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;
198 protected JButton resetButton;
201 * Connections tab components
203 protected JTable linkUrlTable = new JTable();
205 protected JButton editLink = new JButton();
207 protected JButton deleteLink = new JButton();
209 protected JTextField filterTB = new JTextField();
211 protected JButton doReset = new JButton();
213 protected JButton userOnly = new JButton();
215 protected JLabel portLabel = new JLabel();
217 protected JLabel serverLabel = new JLabel();
219 protected JTextField proxyServerTB = new JTextField();
221 protected JTextField proxyPortTB = new JTextField();
223 protected JTextField defaultBrowser = new JTextField();
225 protected JCheckBox useProxy = new JCheckBox();
227 protected JCheckBox usagestats = new JCheckBox();
229 protected JCheckBox questionnaire = new JCheckBox();
231 protected JCheckBox versioncheck = new JCheckBox();
234 * Output tab components
236 protected JComboBox<Object> epsRendering = new JComboBox<>();
238 protected JLabel userIdWidthlabel = new JLabel();
240 protected JCheckBox autoIdWidth = new JCheckBox();
242 protected JTextField userIdWidth = new JTextField();
244 protected JCheckBox blcjv = new JCheckBox();
246 protected JCheckBox pileupjv = new JCheckBox();
248 protected JCheckBox clustaljv = new JCheckBox();
250 protected JCheckBox msfjv = new JCheckBox();
252 protected JCheckBox fastajv = new JCheckBox();
254 protected JCheckBox pfamjv = new JCheckBox();
256 protected JCheckBox pirjv = new JCheckBox();
258 protected JCheckBox modellerOutput = new JCheckBox();
260 protected JCheckBox embbedBioJSON = new JCheckBox();
263 * Editing tab components
265 protected JCheckBox autoCalculateConsCheck = new JCheckBox();
267 protected JCheckBox padGaps = new JCheckBox();
269 protected JCheckBox sortByTree = new JCheckBox();
274 protected JPanel dasTab = new JPanel();
279 protected JPanel wsTab = new JPanel();
282 * Creates a new GPreferences object.
284 public GPreferences()
289 } catch (Exception ex)
291 ex.printStackTrace();
296 * Construct the panel and its tabbed sub-panels.
300 private void jbInit() throws Exception
302 final JTabbedPane tabbedPane = new JTabbedPane();
303 this.setLayout(new BorderLayout());
304 JPanel okCancelPanel = initOkCancelPanel();
305 this.add(tabbedPane, BorderLayout.CENTER);
306 this.add(okCancelPanel, BorderLayout.SOUTH);
308 tabbedPane.add(initVisualTab(),
309 MessageManager.getString("label.visual"));
311 tabbedPane.add(initColoursTab(),
312 MessageManager.getString("label.colours"));
314 tabbedPane.add(initOverviewTab(),
315 MessageManager.getString("label.overview"));
317 tabbedPane.add(initStructureTab(),
318 MessageManager.getString("label.structure"));
320 tabbedPane.add(initConnectionsTab(),
321 MessageManager.getString("label.connections"));
323 tabbedPane.add(initLinksTab(),
324 MessageManager.getString("label.urllinks"));
326 tabbedPane.add(initOutputTab(),
327 MessageManager.getString("label.output"));
329 tabbedPane.add(initEditingTab(),
330 MessageManager.getString("label.editing"));
333 * See DasSourceBrowser for the real work of configuring this tab.
335 dasTab.setLayout(new BorderLayout());
336 tabbedPane.add(dasTab, MessageManager.getString("label.das_settings"));
339 * See WsPreferences for the real work of configuring this tab.
341 wsTab.setLayout(new BorderLayout());
342 tabbedPane.add(wsTab, MessageManager.getString("label.web_services"));
345 * Handler to validate a tab before leaving it - currently only for
348 tabbedPane.addChangeListener(new ChangeListener()
350 private Component lastTab;
353 public void stateChanged(ChangeEvent e)
355 if (lastTab == structureTab
356 && tabbedPane.getSelectedComponent() != structureTab)
358 if (!validateStructure())
360 tabbedPane.setSelectedComponent(structureTab);
364 lastTab = tabbedPane.getSelectedComponent();
371 * Initialises the Editing tabbed panel.
375 private JPanel initEditingTab()
377 JPanel editingTab = new JPanel();
378 editingTab.setLayout(null);
379 autoCalculateConsCheck.setFont(LABEL_FONT);
380 autoCalculateConsCheck.setText(
381 MessageManager.getString("label.autocalculate_consensus"));
382 autoCalculateConsCheck.setBounds(new Rectangle(21, 52, 209, 23));
383 padGaps.setFont(LABEL_FONT);
385 MessageManager.getString("label.pad_gaps_when_editing"));
386 padGaps.setBounds(new Rectangle(22, 94, 168, 23));
387 sortByTree.setFont(LABEL_FONT);
389 .setText(MessageManager.getString("label.sort_with_new_tree"));
390 sortByTree.setToolTipText(MessageManager.getString(
391 "label.any_trees_calculated_or_loaded_alignment_automatically_sort"));
392 sortByTree.setBounds(new Rectangle(22, 136, 168, 23));
393 editingTab.add(autoCalculateConsCheck);
394 editingTab.add(padGaps);
395 editingTab.add(sortByTree);
400 * Initialises the Output tabbed panel.
404 private JPanel initOutputTab()
406 JPanel outputTab = new JPanel();
407 outputTab.setLayout(null);
408 JLabel epsLabel = new JLabel();
409 epsLabel.setFont(LABEL_FONT);
410 epsLabel.setHorizontalAlignment(SwingConstants.RIGHT);
411 epsLabel.setText(MessageManager.getString("label.eps_rendering_style"));
412 epsLabel.setBounds(new Rectangle(9, 31, 140, 24));
413 epsRendering.setFont(LABEL_FONT);
414 epsRendering.setBounds(new Rectangle(154, 34, 187, 21));
415 JLabel jLabel1 = new JLabel();
416 jLabel1.setFont(LABEL_FONT);
417 jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
418 jLabel1.setText(MessageManager.getString("label.append_start_end"));
419 jLabel1.setFont(LABEL_FONT);
420 fastajv.setFont(LABEL_FONT);
421 fastajv.setHorizontalAlignment(SwingConstants.LEFT);
422 clustaljv.setText(MessageManager.getString("label.clustal") + " ");
423 blcjv.setText(MessageManager.getString("label.blc") + " ");
424 fastajv.setText(MessageManager.getString("label.fasta") + " ");
425 msfjv.setText(MessageManager.getString("label.msf") + " ");
426 pfamjv.setText(MessageManager.getString("label.pfam") + " ");
427 pileupjv.setText(MessageManager.getString("label.pileup") + " ");
428 msfjv.setFont(LABEL_FONT);
429 msfjv.setHorizontalAlignment(SwingConstants.LEFT);
430 pirjv.setText(MessageManager.getString("label.pir") + " ");
431 JPanel jPanel11 = new JPanel();
432 jPanel11.setFont(LABEL_FONT);
433 TitledBorder titledBorder2 = new TitledBorder(
434 MessageManager.getString("label.file_output"));
435 jPanel11.setBorder(titledBorder2);
436 jPanel11.setBounds(new Rectangle(30, 72, 196, 182));
437 GridLayout gridLayout3 = new GridLayout();
438 jPanel11.setLayout(gridLayout3);
439 gridLayout3.setRows(8);
440 blcjv.setFont(LABEL_FONT);
441 blcjv.setHorizontalAlignment(SwingConstants.LEFT);
442 clustaljv.setFont(LABEL_FONT);
443 clustaljv.setHorizontalAlignment(SwingConstants.LEFT);
444 pfamjv.setFont(LABEL_FONT);
445 pfamjv.setHorizontalAlignment(SwingConstants.LEFT);
446 pileupjv.setFont(LABEL_FONT);
447 pileupjv.setHorizontalAlignment(SwingConstants.LEFT);
448 pirjv.setFont(LABEL_FONT);
449 pirjv.setHorizontalAlignment(SwingConstants.LEFT);
450 autoIdWidth.setFont(LABEL_FONT);
452 MessageManager.getString("label.automatically_set_id_width"));
453 autoIdWidth.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager
454 .getString("label.adjusts_width_generated_eps_png")));
455 autoIdWidth.setBounds(new Rectangle(228, 96, 188, 23));
456 autoIdWidth.addActionListener(new ActionListener()
460 public void actionPerformed(ActionEvent e)
462 autoIdWidth_actionPerformed();
465 userIdWidthlabel.setFont(LABEL_FONT);
466 userIdWidthlabel.setText(
467 MessageManager.getString("label.figure_id_column_width"));
468 userIdWidth.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager
469 .getString("label.manually_specify_width_left_column")));
470 userIdWidthlabel.setToolTipText(
471 JvSwingUtils.wrapTooltip(true, MessageManager.getString(
472 "label.manually_specify_width_left_column")));
473 userIdWidthlabel.setBounds(new Rectangle(236, 120, 168, 23));
474 userIdWidth.setFont(JvSwingUtils.getTextAreaFont());
475 userIdWidth.setText("");
476 userIdWidth.setBounds(new Rectangle(232, 144, 84, 23));
477 userIdWidth.addActionListener(new ActionListener()
481 public void actionPerformed(ActionEvent e)
483 userIdWidth_actionPerformed();
486 modellerOutput.setFont(LABEL_FONT);
488 .setText(MessageManager.getString("label.use_modeller_output"));
489 modellerOutput.setBounds(new Rectangle(228, 226, 168, 23));
490 embbedBioJSON.setFont(LABEL_FONT);
491 embbedBioJSON.setText(MessageManager.getString("label.embbed_biojson"));
492 embbedBioJSON.setBounds(new Rectangle(228, 200, 250, 23));
494 jPanel11.add(jLabel1);
496 jPanel11.add(clustaljv);
497 jPanel11.add(fastajv);
499 jPanel11.add(pfamjv);
500 jPanel11.add(pileupjv);
502 outputTab.add(autoIdWidth);
503 outputTab.add(userIdWidth);
504 outputTab.add(userIdWidthlabel);
505 outputTab.add(modellerOutput);
506 outputTab.add(embbedBioJSON);
507 outputTab.add(epsLabel);
508 outputTab.add(epsRendering);
509 outputTab.add(jPanel11);
514 * Initialises the Connections tabbed panel.
518 private JPanel initConnectionsTab()
520 JPanel connectTab = new JPanel();
521 connectTab.setLayout(new GridBagLayout());
523 // Label for browser text box
524 JLabel browserLabel = new JLabel();
525 browserLabel.setFont(LABEL_FONT);
526 browserLabel.setHorizontalAlignment(SwingConstants.TRAILING);
527 browserLabel.setText(
528 MessageManager.getString("label.default_browser_unix"));
529 defaultBrowser.setFont(LABEL_FONT);
530 defaultBrowser.setText("");
532 defaultBrowser.addMouseListener(new MouseAdapter()
535 public void mouseClicked(MouseEvent e)
537 if (e.getClickCount() > 1)
539 defaultBrowser_mouseClicked(e);
544 JPanel proxyPanel = initConnTabProxyPanel();
545 initConnTabCheckboxes();
547 // Add default Browser text box
548 connectTab.add(browserLabel,
549 new GridBagConstraints(0, 0, 1, 1, 0.0, 0.0,
550 GridBagConstraints.WEST, GridBagConstraints.NONE,
551 new Insets(10, 0, 5, 5), 5, 1));
552 defaultBrowser.setFont(LABEL_FONT);
553 defaultBrowser.setText("");
555 connectTab.add(defaultBrowser, new GridBagConstraints(1, 0, 1, 1, 1.0,
556 0.0, GridBagConstraints.CENTER, GridBagConstraints.HORIZONTAL,
557 new Insets(10, 0, 5, 10), 30, 1));
559 // Add proxy server panel
560 connectTab.add(proxyPanel, new GridBagConstraints(0, 1, 2, 1, 1.0, 0.0,
561 GridBagConstraints.CENTER, GridBagConstraints.HORIZONTAL,
562 new Insets(10, 0, 5, 12), 4, 10));
564 // Add usage stats, version check and questionnaire checkboxes
565 connectTab.add(usagestats,
566 new GridBagConstraints(0, 2, 1, 1, 1.0, 0.0,
567 GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
568 new Insets(0, 2, 5, 5), 70, 1));
569 connectTab.add(questionnaire,
570 new GridBagConstraints(1, 2, 1, 1, 1.0, 0.0,
571 GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
572 new Insets(0, 2, 5, 10), 70, 1));
573 connectTab.add(versioncheck,
574 new GridBagConstraints(0, 3, 1, 1, 1.0, 0.0,
575 GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
576 new Insets(0, 2, 5, 5), 70, 1));
578 // Add padding so the panel doesn't look ridiculous
579 JPanel spacePanel = new JPanel();
580 connectTab.add(spacePanel,
581 new GridBagConstraints(0, 4, 1, 1, 1.0, 1.0,
582 GridBagConstraints.WEST, GridBagConstraints.BOTH,
583 new Insets(0, 0, 0, 5), 70, 1));
589 * Initialises the Links tabbed panel.
593 private JPanel initLinksTab()
595 JPanel linkTab = new JPanel();
596 linkTab.setLayout(new GridBagLayout());
598 // Set up table for Url links
599 linkUrlTable.setFillsViewportHeight(true);
600 linkUrlTable.setAutoResizeMode(JTable.AUTO_RESIZE_ALL_COLUMNS);
601 linkUrlTable.setAutoCreateRowSorter(true);
602 linkUrlTable.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
604 // adjust row height so radio buttons actually fit
605 // don't do this in the renderer, it causes the awt thread to activate
607 JRadioButton temp = new JRadioButton();
608 linkUrlTable.setRowHeight(temp.getMinimumSize().height);
610 // Table in scrollpane so that the table is given a scrollbar
611 JScrollPane linkScrollPane = new JScrollPane(linkUrlTable);
612 linkScrollPane.setBorder(null);
614 // Panel for links functionality
615 JPanel linkPanel = new JPanel(new GridBagLayout());
616 linkPanel.setBorder(new TitledBorder(
617 MessageManager.getString("label.url_linkfrom_sequence_id")));
619 // Put the Url links panel together
621 // Buttons go at top right, resizing only resizes the blank space vertically
622 JPanel buttonPanel = initLinkTabUrlButtons();
623 GridBagConstraints linkConstraints1 = new GridBagConstraints();
624 linkConstraints1.insets = new Insets(0, 0, 5, 0);
625 linkConstraints1.gridx = 0;
626 linkConstraints1.gridy = 0;
627 linkConstraints1.weightx = 1.0;
628 linkConstraints1.fill = GridBagConstraints.HORIZONTAL;
629 linkTab.add(buttonPanel, linkConstraints1);
631 // Links table goes at top left, resizing resizes the table
632 GridBagConstraints linkConstraints2 = new GridBagConstraints();
633 linkConstraints2.insets = new Insets(0, 0, 5, 5);
634 linkConstraints2.gridx = 0;
635 linkConstraints2.gridy = 1;
636 linkConstraints2.weightx = 1.0;
637 linkConstraints2.weighty = 1.0;
638 linkConstraints2.fill = GridBagConstraints.BOTH;
639 linkTab.add(linkScrollPane, linkConstraints2);
641 // Filter box and buttons goes at bottom left, resizing resizes the text box
642 JPanel filterPanel = initLinkTabFilterPanel();
643 GridBagConstraints linkConstraints3 = new GridBagConstraints();
644 linkConstraints3.insets = new Insets(0, 0, 0, 5);
645 linkConstraints3.gridx = 0;
646 linkConstraints3.gridy = 2;
647 linkConstraints3.weightx = 1.0;
648 linkConstraints3.fill = GridBagConstraints.HORIZONTAL;
649 linkTab.add(filterPanel, linkConstraints3);
654 private JPanel initLinkTabFilterPanel()
656 // Filter textbox and reset button
657 JLabel filterLabel = new JLabel(
658 MessageManager.getString("label.filter"));
659 filterLabel.setFont(LABEL_FONT);
660 filterLabel.setHorizontalAlignment(SwingConstants.RIGHT);
661 filterLabel.setHorizontalTextPosition(SwingConstants.LEADING);
663 filterTB.setFont(LABEL_FONT);
664 filterTB.setText("");
666 doReset.setText(MessageManager.getString("action.showall"));
667 userOnly.setText(MessageManager.getString("action.customfilter"));
669 // Panel for filter functionality
670 JPanel filterPanel = new JPanel(new GridBagLayout());
671 filterPanel.setBorder(new TitledBorder("Filter"));
672 GridBagConstraints gbc = new GridBagConstraints();
675 gbc.fill = GridBagConstraints.NONE;
676 gbc.anchor = GridBagConstraints.WEST;
678 filterPanel.add(filterLabel, gbc);
680 GridBagConstraints gbc1 = new GridBagConstraints();
683 gbc1.fill = GridBagConstraints.HORIZONTAL;
684 gbc1.anchor = GridBagConstraints.WEST;
686 filterPanel.add(filterTB, gbc1);
688 GridBagConstraints gbc2 = new GridBagConstraints();
690 gbc2.fill = GridBagConstraints.NONE;
691 gbc2.anchor = GridBagConstraints.WEST;
692 filterPanel.add(doReset, gbc2);
694 GridBagConstraints gbc3 = new GridBagConstraints();
696 gbc3.fill = GridBagConstraints.NONE;
697 gbc3.anchor = GridBagConstraints.WEST;
698 filterPanel.add(userOnly, gbc3);
703 private JPanel initLinkTabUrlButtons()
705 // Buttons for new / edit / delete Url links
706 JButton newLink = new JButton();
707 newLink.setText(MessageManager.getString("action.new"));
709 editLink.setText(MessageManager.getString("action.edit"));
711 deleteLink.setText(MessageManager.getString("action.delete"));
713 // no current selection, so initially disable delete/edit buttons
714 editLink.setEnabled(false);
715 deleteLink.setEnabled(false);
717 newLink.addActionListener(new java.awt.event.ActionListener()
720 public void actionPerformed(ActionEvent e)
722 newLink_actionPerformed(e);
726 editLink.setText(MessageManager.getString("action.edit"));
727 editLink.addActionListener(new java.awt.event.ActionListener()
730 public void actionPerformed(ActionEvent e)
732 editLink_actionPerformed(e);
736 deleteLink.setText(MessageManager.getString("action.delete"));
737 deleteLink.addActionListener(new java.awt.event.ActionListener()
740 public void actionPerformed(ActionEvent e)
742 deleteLink_actionPerformed(e);
746 JPanel buttonPanel = new JPanel(new GridBagLayout());
747 buttonPanel.setBorder(new TitledBorder("Edit links"));
748 GridBagConstraints gbc = new GridBagConstraints();
751 gbc.fill = GridBagConstraints.NONE;
752 buttonPanel.add(newLink, gbc);
754 GridBagConstraints gbc1 = new GridBagConstraints();
757 gbc1.fill = GridBagConstraints.NONE;
758 buttonPanel.add(editLink, gbc1);
760 GridBagConstraints gbc2 = new GridBagConstraints();
763 gbc2.fill = GridBagConstraints.NONE;
764 buttonPanel.add(deleteLink, gbc2);
766 GridBagConstraints gbc3 = new GridBagConstraints();
769 gbc3.fill = GridBagConstraints.HORIZONTAL;
771 JPanel spacePanel = new JPanel();
772 spacePanel.setBorder(null);
773 buttonPanel.add(spacePanel, gbc3);
779 * Initialises the proxy server panel in the Connections tab
781 * @return the proxy server panel
783 private JPanel initConnTabProxyPanel()
785 // Label for server text box
786 serverLabel.setText(MessageManager.getString("label.address"));
787 serverLabel.setHorizontalAlignment(SwingConstants.RIGHT);
788 serverLabel.setFont(LABEL_FONT);
790 // Proxy server and port text boxes
791 proxyServerTB.setFont(LABEL_FONT);
792 proxyPortTB.setFont(LABEL_FONT);
794 // Label for Port text box
795 portLabel.setFont(LABEL_FONT);
796 portLabel.setHorizontalAlignment(SwingConstants.RIGHT);
797 portLabel.setText(MessageManager.getString("label.port"));
799 // Use proxy server checkbox
800 useProxy.setFont(LABEL_FONT);
801 useProxy.setHorizontalAlignment(SwingConstants.RIGHT);
802 useProxy.setHorizontalTextPosition(SwingConstants.LEADING);
803 useProxy.setText(MessageManager.getString("label.use_proxy_server"));
804 useProxy.addActionListener(new ActionListener()
807 public void actionPerformed(ActionEvent e)
809 useProxy_actionPerformed();
813 // Make proxy server panel
814 JPanel proxyPanel = new JPanel();
815 TitledBorder titledBorder1 = new TitledBorder(
816 MessageManager.getString("label.proxy_server"));
817 proxyPanel.setBorder(titledBorder1);
818 proxyPanel.setLayout(new GridBagLayout());
819 proxyPanel.add(serverLabel,
820 new GridBagConstraints(0, 1, 1, 1, 0.0, 0.0,
821 GridBagConstraints.WEST, GridBagConstraints.NONE,
822 new Insets(0, 2, 2, 0), 5, 0));
823 proxyPanel.add(portLabel,
824 new GridBagConstraints(2, 1, 1, 1, 0.0, 0.0,
825 GridBagConstraints.WEST, GridBagConstraints.NONE,
826 new Insets(0, 0, 2, 0), 11, 0));
827 proxyPanel.add(useProxy,
828 new GridBagConstraints(0, 0, 2, 1, 0.0, 0.0,
829 GridBagConstraints.WEST, GridBagConstraints.NONE,
830 new Insets(0, 2, 5, 185), 2, -4));
831 proxyPanel.add(proxyPortTB,
832 new GridBagConstraints(3, 1, 1, 1, 1.0, 0.0,
833 GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
834 new Insets(0, 2, 2, 2), 54, 1));
835 proxyPanel.add(proxyServerTB,
836 new GridBagConstraints(1, 1, 1, 1, 1.0, 0.0,
837 GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
838 new Insets(0, 2, 2, 0), 263, 1));
844 * Initialises the checkboxes in the Connections tab
846 private void initConnTabCheckboxes()
848 // Usage stats checkbox label
850 MessageManager.getString("label.send_usage_statistics"));
851 usagestats.setFont(LABEL_FONT);
852 usagestats.setHorizontalAlignment(SwingConstants.RIGHT);
853 usagestats.setHorizontalTextPosition(SwingConstants.LEADING);
855 // Questionnaire checkbox label
856 questionnaire.setText(
857 MessageManager.getString("label.check_for_questionnaires"));
858 questionnaire.setFont(LABEL_FONT);
859 questionnaire.setHorizontalAlignment(SwingConstants.RIGHT);
860 questionnaire.setHorizontalTextPosition(SwingConstants.LEADING);
862 // Check for latest version checkbox label
863 versioncheck.setText(
864 MessageManager.getString("label.check_for_latest_version"));
865 versioncheck.setFont(LABEL_FONT);
866 versioncheck.setHorizontalAlignment(SwingConstants.RIGHT);
867 versioncheck.setHorizontalTextPosition(SwingConstants.LEADING);
871 * Initialises the parent panel which contains the tabbed sections.
875 private JPanel initOkCancelPanel()
877 JButton ok = new JButton();
878 ok.setText(MessageManager.getString("action.ok"));
879 ok.addActionListener(new ActionListener()
882 public void actionPerformed(ActionEvent e)
884 ok_actionPerformed(e);
887 JButton cancel = new JButton();
888 cancel.setText(MessageManager.getString("action.cancel"));
889 cancel.addActionListener(new ActionListener()
892 public void actionPerformed(ActionEvent e)
894 cancel_actionPerformed(e);
897 JPanel okCancelPanel = new JPanel();
898 okCancelPanel.add(ok);
899 okCancelPanel.add(cancel);
900 return okCancelPanel;
904 * Initialises the Colours tabbed panel.
908 private JPanel initColoursTab()
910 JPanel coloursTab = new JPanel();
911 coloursTab.setBorder(new TitledBorder(
912 MessageManager.getString("action.open_new_alignment")));
913 coloursTab.setLayout(new FlowLayout());
914 JLabel mincolourLabel = new JLabel();
915 mincolourLabel.setFont(LABEL_FONT);
916 mincolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
917 mincolourLabel.setText(MessageManager.getString("label.min_colour"));
918 minColour.setFont(LABEL_FONT);
919 minColour.setBorder(BorderFactory.createEtchedBorder());
920 minColour.setPreferredSize(new Dimension(40, 20));
921 minColour.addMouseListener(new MouseAdapter()
924 public void mousePressed(MouseEvent e)
926 minColour_actionPerformed(minColour);
929 JLabel maxcolourLabel = new JLabel();
930 maxcolourLabel.setFont(LABEL_FONT);
931 maxcolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
932 maxcolourLabel.setText(MessageManager.getString("label.max_colour"));
933 maxColour.setFont(LABEL_FONT);
934 maxColour.setBorder(BorderFactory.createEtchedBorder());
935 maxColour.setPreferredSize(new Dimension(40, 20));
936 maxColour.addMouseListener(new MouseAdapter()
939 public void mousePressed(MouseEvent e)
941 maxColour_actionPerformed(maxColour);
945 protColour.setFont(LABEL_FONT);
946 protColour.setBounds(new Rectangle(172, 225, 155, 21));
947 JLabel protColourLabel = new JLabel();
948 protColourLabel.setFont(LABEL_FONT);
949 protColourLabel.setHorizontalAlignment(SwingConstants.LEFT);
950 protColourLabel.setText(
951 MessageManager.getString("label.prot_alignment_colour") + " ");
952 JvSwingUtils.addtoLayout(coloursTab,
954 .getString("label.default_colour_scheme_for_alignment"),
955 protColourLabel, protColour);
957 nucColour.setFont(LABEL_FONT);
958 nucColour.setBounds(new Rectangle(172, 240, 155, 21));
959 JLabel nucColourLabel = new JLabel();
960 nucColourLabel.setFont(LABEL_FONT);
961 nucColourLabel.setHorizontalAlignment(SwingConstants.LEFT);
962 nucColourLabel.setText(
963 MessageManager.getString("label.nuc_alignment_colour") + " ");
964 JvSwingUtils.addtoLayout(coloursTab,
966 .getString("label.default_colour_scheme_for_alignment"),
967 nucColourLabel, nucColour);
969 JPanel annotationShding = new JPanel();
970 annotationShding.setBorder(new TitledBorder(
971 MessageManager.getString("label.annotation_shading_default")));
972 annotationShding.setLayout(new GridLayout(1, 2));
973 JvSwingUtils.addtoLayout(annotationShding,
974 MessageManager.getString(
975 "label.default_minimum_colour_annotation_shading"),
976 mincolourLabel, minColour);
977 JvSwingUtils.addtoLayout(annotationShding,
978 MessageManager.getString(
979 "label.default_maximum_colour_annotation_shading"),
980 maxcolourLabel, maxColour);
981 coloursTab.add(annotationShding); // , FlowLayout.LEFT);
986 * Initialises the Overview tabbed panel.
990 private JPanel initOverviewTab()
992 JPanel overviewPanel = new JPanel();
993 overviewPanel.setBorder(new TitledBorder(
994 MessageManager.getString("label.overview_settings")));
996 gapColour.setFont(LABEL_FONT);
997 // fixing the border colours stops apparent colour bleed from the panel
999 BorderFactory.createEtchedBorder(Color.white, Color.lightGray));
1000 gapColour.setPreferredSize(new Dimension(40, 20));
1001 gapColour.addMouseListener(new MouseAdapter()
1004 public void mousePressed(MouseEvent e)
1006 gapColour_actionPerformed(gapColour);
1010 hiddenColour.setFont(LABEL_FONT);
1011 // fixing the border colours stops apparent colour bleed from the panel
1012 hiddenColour.setBorder(
1013 BorderFactory.createEtchedBorder(Color.white, Color.lightGray));
1014 hiddenColour.setPreferredSize(new Dimension(40, 20));
1015 hiddenColour.addMouseListener(new MouseAdapter()
1018 public void mousePressed(MouseEvent e)
1020 hiddenColour_actionPerformed(hiddenColour);
1024 useLegacyGap = new JCheckBox(
1025 MessageManager.getString("label.ov_legacy_gap"));
1026 useLegacyGap.setFont(LABEL_FONT);
1027 useLegacyGap.setHorizontalAlignment(SwingConstants.LEFT);
1028 gapLabel = new JLabel(
1029 MessageManager.getString("label.gap_colour"));
1030 gapLabel.setFont(LABEL_FONT);
1031 gapLabel.setHorizontalAlignment(SwingConstants.LEFT);
1032 showHiddenAtStart = new JCheckBox(
1033 MessageManager.getString("label.ov_show_hide_default"));
1034 showHiddenAtStart.setFont(LABEL_FONT);
1035 showHiddenAtStart.setHorizontalAlignment(SwingConstants.LEFT);
1036 JLabel hiddenLabel = new JLabel(
1037 MessageManager.getString("label.hidden_colour"));
1038 hiddenLabel.setFont(LABEL_FONT);
1039 hiddenLabel.setHorizontalAlignment(SwingConstants.LEFT);
1041 useLegacyGap.addActionListener(new ActionListener()
1044 public void actionPerformed(ActionEvent e)
1046 useLegacyGaps_actionPerformed(e);
1050 overviewPanel.setLayout(new GridBagLayout());
1051 GridBagConstraints c1 = new GridBagConstraints();
1053 c1.fill = GridBagConstraints.HORIZONTAL;
1058 c1.anchor = GridBagConstraints.FIRST_LINE_START;
1059 overviewPanel.add(useLegacyGap, c1);
1061 GridBagConstraints c2 = new GridBagConstraints();
1062 c2.fill = GridBagConstraints.HORIZONTAL;
1065 c2.insets = new Insets(0, 15, 0, 10);
1066 overviewPanel.add(gapLabel, c2);
1068 GridBagConstraints c3 = new GridBagConstraints();
1069 c3.fill = GridBagConstraints.HORIZONTAL;
1072 c3.insets = new Insets(0, 0, 0, 15);
1073 overviewPanel.add(gapColour, c3);
1075 GridBagConstraints c4 = new GridBagConstraints();
1076 c4.fill = GridBagConstraints.HORIZONTAL;
1080 overviewPanel.add(showHiddenAtStart, c4);
1082 GridBagConstraints c5 = new GridBagConstraints();
1083 c5.fill = GridBagConstraints.HORIZONTAL;
1086 c5.insets = new Insets(0, 15, 0, 10);
1087 overviewPanel.add(hiddenLabel, c5);
1089 GridBagConstraints c6 = new GridBagConstraints();
1090 c6.fill = GridBagConstraints.HORIZONTAL;
1093 c6.insets = new Insets(0, 0, 0, 15);
1094 overviewPanel.add(hiddenColour, c6);
1096 resetButton = new JButton(
1097 MessageManager.getString("label.reset_to_defaults"));
1099 resetButton.addActionListener(new ActionListener()
1102 public void actionPerformed(ActionEvent e)
1104 resetOvDefaults_actionPerformed(e);
1108 GridBagConstraints c7 = new GridBagConstraints();
1109 c7.fill = GridBagConstraints.NONE;
1112 c7.insets = new Insets(10, 0, 0, 0);
1113 c7.anchor = GridBagConstraints.WEST;
1114 overviewPanel.add(resetButton, c7);
1116 // Add padding so the panel doesn't look ridiculous
1117 JPanel spacePanel = new JPanel();
1118 overviewPanel.add(spacePanel,
1119 new GridBagConstraints(0, 3, 1, 1, 1.0, 1.0,
1120 GridBagConstraints.WEST, GridBagConstraints.BOTH,
1121 new Insets(0, 0, 0, 5), 0, 0));
1123 return overviewPanel;
1127 * Initialises the Structure tabbed panel.
1131 private JPanel initStructureTab()
1133 structureTab = new JPanel();
1135 structureTab.setBorder(new TitledBorder(
1136 MessageManager.getString("label.structure_options")));
1137 structureTab.setLayout(null);
1138 final int width = 400;
1139 final int height = 22;
1140 final int lineSpacing = 25;
1143 structFromPdb.setFont(LABEL_FONT);
1145 .setText(MessageManager.getString("label.struct_from_pdb"));
1146 structFromPdb.setBounds(new Rectangle(5, ypos, width, height));
1147 structFromPdb.addActionListener(new ActionListener()
1150 public void actionPerformed(ActionEvent e)
1152 boolean selected = structFromPdb.isSelected();
1153 // enable other options only when the first is checked
1154 useRnaView.setEnabled(selected);
1155 addSecondaryStructure.setEnabled(selected);
1156 addTempFactor.setEnabled(selected);
1159 structureTab.add(structFromPdb);
1161 // indent checkboxes that are conditional on the first one
1162 ypos += lineSpacing;
1163 useRnaView.setFont(LABEL_FONT);
1164 useRnaView.setText(MessageManager.getString("label.use_rnaview"));
1165 useRnaView.setBounds(new Rectangle(25, ypos, width, height));
1166 structureTab.add(useRnaView);
1168 ypos += lineSpacing;
1169 addSecondaryStructure.setFont(LABEL_FONT);
1170 addSecondaryStructure
1171 .setText(MessageManager.getString("label.autoadd_secstr"));
1172 addSecondaryStructure.setBounds(new Rectangle(25, ypos, width, height));
1173 structureTab.add(addSecondaryStructure);
1175 ypos += lineSpacing;
1176 addTempFactor.setFont(LABEL_FONT);
1177 addTempFactor.setText(MessageManager.getString("label.autoadd_temp"));
1178 addTempFactor.setBounds(new Rectangle(25, ypos, width, height));
1179 structureTab.add(addTempFactor);
1181 ypos += lineSpacing;
1182 JLabel viewerLabel = new JLabel();
1183 viewerLabel.setFont(LABEL_FONT);
1184 viewerLabel.setHorizontalAlignment(SwingConstants.LEFT);
1185 viewerLabel.setText(MessageManager.getString("label.structure_viewer"));
1186 viewerLabel.setBounds(new Rectangle(10, ypos, 200, height));
1187 structureTab.add(viewerLabel);
1189 structViewer.setFont(LABEL_FONT);
1190 structViewer.setBounds(new Rectangle(160, ypos, 120, height));
1191 structViewer.addItem(ViewerType.JMOL.name());
1192 structViewer.addItem(ViewerType.CHIMERA.name());
1193 structViewer.addActionListener(new ActionListener()
1196 public void actionPerformed(ActionEvent e)
1198 structureViewer_actionPerformed(
1199 (String) structViewer.getSelectedItem());
1202 structureTab.add(structViewer);
1204 ypos += lineSpacing;
1205 JLabel pathLabel = new JLabel();
1206 pathLabel.setFont(new java.awt.Font("SansSerif", 0, 11));
1207 pathLabel.setHorizontalAlignment(SwingConstants.LEFT);
1208 pathLabel.setText(MessageManager.getString("label.chimera_path"));
1209 final String tooltip = JvSwingUtils.wrapTooltip(true,
1210 MessageManager.getString("label.chimera_path_tip"));
1211 pathLabel.setToolTipText(tooltip);
1212 pathLabel.setBounds(new Rectangle(10, ypos, 140, height));
1213 structureTab.add(pathLabel);
1215 chimeraPath.setFont(LABEL_FONT);
1216 chimeraPath.setText("");
1217 chimeraPath.setBounds(new Rectangle(160, ypos, 300, height));
1218 chimeraPath.addMouseListener(new MouseAdapter()
1221 public void mouseClicked(MouseEvent e)
1223 if (e.getClickCount() == 2)
1225 String chosen = openFileChooser();
1228 chimeraPath.setText(chosen);
1233 structureTab.add(chimeraPath);
1235 ypos += lineSpacing;
1236 nwMapping.setFont(LABEL_FONT);
1237 nwMapping.setText(MessageManager.getString("label.nw_mapping"));
1238 siftsMapping.setFont(LABEL_FONT);
1239 siftsMapping.setText(MessageManager.getString("label.sifts_mapping"));
1240 mappingMethod.add(nwMapping);
1241 mappingMethod.add(siftsMapping);
1242 JPanel mappingPanel = new JPanel();
1243 mappingPanel.setFont(LABEL_FONT);
1244 TitledBorder mmTitledBorder = new TitledBorder(
1245 MessageManager.getString("label.mapping_method"));
1246 mmTitledBorder.setTitleFont(LABEL_FONT);
1247 mappingPanel.setBorder(mmTitledBorder);
1248 mappingPanel.setBounds(new Rectangle(10, ypos, 452, 45));
1249 // GridLayout mappingLayout = new GridLayout();
1250 mappingPanel.setLayout(new GridLayout());
1251 mappingPanel.add(nwMapping);
1252 mappingPanel.add(siftsMapping);
1253 structureTab.add(mappingPanel);
1255 ypos += lineSpacing;
1256 ypos += lineSpacing;
1257 FTSDataColumnPreferences docFieldPref = new FTSDataColumnPreferences(
1258 PreferenceSource.PREFERENCES, PDBFTSRestClient.getInstance());
1259 docFieldPref.setBounds(new Rectangle(10, ypos, 450, 120));
1260 structureTab.add(docFieldPref);
1262 return structureTab;
1266 * Action on choosing a structure viewer from combobox options.
1268 * @param selectedItem
1270 protected void structureViewer_actionPerformed(String selectedItem)
1275 * Show a dialog for the user to choose a file. Returns the chosen path, or
1280 protected String openFileChooser()
1282 String choice = null;
1283 JFileChooser chooser = new JFileChooser();
1285 // chooser.setFileView(new JalviewFileView());
1286 chooser.setDialogTitle(
1287 MessageManager.getString("label.open_local_file"));
1288 chooser.setToolTipText(MessageManager.getString("action.open"));
1290 int value = chooser.showOpenDialog(this);
1292 if (value == JFileChooser.APPROVE_OPTION)
1294 choice = chooser.getSelectedFile().getPath();
1300 * Validate the structure tab preferences; if invalid, set focus on this tab.
1304 protected boolean validateStructure(FocusEvent e)
1306 if (!validateStructure())
1308 e.getComponent().requestFocusInWindow();
1314 protected boolean validateStructure()
1320 * Initialises the Visual tabbed panel.
1324 private JPanel initVisualTab()
1326 JPanel visualTab = new JPanel();
1327 visualTab.setBorder(new TitledBorder(
1328 MessageManager.getString("action.open_new_alignment")));
1329 visualTab.setLayout(null);
1330 fullScreen.setFont(LABEL_FONT);
1331 fullScreen.setHorizontalAlignment(SwingConstants.RIGHT);
1332 fullScreen.setHorizontalTextPosition(SwingConstants.LEFT);
1333 fullScreen.setText(MessageManager.getString("label.maximize_window"));
1334 quality.setEnabled(false);
1335 quality.setFont(LABEL_FONT);
1336 quality.setHorizontalAlignment(SwingConstants.RIGHT);
1337 quality.setHorizontalTextPosition(SwingConstants.LEFT);
1338 quality.setSelected(true);
1339 quality.setText(MessageManager.getString("label.quality"));
1340 conservation.setEnabled(false);
1341 conservation.setFont(LABEL_FONT);
1342 conservation.setHorizontalAlignment(SwingConstants.RIGHT);
1343 conservation.setHorizontalTextPosition(SwingConstants.LEFT);
1344 conservation.setSelected(true);
1345 conservation.setText(MessageManager.getString("label.conservation"));
1346 identity.setEnabled(false);
1347 identity.setFont(LABEL_FONT);
1348 identity.setHorizontalAlignment(SwingConstants.RIGHT);
1349 identity.setHorizontalTextPosition(SwingConstants.LEFT);
1350 identity.setSelected(true);
1351 identity.setText(MessageManager.getString("label.consensus"));
1352 showOccupancy.setFont(LABEL_FONT);
1353 showOccupancy.setEnabled(false);
1354 showOccupancy.setHorizontalAlignment(SwingConstants.RIGHT);
1355 showOccupancy.setHorizontalTextPosition(SwingConstants.LEFT);
1356 showOccupancy.setSelected(true);
1357 showOccupancy.setText(MessageManager.getString("label.occupancy"));
1359 JLabel showGroupbits = new JLabel();
1360 showGroupbits.setFont(LABEL_FONT);
1361 showGroupbits.setHorizontalAlignment(SwingConstants.RIGHT);
1362 showGroupbits.setHorizontalTextPosition(SwingConstants.LEFT);
1364 .setText(MessageManager.getString("action.show_group") + ":");
1365 JLabel showConsensbits = new JLabel();
1366 showConsensbits.setFont(LABEL_FONT);
1367 showConsensbits.setHorizontalAlignment(SwingConstants.RIGHT);
1368 showConsensbits.setHorizontalTextPosition(SwingConstants.LEFT);
1370 .setText(MessageManager.getString("label.consensus") + ":");
1371 showConsensHistogram.setEnabled(false);
1372 showConsensHistogram.setFont(LABEL_FONT);
1373 showConsensHistogram.setHorizontalAlignment(SwingConstants.RIGHT);
1374 showConsensHistogram.setHorizontalTextPosition(SwingConstants.LEFT);
1375 showConsensHistogram.setSelected(true);
1376 showConsensHistogram
1377 .setText(MessageManager.getString("label.histogram"));
1378 showConsensLogo.setEnabled(false);
1379 showConsensLogo.setFont(LABEL_FONT);
1380 showConsensLogo.setHorizontalAlignment(SwingConstants.RIGHT);
1381 showConsensLogo.setHorizontalTextPosition(SwingConstants.LEFT);
1382 showConsensLogo.setSelected(true);
1383 showConsensLogo.setText(MessageManager.getString("label.logo"));
1384 showGroupConsensus.setEnabled(false);
1385 showGroupConsensus.setFont(LABEL_FONT);
1386 showGroupConsensus.setHorizontalAlignment(SwingConstants.RIGHT);
1387 showGroupConsensus.setHorizontalTextPosition(SwingConstants.LEFT);
1388 showGroupConsensus.setSelected(true);
1389 showGroupConsensus.setText(MessageManager.getString("label.consensus"));
1390 showGroupConservation.setEnabled(false);
1391 showGroupConservation.setFont(LABEL_FONT);
1392 showGroupConservation.setHorizontalAlignment(SwingConstants.RIGHT);
1393 showGroupConservation.setHorizontalTextPosition(SwingConstants.LEFT);
1394 showGroupConservation.setSelected(true);
1395 showGroupConservation
1396 .setText(MessageManager.getString("label.conservation"));
1397 showNpTooltip.setEnabled(true);
1398 showNpTooltip.setFont(LABEL_FONT);
1399 showNpTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
1400 showNpTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
1401 showNpTooltip.setSelected(true);
1402 showNpTooltip.setText(
1403 MessageManager.getString("label.non_positional_features"));
1404 showDbRefTooltip.setEnabled(true);
1405 showDbRefTooltip.setFont(LABEL_FONT);
1406 showDbRefTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
1407 showDbRefTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
1408 showDbRefTooltip.setSelected(true);
1410 .setText(MessageManager.getString("label.database_references"));
1411 annotations.setFont(LABEL_FONT);
1412 annotations.setHorizontalAlignment(SwingConstants.RIGHT);
1413 annotations.setHorizontalTextPosition(SwingConstants.LEFT);
1414 annotations.setSelected(true);
1415 annotations.setText(MessageManager.getString("label.show_annotations"));
1416 // annotations.setBounds(new Rectangle(169, 12, 200, 23));
1417 annotations.addActionListener(new ActionListener()
1420 public void actionPerformed(ActionEvent e)
1422 annotations_actionPerformed(e);
1425 identity.addActionListener(new ActionListener()
1428 public void actionPerformed(ActionEvent e)
1430 annotations_actionPerformed(e);
1433 showGroupConsensus.addActionListener(new ActionListener()
1436 public void actionPerformed(ActionEvent e)
1438 annotations_actionPerformed(e);
1441 showUnconserved.setFont(LABEL_FONT);
1442 showUnconserved.setHorizontalAlignment(SwingConstants.RIGHT);
1443 showUnconserved.setHorizontalTextPosition(SwingConstants.LEFT);
1444 showUnconserved.setSelected(true);
1446 .setText(MessageManager.getString("action.show_unconserved"));
1447 showUnconserved.addActionListener(new ActionListener()
1450 public void actionPerformed(ActionEvent e)
1452 showunconserved_actionPerformed(e);
1456 // TODO these are not yet added to / action from Preferences
1457 // JCheckBox shareSelections = new JCheckBox();
1458 // shareSelections.setFont(verdana11);
1459 // shareSelections.setHorizontalAlignment(SwingConstants.RIGHT);
1460 // shareSelections.setHorizontalTextPosition(SwingConstants.LEFT);
1461 // shareSelections.setSelected(true);
1462 // shareSelections.setText(MessageManager
1463 // .getString("label.share_selection_across_views"));
1464 // JCheckBox followHighlight = new JCheckBox();
1465 // followHighlight.setFont(verdana11);
1466 // followHighlight.setHorizontalAlignment(SwingConstants.RIGHT);
1467 // followHighlight.setHorizontalTextPosition(SwingConstants.LEFT);
1468 // // showUnconserved.setBounds(new Rectangle(169, 40, 200, 23));
1469 // followHighlight.setSelected(true);
1470 // followHighlight.setText(MessageManager
1471 // .getString("label.scroll_highlighted_regions"));
1473 seqLimit.setFont(LABEL_FONT);
1474 seqLimit.setHorizontalAlignment(SwingConstants.RIGHT);
1475 seqLimit.setHorizontalTextPosition(SwingConstants.LEFT);
1476 seqLimit.setText(MessageManager.getString("label.full_sequence_id"));
1477 smoothFont.setFont(LABEL_FONT);
1478 smoothFont.setHorizontalAlignment(SwingConstants.RIGHT);
1479 smoothFont.setHorizontalTextPosition(SwingConstants.LEADING);
1480 smoothFont.setText(MessageManager.getString("label.smooth_font"));
1481 scaleProteinToCdna.setFont(LABEL_FONT);
1482 scaleProteinToCdna.setHorizontalAlignment(SwingConstants.RIGHT);
1483 scaleProteinToCdna.setHorizontalTextPosition(SwingConstants.LEADING);
1484 scaleProteinToCdna.setText(
1485 MessageManager.getString("label.scale_protein_to_cdna"));
1486 scaleProteinToCdna.setToolTipText(
1487 MessageManager.getString("label.scale_protein_to_cdna_tip"));
1488 JLabel gapLabel = new JLabel();
1489 gapLabel.setFont(LABEL_FONT);
1490 gapLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1491 gapLabel.setText(MessageManager.getString("label.gap_symbol") + " ");
1492 JLabel fontLabel = new JLabel();
1493 fontLabel.setFont(LABEL_FONT);
1494 fontLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1495 fontLabel.setText(MessageManager.getString("label.font"));
1496 fontSizeCB.setFont(LABEL_FONT);
1497 fontSizeCB.setBounds(new Rectangle(320, 112, 65, 23));
1498 fontStyleCB.setFont(LABEL_FONT);
1499 fontStyleCB.setBounds(new Rectangle(382, 112, 80, 23));
1500 fontNameCB.setFont(LABEL_FONT);
1501 fontNameCB.setBounds(new Rectangle(172, 112, 147, 23));
1502 gapSymbolCB.setFont(LABEL_FONT);
1503 gapSymbolCB.setBounds(new Rectangle(172, 215, 69, 23));
1504 DefaultListCellRenderer dlcr = new DefaultListCellRenderer();
1505 dlcr.setHorizontalAlignment(DefaultListCellRenderer.CENTER);
1506 gapSymbolCB.setRenderer(dlcr);
1508 startupCheckbox.setText(MessageManager.getString("action.open_file"));
1509 startupCheckbox.setFont(LABEL_FONT);
1510 startupCheckbox.setHorizontalAlignment(SwingConstants.RIGHT);
1511 startupCheckbox.setHorizontalTextPosition(SwingConstants.LEFT);
1512 startupCheckbox.setSelected(true);
1513 startupFileTextfield.setFont(LABEL_FONT);
1514 startupFileTextfield.setBounds(new Rectangle(172, 310, 330, 20));
1515 startupFileTextfield.addMouseListener(new MouseAdapter()
1518 public void mouseClicked(MouseEvent e)
1520 if (e.getClickCount() > 1)
1522 startupFileTextfield_mouseClicked();
1527 sortby.setFont(LABEL_FONT);
1528 sortby.setBounds(new Rectangle(172, 260, 155, 21));
1529 JLabel sortLabel = new JLabel();
1530 sortLabel.setFont(LABEL_FONT);
1531 sortLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1532 sortLabel.setText(MessageManager.getString("label.sort_by"));
1533 sortAnnBy.setFont(LABEL_FONT);
1534 sortAnnBy.setBounds(new Rectangle(172, 285, 110, 21));
1535 JLabel sortAnnLabel = new JLabel();
1536 sortAnnLabel.setFont(LABEL_FONT);
1537 sortAnnLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1538 sortAnnLabel.setText(MessageManager.getString("label.sort_ann_by"));
1539 sortAutocalc.setFont(LABEL_FONT);
1540 sortAutocalc.setBounds(new Rectangle(290, 285, 165, 21));
1542 JPanel annsettingsPanel = new JPanel();
1543 annsettingsPanel.setBounds(new Rectangle(173, 13, 320, 96));
1544 annsettingsPanel.setLayout(new FlowLayout(FlowLayout.LEFT, 0, 0));
1545 annsettingsPanel.setBorder(new EtchedBorder());
1546 visualTab.add(annsettingsPanel);
1547 Border jb = new EmptyBorder(1, 1, 4, 5);
1548 annotations.setBorder(jb);
1549 showOccupancy.setBorder(jb);
1550 quality.setBorder(jb);
1551 conservation.setBorder(jb);
1552 identity.setBorder(jb);
1553 showConsensbits.setBorder(jb);
1554 showGroupbits.setBorder(jb);
1555 showGroupConsensus.setBorder(jb);
1556 showGroupConservation.setBorder(jb);
1557 showConsensHistogram.setBorder(jb);
1558 showConsensLogo.setBorder(jb);
1560 JPanel autoAnnotSettings = new JPanel();
1561 annsettingsPanel.add(autoAnnotSettings);
1562 autoAnnotSettings.setLayout(new GridLayout(0, 2));
1563 autoAnnotSettings.add(annotations);
1564 autoAnnotSettings.add(quality);
1565 // second row of autoannotation box
1566 autoAnnotSettings = new JPanel();
1567 annsettingsPanel.add(autoAnnotSettings);
1569 autoAnnotSettings.setLayout(new GridLayout(0, 3));
1570 autoAnnotSettings.add(conservation);
1571 autoAnnotSettings.add(identity);
1572 autoAnnotSettings.add(showOccupancy);
1573 autoAnnotSettings.add(showGroupbits);
1574 autoAnnotSettings.add(showGroupConservation);
1575 autoAnnotSettings.add(showGroupConsensus);
1576 autoAnnotSettings.add(showConsensbits);
1577 autoAnnotSettings.add(showConsensHistogram);
1578 autoAnnotSettings.add(showConsensLogo);
1580 JPanel tooltipSettings = new JPanel();
1581 tooltipSettings.setBorder(new TitledBorder(
1582 MessageManager.getString("label.sequence_id_tooltip")));
1583 tooltipSettings.setBounds(173, 140, 220, 62);
1584 tooltipSettings.setLayout(new GridLayout(2, 1));
1585 tooltipSettings.add(showDbRefTooltip);
1586 tooltipSettings.add(showNpTooltip);
1587 visualTab.add(tooltipSettings);
1589 wrap.setFont(LABEL_FONT);
1590 wrap.setHorizontalAlignment(SwingConstants.TRAILING);
1591 wrap.setHorizontalTextPosition(SwingConstants.LEADING);
1592 wrap.setText(MessageManager.getString("label.wrap_alignment"));
1593 rightAlign.setFont(LABEL_FONT);
1594 rightAlign.setForeground(Color.black);
1595 rightAlign.setHorizontalAlignment(SwingConstants.RIGHT);
1596 rightAlign.setHorizontalTextPosition(SwingConstants.LEFT);
1597 rightAlign.setText(MessageManager.getString("label.right_align_ids"));
1598 idItalics.setFont(LABEL_FONT_ITALIC);
1599 idItalics.setHorizontalAlignment(SwingConstants.RIGHT);
1600 idItalics.setHorizontalTextPosition(SwingConstants.LEADING);
1602 MessageManager.getString("label.sequence_name_italics"));
1603 openoverv.setFont(LABEL_FONT);
1604 openoverv.setActionCommand(
1605 MessageManager.getString("label.open_overview"));
1606 openoverv.setHorizontalAlignment(SwingConstants.RIGHT);
1607 openoverv.setHorizontalTextPosition(SwingConstants.LEFT);
1608 openoverv.setText(MessageManager.getString("label.open_overview"));
1609 JPanel jPanel2 = new JPanel();
1610 jPanel2.setBounds(new Rectangle(7, 17, 158, 310));
1611 jPanel2.setLayout(new GridLayout(14, 1));
1612 jPanel2.add(fullScreen);
1613 jPanel2.add(openoverv);
1614 jPanel2.add(seqLimit);
1615 jPanel2.add(rightAlign);
1616 jPanel2.add(fontLabel);
1617 jPanel2.add(showUnconserved);
1618 jPanel2.add(idItalics);
1619 jPanel2.add(smoothFont);
1620 jPanel2.add(scaleProteinToCdna);
1621 jPanel2.add(gapLabel);
1623 jPanel2.add(sortLabel);
1624 jPanel2.add(sortAnnLabel);
1625 jPanel2.add(startupCheckbox);
1626 visualTab.add(jPanel2);
1627 visualTab.add(startupFileTextfield);
1628 visualTab.add(sortby);
1629 visualTab.add(sortAnnBy);
1630 visualTab.add(sortAutocalc);
1631 visualTab.add(gapSymbolCB);
1632 visualTab.add(fontNameCB);
1633 visualTab.add(fontSizeCB);
1634 visualTab.add(fontStyleCB);
1638 protected void autoIdWidth_actionPerformed()
1640 // TODO Auto-generated method stub
1644 protected void userIdWidth_actionPerformed()
1646 // TODO Auto-generated method stub
1650 protected void maxColour_actionPerformed(JPanel panel)
1654 protected void minColour_actionPerformed(JPanel panel)
1658 protected void gapColour_actionPerformed(JPanel panel)
1662 protected void hiddenColour_actionPerformed(JPanel panel)
1666 protected void showunconserved_actionPerformed(ActionEvent e)
1668 // TODO Auto-generated method stub
1672 protected void useLegacyGaps_actionPerformed(ActionEvent e)
1676 protected void resetOvDefaults_actionPerformed(ActionEvent e)
1686 public void ok_actionPerformed(ActionEvent e)
1696 public void cancel_actionPerformed(ActionEvent e)
1706 public void annotations_actionPerformed(ActionEvent e)
1713 public void startupFileTextfield_mouseClicked()
1717 public void newLink_actionPerformed(ActionEvent e)
1722 public void editLink_actionPerformed(ActionEvent e)
1727 public void deleteLink_actionPerformed(ActionEvent e)
1732 public void defaultBrowser_mouseClicked(MouseEvent e)
1737 public void linkURLList_keyTyped(KeyEvent e)
1742 public void useProxy_actionPerformed()
1744 boolean enabled = useProxy.isSelected();
1745 portLabel.setEnabled(enabled);
1746 serverLabel.setEnabled(enabled);
1747 proxyServerTB.setEnabled(enabled);
1748 proxyPortTB.setEnabled(enabled);
1752 * Customer renderer for JTable: supports column of radio buttons
1754 public class RadioButtonRenderer extends JRadioButton
1755 implements TableCellRenderer
1757 public RadioButtonRenderer()
1759 setHorizontalAlignment(CENTER);
1760 setToolTipText(MessageManager.getString("label.urltooltip"));
1764 public Component getTableCellRendererComponent(JTable table,
1765 Object value, boolean isSelected, boolean hasFocus, int row,
1768 setSelected((boolean) value);
1770 // set colours to match rest of table
1773 setBackground(table.getSelectionBackground());
1774 setForeground(table.getSelectionForeground());
1778 setBackground(table.getBackground());
1779 setForeground(table.getForeground());
1786 * Customer cell editor for JTable: supports column of radio buttons in
1787 * conjunction with renderer
1789 public class RadioButtonEditor extends AbstractCellEditor
1790 implements TableCellEditor
1792 private JRadioButton button = new JRadioButton();
1794 public RadioButtonEditor()
1796 button.setHorizontalAlignment(SwingConstants.CENTER);
1797 this.button.addActionListener(new ActionListener()
1800 public void actionPerformed(ActionEvent e)
1802 fireEditingStopped();
1808 public Component getTableCellEditorComponent(JTable table, Object value,
1809 boolean isSelected, int row, int column)
1811 button.setSelected((boolean) value);
1816 public Object getCellEditorValue()
1818 return button.isSelected();