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 overviewTab;
188 protected JPanel gapColour = new JPanel();
190 protected JPanel hiddenColour = new JPanel();
192 protected JCheckBox useLegacyGap;
194 protected JCheckBox showHiddenAtStart;
196 protected JLabel gapLabel;
199 * Connections tab components
201 protected JTable linkUrlTable = new JTable();
203 protected JButton editLink = new JButton();
205 protected JButton deleteLink = new JButton();
207 protected JTextField filterTB = new JTextField();
209 protected JButton doReset = new JButton();
211 protected JButton userOnly = new JButton();
213 protected JLabel portLabel = new JLabel();
215 protected JLabel serverLabel = new JLabel();
217 protected JTextField proxyServerTB = new JTextField();
219 protected JTextField proxyPortTB = new JTextField();
221 protected JTextField defaultBrowser = new JTextField();
223 protected JCheckBox useProxy = new JCheckBox();
225 protected JCheckBox usagestats = new JCheckBox();
227 protected JCheckBox questionnaire = new JCheckBox();
229 protected JCheckBox versioncheck = new JCheckBox();
232 * Output tab components
234 protected JComboBox<Object> epsRendering = new JComboBox<>();
236 protected JLabel userIdWidthlabel = new JLabel();
238 protected JCheckBox autoIdWidth = new JCheckBox();
240 protected JTextField userIdWidth = new JTextField();
242 protected JCheckBox blcjv = new JCheckBox();
244 protected JCheckBox pileupjv = new JCheckBox();
246 protected JCheckBox clustaljv = new JCheckBox();
248 protected JCheckBox msfjv = new JCheckBox();
250 protected JCheckBox fastajv = new JCheckBox();
252 protected JCheckBox pfamjv = new JCheckBox();
254 protected JCheckBox pirjv = new JCheckBox();
256 protected JCheckBox modellerOutput = new JCheckBox();
258 protected JCheckBox embbedBioJSON = new JCheckBox();
261 * Editing tab components
263 protected JCheckBox autoCalculateConsCheck = new JCheckBox();
265 protected JCheckBox padGaps = new JCheckBox();
267 protected JCheckBox sortByTree = new JCheckBox();
272 protected JPanel dasTab = new JPanel();
277 protected JPanel wsTab = new JPanel();
280 * Creates a new GPreferences object.
282 public GPreferences()
287 } catch (Exception ex)
289 ex.printStackTrace();
294 * Construct the panel and its tabbed sub-panels.
298 private void jbInit() throws Exception
300 final JTabbedPane tabbedPane = new JTabbedPane();
301 this.setLayout(new BorderLayout());
302 JPanel okCancelPanel = initOkCancelPanel();
303 this.add(tabbedPane, BorderLayout.CENTER);
304 this.add(okCancelPanel, BorderLayout.SOUTH);
306 tabbedPane.add(initVisualTab(),
307 MessageManager.getString("label.visual"));
309 tabbedPane.add(initColoursTab(),
310 MessageManager.getString("label.colours"));
312 tabbedPane.add(initOverviewTab(),
313 MessageManager.getString("label.overview"));
315 tabbedPane.add(initStructureTab(),
316 MessageManager.getString("label.structure"));
318 tabbedPane.add(initConnectionsTab(),
319 MessageManager.getString("label.connections"));
321 tabbedPane.add(initLinksTab(),
322 MessageManager.getString("label.urllinks"));
324 tabbedPane.add(initOutputTab(),
325 MessageManager.getString("label.output"));
327 tabbedPane.add(initEditingTab(),
328 MessageManager.getString("label.editing"));
331 * See DasSourceBrowser for the real work of configuring this tab.
333 dasTab.setLayout(new BorderLayout());
334 tabbedPane.add(dasTab, MessageManager.getString("label.das_settings"));
337 * See WsPreferences for the real work of configuring this tab.
339 wsTab.setLayout(new BorderLayout());
340 tabbedPane.add(wsTab, MessageManager.getString("label.web_services"));
343 * Handler to validate a tab before leaving it - currently only for
346 tabbedPane.addChangeListener(new ChangeListener()
348 private Component lastTab;
351 public void stateChanged(ChangeEvent e)
353 if (lastTab == structureTab
354 && tabbedPane.getSelectedComponent() != structureTab)
356 if (!validateStructure())
358 tabbedPane.setSelectedComponent(structureTab);
362 lastTab = tabbedPane.getSelectedComponent();
369 * Initialises the Editing tabbed panel.
373 private JPanel initEditingTab()
375 JPanel editingTab = new JPanel();
376 editingTab.setLayout(null);
377 autoCalculateConsCheck.setFont(LABEL_FONT);
378 autoCalculateConsCheck.setText(
379 MessageManager.getString("label.autocalculate_consensus"));
380 autoCalculateConsCheck.setBounds(new Rectangle(21, 52, 209, 23));
381 padGaps.setFont(LABEL_FONT);
383 MessageManager.getString("label.pad_gaps_when_editing"));
384 padGaps.setBounds(new Rectangle(22, 94, 168, 23));
385 sortByTree.setFont(LABEL_FONT);
387 .setText(MessageManager.getString("label.sort_with_new_tree"));
388 sortByTree.setToolTipText(MessageManager.getString(
389 "label.any_trees_calculated_or_loaded_alignment_automatically_sort"));
390 sortByTree.setBounds(new Rectangle(22, 136, 168, 23));
391 editingTab.add(autoCalculateConsCheck);
392 editingTab.add(padGaps);
393 editingTab.add(sortByTree);
398 * Initialises the Output tabbed panel.
402 private JPanel initOutputTab()
404 JPanel outputTab = new JPanel();
405 outputTab.setLayout(null);
406 JLabel epsLabel = new JLabel();
407 epsLabel.setFont(LABEL_FONT);
408 epsLabel.setHorizontalAlignment(SwingConstants.RIGHT);
409 epsLabel.setText(MessageManager.getString("label.eps_rendering_style"));
410 epsLabel.setBounds(new Rectangle(9, 31, 140, 24));
411 epsRendering.setFont(LABEL_FONT);
412 epsRendering.setBounds(new Rectangle(154, 34, 187, 21));
413 JLabel jLabel1 = new JLabel();
414 jLabel1.setFont(LABEL_FONT);
415 jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
416 jLabel1.setText(MessageManager.getString("label.append_start_end"));
417 jLabel1.setFont(LABEL_FONT);
418 fastajv.setFont(LABEL_FONT);
419 fastajv.setHorizontalAlignment(SwingConstants.LEFT);
420 clustaljv.setText(MessageManager.getString("label.clustal") + " ");
421 blcjv.setText(MessageManager.getString("label.blc") + " ");
422 fastajv.setText(MessageManager.getString("label.fasta") + " ");
423 msfjv.setText(MessageManager.getString("label.msf") + " ");
424 pfamjv.setText(MessageManager.getString("label.pfam") + " ");
425 pileupjv.setText(MessageManager.getString("label.pileup") + " ");
426 msfjv.setFont(LABEL_FONT);
427 msfjv.setHorizontalAlignment(SwingConstants.LEFT);
428 pirjv.setText(MessageManager.getString("label.pir") + " ");
429 JPanel jPanel11 = new JPanel();
430 jPanel11.setFont(LABEL_FONT);
431 TitledBorder titledBorder2 = new TitledBorder(
432 MessageManager.getString("label.file_output"));
433 jPanel11.setBorder(titledBorder2);
434 jPanel11.setBounds(new Rectangle(30, 72, 196, 182));
435 GridLayout gridLayout3 = new GridLayout();
436 jPanel11.setLayout(gridLayout3);
437 gridLayout3.setRows(8);
438 blcjv.setFont(LABEL_FONT);
439 blcjv.setHorizontalAlignment(SwingConstants.LEFT);
440 clustaljv.setFont(LABEL_FONT);
441 clustaljv.setHorizontalAlignment(SwingConstants.LEFT);
442 pfamjv.setFont(LABEL_FONT);
443 pfamjv.setHorizontalAlignment(SwingConstants.LEFT);
444 pileupjv.setFont(LABEL_FONT);
445 pileupjv.setHorizontalAlignment(SwingConstants.LEFT);
446 pirjv.setFont(LABEL_FONT);
447 pirjv.setHorizontalAlignment(SwingConstants.LEFT);
448 autoIdWidth.setFont(LABEL_FONT);
450 MessageManager.getString("label.automatically_set_id_width"));
451 autoIdWidth.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager
452 .getString("label.adjusts_width_generated_eps_png")));
453 autoIdWidth.setBounds(new Rectangle(228, 96, 188, 23));
454 autoIdWidth.addActionListener(new ActionListener()
458 public void actionPerformed(ActionEvent e)
460 autoIdWidth_actionPerformed();
463 userIdWidthlabel.setFont(LABEL_FONT);
464 userIdWidthlabel.setText(
465 MessageManager.getString("label.figure_id_column_width"));
466 userIdWidth.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager
467 .getString("label.manually_specify_width_left_column")));
468 userIdWidthlabel.setToolTipText(
469 JvSwingUtils.wrapTooltip(true, MessageManager.getString(
470 "label.manually_specify_width_left_column")));
471 userIdWidthlabel.setBounds(new Rectangle(236, 120, 168, 23));
472 userIdWidth.setFont(JvSwingUtils.getTextAreaFont());
473 userIdWidth.setText("");
474 userIdWidth.setBounds(new Rectangle(232, 144, 84, 23));
475 userIdWidth.addActionListener(new ActionListener()
479 public void actionPerformed(ActionEvent e)
481 userIdWidth_actionPerformed();
484 modellerOutput.setFont(LABEL_FONT);
486 .setText(MessageManager.getString("label.use_modeller_output"));
487 modellerOutput.setBounds(new Rectangle(228, 226, 168, 23));
488 embbedBioJSON.setFont(LABEL_FONT);
489 embbedBioJSON.setText(MessageManager.getString("label.embbed_biojson"));
490 embbedBioJSON.setBounds(new Rectangle(228, 200, 250, 23));
492 jPanel11.add(jLabel1);
494 jPanel11.add(clustaljv);
495 jPanel11.add(fastajv);
497 jPanel11.add(pfamjv);
498 jPanel11.add(pileupjv);
500 outputTab.add(autoIdWidth);
501 outputTab.add(userIdWidth);
502 outputTab.add(userIdWidthlabel);
503 outputTab.add(modellerOutput);
504 outputTab.add(embbedBioJSON);
505 outputTab.add(epsLabel);
506 outputTab.add(epsRendering);
507 outputTab.add(jPanel11);
512 * Initialises the Connections tabbed panel.
516 private JPanel initConnectionsTab()
518 JPanel connectTab = new JPanel();
519 connectTab.setLayout(new GridBagLayout());
521 // Label for browser text box
522 JLabel browserLabel = new JLabel();
523 browserLabel.setFont(LABEL_FONT);
524 browserLabel.setHorizontalAlignment(SwingConstants.TRAILING);
525 browserLabel.setText(
526 MessageManager.getString("label.default_browser_unix"));
527 defaultBrowser.setFont(LABEL_FONT);
528 defaultBrowser.setText("");
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 gapLabel = new JLabel(
1027 MessageManager.getString("label.gap_colour"));
1028 gapLabel.setFont(LABEL_FONT);
1029 gapLabel.setHorizontalAlignment(SwingConstants.LEFT);
1030 showHiddenAtStart = new JCheckBox(
1031 MessageManager.getString("label.ov_show_hide_default"));
1032 showHiddenAtStart.setFont(LABEL_FONT);
1033 showHiddenAtStart.setHorizontalAlignment(SwingConstants.LEFT);
1034 JLabel hiddenLabel = new JLabel(
1035 MessageManager.getString("label.hidden_colour"));
1036 hiddenLabel.setFont(LABEL_FONT);
1037 hiddenLabel.setHorizontalAlignment(SwingConstants.LEFT);
1039 useLegacyGap.addActionListener(new ActionListener()
1042 public void actionPerformed(ActionEvent e)
1044 useLegacyGaps_actionPerformed(e);
1048 overviewPanel.setLayout(new GridBagLayout());
1049 GridBagConstraints c1 = new GridBagConstraints();
1051 c1.fill = GridBagConstraints.HORIZONTAL;
1056 c1.anchor = GridBagConstraints.FIRST_LINE_START;
1057 overviewPanel.add(useLegacyGap, c1);
1059 GridBagConstraints c2 = new GridBagConstraints();
1060 c2.fill = GridBagConstraints.HORIZONTAL;
1063 c2.insets = new Insets(0, 15, 0, 10);
1064 overviewPanel.add(gapLabel, c2);
1066 GridBagConstraints c3 = new GridBagConstraints();
1067 c3.fill = GridBagConstraints.HORIZONTAL;
1070 c3.insets = new Insets(0, 0, 0, 15);
1071 overviewPanel.add(gapColour, c3);
1073 GridBagConstraints c4 = new GridBagConstraints();
1074 c4.fill = GridBagConstraints.HORIZONTAL;
1078 overviewPanel.add(showHiddenAtStart, c4);
1080 GridBagConstraints c5 = new GridBagConstraints();
1081 c5.fill = GridBagConstraints.HORIZONTAL;
1084 c5.insets = new Insets(0, 15, 0, 10);
1085 overviewPanel.add(hiddenLabel, c5);
1087 GridBagConstraints c6 = new GridBagConstraints();
1088 c6.fill = GridBagConstraints.HORIZONTAL;
1091 c6.insets = new Insets(0, 0, 0, 15);
1092 overviewPanel.add(hiddenColour, c6);
1094 // Add padding so the panel doesn't look ridiculous
1095 JPanel spacePanel = new JPanel();
1096 overviewPanel.add(spacePanel,
1097 new GridBagConstraints(0, 2, 1, 1, 1.0, 1.0,
1098 GridBagConstraints.WEST, GridBagConstraints.BOTH,
1099 new Insets(0, 0, 0, 5), 0, 0));
1101 return overviewPanel;
1105 * Initialises the Structure tabbed panel.
1109 private JPanel initStructureTab()
1111 structureTab = new JPanel();
1113 structureTab.setBorder(new TitledBorder(
1114 MessageManager.getString("label.structure_options")));
1115 structureTab.setLayout(null);
1116 final int width = 400;
1117 final int height = 22;
1118 final int lineSpacing = 25;
1121 structFromPdb.setFont(LABEL_FONT);
1123 .setText(MessageManager.getString("label.struct_from_pdb"));
1124 structFromPdb.setBounds(new Rectangle(5, ypos, width, height));
1125 structFromPdb.addActionListener(new ActionListener()
1128 public void actionPerformed(ActionEvent e)
1130 boolean selected = structFromPdb.isSelected();
1131 // enable other options only when the first is checked
1132 useRnaView.setEnabled(selected);
1133 addSecondaryStructure.setEnabled(selected);
1134 addTempFactor.setEnabled(selected);
1137 structureTab.add(structFromPdb);
1139 // indent checkboxes that are conditional on the first one
1140 ypos += lineSpacing;
1141 useRnaView.setFont(LABEL_FONT);
1142 useRnaView.setText(MessageManager.getString("label.use_rnaview"));
1143 useRnaView.setBounds(new Rectangle(25, ypos, width, height));
1144 structureTab.add(useRnaView);
1146 ypos += lineSpacing;
1147 addSecondaryStructure.setFont(LABEL_FONT);
1148 addSecondaryStructure
1149 .setText(MessageManager.getString("label.autoadd_secstr"));
1150 addSecondaryStructure.setBounds(new Rectangle(25, ypos, width, height));
1151 structureTab.add(addSecondaryStructure);
1153 ypos += lineSpacing;
1154 addTempFactor.setFont(LABEL_FONT);
1155 addTempFactor.setText(MessageManager.getString("label.autoadd_temp"));
1156 addTempFactor.setBounds(new Rectangle(25, ypos, width, height));
1157 structureTab.add(addTempFactor);
1159 ypos += lineSpacing;
1160 JLabel viewerLabel = new JLabel();
1161 viewerLabel.setFont(LABEL_FONT);
1162 viewerLabel.setHorizontalAlignment(SwingConstants.LEFT);
1163 viewerLabel.setText(MessageManager.getString("label.structure_viewer"));
1164 viewerLabel.setBounds(new Rectangle(10, ypos, 200, height));
1165 structureTab.add(viewerLabel);
1167 structViewer.setFont(LABEL_FONT);
1168 structViewer.setBounds(new Rectangle(160, ypos, 120, height));
1169 structViewer.addItem(ViewerType.JMOL.name());
1170 structViewer.addItem(ViewerType.CHIMERA.name());
1171 structViewer.addActionListener(new ActionListener()
1174 public void actionPerformed(ActionEvent e)
1176 structureViewer_actionPerformed(
1177 (String) structViewer.getSelectedItem());
1180 structureTab.add(structViewer);
1182 ypos += lineSpacing;
1183 JLabel pathLabel = new JLabel();
1184 pathLabel.setFont(new java.awt.Font("SansSerif", 0, 11));
1185 pathLabel.setHorizontalAlignment(SwingConstants.LEFT);
1186 pathLabel.setText(MessageManager.getString("label.chimera_path"));
1187 final String tooltip = JvSwingUtils.wrapTooltip(true,
1188 MessageManager.getString("label.chimera_path_tip"));
1189 pathLabel.setToolTipText(tooltip);
1190 pathLabel.setBounds(new Rectangle(10, ypos, 140, height));
1191 structureTab.add(pathLabel);
1193 chimeraPath.setFont(LABEL_FONT);
1194 chimeraPath.setText("");
1195 chimeraPath.setBounds(new Rectangle(160, ypos, 300, height));
1196 chimeraPath.addMouseListener(new MouseAdapter()
1199 public void mouseClicked(MouseEvent e)
1201 if (e.getClickCount() == 2)
1203 String chosen = openFileChooser();
1206 chimeraPath.setText(chosen);
1211 structureTab.add(chimeraPath);
1213 ypos += lineSpacing;
1214 nwMapping.setFont(LABEL_FONT);
1215 nwMapping.setText(MessageManager.getString("label.nw_mapping"));
1216 siftsMapping.setFont(LABEL_FONT);
1217 siftsMapping.setText(MessageManager.getString("label.sifts_mapping"));
1218 mappingMethod.add(nwMapping);
1219 mappingMethod.add(siftsMapping);
1220 JPanel mappingPanel = new JPanel();
1221 mappingPanel.setFont(LABEL_FONT);
1222 TitledBorder mmTitledBorder = new TitledBorder(
1223 MessageManager.getString("label.mapping_method"));
1224 mmTitledBorder.setTitleFont(LABEL_FONT);
1225 mappingPanel.setBorder(mmTitledBorder);
1226 mappingPanel.setBounds(new Rectangle(10, ypos, 452, 45));
1227 // GridLayout mappingLayout = new GridLayout();
1228 mappingPanel.setLayout(new GridLayout());
1229 mappingPanel.add(nwMapping);
1230 mappingPanel.add(siftsMapping);
1231 structureTab.add(mappingPanel);
1233 ypos += lineSpacing;
1234 ypos += lineSpacing;
1235 FTSDataColumnPreferences docFieldPref = new FTSDataColumnPreferences(
1236 PreferenceSource.PREFERENCES, PDBFTSRestClient.getInstance());
1237 docFieldPref.setBounds(new Rectangle(10, ypos, 450, 120));
1238 structureTab.add(docFieldPref);
1240 return structureTab;
1244 * Action on choosing a structure viewer from combobox options.
1246 * @param selectedItem
1248 protected void structureViewer_actionPerformed(String selectedItem)
1253 * Show a dialog for the user to choose a file. Returns the chosen path, or
1258 protected String openFileChooser()
1260 String choice = null;
1261 JFileChooser chooser = new JFileChooser();
1263 // chooser.setFileView(new JalviewFileView());
1264 chooser.setDialogTitle(
1265 MessageManager.getString("label.open_local_file"));
1266 chooser.setToolTipText(MessageManager.getString("action.open"));
1268 int value = chooser.showOpenDialog(this);
1270 if (value == JFileChooser.APPROVE_OPTION)
1272 choice = chooser.getSelectedFile().getPath();
1278 * Validate the structure tab preferences; if invalid, set focus on this tab.
1282 protected boolean validateStructure(FocusEvent e)
1284 if (!validateStructure())
1286 e.getComponent().requestFocusInWindow();
1292 protected boolean validateStructure()
1298 * Initialises the Visual tabbed panel.
1302 private JPanel initVisualTab()
1304 JPanel visualTab = new JPanel();
1305 visualTab.setBorder(new TitledBorder(
1306 MessageManager.getString("action.open_new_alignment")));
1307 visualTab.setLayout(null);
1308 fullScreen.setFont(LABEL_FONT);
1309 fullScreen.setHorizontalAlignment(SwingConstants.RIGHT);
1310 fullScreen.setHorizontalTextPosition(SwingConstants.LEFT);
1311 fullScreen.setText(MessageManager.getString("label.maximize_window"));
1312 quality.setEnabled(false);
1313 quality.setFont(LABEL_FONT);
1314 quality.setHorizontalAlignment(SwingConstants.RIGHT);
1315 quality.setHorizontalTextPosition(SwingConstants.LEFT);
1316 quality.setSelected(true);
1317 quality.setText(MessageManager.getString("label.quality"));
1318 conservation.setEnabled(false);
1319 conservation.setFont(LABEL_FONT);
1320 conservation.setHorizontalAlignment(SwingConstants.RIGHT);
1321 conservation.setHorizontalTextPosition(SwingConstants.LEFT);
1322 conservation.setSelected(true);
1323 conservation.setText(MessageManager.getString("label.conservation"));
1324 identity.setEnabled(false);
1325 identity.setFont(LABEL_FONT);
1326 identity.setHorizontalAlignment(SwingConstants.RIGHT);
1327 identity.setHorizontalTextPosition(SwingConstants.LEFT);
1328 identity.setSelected(true);
1329 identity.setText(MessageManager.getString("label.consensus"));
1330 showOccupancy.setFont(LABEL_FONT);
1331 showOccupancy.setEnabled(false);
1332 showOccupancy.setHorizontalAlignment(SwingConstants.RIGHT);
1333 showOccupancy.setHorizontalTextPosition(SwingConstants.LEFT);
1334 showOccupancy.setSelected(true);
1335 showOccupancy.setText(MessageManager.getString("label.occupancy"));
1337 JLabel showGroupbits = new JLabel();
1338 showGroupbits.setFont(LABEL_FONT);
1339 showGroupbits.setHorizontalAlignment(SwingConstants.RIGHT);
1340 showGroupbits.setHorizontalTextPosition(SwingConstants.LEFT);
1342 .setText(MessageManager.getString("action.show_group") + ":");
1343 JLabel showConsensbits = new JLabel();
1344 showConsensbits.setFont(LABEL_FONT);
1345 showConsensbits.setHorizontalAlignment(SwingConstants.RIGHT);
1346 showConsensbits.setHorizontalTextPosition(SwingConstants.LEFT);
1348 .setText(MessageManager.getString("label.consensus") + ":");
1349 showConsensHistogram.setEnabled(false);
1350 showConsensHistogram.setFont(LABEL_FONT);
1351 showConsensHistogram.setHorizontalAlignment(SwingConstants.RIGHT);
1352 showConsensHistogram.setHorizontalTextPosition(SwingConstants.LEFT);
1353 showConsensHistogram.setSelected(true);
1354 showConsensHistogram
1355 .setText(MessageManager.getString("label.histogram"));
1356 showConsensLogo.setEnabled(false);
1357 showConsensLogo.setFont(LABEL_FONT);
1358 showConsensLogo.setHorizontalAlignment(SwingConstants.RIGHT);
1359 showConsensLogo.setHorizontalTextPosition(SwingConstants.LEFT);
1360 showConsensLogo.setSelected(true);
1361 showConsensLogo.setText(MessageManager.getString("label.logo"));
1362 showGroupConsensus.setEnabled(false);
1363 showGroupConsensus.setFont(LABEL_FONT);
1364 showGroupConsensus.setHorizontalAlignment(SwingConstants.RIGHT);
1365 showGroupConsensus.setHorizontalTextPosition(SwingConstants.LEFT);
1366 showGroupConsensus.setSelected(true);
1367 showGroupConsensus.setText(MessageManager.getString("label.consensus"));
1368 showGroupConservation.setEnabled(false);
1369 showGroupConservation.setFont(LABEL_FONT);
1370 showGroupConservation.setHorizontalAlignment(SwingConstants.RIGHT);
1371 showGroupConservation.setHorizontalTextPosition(SwingConstants.LEFT);
1372 showGroupConservation.setSelected(true);
1373 showGroupConservation
1374 .setText(MessageManager.getString("label.conservation"));
1375 showNpTooltip.setEnabled(true);
1376 showNpTooltip.setFont(LABEL_FONT);
1377 showNpTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
1378 showNpTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
1379 showNpTooltip.setSelected(true);
1380 showNpTooltip.setText(
1381 MessageManager.getString("label.non_positional_features"));
1382 showDbRefTooltip.setEnabled(true);
1383 showDbRefTooltip.setFont(LABEL_FONT);
1384 showDbRefTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
1385 showDbRefTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
1386 showDbRefTooltip.setSelected(true);
1388 .setText(MessageManager.getString("label.database_references"));
1389 annotations.setFont(LABEL_FONT);
1390 annotations.setHorizontalAlignment(SwingConstants.RIGHT);
1391 annotations.setHorizontalTextPosition(SwingConstants.LEFT);
1392 annotations.setSelected(true);
1393 annotations.setText(MessageManager.getString("label.show_annotations"));
1394 // annotations.setBounds(new Rectangle(169, 12, 200, 23));
1395 annotations.addActionListener(new ActionListener()
1398 public void actionPerformed(ActionEvent e)
1400 annotations_actionPerformed(e);
1403 identity.addActionListener(new ActionListener()
1406 public void actionPerformed(ActionEvent e)
1408 annotations_actionPerformed(e);
1411 showGroupConsensus.addActionListener(new ActionListener()
1414 public void actionPerformed(ActionEvent e)
1416 annotations_actionPerformed(e);
1419 showUnconserved.setFont(LABEL_FONT);
1420 showUnconserved.setHorizontalAlignment(SwingConstants.RIGHT);
1421 showUnconserved.setHorizontalTextPosition(SwingConstants.LEFT);
1422 showUnconserved.setSelected(true);
1424 .setText(MessageManager.getString("action.show_unconserved"));
1425 showUnconserved.addActionListener(new ActionListener()
1428 public void actionPerformed(ActionEvent e)
1430 showunconserved_actionPerformed(e);
1434 // TODO these are not yet added to / action from Preferences
1435 // JCheckBox shareSelections = new JCheckBox();
1436 // shareSelections.setFont(verdana11);
1437 // shareSelections.setHorizontalAlignment(SwingConstants.RIGHT);
1438 // shareSelections.setHorizontalTextPosition(SwingConstants.LEFT);
1439 // shareSelections.setSelected(true);
1440 // shareSelections.setText(MessageManager
1441 // .getString("label.share_selection_across_views"));
1442 // JCheckBox followHighlight = new JCheckBox();
1443 // followHighlight.setFont(verdana11);
1444 // followHighlight.setHorizontalAlignment(SwingConstants.RIGHT);
1445 // followHighlight.setHorizontalTextPosition(SwingConstants.LEFT);
1446 // // showUnconserved.setBounds(new Rectangle(169, 40, 200, 23));
1447 // followHighlight.setSelected(true);
1448 // followHighlight.setText(MessageManager
1449 // .getString("label.scroll_highlighted_regions"));
1451 seqLimit.setFont(LABEL_FONT);
1452 seqLimit.setHorizontalAlignment(SwingConstants.RIGHT);
1453 seqLimit.setHorizontalTextPosition(SwingConstants.LEFT);
1454 seqLimit.setText(MessageManager.getString("label.full_sequence_id"));
1455 smoothFont.setFont(LABEL_FONT);
1456 smoothFont.setHorizontalAlignment(SwingConstants.RIGHT);
1457 smoothFont.setHorizontalTextPosition(SwingConstants.LEADING);
1458 smoothFont.setText(MessageManager.getString("label.smooth_font"));
1459 scaleProteinToCdna.setFont(LABEL_FONT);
1460 scaleProteinToCdna.setHorizontalAlignment(SwingConstants.RIGHT);
1461 scaleProteinToCdna.setHorizontalTextPosition(SwingConstants.LEADING);
1462 scaleProteinToCdna.setText(
1463 MessageManager.getString("label.scale_protein_to_cdna"));
1464 scaleProteinToCdna.setToolTipText(
1465 MessageManager.getString("label.scale_protein_to_cdna_tip"));
1466 JLabel gapLabel = new JLabel();
1467 gapLabel.setFont(LABEL_FONT);
1468 gapLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1469 gapLabel.setText(MessageManager.getString("label.gap_symbol") + " ");
1470 JLabel fontLabel = new JLabel();
1471 fontLabel.setFont(LABEL_FONT);
1472 fontLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1473 fontLabel.setText(MessageManager.getString("label.font"));
1474 fontSizeCB.setFont(LABEL_FONT);
1475 fontSizeCB.setBounds(new Rectangle(320, 112, 65, 23));
1476 fontStyleCB.setFont(LABEL_FONT);
1477 fontStyleCB.setBounds(new Rectangle(382, 112, 80, 23));
1478 fontNameCB.setFont(LABEL_FONT);
1479 fontNameCB.setBounds(new Rectangle(172, 112, 147, 23));
1480 gapSymbolCB.setFont(LABEL_FONT);
1481 gapSymbolCB.setBounds(new Rectangle(172, 215, 69, 23));
1482 DefaultListCellRenderer dlcr = new DefaultListCellRenderer();
1483 dlcr.setHorizontalAlignment(DefaultListCellRenderer.CENTER);
1484 gapSymbolCB.setRenderer(dlcr);
1486 startupCheckbox.setText(MessageManager.getString("action.open_file"));
1487 startupCheckbox.setFont(LABEL_FONT);
1488 startupCheckbox.setHorizontalAlignment(SwingConstants.RIGHT);
1489 startupCheckbox.setHorizontalTextPosition(SwingConstants.LEFT);
1490 startupCheckbox.setSelected(true);
1491 startupFileTextfield.setFont(LABEL_FONT);
1492 startupFileTextfield.setBounds(new Rectangle(172, 310, 330, 20));
1493 startupFileTextfield.addMouseListener(new MouseAdapter()
1496 public void mouseClicked(MouseEvent e)
1498 if (e.getClickCount() > 1)
1500 startupFileTextfield_mouseClicked();
1505 sortby.setFont(LABEL_FONT);
1506 sortby.setBounds(new Rectangle(172, 260, 155, 21));
1507 JLabel sortLabel = new JLabel();
1508 sortLabel.setFont(LABEL_FONT);
1509 sortLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1510 sortLabel.setText(MessageManager.getString("label.sort_by"));
1511 sortAnnBy.setFont(LABEL_FONT);
1512 sortAnnBy.setBounds(new Rectangle(172, 285, 110, 21));
1513 JLabel sortAnnLabel = new JLabel();
1514 sortAnnLabel.setFont(LABEL_FONT);
1515 sortAnnLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1516 sortAnnLabel.setText(MessageManager.getString("label.sort_ann_by"));
1517 sortAutocalc.setFont(LABEL_FONT);
1518 sortAutocalc.setBounds(new Rectangle(290, 285, 165, 21));
1520 JPanel annsettingsPanel = new JPanel();
1521 annsettingsPanel.setBounds(new Rectangle(173, 13, 320, 96));
1522 annsettingsPanel.setLayout(new FlowLayout(FlowLayout.LEFT, 0, 0));
1523 annsettingsPanel.setBorder(new EtchedBorder());
1524 visualTab.add(annsettingsPanel);
1525 Border jb = new EmptyBorder(1, 1, 4, 5);
1526 annotations.setBorder(jb);
1527 showOccupancy.setBorder(jb);
1528 quality.setBorder(jb);
1529 conservation.setBorder(jb);
1530 identity.setBorder(jb);
1531 showConsensbits.setBorder(jb);
1532 showGroupbits.setBorder(jb);
1533 showGroupConsensus.setBorder(jb);
1534 showGroupConservation.setBorder(jb);
1535 showConsensHistogram.setBorder(jb);
1536 showConsensLogo.setBorder(jb);
1538 JPanel autoAnnotSettings = new JPanel();
1539 annsettingsPanel.add(autoAnnotSettings);
1540 autoAnnotSettings.setLayout(new GridLayout(0, 2));
1541 autoAnnotSettings.add(annotations);
1542 autoAnnotSettings.add(quality);
1543 // second row of autoannotation box
1544 autoAnnotSettings = new JPanel();
1545 annsettingsPanel.add(autoAnnotSettings);
1547 autoAnnotSettings.setLayout(new GridLayout(0, 3));
1548 autoAnnotSettings.add(conservation);
1549 autoAnnotSettings.add(identity);
1550 autoAnnotSettings.add(showOccupancy);
1551 autoAnnotSettings.add(showGroupbits);
1552 autoAnnotSettings.add(showGroupConservation);
1553 autoAnnotSettings.add(showGroupConsensus);
1554 autoAnnotSettings.add(showConsensbits);
1555 autoAnnotSettings.add(showConsensHistogram);
1556 autoAnnotSettings.add(showConsensLogo);
1558 JPanel tooltipSettings = new JPanel();
1559 tooltipSettings.setBorder(new TitledBorder(
1560 MessageManager.getString("label.sequence_id_tooltip")));
1561 tooltipSettings.setBounds(173, 140, 220, 62);
1562 tooltipSettings.setLayout(new GridLayout(2, 1));
1563 tooltipSettings.add(showDbRefTooltip);
1564 tooltipSettings.add(showNpTooltip);
1565 visualTab.add(tooltipSettings);
1567 wrap.setFont(LABEL_FONT);
1568 wrap.setHorizontalAlignment(SwingConstants.TRAILING);
1569 wrap.setHorizontalTextPosition(SwingConstants.LEADING);
1570 wrap.setText(MessageManager.getString("label.wrap_alignment"));
1571 rightAlign.setFont(LABEL_FONT);
1572 rightAlign.setForeground(Color.black);
1573 rightAlign.setHorizontalAlignment(SwingConstants.RIGHT);
1574 rightAlign.setHorizontalTextPosition(SwingConstants.LEFT);
1575 rightAlign.setText(MessageManager.getString("label.right_align_ids"));
1576 idItalics.setFont(LABEL_FONT_ITALIC);
1577 idItalics.setHorizontalAlignment(SwingConstants.RIGHT);
1578 idItalics.setHorizontalTextPosition(SwingConstants.LEADING);
1580 MessageManager.getString("label.sequence_name_italics"));
1581 openoverv.setFont(LABEL_FONT);
1582 openoverv.setActionCommand(
1583 MessageManager.getString("label.open_overview"));
1584 openoverv.setHorizontalAlignment(SwingConstants.RIGHT);
1585 openoverv.setHorizontalTextPosition(SwingConstants.LEFT);
1586 openoverv.setText(MessageManager.getString("label.open_overview"));
1587 JPanel jPanel2 = new JPanel();
1588 jPanel2.setBounds(new Rectangle(7, 17, 158, 310));
1589 jPanel2.setLayout(new GridLayout(14, 1));
1590 jPanel2.add(fullScreen);
1591 jPanel2.add(openoverv);
1592 jPanel2.add(seqLimit);
1593 jPanel2.add(rightAlign);
1594 jPanel2.add(fontLabel);
1595 jPanel2.add(showUnconserved);
1596 jPanel2.add(idItalics);
1597 jPanel2.add(smoothFont);
1598 jPanel2.add(scaleProteinToCdna);
1599 jPanel2.add(gapLabel);
1601 jPanel2.add(sortLabel);
1602 jPanel2.add(sortAnnLabel);
1603 jPanel2.add(startupCheckbox);
1604 visualTab.add(jPanel2);
1605 visualTab.add(startupFileTextfield);
1606 visualTab.add(sortby);
1607 visualTab.add(sortAnnBy);
1608 visualTab.add(sortAutocalc);
1609 visualTab.add(gapSymbolCB);
1610 visualTab.add(fontNameCB);
1611 visualTab.add(fontSizeCB);
1612 visualTab.add(fontStyleCB);
1616 protected void autoIdWidth_actionPerformed()
1618 // TODO Auto-generated method stub
1622 protected void userIdWidth_actionPerformed()
1624 // TODO Auto-generated method stub
1628 protected void maxColour_actionPerformed(JPanel panel)
1632 protected void minColour_actionPerformed(JPanel panel)
1636 protected void gapColour_actionPerformed(JPanel panel)
1640 protected void hiddenColour_actionPerformed(JPanel panel)
1644 protected void showunconserved_actionPerformed(ActionEvent e)
1646 // TODO Auto-generated method stub
1650 protected void useLegacyGaps_actionPerformed(ActionEvent e)
1652 boolean enabled = useLegacyGap.isSelected();
1655 gapColour.setBackground(Color.WHITE);
1657 gapColour.setEnabled(!enabled);
1658 gapLabel.setEnabled(!enabled);
1667 public void ok_actionPerformed(ActionEvent e)
1677 public void cancel_actionPerformed(ActionEvent e)
1687 public void annotations_actionPerformed(ActionEvent e)
1694 public void startupFileTextfield_mouseClicked()
1698 public void newLink_actionPerformed(ActionEvent e)
1703 public void editLink_actionPerformed(ActionEvent e)
1708 public void deleteLink_actionPerformed(ActionEvent e)
1713 public void defaultBrowser_mouseClicked(MouseEvent e)
1718 public void linkURLList_keyTyped(KeyEvent e)
1723 public void useProxy_actionPerformed()
1725 boolean enabled = useProxy.isSelected();
1726 portLabel.setEnabled(enabled);
1727 serverLabel.setEnabled(enabled);
1728 proxyServerTB.setEnabled(enabled);
1729 proxyPortTB.setEnabled(enabled);
1733 * Customer renderer for JTable: supports column of radio buttons
1735 public class RadioButtonRenderer extends JRadioButton
1736 implements TableCellRenderer
1738 public RadioButtonRenderer()
1740 setHorizontalAlignment(CENTER);
1741 setToolTipText(MessageManager.getString("label.urltooltip"));
1745 public Component getTableCellRendererComponent(JTable table,
1746 Object value, boolean isSelected, boolean hasFocus, int row,
1749 setSelected((boolean) value);
1751 // set colours to match rest of table
1754 setBackground(table.getSelectionBackground());
1755 setForeground(table.getSelectionForeground());
1759 setBackground(table.getBackground());
1760 setForeground(table.getForeground());
1767 * Customer cell editor for JTable: supports column of radio buttons in
1768 * conjunction with renderer
1770 public class RadioButtonEditor extends AbstractCellEditor
1771 implements TableCellEditor
1773 private JRadioButton button = new JRadioButton();
1775 public RadioButtonEditor()
1777 button.setHorizontalAlignment(SwingConstants.CENTER);
1778 this.button.addActionListener(new ActionListener()
1781 public void actionPerformed(ActionEvent e)
1783 fireEditingStopped();
1789 public Component getTableCellEditorComponent(JTable table, Object value,
1790 boolean isSelected, int row, int column)
1792 button.setSelected((boolean) value);
1797 public Object getCellEditorValue()
1799 return button.isSelected();