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.fts.core.FTSDataColumnPreferences;
24 import jalview.fts.core.FTSDataColumnPreferences.PreferenceSource;
25 import jalview.fts.service.pdb.PDBFTSRestClient;
26 import jalview.gui.JvSwingUtils;
27 import jalview.gui.StructureViewer.ViewerType;
28 import jalview.util.MessageManager;
30 import java.awt.BorderLayout;
31 import java.awt.Color;
32 import java.awt.Component;
33 import java.awt.Dimension;
34 import java.awt.FlowLayout;
36 import java.awt.GridBagConstraints;
37 import java.awt.GridBagLayout;
38 import java.awt.GridLayout;
39 import java.awt.Insets;
40 import java.awt.Rectangle;
41 import java.awt.event.ActionEvent;
42 import java.awt.event.ActionListener;
43 import java.awt.event.FocusEvent;
44 import java.awt.event.KeyEvent;
45 import java.awt.event.MouseAdapter;
46 import java.awt.event.MouseEvent;
48 import javax.swing.AbstractCellEditor;
49 import javax.swing.BorderFactory;
50 import javax.swing.ButtonGroup;
51 import javax.swing.DefaultListCellRenderer;
52 import javax.swing.JButton;
53 import javax.swing.JCheckBox;
54 import javax.swing.JComboBox;
55 import javax.swing.JFileChooser;
56 import javax.swing.JLabel;
57 import javax.swing.JPanel;
58 import javax.swing.JRadioButton;
59 import javax.swing.JScrollPane;
60 import javax.swing.JTabbedPane;
61 import javax.swing.JTable;
62 import javax.swing.JTextField;
63 import javax.swing.ListSelectionModel;
64 import javax.swing.SwingConstants;
65 import javax.swing.border.Border;
66 import javax.swing.border.EmptyBorder;
67 import javax.swing.border.EtchedBorder;
68 import javax.swing.border.TitledBorder;
69 import javax.swing.event.ChangeEvent;
70 import javax.swing.event.ChangeListener;
71 import javax.swing.table.TableCellEditor;
72 import javax.swing.table.TableCellRenderer;
75 * Base class for the Preferences panel.
80 public class GPreferences extends JPanel
82 private static final Font LABEL_FONT = JvSwingUtils.getLabelFont();
84 private static final Font LABEL_FONT_ITALIC = JvSwingUtils
85 .getLabelFont(false, true);
88 * Visual tab components
90 protected JCheckBox fullScreen = new JCheckBox();
92 protected JCheckBox openoverv = new JCheckBox();
94 protected JCheckBox seqLimit = new JCheckBox();
96 protected JCheckBox rightAlign = new JCheckBox();
98 protected JComboBox<String> fontSizeCB = new JComboBox<>();
100 protected JComboBox<String> fontStyleCB = new JComboBox<>();
102 protected JComboBox<String> fontNameCB = new JComboBox<>();
104 protected JCheckBox showOccupancy = new JCheckBox();
106 protected JCheckBox showUnconserved = new JCheckBox();
108 protected JCheckBox idItalics = new JCheckBox();
110 protected JCheckBox smoothFont = new JCheckBox();
112 protected JCheckBox scaleProteinToCdna = new JCheckBox();
114 protected JComboBox<String> gapSymbolCB = new JComboBox<>();
116 protected JCheckBox wrap = new JCheckBox();
118 protected JComboBox<String> sortby = new JComboBox<>();
120 protected JComboBox<String> sortAnnBy = new JComboBox<>();
122 protected JComboBox<String> sortAutocalc = new JComboBox<>();
124 protected JCheckBox startupCheckbox = new JCheckBox();
126 protected JTextField startupFileTextfield = new JTextField();
128 // below are in the 'second column'
129 protected JCheckBox annotations = new JCheckBox();
131 protected JCheckBox quality = new JCheckBox();
133 protected JCheckBox conservation = new JCheckBox();
135 protected JCheckBox identity = new JCheckBox();
137 protected JCheckBox showGroupConsensus = new JCheckBox();
139 protected JCheckBox showGroupConservation = new JCheckBox();
141 protected JCheckBox showConsensHistogram = new JCheckBox();
143 protected JCheckBox showConsensLogo = new JCheckBox();
145 protected JCheckBox showDbRefTooltip = new JCheckBox();
147 protected JCheckBox showNpTooltip = new JCheckBox();
150 * Structure tab and components
152 protected JPanel structureTab;
154 protected JCheckBox structFromPdb = new JCheckBox();
156 protected JCheckBox useRnaView = new JCheckBox();
158 protected JCheckBox addSecondaryStructure = new JCheckBox();
160 protected JCheckBox addTempFactor = new JCheckBox();
162 protected JComboBox<String> structViewer = new JComboBox<>();
164 protected JTextField chimeraPath = new JTextField();
166 protected ButtonGroup mappingMethod = new ButtonGroup();
168 protected JRadioButton siftsMapping = new JRadioButton();
170 protected JRadioButton nwMapping = new JRadioButton();
173 * Colours tab components
175 protected JPanel minColour = new JPanel();
177 protected JPanel maxColour = new JPanel();
179 protected JComboBox<String> protColour = new JComboBox<>();
181 protected JComboBox<String> nucColour = new JComboBox<>();
184 * Overview tab components
186 protected JPanel gapColour = new JPanel();
188 protected JPanel hiddenColour = new JPanel();
190 protected JCheckBox useLegacyGap;
192 protected JCheckBox showHiddenAtStart;
194 protected JLabel gapLabel;
197 * Connections tab components
199 protected JTable linkUrlTable = new JTable();
201 protected JButton editLink = new JButton();
203 protected JButton deleteLink = new JButton();
205 protected JTextField filterTB = new JTextField();
207 protected JButton doReset = new JButton();
209 protected JButton userOnly = new JButton();
211 protected JLabel portLabel = new JLabel();
213 protected JLabel serverLabel = new JLabel();
215 protected JTextField proxyServerTB = new JTextField();
217 protected JTextField proxyPortTB = new JTextField();
219 protected JTextField defaultBrowser = new JTextField();
221 protected JCheckBox useProxy = new JCheckBox();
223 protected JCheckBox usagestats = new JCheckBox();
225 protected JCheckBox questionnaire = new JCheckBox();
227 protected JCheckBox versioncheck = new JCheckBox();
230 * Output tab components
232 protected JComboBox<Object> epsRendering = new JComboBox<>();
234 protected JLabel userIdWidthlabel = new JLabel();
236 protected JCheckBox autoIdWidth = new JCheckBox();
238 protected JTextField userIdWidth = new JTextField();
240 protected JCheckBox blcjv = new JCheckBox();
242 protected JCheckBox pileupjv = new JCheckBox();
244 protected JCheckBox clustaljv = new JCheckBox();
246 protected JCheckBox msfjv = new JCheckBox();
248 protected JCheckBox fastajv = new JCheckBox();
250 protected JCheckBox pfamjv = new JCheckBox();
252 protected JCheckBox pirjv = new JCheckBox();
254 protected JCheckBox modellerOutput = new JCheckBox();
256 protected JCheckBox embbedBioJSON = new JCheckBox();
259 * Editing tab components
261 protected JCheckBox autoCalculateConsCheck = new JCheckBox();
263 protected JCheckBox padGaps = new JCheckBox();
265 protected JCheckBox sortByTree = new JCheckBox();
270 protected JPanel dasTab = new JPanel();
275 protected JPanel wsTab = new JPanel();
278 * Creates a new GPreferences object.
280 public GPreferences()
285 } catch (Exception ex)
287 ex.printStackTrace();
292 * Construct the panel and its tabbed sub-panels.
296 private void jbInit() throws Exception
298 final JTabbedPane tabbedPane = new JTabbedPane();
299 this.setLayout(new BorderLayout());
300 JPanel okCancelPanel = initOkCancelPanel();
301 this.add(tabbedPane, BorderLayout.CENTER);
302 this.add(okCancelPanel, BorderLayout.SOUTH);
304 tabbedPane.add(initVisualTab(),
305 MessageManager.getString("label.visual"));
307 tabbedPane.add(initColoursTab(),
308 MessageManager.getString("label.colours"));
310 tabbedPane.add(initOverviewTab(),
311 MessageManager.getString("label.overview"));
313 tabbedPane.add(initStructureTab(),
314 MessageManager.getString("label.structure"));
316 tabbedPane.add(initConnectionsTab(),
317 MessageManager.getString("label.connections"));
319 tabbedPane.add(initLinksTab(),
320 MessageManager.getString("label.urllinks"));
322 tabbedPane.add(initOutputTab(),
323 MessageManager.getString("label.output"));
325 tabbedPane.add(initEditingTab(),
326 MessageManager.getString("label.editing"));
329 * See DasSourceBrowser for the real work of configuring this tab.
331 dasTab.setLayout(new BorderLayout());
332 tabbedPane.add(dasTab, MessageManager.getString("label.das_settings"));
335 * See WsPreferences for the real work of configuring this tab.
337 wsTab.setLayout(new BorderLayout());
338 tabbedPane.add(wsTab, MessageManager.getString("label.web_services"));
341 * Handler to validate a tab before leaving it - currently only for
344 tabbedPane.addChangeListener(new ChangeListener()
346 private Component lastTab;
349 public void stateChanged(ChangeEvent e)
351 if (lastTab == structureTab
352 && tabbedPane.getSelectedComponent() != structureTab)
354 if (!validateStructure())
356 tabbedPane.setSelectedComponent(structureTab);
360 lastTab = tabbedPane.getSelectedComponent();
367 * Initialises the Editing tabbed panel.
371 private JPanel initEditingTab()
373 JPanel editingTab = new JPanel();
374 editingTab.setLayout(null);
375 autoCalculateConsCheck.setFont(LABEL_FONT);
376 autoCalculateConsCheck.setText(
377 MessageManager.getString("label.autocalculate_consensus"));
378 autoCalculateConsCheck.setBounds(new Rectangle(21, 52, 209, 23));
379 padGaps.setFont(LABEL_FONT);
381 MessageManager.getString("label.pad_gaps_when_editing"));
382 padGaps.setBounds(new Rectangle(22, 94, 168, 23));
383 sortByTree.setFont(LABEL_FONT);
385 .setText(MessageManager.getString("label.sort_with_new_tree"));
386 sortByTree.setToolTipText(MessageManager.getString(
387 "label.any_trees_calculated_or_loaded_alignment_automatically_sort"));
388 sortByTree.setBounds(new Rectangle(22, 136, 168, 23));
389 editingTab.add(autoCalculateConsCheck);
390 editingTab.add(padGaps);
391 editingTab.add(sortByTree);
396 * Initialises the Output tabbed panel.
400 private JPanel initOutputTab()
402 JPanel outputTab = new JPanel();
403 outputTab.setLayout(null);
404 JLabel epsLabel = new JLabel();
405 epsLabel.setFont(LABEL_FONT);
406 epsLabel.setHorizontalAlignment(SwingConstants.RIGHT);
407 epsLabel.setText(MessageManager.getString("label.eps_rendering_style"));
408 epsLabel.setBounds(new Rectangle(9, 31, 140, 24));
409 epsRendering.setFont(LABEL_FONT);
410 epsRendering.setBounds(new Rectangle(154, 34, 187, 21));
411 JLabel jLabel1 = new JLabel();
412 jLabel1.setFont(LABEL_FONT);
413 jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
414 jLabel1.setText(MessageManager.getString("label.append_start_end"));
415 jLabel1.setFont(LABEL_FONT);
416 fastajv.setFont(LABEL_FONT);
417 fastajv.setHorizontalAlignment(SwingConstants.LEFT);
418 clustaljv.setText(MessageManager.getString("label.clustal") + " ");
419 blcjv.setText(MessageManager.getString("label.blc") + " ");
420 fastajv.setText(MessageManager.getString("label.fasta") + " ");
421 msfjv.setText(MessageManager.getString("label.msf") + " ");
422 pfamjv.setText(MessageManager.getString("label.pfam") + " ");
423 pileupjv.setText(MessageManager.getString("label.pileup") + " ");
424 msfjv.setFont(LABEL_FONT);
425 msfjv.setHorizontalAlignment(SwingConstants.LEFT);
426 pirjv.setText(MessageManager.getString("label.pir") + " ");
427 JPanel jPanel11 = new JPanel();
428 jPanel11.setFont(LABEL_FONT);
429 TitledBorder titledBorder2 = new TitledBorder(
430 MessageManager.getString("label.file_output"));
431 jPanel11.setBorder(titledBorder2);
432 jPanel11.setBounds(new Rectangle(30, 72, 196, 182));
433 GridLayout gridLayout3 = new GridLayout();
434 jPanel11.setLayout(gridLayout3);
435 gridLayout3.setRows(8);
436 blcjv.setFont(LABEL_FONT);
437 blcjv.setHorizontalAlignment(SwingConstants.LEFT);
438 clustaljv.setFont(LABEL_FONT);
439 clustaljv.setHorizontalAlignment(SwingConstants.LEFT);
440 pfamjv.setFont(LABEL_FONT);
441 pfamjv.setHorizontalAlignment(SwingConstants.LEFT);
442 pileupjv.setFont(LABEL_FONT);
443 pileupjv.setHorizontalAlignment(SwingConstants.LEFT);
444 pirjv.setFont(LABEL_FONT);
445 pirjv.setHorizontalAlignment(SwingConstants.LEFT);
446 autoIdWidth.setFont(LABEL_FONT);
448 MessageManager.getString("label.automatically_set_id_width"));
449 autoIdWidth.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager
450 .getString("label.adjusts_width_generated_eps_png")));
451 autoIdWidth.setBounds(new Rectangle(228, 96, 188, 23));
452 autoIdWidth.addActionListener(new ActionListener()
456 public void actionPerformed(ActionEvent e)
458 autoIdWidth_actionPerformed();
461 userIdWidthlabel.setFont(LABEL_FONT);
462 userIdWidthlabel.setText(
463 MessageManager.getString("label.figure_id_column_width"));
464 userIdWidth.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager
465 .getString("label.manually_specify_width_left_column")));
466 userIdWidthlabel.setToolTipText(
467 JvSwingUtils.wrapTooltip(true, MessageManager.getString(
468 "label.manually_specify_width_left_column")));
469 userIdWidthlabel.setBounds(new Rectangle(236, 120, 168, 23));
470 userIdWidth.setFont(JvSwingUtils.getTextAreaFont());
471 userIdWidth.setText("");
472 userIdWidth.setBounds(new Rectangle(232, 144, 84, 23));
473 userIdWidth.addActionListener(new ActionListener()
477 public void actionPerformed(ActionEvent e)
479 userIdWidth_actionPerformed();
482 modellerOutput.setFont(LABEL_FONT);
484 .setText(MessageManager.getString("label.use_modeller_output"));
485 modellerOutput.setBounds(new Rectangle(228, 226, 168, 23));
486 embbedBioJSON.setFont(LABEL_FONT);
487 embbedBioJSON.setText(MessageManager.getString("label.embbed_biojson"));
488 embbedBioJSON.setBounds(new Rectangle(228, 200, 250, 23));
490 jPanel11.add(jLabel1);
492 jPanel11.add(clustaljv);
493 jPanel11.add(fastajv);
495 jPanel11.add(pfamjv);
496 jPanel11.add(pileupjv);
498 outputTab.add(autoIdWidth);
499 outputTab.add(userIdWidth);
500 outputTab.add(userIdWidthlabel);
501 outputTab.add(modellerOutput);
502 outputTab.add(embbedBioJSON);
503 outputTab.add(epsLabel);
504 outputTab.add(epsRendering);
505 outputTab.add(jPanel11);
510 * Initialises the Connections tabbed panel.
514 private JPanel initConnectionsTab()
516 JPanel connectTab = new JPanel();
517 connectTab.setLayout(new GridBagLayout());
519 // Label for browser text box
520 JLabel browserLabel = new JLabel();
521 browserLabel.setFont(LABEL_FONT);
522 browserLabel.setHorizontalAlignment(SwingConstants.TRAILING);
523 browserLabel.setText(
524 MessageManager.getString("label.default_browser_unix"));
525 defaultBrowser.setFont(LABEL_FONT);
526 defaultBrowser.setText("");
527 final String tooltip = JvSwingUtils.wrapTooltip(true,
528 MessageManager.getString("label.double_click_to_browse"));
529 defaultBrowser.setToolTipText(tooltip);
530 defaultBrowser.addMouseListener(new MouseAdapter()
533 public void mouseClicked(MouseEvent e)
535 if (e.getClickCount() > 1)
537 defaultBrowser_mouseClicked(e);
542 JPanel proxyPanel = initConnTabProxyPanel();
543 initConnTabCheckboxes();
545 // Add default Browser text box
546 connectTab.add(browserLabel,
547 new GridBagConstraints(0, 0, 1, 1, 0.0, 0.0,
548 GridBagConstraints.WEST, GridBagConstraints.NONE,
549 new Insets(10, 0, 5, 5), 5, 1));
550 defaultBrowser.setFont(LABEL_FONT);
551 defaultBrowser.setText("");
553 connectTab.add(defaultBrowser, new GridBagConstraints(1, 0, 1, 1, 1.0,
554 0.0, GridBagConstraints.CENTER, GridBagConstraints.HORIZONTAL,
555 new Insets(10, 0, 5, 10), 30, 1));
557 // Add proxy server panel
558 connectTab.add(proxyPanel, new GridBagConstraints(0, 1, 2, 1, 1.0, 0.0,
559 GridBagConstraints.CENTER, GridBagConstraints.HORIZONTAL,
560 new Insets(10, 0, 5, 12), 4, 10));
562 // Add usage stats, version check and questionnaire checkboxes
563 connectTab.add(usagestats,
564 new GridBagConstraints(0, 2, 1, 1, 1.0, 0.0,
565 GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
566 new Insets(0, 2, 5, 5), 70, 1));
567 connectTab.add(questionnaire,
568 new GridBagConstraints(1, 2, 1, 1, 1.0, 0.0,
569 GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
570 new Insets(0, 2, 5, 10), 70, 1));
571 connectTab.add(versioncheck,
572 new GridBagConstraints(0, 3, 1, 1, 1.0, 0.0,
573 GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
574 new Insets(0, 2, 5, 5), 70, 1));
576 // Add padding so the panel doesn't look ridiculous
577 JPanel spacePanel = new JPanel();
578 connectTab.add(spacePanel,
579 new GridBagConstraints(0, 4, 1, 1, 1.0, 1.0,
580 GridBagConstraints.WEST, GridBagConstraints.BOTH,
581 new Insets(0, 0, 0, 5), 70, 1));
587 * Initialises the Links tabbed panel.
591 private JPanel initLinksTab()
593 JPanel linkTab = new JPanel();
594 linkTab.setLayout(new GridBagLayout());
596 // Set up table for Url links
597 linkUrlTable.setFillsViewportHeight(true);
598 linkUrlTable.setAutoResizeMode(JTable.AUTO_RESIZE_ALL_COLUMNS);
599 linkUrlTable.setAutoCreateRowSorter(true);
600 linkUrlTable.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
602 // adjust row height so radio buttons actually fit
603 // don't do this in the renderer, it causes the awt thread to activate
605 JRadioButton temp = new JRadioButton();
606 linkUrlTable.setRowHeight(temp.getMinimumSize().height);
608 // Table in scrollpane so that the table is given a scrollbar
609 JScrollPane linkScrollPane = new JScrollPane(linkUrlTable);
610 linkScrollPane.setBorder(null);
612 // Panel for links functionality
613 JPanel linkPanel = new JPanel(new GridBagLayout());
614 linkPanel.setBorder(new TitledBorder(
615 MessageManager.getString("label.url_linkfrom_sequence_id")));
617 // Put the Url links panel together
619 // Buttons go at top right, resizing only resizes the blank space vertically
620 JPanel buttonPanel = initLinkTabUrlButtons();
621 GridBagConstraints linkConstraints1 = new GridBagConstraints();
622 linkConstraints1.insets = new Insets(0, 0, 5, 0);
623 linkConstraints1.gridx = 0;
624 linkConstraints1.gridy = 0;
625 linkConstraints1.weightx = 1.0;
626 linkConstraints1.fill = GridBagConstraints.HORIZONTAL;
627 linkTab.add(buttonPanel, linkConstraints1);
629 // Links table goes at top left, resizing resizes the table
630 GridBagConstraints linkConstraints2 = new GridBagConstraints();
631 linkConstraints2.insets = new Insets(0, 0, 5, 5);
632 linkConstraints2.gridx = 0;
633 linkConstraints2.gridy = 1;
634 linkConstraints2.weightx = 1.0;
635 linkConstraints2.weighty = 1.0;
636 linkConstraints2.fill = GridBagConstraints.BOTH;
637 linkTab.add(linkScrollPane, linkConstraints2);
639 // Filter box and buttons goes at bottom left, resizing resizes the text box
640 JPanel filterPanel = initLinkTabFilterPanel();
641 GridBagConstraints linkConstraints3 = new GridBagConstraints();
642 linkConstraints3.insets = new Insets(0, 0, 0, 5);
643 linkConstraints3.gridx = 0;
644 linkConstraints3.gridy = 2;
645 linkConstraints3.weightx = 1.0;
646 linkConstraints3.fill = GridBagConstraints.HORIZONTAL;
647 linkTab.add(filterPanel, linkConstraints3);
652 private JPanel initLinkTabFilterPanel()
654 // Filter textbox and reset button
655 JLabel filterLabel = new JLabel(
656 MessageManager.getString("label.filter"));
657 filterLabel.setFont(LABEL_FONT);
658 filterLabel.setHorizontalAlignment(SwingConstants.RIGHT);
659 filterLabel.setHorizontalTextPosition(SwingConstants.LEADING);
661 filterTB.setFont(LABEL_FONT);
662 filterTB.setText("");
664 doReset.setText(MessageManager.getString("action.showall"));
665 userOnly.setText(MessageManager.getString("action.customfilter"));
667 // Panel for filter functionality
668 JPanel filterPanel = new JPanel(new GridBagLayout());
669 filterPanel.setBorder(new TitledBorder("Filter"));
670 GridBagConstraints gbc = new GridBagConstraints();
673 gbc.fill = GridBagConstraints.NONE;
674 gbc.anchor = GridBagConstraints.WEST;
676 filterPanel.add(filterLabel, gbc);
678 GridBagConstraints gbc1 = new GridBagConstraints();
681 gbc1.fill = GridBagConstraints.HORIZONTAL;
682 gbc1.anchor = GridBagConstraints.WEST;
684 filterPanel.add(filterTB, gbc1);
686 GridBagConstraints gbc2 = new GridBagConstraints();
688 gbc2.fill = GridBagConstraints.NONE;
689 gbc2.anchor = GridBagConstraints.WEST;
690 filterPanel.add(doReset, gbc2);
692 GridBagConstraints gbc3 = new GridBagConstraints();
694 gbc3.fill = GridBagConstraints.NONE;
695 gbc3.anchor = GridBagConstraints.WEST;
696 filterPanel.add(userOnly, gbc3);
701 private JPanel initLinkTabUrlButtons()
703 // Buttons for new / edit / delete Url links
704 JButton newLink = new JButton();
705 newLink.setText(MessageManager.getString("action.new"));
707 editLink.setText(MessageManager.getString("action.edit"));
709 deleteLink.setText(MessageManager.getString("action.delete"));
711 // no current selection, so initially disable delete/edit buttons
712 editLink.setEnabled(false);
713 deleteLink.setEnabled(false);
715 newLink.addActionListener(new java.awt.event.ActionListener()
718 public void actionPerformed(ActionEvent e)
720 newLink_actionPerformed(e);
724 editLink.setText(MessageManager.getString("action.edit"));
725 editLink.addActionListener(new java.awt.event.ActionListener()
728 public void actionPerformed(ActionEvent e)
730 editLink_actionPerformed(e);
734 deleteLink.setText(MessageManager.getString("action.delete"));
735 deleteLink.addActionListener(new java.awt.event.ActionListener()
738 public void actionPerformed(ActionEvent e)
740 deleteLink_actionPerformed(e);
744 JPanel buttonPanel = new JPanel(new GridBagLayout());
745 buttonPanel.setBorder(new TitledBorder("Edit links"));
746 GridBagConstraints gbc = new GridBagConstraints();
749 gbc.fill = GridBagConstraints.NONE;
750 buttonPanel.add(newLink, gbc);
752 GridBagConstraints gbc1 = new GridBagConstraints();
755 gbc1.fill = GridBagConstraints.NONE;
756 buttonPanel.add(editLink, gbc1);
758 GridBagConstraints gbc2 = new GridBagConstraints();
761 gbc2.fill = GridBagConstraints.NONE;
762 buttonPanel.add(deleteLink, gbc2);
764 GridBagConstraints gbc3 = new GridBagConstraints();
767 gbc3.fill = GridBagConstraints.HORIZONTAL;
769 JPanel spacePanel = new JPanel();
770 spacePanel.setBorder(null);
771 buttonPanel.add(spacePanel, gbc3);
777 * Initialises the proxy server panel in the Connections tab
779 * @return the proxy server panel
781 private JPanel initConnTabProxyPanel()
783 // Label for server text box
784 serverLabel.setText(MessageManager.getString("label.address"));
785 serverLabel.setHorizontalAlignment(SwingConstants.RIGHT);
786 serverLabel.setFont(LABEL_FONT);
788 // Proxy server and port text boxes
789 proxyServerTB.setFont(LABEL_FONT);
790 proxyPortTB.setFont(LABEL_FONT);
792 // Label for Port text box
793 portLabel.setFont(LABEL_FONT);
794 portLabel.setHorizontalAlignment(SwingConstants.RIGHT);
795 portLabel.setText(MessageManager.getString("label.port"));
797 // Use proxy server checkbox
798 useProxy.setFont(LABEL_FONT);
799 useProxy.setHorizontalAlignment(SwingConstants.RIGHT);
800 useProxy.setHorizontalTextPosition(SwingConstants.LEADING);
801 useProxy.setText(MessageManager.getString("label.use_proxy_server"));
802 useProxy.addActionListener(new ActionListener()
805 public void actionPerformed(ActionEvent e)
807 useProxy_actionPerformed();
811 // Make proxy server panel
812 JPanel proxyPanel = new JPanel();
813 TitledBorder titledBorder1 = new TitledBorder(
814 MessageManager.getString("label.proxy_server"));
815 proxyPanel.setBorder(titledBorder1);
816 proxyPanel.setLayout(new GridBagLayout());
817 proxyPanel.add(serverLabel,
818 new GridBagConstraints(0, 1, 1, 1, 0.0, 0.0,
819 GridBagConstraints.WEST, GridBagConstraints.NONE,
820 new Insets(0, 2, 2, 0), 5, 0));
821 proxyPanel.add(portLabel,
822 new GridBagConstraints(2, 1, 1, 1, 0.0, 0.0,
823 GridBagConstraints.WEST, GridBagConstraints.NONE,
824 new Insets(0, 0, 2, 0), 11, 0));
825 proxyPanel.add(useProxy,
826 new GridBagConstraints(0, 0, 2, 1, 0.0, 0.0,
827 GridBagConstraints.WEST, GridBagConstraints.NONE,
828 new Insets(0, 2, 5, 185), 2, -4));
829 proxyPanel.add(proxyPortTB,
830 new GridBagConstraints(3, 1, 1, 1, 1.0, 0.0,
831 GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
832 new Insets(0, 2, 2, 2), 54, 1));
833 proxyPanel.add(proxyServerTB,
834 new GridBagConstraints(1, 1, 1, 1, 1.0, 0.0,
835 GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
836 new Insets(0, 2, 2, 0), 263, 1));
842 * Initialises the checkboxes in the Connections tab
844 private void initConnTabCheckboxes()
846 // Usage stats checkbox label
848 MessageManager.getString("label.send_usage_statistics"));
849 usagestats.setFont(LABEL_FONT);
850 usagestats.setHorizontalAlignment(SwingConstants.RIGHT);
851 usagestats.setHorizontalTextPosition(SwingConstants.LEADING);
853 // Questionnaire checkbox label
854 questionnaire.setText(
855 MessageManager.getString("label.check_for_questionnaires"));
856 questionnaire.setFont(LABEL_FONT);
857 questionnaire.setHorizontalAlignment(SwingConstants.RIGHT);
858 questionnaire.setHorizontalTextPosition(SwingConstants.LEADING);
860 // Check for latest version checkbox label
861 versioncheck.setText(
862 MessageManager.getString("label.check_for_latest_version"));
863 versioncheck.setFont(LABEL_FONT);
864 versioncheck.setHorizontalAlignment(SwingConstants.RIGHT);
865 versioncheck.setHorizontalTextPosition(SwingConstants.LEADING);
869 * Initialises the parent panel which contains the tabbed sections.
873 private JPanel initOkCancelPanel()
875 JButton ok = new JButton();
876 ok.setText(MessageManager.getString("action.ok"));
877 ok.addActionListener(new ActionListener()
880 public void actionPerformed(ActionEvent e)
882 ok_actionPerformed(e);
885 JButton cancel = new JButton();
886 cancel.setText(MessageManager.getString("action.cancel"));
887 cancel.addActionListener(new ActionListener()
890 public void actionPerformed(ActionEvent e)
892 cancel_actionPerformed(e);
895 JPanel okCancelPanel = new JPanel();
896 okCancelPanel.add(ok);
897 okCancelPanel.add(cancel);
898 return okCancelPanel;
902 * Initialises the Colours tabbed panel.
906 private JPanel initColoursTab()
908 JPanel coloursTab = new JPanel();
909 coloursTab.setBorder(new TitledBorder(
910 MessageManager.getString("action.open_new_alignment")));
911 coloursTab.setLayout(new FlowLayout());
912 JLabel mincolourLabel = new JLabel();
913 mincolourLabel.setFont(LABEL_FONT);
914 mincolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
915 mincolourLabel.setText(MessageManager.getString("label.min_colour"));
916 minColour.setFont(LABEL_FONT);
917 minColour.setBorder(BorderFactory.createEtchedBorder());
918 minColour.setPreferredSize(new Dimension(40, 20));
919 minColour.addMouseListener(new MouseAdapter()
922 public void mousePressed(MouseEvent e)
924 minColour_actionPerformed(minColour);
927 JLabel maxcolourLabel = new JLabel();
928 maxcolourLabel.setFont(LABEL_FONT);
929 maxcolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
930 maxcolourLabel.setText(MessageManager.getString("label.max_colour"));
931 maxColour.setFont(LABEL_FONT);
932 maxColour.setBorder(BorderFactory.createEtchedBorder());
933 maxColour.setPreferredSize(new Dimension(40, 20));
934 maxColour.addMouseListener(new MouseAdapter()
937 public void mousePressed(MouseEvent e)
939 maxColour_actionPerformed(maxColour);
943 protColour.setFont(LABEL_FONT);
944 protColour.setBounds(new Rectangle(172, 225, 155, 21));
945 JLabel protColourLabel = new JLabel();
946 protColourLabel.setFont(LABEL_FONT);
947 protColourLabel.setHorizontalAlignment(SwingConstants.LEFT);
948 protColourLabel.setText(
949 MessageManager.getString("label.prot_alignment_colour") + " ");
950 JvSwingUtils.addtoLayout(coloursTab,
952 .getString("label.default_colour_scheme_for_alignment"),
953 protColourLabel, protColour);
955 nucColour.setFont(LABEL_FONT);
956 nucColour.setBounds(new Rectangle(172, 240, 155, 21));
957 JLabel nucColourLabel = new JLabel();
958 nucColourLabel.setFont(LABEL_FONT);
959 nucColourLabel.setHorizontalAlignment(SwingConstants.LEFT);
960 nucColourLabel.setText(
961 MessageManager.getString("label.nuc_alignment_colour") + " ");
962 JvSwingUtils.addtoLayout(coloursTab,
964 .getString("label.default_colour_scheme_for_alignment"),
965 nucColourLabel, nucColour);
967 JPanel annotationShding = new JPanel();
968 annotationShding.setBorder(new TitledBorder(
969 MessageManager.getString("label.annotation_shading_default")));
970 annotationShding.setLayout(new GridLayout(1, 2));
971 JvSwingUtils.addtoLayout(annotationShding,
972 MessageManager.getString(
973 "label.default_minimum_colour_annotation_shading"),
974 mincolourLabel, minColour);
975 JvSwingUtils.addtoLayout(annotationShding,
976 MessageManager.getString(
977 "label.default_maximum_colour_annotation_shading"),
978 maxcolourLabel, maxColour);
979 coloursTab.add(annotationShding); // , FlowLayout.LEFT);
984 * Initialises the Overview tabbed panel.
988 private JPanel initOverviewTab()
990 JPanel overviewPanel = new JPanel();
991 overviewPanel.setBorder(new TitledBorder(
992 MessageManager.getString("label.overview_settings")));
994 gapColour.setFont(LABEL_FONT);
995 // fixing the border colours stops apparent colour bleed from the panel
997 BorderFactory.createEtchedBorder(Color.white, Color.lightGray));
998 gapColour.setPreferredSize(new Dimension(40, 20));
999 gapColour.addMouseListener(new MouseAdapter()
1002 public void mousePressed(MouseEvent e)
1004 gapColour_actionPerformed(gapColour);
1008 hiddenColour.setFont(LABEL_FONT);
1009 // fixing the border colours stops apparent colour bleed from the panel
1010 hiddenColour.setBorder(
1011 BorderFactory.createEtchedBorder(Color.white, Color.lightGray));
1012 hiddenColour.setPreferredSize(new Dimension(40, 20));
1013 hiddenColour.addMouseListener(new MouseAdapter()
1016 public void mousePressed(MouseEvent e)
1018 hiddenColour_actionPerformed(hiddenColour);
1022 useLegacyGap = new JCheckBox(
1023 MessageManager.getString("label.ov_legacy_gap"));
1024 useLegacyGap.setFont(LABEL_FONT);
1025 useLegacyGap.setHorizontalAlignment(SwingConstants.LEFT);
1026 useLegacyGap.setVerticalTextPosition(SwingConstants.TOP);
1027 gapLabel = new JLabel(
1028 MessageManager.getString("label.gap_colour"));
1029 gapLabel.setFont(LABEL_FONT);
1030 gapLabel.setHorizontalAlignment(SwingConstants.LEFT);
1031 gapLabel.setVerticalTextPosition(SwingConstants.TOP);
1032 showHiddenAtStart = new JCheckBox(
1033 MessageManager.getString("label.ov_show_hide_default"));
1034 showHiddenAtStart.setFont(LABEL_FONT);
1035 showHiddenAtStart.setHorizontalAlignment(SwingConstants.LEFT);
1036 showHiddenAtStart.setVerticalTextPosition(SwingConstants.TOP);
1037 JLabel hiddenLabel = new JLabel(
1038 MessageManager.getString("label.hidden_colour"));
1039 hiddenLabel.setFont(LABEL_FONT);
1040 hiddenLabel.setHorizontalAlignment(SwingConstants.LEFT);
1041 hiddenLabel.setVerticalTextPosition(SwingConstants.TOP);
1043 useLegacyGap.addActionListener(new ActionListener()
1046 public void actionPerformed(ActionEvent e)
1048 useLegacyGaps_actionPerformed(e);
1052 overviewPanel.setLayout(new GridBagLayout());
1053 GridBagConstraints c1 = new GridBagConstraints();
1055 c1.fill = GridBagConstraints.HORIZONTAL;
1060 c1.anchor = GridBagConstraints.FIRST_LINE_START;
1061 overviewPanel.add(useLegacyGap, c1);
1063 GridBagConstraints c2 = new GridBagConstraints();
1064 c2.fill = GridBagConstraints.HORIZONTAL;
1067 c2.insets = new Insets(0, 15, 0, 10);
1068 overviewPanel.add(gapLabel, c2);
1070 GridBagConstraints c3 = new GridBagConstraints();
1071 c3.fill = GridBagConstraints.HORIZONTAL;
1074 c3.insets = new Insets(0, 0, 0, 15);
1075 overviewPanel.add(gapColour, c3);
1077 GridBagConstraints c4 = new GridBagConstraints();
1078 c4.fill = GridBagConstraints.HORIZONTAL;
1082 overviewPanel.add(showHiddenAtStart, c4);
1084 GridBagConstraints c5 = new GridBagConstraints();
1085 c5.fill = GridBagConstraints.HORIZONTAL;
1088 c5.insets = new Insets(0, 15, 0, 10);
1089 overviewPanel.add(hiddenLabel, c5);
1091 GridBagConstraints c6 = new GridBagConstraints();
1092 c6.fill = GridBagConstraints.HORIZONTAL;
1095 c6.insets = new Insets(0, 0, 0, 15);
1096 overviewPanel.add(hiddenColour, c6);
1098 JButton resetButton = new JButton(
1099 MessageManager.getString("label.reset_to_defaults"));
1101 resetButton.addActionListener(new ActionListener()
1104 public void actionPerformed(ActionEvent e)
1106 resetOvDefaults_actionPerformed(e);
1110 GridBagConstraints c7 = new GridBagConstraints();
1111 c7.fill = GridBagConstraints.NONE;
1114 c7.insets = new Insets(10, 0, 0, 0);
1115 c7.anchor = GridBagConstraints.WEST;
1116 overviewPanel.add(resetButton, c7);
1118 // Add padding so the panel doesn't look ridiculous
1119 JPanel spacePanel = new JPanel();
1120 overviewPanel.add(spacePanel,
1121 new GridBagConstraints(0, 3, 1, 1, 1.0, 1.0,
1122 GridBagConstraints.WEST, GridBagConstraints.BOTH,
1123 new Insets(0, 0, 0, 5), 0, 0));
1125 return overviewPanel;
1129 * Initialises the Structure tabbed panel.
1133 private JPanel initStructureTab()
1135 structureTab = new JPanel();
1137 structureTab.setBorder(new TitledBorder(
1138 MessageManager.getString("label.structure_options")));
1139 structureTab.setLayout(null);
1140 final int width = 400;
1141 final int height = 22;
1142 final int lineSpacing = 25;
1145 structFromPdb.setFont(LABEL_FONT);
1147 .setText(MessageManager.getString("label.struct_from_pdb"));
1148 structFromPdb.setBounds(new Rectangle(5, ypos, width, height));
1149 structFromPdb.addActionListener(new ActionListener()
1152 public void actionPerformed(ActionEvent e)
1154 boolean selected = structFromPdb.isSelected();
1155 // enable other options only when the first is checked
1156 useRnaView.setEnabled(selected);
1157 addSecondaryStructure.setEnabled(selected);
1158 addTempFactor.setEnabled(selected);
1161 structureTab.add(structFromPdb);
1163 // indent checkboxes that are conditional on the first one
1164 ypos += lineSpacing;
1165 useRnaView.setFont(LABEL_FONT);
1166 useRnaView.setText(MessageManager.getString("label.use_rnaview"));
1167 useRnaView.setBounds(new Rectangle(25, ypos, width, height));
1168 structureTab.add(useRnaView);
1170 ypos += lineSpacing;
1171 addSecondaryStructure.setFont(LABEL_FONT);
1172 addSecondaryStructure
1173 .setText(MessageManager.getString("label.autoadd_secstr"));
1174 addSecondaryStructure.setBounds(new Rectangle(25, ypos, width, height));
1175 structureTab.add(addSecondaryStructure);
1177 ypos += lineSpacing;
1178 addTempFactor.setFont(LABEL_FONT);
1179 addTempFactor.setText(MessageManager.getString("label.autoadd_temp"));
1180 addTempFactor.setBounds(new Rectangle(25, ypos, width, height));
1181 structureTab.add(addTempFactor);
1183 ypos += lineSpacing;
1184 JLabel viewerLabel = new JLabel();
1185 viewerLabel.setFont(LABEL_FONT);
1186 viewerLabel.setHorizontalAlignment(SwingConstants.LEFT);
1187 viewerLabel.setText(MessageManager.getString("label.structure_viewer"));
1188 viewerLabel.setBounds(new Rectangle(10, ypos, 200, height));
1189 structureTab.add(viewerLabel);
1191 structViewer.setFont(LABEL_FONT);
1192 structViewer.setBounds(new Rectangle(160, ypos, 120, height));
1193 structViewer.addItem(ViewerType.JMOL.name());
1194 structViewer.addItem(ViewerType.CHIMERA.name());
1195 structViewer.addActionListener(new ActionListener()
1198 public void actionPerformed(ActionEvent e)
1200 structureViewer_actionPerformed(
1201 (String) structViewer.getSelectedItem());
1204 structureTab.add(structViewer);
1206 ypos += lineSpacing;
1207 JLabel pathLabel = new JLabel();
1208 pathLabel.setFont(new java.awt.Font("SansSerif", 0, 11));
1209 pathLabel.setHorizontalAlignment(SwingConstants.LEFT);
1210 pathLabel.setText(MessageManager.getString("label.chimera_path"));
1211 pathLabel.setBounds(new Rectangle(10, ypos, 140, height));
1212 structureTab.add(pathLabel);
1214 chimeraPath.setFont(LABEL_FONT);
1215 chimeraPath.setText("");
1216 final String tooltip = JvSwingUtils.wrapTooltip(true,
1217 MessageManager.getString("label.chimera_path_tip"));
1218 chimeraPath.setToolTipText(tooltip);
1219 chimeraPath.setBounds(new Rectangle(160, ypos, 300, height));
1220 chimeraPath.addMouseListener(new MouseAdapter()
1223 public void mouseClicked(MouseEvent e)
1225 if (e.getClickCount() == 2)
1227 String chosen = openFileChooser();
1230 chimeraPath.setText(chosen);
1235 structureTab.add(chimeraPath);
1237 ypos += lineSpacing;
1238 nwMapping.setFont(LABEL_FONT);
1239 nwMapping.setText(MessageManager.getString("label.nw_mapping"));
1240 siftsMapping.setFont(LABEL_FONT);
1241 siftsMapping.setText(MessageManager.getString("label.sifts_mapping"));
1242 mappingMethod.add(nwMapping);
1243 mappingMethod.add(siftsMapping);
1244 JPanel mappingPanel = new JPanel();
1245 mappingPanel.setFont(LABEL_FONT);
1246 TitledBorder mmTitledBorder = new TitledBorder(
1247 MessageManager.getString("label.mapping_method"));
1248 mmTitledBorder.setTitleFont(LABEL_FONT);
1249 mappingPanel.setBorder(mmTitledBorder);
1250 mappingPanel.setBounds(new Rectangle(10, ypos, 452, 45));
1251 // GridLayout mappingLayout = new GridLayout();
1252 mappingPanel.setLayout(new GridLayout());
1253 mappingPanel.add(nwMapping);
1254 mappingPanel.add(siftsMapping);
1255 structureTab.add(mappingPanel);
1257 ypos += lineSpacing;
1258 ypos += lineSpacing;
1259 FTSDataColumnPreferences docFieldPref = new FTSDataColumnPreferences(
1260 PreferenceSource.PREFERENCES, PDBFTSRestClient.getInstance());
1261 docFieldPref.setBounds(new Rectangle(10, ypos, 450, 120));
1262 structureTab.add(docFieldPref);
1264 return structureTab;
1268 * Action on choosing a structure viewer from combobox options.
1270 * @param selectedItem
1272 protected void structureViewer_actionPerformed(String selectedItem)
1277 * Show a dialog for the user to choose a file. Returns the chosen path, or
1282 protected String openFileChooser()
1284 String choice = null;
1285 JFileChooser chooser = new JFileChooser();
1287 // chooser.setFileView(new JalviewFileView());
1288 chooser.setDialogTitle(
1289 MessageManager.getString("label.open_local_file"));
1290 chooser.setToolTipText(MessageManager.getString("action.open"));
1292 int value = chooser.showOpenDialog(this);
1294 if (value == JFileChooser.APPROVE_OPTION)
1296 choice = chooser.getSelectedFile().getPath();
1302 * Validate the structure tab preferences; if invalid, set focus on this tab.
1306 protected boolean validateStructure(FocusEvent e)
1308 if (!validateStructure())
1310 e.getComponent().requestFocusInWindow();
1316 protected boolean validateStructure()
1322 * Initialises the Visual tabbed panel.
1326 private JPanel initVisualTab()
1328 JPanel visualTab = new JPanel();
1329 visualTab.setBorder(new TitledBorder(
1330 MessageManager.getString("action.open_new_alignment")));
1331 visualTab.setLayout(null);
1332 fullScreen.setFont(LABEL_FONT);
1333 fullScreen.setHorizontalAlignment(SwingConstants.RIGHT);
1334 fullScreen.setHorizontalTextPosition(SwingConstants.LEFT);
1335 fullScreen.setText(MessageManager.getString("label.maximize_window"));
1336 quality.setEnabled(false);
1337 quality.setFont(LABEL_FONT);
1338 quality.setHorizontalAlignment(SwingConstants.RIGHT);
1339 quality.setHorizontalTextPosition(SwingConstants.LEFT);
1340 quality.setSelected(true);
1341 quality.setText(MessageManager.getString("label.quality"));
1342 conservation.setEnabled(false);
1343 conservation.setFont(LABEL_FONT);
1344 conservation.setHorizontalAlignment(SwingConstants.RIGHT);
1345 conservation.setHorizontalTextPosition(SwingConstants.LEFT);
1346 conservation.setSelected(true);
1347 conservation.setText(MessageManager.getString("label.conservation"));
1348 identity.setEnabled(false);
1349 identity.setFont(LABEL_FONT);
1350 identity.setHorizontalAlignment(SwingConstants.RIGHT);
1351 identity.setHorizontalTextPosition(SwingConstants.LEFT);
1352 identity.setSelected(true);
1353 identity.setText(MessageManager.getString("label.consensus"));
1354 showOccupancy.setFont(LABEL_FONT);
1355 showOccupancy.setEnabled(false);
1356 showOccupancy.setHorizontalAlignment(SwingConstants.RIGHT);
1357 showOccupancy.setHorizontalTextPosition(SwingConstants.LEFT);
1358 showOccupancy.setSelected(true);
1359 showOccupancy.setText(MessageManager.getString("label.occupancy"));
1361 JLabel showGroupbits = new JLabel();
1362 showGroupbits.setFont(LABEL_FONT);
1363 showGroupbits.setHorizontalAlignment(SwingConstants.RIGHT);
1364 showGroupbits.setHorizontalTextPosition(SwingConstants.LEFT);
1366 .setText(MessageManager.getString("action.show_group") + ":");
1367 JLabel showConsensbits = new JLabel();
1368 showConsensbits.setFont(LABEL_FONT);
1369 showConsensbits.setHorizontalAlignment(SwingConstants.RIGHT);
1370 showConsensbits.setHorizontalTextPosition(SwingConstants.LEFT);
1372 .setText(MessageManager.getString("label.consensus") + ":");
1373 showConsensHistogram.setEnabled(false);
1374 showConsensHistogram.setFont(LABEL_FONT);
1375 showConsensHistogram.setHorizontalAlignment(SwingConstants.RIGHT);
1376 showConsensHistogram.setHorizontalTextPosition(SwingConstants.LEFT);
1377 showConsensHistogram.setSelected(true);
1378 showConsensHistogram
1379 .setText(MessageManager.getString("label.histogram"));
1380 showConsensLogo.setEnabled(false);
1381 showConsensLogo.setFont(LABEL_FONT);
1382 showConsensLogo.setHorizontalAlignment(SwingConstants.RIGHT);
1383 showConsensLogo.setHorizontalTextPosition(SwingConstants.LEFT);
1384 showConsensLogo.setSelected(true);
1385 showConsensLogo.setText(MessageManager.getString("label.logo"));
1386 showGroupConsensus.setEnabled(false);
1387 showGroupConsensus.setFont(LABEL_FONT);
1388 showGroupConsensus.setHorizontalAlignment(SwingConstants.RIGHT);
1389 showGroupConsensus.setHorizontalTextPosition(SwingConstants.LEFT);
1390 showGroupConsensus.setSelected(true);
1391 showGroupConsensus.setText(MessageManager.getString("label.consensus"));
1392 showGroupConservation.setEnabled(false);
1393 showGroupConservation.setFont(LABEL_FONT);
1394 showGroupConservation.setHorizontalAlignment(SwingConstants.RIGHT);
1395 showGroupConservation.setHorizontalTextPosition(SwingConstants.LEFT);
1396 showGroupConservation.setSelected(true);
1397 showGroupConservation
1398 .setText(MessageManager.getString("label.conservation"));
1399 showNpTooltip.setEnabled(true);
1400 showNpTooltip.setFont(LABEL_FONT);
1401 showNpTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
1402 showNpTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
1403 showNpTooltip.setSelected(true);
1404 showNpTooltip.setText(
1405 MessageManager.getString("label.non_positional_features"));
1406 showDbRefTooltip.setEnabled(true);
1407 showDbRefTooltip.setFont(LABEL_FONT);
1408 showDbRefTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
1409 showDbRefTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
1410 showDbRefTooltip.setSelected(true);
1412 .setText(MessageManager.getString("label.database_references"));
1413 annotations.setFont(LABEL_FONT);
1414 annotations.setHorizontalAlignment(SwingConstants.RIGHT);
1415 annotations.setHorizontalTextPosition(SwingConstants.LEFT);
1416 annotations.setSelected(true);
1417 annotations.setText(MessageManager.getString("label.show_annotations"));
1418 // annotations.setBounds(new Rectangle(169, 12, 200, 23));
1419 annotations.addActionListener(new ActionListener()
1422 public void actionPerformed(ActionEvent e)
1424 annotations_actionPerformed(e);
1427 identity.addActionListener(new ActionListener()
1430 public void actionPerformed(ActionEvent e)
1432 annotations_actionPerformed(e);
1435 showGroupConsensus.addActionListener(new ActionListener()
1438 public void actionPerformed(ActionEvent e)
1440 annotations_actionPerformed(e);
1443 showUnconserved.setFont(LABEL_FONT);
1444 showUnconserved.setHorizontalAlignment(SwingConstants.RIGHT);
1445 showUnconserved.setHorizontalTextPosition(SwingConstants.LEFT);
1446 showUnconserved.setSelected(true);
1448 .setText(MessageManager.getString("action.show_unconserved"));
1449 showUnconserved.addActionListener(new ActionListener()
1452 public void actionPerformed(ActionEvent e)
1454 showunconserved_actionPerformed(e);
1458 // TODO these are not yet added to / action from Preferences
1459 // JCheckBox shareSelections = new JCheckBox();
1460 // shareSelections.setFont(verdana11);
1461 // shareSelections.setHorizontalAlignment(SwingConstants.RIGHT);
1462 // shareSelections.setHorizontalTextPosition(SwingConstants.LEFT);
1463 // shareSelections.setSelected(true);
1464 // shareSelections.setText(MessageManager
1465 // .getString("label.share_selection_across_views"));
1466 // JCheckBox followHighlight = new JCheckBox();
1467 // followHighlight.setFont(verdana11);
1468 // followHighlight.setHorizontalAlignment(SwingConstants.RIGHT);
1469 // followHighlight.setHorizontalTextPosition(SwingConstants.LEFT);
1470 // // showUnconserved.setBounds(new Rectangle(169, 40, 200, 23));
1471 // followHighlight.setSelected(true);
1472 // followHighlight.setText(MessageManager
1473 // .getString("label.scroll_highlighted_regions"));
1475 seqLimit.setFont(LABEL_FONT);
1476 seqLimit.setHorizontalAlignment(SwingConstants.RIGHT);
1477 seqLimit.setHorizontalTextPosition(SwingConstants.LEFT);
1478 seqLimit.setText(MessageManager.getString("label.full_sequence_id"));
1479 smoothFont.setFont(LABEL_FONT);
1480 smoothFont.setHorizontalAlignment(SwingConstants.RIGHT);
1481 smoothFont.setHorizontalTextPosition(SwingConstants.LEADING);
1482 smoothFont.setText(MessageManager.getString("label.smooth_font"));
1483 scaleProteinToCdna.setFont(LABEL_FONT);
1484 scaleProteinToCdna.setHorizontalAlignment(SwingConstants.RIGHT);
1485 scaleProteinToCdna.setHorizontalTextPosition(SwingConstants.LEADING);
1486 scaleProteinToCdna.setText(
1487 MessageManager.getString("label.scale_protein_to_cdna"));
1488 scaleProteinToCdna.setToolTipText(
1489 MessageManager.getString("label.scale_protein_to_cdna_tip"));
1490 JLabel gapLabel = new JLabel();
1491 gapLabel.setFont(LABEL_FONT);
1492 gapLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1493 gapLabel.setText(MessageManager.getString("label.gap_symbol") + " ");
1494 JLabel fontLabel = new JLabel();
1495 fontLabel.setFont(LABEL_FONT);
1496 fontLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1497 fontLabel.setText(MessageManager.getString("label.font"));
1498 fontSizeCB.setFont(LABEL_FONT);
1499 fontSizeCB.setBounds(new Rectangle(320, 112, 65, 23));
1500 fontStyleCB.setFont(LABEL_FONT);
1501 fontStyleCB.setBounds(new Rectangle(382, 112, 80, 23));
1502 fontNameCB.setFont(LABEL_FONT);
1503 fontNameCB.setBounds(new Rectangle(172, 112, 147, 23));
1504 gapSymbolCB.setFont(LABEL_FONT);
1505 gapSymbolCB.setBounds(new Rectangle(172, 215, 69, 23));
1506 DefaultListCellRenderer dlcr = new DefaultListCellRenderer();
1507 dlcr.setHorizontalAlignment(DefaultListCellRenderer.CENTER);
1508 gapSymbolCB.setRenderer(dlcr);
1510 startupCheckbox.setText(MessageManager.getString("action.open_file"));
1511 startupCheckbox.setFont(LABEL_FONT);
1512 startupCheckbox.setHorizontalAlignment(SwingConstants.RIGHT);
1513 startupCheckbox.setHorizontalTextPosition(SwingConstants.LEFT);
1514 startupCheckbox.setSelected(true);
1515 startupFileTextfield.setFont(LABEL_FONT);
1516 startupFileTextfield.setBounds(new Rectangle(172, 310, 330, 20));
1517 final String tooltip = JvSwingUtils.wrapTooltip(true,
1518 MessageManager.getString("label.double_click_to_browse"));
1519 startupFileTextfield.setToolTipText(tooltip);
1520 startupFileTextfield.addMouseListener(new MouseAdapter()
1523 public void mouseClicked(MouseEvent e)
1525 if (e.getClickCount() > 1)
1527 startupFileTextfield_mouseClicked();
1532 sortby.setFont(LABEL_FONT);
1533 sortby.setBounds(new Rectangle(172, 260, 155, 21));
1534 JLabel sortLabel = new JLabel();
1535 sortLabel.setFont(LABEL_FONT);
1536 sortLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1537 sortLabel.setText(MessageManager.getString("label.sort_by"));
1538 sortAnnBy.setFont(LABEL_FONT);
1539 sortAnnBy.setBounds(new Rectangle(172, 285, 110, 21));
1540 JLabel sortAnnLabel = new JLabel();
1541 sortAnnLabel.setFont(LABEL_FONT);
1542 sortAnnLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1543 sortAnnLabel.setText(MessageManager.getString("label.sort_ann_by"));
1544 sortAutocalc.setFont(LABEL_FONT);
1545 sortAutocalc.setBounds(new Rectangle(290, 285, 165, 21));
1547 JPanel annsettingsPanel = new JPanel();
1548 annsettingsPanel.setBounds(new Rectangle(173, 13, 320, 96));
1549 annsettingsPanel.setLayout(new FlowLayout(FlowLayout.LEFT, 0, 0));
1550 annsettingsPanel.setBorder(new EtchedBorder());
1551 visualTab.add(annsettingsPanel);
1552 Border jb = new EmptyBorder(1, 1, 4, 5);
1553 annotations.setBorder(jb);
1554 showOccupancy.setBorder(jb);
1555 quality.setBorder(jb);
1556 conservation.setBorder(jb);
1557 identity.setBorder(jb);
1558 showConsensbits.setBorder(jb);
1559 showGroupbits.setBorder(jb);
1560 showGroupConsensus.setBorder(jb);
1561 showGroupConservation.setBorder(jb);
1562 showConsensHistogram.setBorder(jb);
1563 showConsensLogo.setBorder(jb);
1565 JPanel autoAnnotSettings = new JPanel();
1566 annsettingsPanel.add(autoAnnotSettings);
1567 autoAnnotSettings.setLayout(new GridLayout(0, 2));
1568 autoAnnotSettings.add(annotations);
1569 autoAnnotSettings.add(quality);
1570 // second row of autoannotation box
1571 autoAnnotSettings = new JPanel();
1572 annsettingsPanel.add(autoAnnotSettings);
1574 autoAnnotSettings.setLayout(new GridLayout(0, 3));
1575 autoAnnotSettings.add(conservation);
1576 autoAnnotSettings.add(identity);
1577 autoAnnotSettings.add(showOccupancy);
1578 autoAnnotSettings.add(showGroupbits);
1579 autoAnnotSettings.add(showGroupConservation);
1580 autoAnnotSettings.add(showGroupConsensus);
1581 autoAnnotSettings.add(showConsensbits);
1582 autoAnnotSettings.add(showConsensHistogram);
1583 autoAnnotSettings.add(showConsensLogo);
1585 JPanel tooltipSettings = new JPanel();
1586 tooltipSettings.setBorder(new TitledBorder(
1587 MessageManager.getString("label.sequence_id_tooltip")));
1588 tooltipSettings.setBounds(173, 140, 220, 62);
1589 tooltipSettings.setLayout(new GridLayout(2, 1));
1590 tooltipSettings.add(showDbRefTooltip);
1591 tooltipSettings.add(showNpTooltip);
1592 visualTab.add(tooltipSettings);
1594 wrap.setFont(LABEL_FONT);
1595 wrap.setHorizontalAlignment(SwingConstants.TRAILING);
1596 wrap.setHorizontalTextPosition(SwingConstants.LEADING);
1597 wrap.setText(MessageManager.getString("label.wrap_alignment"));
1598 rightAlign.setFont(LABEL_FONT);
1599 rightAlign.setForeground(Color.black);
1600 rightAlign.setHorizontalAlignment(SwingConstants.RIGHT);
1601 rightAlign.setHorizontalTextPosition(SwingConstants.LEFT);
1602 rightAlign.setText(MessageManager.getString("label.right_align_ids"));
1603 idItalics.setFont(LABEL_FONT_ITALIC);
1604 idItalics.setHorizontalAlignment(SwingConstants.RIGHT);
1605 idItalics.setHorizontalTextPosition(SwingConstants.LEADING);
1607 MessageManager.getString("label.sequence_name_italics"));
1608 openoverv.setFont(LABEL_FONT);
1609 openoverv.setActionCommand(
1610 MessageManager.getString("label.open_overview"));
1611 openoverv.setHorizontalAlignment(SwingConstants.RIGHT);
1612 openoverv.setHorizontalTextPosition(SwingConstants.LEFT);
1613 openoverv.setText(MessageManager.getString("label.open_overview"));
1614 JPanel jPanel2 = new JPanel();
1615 jPanel2.setBounds(new Rectangle(7, 17, 158, 310));
1616 jPanel2.setLayout(new GridLayout(14, 1));
1617 jPanel2.add(fullScreen);
1618 jPanel2.add(openoverv);
1619 jPanel2.add(seqLimit);
1620 jPanel2.add(rightAlign);
1621 jPanel2.add(fontLabel);
1622 jPanel2.add(showUnconserved);
1623 jPanel2.add(idItalics);
1624 jPanel2.add(smoothFont);
1625 jPanel2.add(scaleProteinToCdna);
1626 jPanel2.add(gapLabel);
1628 jPanel2.add(sortLabel);
1629 jPanel2.add(sortAnnLabel);
1630 jPanel2.add(startupCheckbox);
1631 visualTab.add(jPanel2);
1632 visualTab.add(startupFileTextfield);
1633 visualTab.add(sortby);
1634 visualTab.add(sortAnnBy);
1635 visualTab.add(sortAutocalc);
1636 visualTab.add(gapSymbolCB);
1637 visualTab.add(fontNameCB);
1638 visualTab.add(fontSizeCB);
1639 visualTab.add(fontStyleCB);
1643 protected void autoIdWidth_actionPerformed()
1645 // TODO Auto-generated method stub
1649 protected void userIdWidth_actionPerformed()
1651 // TODO Auto-generated method stub
1655 protected void maxColour_actionPerformed(JPanel panel)
1659 protected void minColour_actionPerformed(JPanel panel)
1663 protected void gapColour_actionPerformed(JPanel panel)
1667 protected void hiddenColour_actionPerformed(JPanel panel)
1671 protected void showunconserved_actionPerformed(ActionEvent e)
1673 // TODO Auto-generated method stub
1677 protected void useLegacyGaps_actionPerformed(ActionEvent e)
1681 protected void resetOvDefaults_actionPerformed(ActionEvent e)
1691 public void ok_actionPerformed(ActionEvent e)
1701 public void cancel_actionPerformed(ActionEvent e)
1711 public void annotations_actionPerformed(ActionEvent e)
1718 public void startupFileTextfield_mouseClicked()
1722 public void newLink_actionPerformed(ActionEvent e)
1727 public void editLink_actionPerformed(ActionEvent e)
1732 public void deleteLink_actionPerformed(ActionEvent e)
1737 public void defaultBrowser_mouseClicked(MouseEvent e)
1742 public void linkURLList_keyTyped(KeyEvent e)
1747 public void useProxy_actionPerformed()
1749 boolean enabled = useProxy.isSelected();
1750 portLabel.setEnabled(enabled);
1751 serverLabel.setEnabled(enabled);
1752 proxyServerTB.setEnabled(enabled);
1753 proxyPortTB.setEnabled(enabled);
1757 * Customer renderer for JTable: supports column of radio buttons
1759 public class RadioButtonRenderer extends JRadioButton
1760 implements TableCellRenderer
1762 public RadioButtonRenderer()
1764 setHorizontalAlignment(CENTER);
1765 setToolTipText(MessageManager.getString("label.urltooltip"));
1769 public Component getTableCellRendererComponent(JTable table,
1770 Object value, boolean isSelected, boolean hasFocus, int row,
1773 setSelected((boolean) value);
1775 // set colours to match rest of table
1778 setBackground(table.getSelectionBackground());
1779 setForeground(table.getSelectionForeground());
1783 setBackground(table.getBackground());
1784 setForeground(table.getForeground());
1791 * Customer cell editor for JTable: supports column of radio buttons in
1792 * conjunction with renderer
1794 public class RadioButtonEditor extends AbstractCellEditor
1795 implements TableCellEditor
1797 private JRadioButton button = new JRadioButton();
1799 public RadioButtonEditor()
1801 button.setHorizontalAlignment(SwingConstants.CENTER);
1802 this.button.addActionListener(new ActionListener()
1805 public void actionPerformed(ActionEvent e)
1807 fireEditingStopped();
1813 public Component getTableCellEditorComponent(JTable table, Object value,
1814 boolean isSelected, int row, int column)
1816 button.setSelected((boolean) value);
1821 public Object getCellEditorValue()
1823 return button.isSelected();