getComboIntStringKey(backupfilesPresetsCombo);
1935 if (customiseCheckbox.isSelected())
1937 backupfilesPresetsComboLastSelected = currently;
1938 setComboIntStringKey(backupfilesPresetsCombo,
1939 BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM);
1943 setComboIntStringKey(backupfilesPresetsCombo,
1944 backupfilesPresetsComboLastSelected);
1947 backupfilesCustomOptionsSetEnabled();
1950 customiseCheckbox.setToolTipText(
1951 MessageManager.getString("label.customise_description"));
1953 // customise checkbox
1956 presetsPanel.add(customiseCheckbox, gbc);
1958 // "Cancel changes" button (aligned with combo box above)
1960 presetsPanel.add(revertButton, gbc);
1962 return presetsPanel;
1965 private JPanel initBackupsTabFilenameExamplesPanel()
1967 String title = MessageManager
1968 .getString("label.scheme_examples");
1969 TitledBorder tb = new TitledBorder(title);
1970 exampleFilesPanel.setBorder(tb);
1971 exampleFilesPanel.setLayout(new GridBagLayout());
1974 backupfilesExampleLabel.setEditable(false);
1975 backupfilesExampleLabel
1976 .setBackground(exampleFilesPanel.getBackground());
1978 updateBackupFilesExampleLabel();
1980 GridBagConstraints gbc = new GridBagConstraints();
1983 gbc.fill = GridBagConstraints.NONE;
1984 gbc.anchor = GridBagConstraints.FIRST_LINE_START;
1986 exampleFilesPanel.add(backupfilesExampleLabel, gbc);
1987 return exampleFilesPanel;
1990 private void backupsTabUpdatePresets()
1992 IntKeyStringValueEntry entry = (IntKeyStringValueEntry) backupfilesPresetsCombo
1995 String value = entry.v;
1997 if (BackupFilesPresetEntry.backupfilesPresetEntriesValues
2001 BackupFilesPresetEntry.backupfilesPresetEntriesValues
2007 "Preset '" + value + "' [key:" + key + "] not implemented");
2010 // Custom options will now be enabled when the customiseCheckbox is checked
2011 // (performed above)
2012 // backupfilesCustomOptionsSetEnabled();
2013 updateBackupFilesExampleLabel();
2016 protected int getComboIntStringKey(
2017 JComboBox<Object> backupfilesPresetsCombo2)
2019 IntKeyStringValueEntry e;
2022 e = (IntKeyStringValueEntry) backupfilesPresetsCombo2
2024 } catch (Exception ex)
2027 "Problem casting Combo entry to IntKeyStringValueEntry.");
2030 return e != null ? e.k : 0;
2033 protected void setComboIntStringKey(
2034 JComboBox<Object> backupfilesPresetsCombo2,
2037 for (int i = 0; i < backupfilesPresetsCombo2.getItemCount(); i++)
2039 IntKeyStringValueEntry e;
2042 e = (IntKeyStringValueEntry) backupfilesPresetsCombo2.getItemAt(i);
2043 } catch (Exception ex)
2046 "Problem casting Combo entry to IntKeyStringValueEntry. Skipping item. ");
2051 backupfilesPresetsCombo2.setSelectedIndex(i);
2055 // backupsTabUpdatePresets();
2058 private JPanel initBackupsTabSuffixPanel()
2060 suffixPanel.setBorder(new TitledBorder(
2061 MessageManager.getString("label.backup_filename_strategy")));
2062 suffixPanel.setLayout(new GridBagLayout());
2065 .setText(MessageManager.getString("label.append_to_filename"));
2066 suffixTemplateLabel.setHorizontalAlignment(SwingConstants.LEFT);
2067 suffixTemplateLabel.setFont(LABEL_FONT);
2069 final String tooltip = JvSwingUtils.wrapTooltip(true,
2070 MessageManager.getString("label.append_to_filename_tooltip"));
2071 suffixTemplate.setToolTipText(tooltip);
2072 suffixTemplate.addActionListener(new ActionListener()
2075 public void actionPerformed(ActionEvent e)
2077 updateBackupFilesExampleLabel();
2078 backupfilesCustomOptionsSetEnabled();
2079 backupfilesRevertButtonSetEnabled(true);
2083 suffixTemplate.addKeyListener(new KeyListener()
2086 public void keyReleased(KeyEvent e)
2088 updateBackupFilesExampleLabel();
2089 backupfilesCustomOptionsSetEnabled();
2090 backupfilesRevertButtonSetEnabled(true);
2094 public void keyPressed(KeyEvent e)
2098 // disable use of ':' or '/' or '\'
2100 public void keyTyped(KeyEvent e)
2102 char c = e.getKeyChar();
2103 if (c == ':' || c == '/' || c == '\\')
2105 // don't process ':' or '/' or '\'
2114 .setText(MessageManager.getString("label.index_digits"));
2115 suffixDigitsLabel.setHorizontalAlignment(SwingConstants.LEFT);
2116 suffixDigitsLabel.setFont(LABEL_FONT);
2117 ChangeListener c = new ChangeListener()
2120 public void stateChanged(ChangeEvent e)
2122 backupfilesRevertButtonSetEnabled(true);
2123 updateBackupFilesExampleLabel();
2127 setIntegerSpinner(suffixDigitsSpinner, BackupFilesPresetEntry.DIGITSMIN,
2128 BackupFilesPresetEntry.DIGITSMAX, 3, c);
2130 suffixReverse.setLabels(MessageManager.getString("label.reverse_roll"),
2131 MessageManager.getString("label.increment_index"));
2132 suffixReverse.addActionListener(new ActionListener()
2135 public void actionPerformed(ActionEvent e)
2137 boolean okay = true;
2138 if (warnAboutSuffixReverseChange())
2141 okay = confirmSuffixReverseChange();
2145 backupfilesRevertButtonSetEnabled(true);
2146 updateBackupFilesExampleLabel();
2150 boolean savedSuffixReverse = BackupFilesPresetEntry
2151 .getSavedBackupEntry().reverse;
2152 suffixReverse.setSelected(savedSuffixReverse);
2157 GridBagConstraints sgbc = new GridBagConstraints();
2159 // first row (template text box)
2160 sgbc.anchor = GridBagConstraints.WEST;
2164 sgbc.gridheight = 1;
2167 sgbc.fill = GridBagConstraints.NONE;
2168 suffixPanel.add(suffixTemplateLabel, sgbc);
2171 sgbc.fill = GridBagConstraints.HORIZONTAL;
2172 suffixPanel.add(suffixTemplate, sgbc);
2174 // second row (number of digits spinner)
2178 sgbc.fill = GridBagConstraints.NONE;
2179 suffixPanel.add(suffixDigitsLabel, sgbc);
2182 sgbc.fill = GridBagConstraints.HORIZONTAL;
2183 suffixPanel.add(suffixDigitsSpinner, sgbc);
2185 // third row (forward order radio selection)
2188 sgbc.gridwidth = GridBagConstraints.REMAINDER;
2189 sgbc.fill = GridBagConstraints.HORIZONTAL;
2190 suffixPanel.add(suffixReverse.getFalseButton(), sgbc);
2192 // fourth row (reverse order radio selection)
2194 suffixPanel.add(suffixReverse.getTrueButton(), sgbc);
2198 private boolean confirmSuffixReverseChange()
2200 boolean ret = false;
2201 String warningMessage = MessageManager
2202 .getString("label.warning_confirm_change_reverse");
2203 int confirm = JvOptionPane.showConfirmDialog(Desktop.desktop,
2205 MessageManager.getString("label.change_increment_decrement"),
2206 JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE);
2208 ret = (confirm == JvOptionPane.YES_OPTION);
2212 private JPanel initBackupsTabKeepFilesPanel()
2214 keepfilesPanel.setBorder(
2215 new TitledBorder(MessageManager.getString("label.keep_files")));
2216 keepfilesPanel.setLayout(new GridBagLayout());
2218 backupfilesKeepAll.setLabels(
2219 MessageManager.getString("label.keep_all_backup_files"),
2220 MessageManager.getString(
2221 "label.keep_only_this_number_of_backup_files"));
2222 backupfilesKeepAll.addTrueActionListener(new ActionListener()
2225 public void actionPerformed(ActionEvent e)
2227 backupfilesRevertButtonSetEnabled(true);
2228 updateBackupFilesExampleLabel();
2231 backupfilesKeepAll.addActionListener(new ActionListener()
2234 public void actionPerformed(ActionEvent e)
2236 backupfilesRevertButtonSetEnabled(true);
2237 keepRollMaxOptionsEnabled();
2238 updateBackupFilesExampleLabel();
2242 ChangeListener c = new ChangeListener()
2245 public void stateChanged(ChangeEvent e)
2247 backupfilesRevertButtonSetEnabled(true);
2248 updateBackupFilesExampleLabel();
2252 setIntegerSpinner(backupfilesRollMaxSpinner,
2253 BackupFilesPresetEntry.ROLLMAXMIN,
2254 BackupFilesPresetEntry.ROLLMAXMAX, 4, true, c);
2256 backupfilesConfirmDelete.setLabels(
2257 MessageManager.getString("label.always_ask"),
2258 MessageManager.getString("label.auto_delete"));
2259 backupfilesConfirmDelete.addActionListener(new ActionListener()
2262 public void actionPerformed(ActionEvent e)
2264 backupfilesRevertButtonSetEnabled(true);
2267 // update the enabled section
2268 keepRollMaxOptionsEnabled();
2270 GridBagConstraints kgbc = new GridBagConstraints();
2272 // first row (template text box)
2273 kgbc.anchor = GridBagConstraints.WEST;
2276 kgbc.gridwidth = GridBagConstraints.REMAINDER;
2277 kgbc.gridheight = 1;
2280 kgbc.fill = GridBagConstraints.HORIZONTAL;
2281 keepfilesPanel.add(backupfilesKeepAll.getTrueButton(), kgbc);
2287 kgbc.gridwidth = GridBagConstraints.RELATIVE;
2288 keepfilesPanel.add(backupfilesKeepAll.getFalseButton(), kgbc);
2291 kgbc.gridwidth = GridBagConstraints.REMAINDER;
2292 keepfilesPanel.add(backupfilesRollMaxSpinner, kgbc);
2294 // third row (indented)
2296 kgbc.insets = new Insets(0, 20, 0, 0);
2299 kgbc.gridwidth = GridBagConstraints.REMAINDER;
2300 kgbc.fill = GridBagConstraints.HORIZONTAL;
2303 JPanel jp = new JPanel();
2304 jp.setLayout(new FlowLayout());
2306 .setText(MessageManager
2307 .getString("label.autodelete_old_backup_files"));
2308 oldBackupFilesLabel.setFont(LABEL_FONT);
2309 oldBackupFilesLabel.setHorizontalAlignment(SwingConstants.LEFT);
2310 jp.add(oldBackupFilesLabel);
2311 jp.add(backupfilesConfirmDelete.getTrueButton());
2312 jp.add(backupfilesConfirmDelete.getFalseButton());
2313 keepfilesPanel.add(jp, kgbc);
2315 return keepfilesPanel;
2318 protected void updateBackupFilesExampleLabel()
2320 int exampleindex = 12;
2321 String base = MessageManager.getString("label.filename") + ".fa";
2322 if (base == null || base.length() == 0)
2324 base = "file_name.fa";
2327 boolean reverse = suffixReverse.isSelected();
2328 boolean keepAll = backupfilesKeepAll.isSelected();
2330 String suffix = suffixTemplate.getText();
2333 backupfilesExampleLabel.setFont(LABEL_FONT_ITALIC);
2334 if (suffix == null || suffix.length() == 0)
2336 backupfilesExampleLabel
2337 .setText(MessageManager.getString("label.no_backup_files"));
2338 backupfilesExampleLabel.setFont(LABEL_FONT_BOLD);
2342 rollMax = getSpinnerInt(backupfilesRollMaxSpinner, 4);
2343 rollMax = rollMax < 1 ? 1 : rollMax;
2345 if (suffix.indexOf(BackupFiles.NUM_PLACEHOLDER) == -1)
2350 digits = getSpinnerInt(suffixDigitsSpinner, 3);
2351 digits = digits < 1 ? 1 : digits;
2353 int lowersurround = 2;
2354 int uppersurround = 0;
2355 StringBuilder exampleSB = new StringBuilder();
2356 boolean firstLine = true;
2362 int max = keepAll ? exampleindex : rollMax;
2363 for (int index = min; index <= max; index++)
2365 if (index == min + lowersurround && index < max - uppersurround - 1)
2367 exampleSB.append("\n...");
2370 else if (index > min + lowersurround && index < max - uppersurround)
2382 exampleSB.append("\n");
2385 exampleSB.append(BackupFilenameParts.getBackupFilename(index,
2386 base, suffix, digits));
2389 // no extra text needed
2391 else if (index == min)
2393 String newest = MessageManager.getString("label.braced_newest");
2394 if (newest != null && newest.length() > 0)
2396 exampleSB.append(" " + newest);
2399 else if (index == max)
2401 String oldest = MessageManager.getString("label.braced_oldest");
2402 if (oldest != null && oldest.length() > 0)
2404 exampleSB.append(" " + oldest);
2413 int min = (keepAll || exampleindex - rollMax < 0) ? 1
2414 : exampleindex - rollMax + 1;
2415 int max = exampleindex;
2417 for (int index = min; index <= max; index++)
2420 if (index == min + lowersurround && index < max - uppersurround - 1)
2422 exampleSB.append("\n...");
2425 else if (index > min + lowersurround && index < max - uppersurround)
2437 exampleSB.append("\n");
2440 exampleSB.append(BackupFilenameParts.getBackupFilename(index,
2441 base, suffix, digits));
2444 // no extra text needed
2446 else if (index == min)
2448 String oldest = MessageManager.getString("label.braced_oldest");
2449 if (oldest != null && oldest.length() > 0)
2451 exampleSB.append(" " + oldest);
2454 else if (index == max)
2456 String newest = MessageManager.getString("label.braced_newest");
2457 if (newest != null && newest.length() > 0)
2459 exampleSB.append(" " + newest);
2467 // add some extra empty lines to pad out the example files box. ugh, please tell
2468 // me how to do this better
2469 int remainingLines = lowersurround + uppersurround + 1 - lineNumber;
2470 if (remainingLines > 0)
2472 for (int i = 0; i < remainingLines; i++)
2474 exampleSB.append("\n ");
2479 backupfilesExampleLabel.setText(exampleSB.toString());
2482 protected void setIntegerSpinner(JSpinner s, int min, int max, int def,
2483 boolean useExistingVal, ChangeListener c)
2490 i = ((Integer) s.getValue()).intValue();
2491 } catch (Exception e)
2494 "Exception casting the initial value of s.getValue()");
2498 setIntegerSpinner(s, min, max, i, c);
2501 protected void setIntegerSpinner(JSpinner s, int min, int max, int def,
2504 // integer spinner for number of digits
2513 SpinnerModel sModel = new SpinnerNumberModel(def, min, max, 1);
2516 s.addChangeListener(c);
2520 protected static int getSpinnerInt(JSpinner s, int def)
2526 i = (Integer) s.getValue();
2527 } catch (Exception e)
2529 Cache.log.error("Failed casting (Integer) JSpinner s.getValue()");
2534 private void keepRollMaxOptionsEnabled()
2536 boolean enabled = backupfilesKeepAll.isEnabled()
2537 && !backupfilesKeepAll.isSelected();
2538 oldBackupFilesLabel.setEnabled(enabled);
2539 backupfilesRollMaxSpinner.setEnabled(enabled);
2540 backupfilesConfirmDelete.setEnabled(enabled);
2543 private void backupfilesKeepAllSetEnabled(boolean tryEnabled)
2545 boolean enabled = tryEnabled && enableBackupFiles.isSelected()
2546 && customiseCheckbox.isSelected()
2547 && suffixTemplate.getText()
2548 .indexOf(BackupFiles.NUM_PLACEHOLDER) > -1;
2549 keepfilesPanel.setEnabled(enabled);
2550 backupfilesKeepAll.setEnabled(enabled);
2551 oldBackupFilesLabel.setEnabled(enabled);
2552 keepRollMaxOptionsEnabled();
2555 private void backupfilesSuffixTemplateDigitsSetEnabled()
2557 boolean enabled = suffixTemplate.isEnabled() && suffixTemplate.getText()
2558 .indexOf(BackupFiles.NUM_PLACEHOLDER) > -1;
2559 suffixDigitsLabel.setEnabled(enabled);
2560 suffixDigitsSpinner.setEnabled(enabled);
2561 suffixReverse.setEnabled(enabled);
2564 private void backupfilesSuffixTemplateSetEnabled(boolean tryEnabled)
2566 boolean enabled = tryEnabled && enableBackupFiles.isSelected()
2567 && customiseCheckbox.isSelected();
2568 suffixPanel.setEnabled(enabled);
2569 suffixTemplateLabel.setEnabled(enabled);
2570 suffixTemplate.setEnabled(enabled);
2571 backupfilesSuffixTemplateDigitsSetEnabled();
2574 private void backupfilesRevertButtonSetEnabled(boolean tryEnabled)
2576 boolean enabled = tryEnabled && enableBackupFiles.isSelected()
2577 && customiseCheckbox.isSelected() && backupfilesCustomChanged();
2578 revertButton.setEnabled(enabled);
2581 private boolean backupfilesCustomChanged()
2583 BackupFilesPresetEntry custom = BackupFilesPresetEntry.backupfilesPresetEntriesValues
2584 .get(BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM);
2585 BackupFilesPresetEntry current = getBackupfilesCurrentEntry();
2586 return !custom.equals(current);
2589 protected BackupFilesPresetEntry getBackupfilesCurrentEntry()
2591 String suffix = suffixTemplate.getText();
2592 int digits = getSpinnerInt(suffixDigitsSpinner, 3);
2593 boolean reverse = suffixReverse.isSelected();
2594 boolean keepAll = backupfilesKeepAll.isSelected();
2595 int rollMax = getSpinnerInt(backupfilesRollMaxSpinner, 3);
2596 boolean confirmDelete = backupfilesConfirmDelete.isSelected();
2598 BackupFilesPresetEntry bfpe = new BackupFilesPresetEntry(suffix, digits,
2599 reverse, keepAll, rollMax, confirmDelete);
2604 protected void backupfilesCustomOptionsSetEnabled()
2606 boolean enabled = customiseCheckbox.isSelected();
2608 backupfilesRevertButtonSetEnabled(enabled);
2609 backupfilesSuffixTemplateSetEnabled(enabled);
2610 backupfilesKeepAllSetEnabled(enabled);
2613 private void backupfilesSummarySetEnabled()
2615 boolean enabled = enableBackupFiles.isSelected();
2616 backupfilesExampleLabel.setEnabled(enabled);
2617 exampleFilesPanel.setEnabled(enabled);
2620 private void backupfilesPresetsSetEnabled()
2622 boolean enabled = enableBackupFiles.isSelected();
2623 presetsPanel.setEnabled(enabled);
2624 presetsComboLabel.setEnabled(enabled);
2625 backupfilesPresetsCombo.setEnabled(enabled);
2626 customiseCheckbox.setEnabled(enabled);
2627 revertButton.setEnabled(enabled);
2630 protected void backupsOptionsSetEnabled()
2632 backupfilesPresetsSetEnabled();
2633 backupfilesSummarySetEnabled();
2634 backupfilesCustomOptionsSetEnabled();
2637 protected void backupsSetOptions(String suffix, int digits,
2638 boolean reverse, boolean keepAll, int rollMax,
2639 boolean confirmDelete)
2641 suffixTemplate.setText(suffix);
2642 suffixDigitsSpinner.setValue(digits);
2643 suffixReverse.setSelected(reverse);
2644 backupfilesKeepAll.setSelected(keepAll);
2645 backupfilesRollMaxSpinner.setValue(rollMax);
2646 backupfilesConfirmDelete.setSelected(confirmDelete);
2649 protected void backupsSetOptions(BackupFilesPresetEntry p)
2651 backupsSetOptions(p.suffix, p.digits, p.reverse, p.keepAll, p.rollMax,
2655 protected void autoIdWidth_actionPerformed()
2657 // TODO Auto-generated method stub
2661 protected void userIdWidth_actionPerformed()
2663 // TODO Auto-generated method stub
2667 protected void maxColour_actionPerformed(JPanel panel)
2671 protected void minColour_actionPerformed(JPanel panel)
2675 protected void gapColour_actionPerformed(JPanel panel)
2679 protected void hiddenColour_actionPerformed(JPanel panel)
2683 protected void showunconserved_actionPerformed(ActionEvent e)
2685 // TODO Auto-generated method stub
2689 protected void useLegacyGaps_actionPerformed(ActionEvent e)
2693 protected void resetOvDefaults_actionPerformed(ActionEvent e)
2703 public void ok_actionPerformed(ActionEvent e)
2713 public void cancel_actionPerformed(ActionEvent e)
2723 public void annotations_actionPerformed(ActionEvent e)
2730 public void startupFileTextfield_mouseClicked()
2734 public void newLink_actionPerformed(ActionEvent e)
2739 public void editLink_actionPerformed(ActionEvent e)
2744 public void deleteLink_actionPerformed(ActionEvent e)
2749 public void defaultBrowser_mouseClicked(MouseEvent e)
2754 public void linkURLList_keyTyped(KeyEvent e)
2759 public void useProxy_actionPerformed()
2761 boolean enabled = useProxy.isSelected();
2762 portLabel.setEnabled(enabled);
2763 serverLabel.setEnabled(enabled);
2764 proxyServerTB.setEnabled(enabled);
2765 proxyPortTB.setEnabled(enabled);
2769 * Customer renderer for JTable: supports column of radio buttons
2771 public class RadioButtonRenderer extends JRadioButton
2772 implements TableCellRenderer
2774 public RadioButtonRenderer()
2776 setHorizontalAlignment(CENTER);
2777 setToolTipText(MessageManager.getString("label.urltooltip"));
2781 public Component getTableCellRendererComponent(JTable table,
2782 Object value, boolean isSelected, boolean hasFocus, int row,
2785 setSelected((boolean) value);
2787 // set colours to match rest of table
2790 setBackground(table.getSelectionBackground());
2791 setForeground(table.getSelectionForeground());
2795 setBackground(table.getBackground());
2796 setForeground(table.getForeground());
2803 * Customer cell editor for JTable: supports column of radio buttons in
2804 * conjunction with renderer
2806 public class RadioButtonEditor extends AbstractCellEditor
2807 implements TableCellEditor
2809 private JRadioButton button = new JRadioButton();
2811 public RadioButtonEditor()
2813 button.setHorizontalAlignment(SwingConstants.CENTER);
2814 this.button.addActionListener(new ActionListener()
2817 public void actionPerformed(ActionEvent e)
2819 fireEditingStopped();
2825 public Component getTableCellEditorComponent(JTable table, Object value,
2826 boolean isSelected, int row, int column)
2828 button.setSelected((boolean) value);
2833 public Object getCellEditorValue()
2835 return button.isSelected();