2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.jbgui;
23 import jalview.fts.core.FTSDataColumnPreferences;
24 import jalview.fts.core.FTSDataColumnPreferences.PreferenceSource;
25 import jalview.fts.service.pdb.PDBFTSRestClient;
26 import jalview.gui.JvSwingUtils;
27 import jalview.gui.StructureViewer.ViewerType;
28 import jalview.util.MessageManager;
30 import java.awt.BorderLayout;
31 import java.awt.Color;
32 import java.awt.Component;
33 import java.awt.Dimension;
34 import java.awt.FlowLayout;
36 import java.awt.GridBagConstraints;
37 import java.awt.GridBagLayout;
38 import java.awt.GridLayout;
39 import java.awt.Insets;
40 import java.awt.Rectangle;
41 import java.awt.event.ActionEvent;
42 import java.awt.event.ActionListener;
43 import java.awt.event.FocusEvent;
44 import java.awt.event.KeyEvent;
45 import java.awt.event.MouseAdapter;
46 import java.awt.event.MouseEvent;
48 import javax.swing.AbstractCellEditor;
49 import javax.swing.BorderFactory;
50 import javax.swing.ButtonGroup;
51 import javax.swing.DefaultListCellRenderer;
52 import javax.swing.JButton;
53 import javax.swing.JCheckBox;
54 import javax.swing.JComboBox;
55 import javax.swing.JFileChooser;
56 import javax.swing.JLabel;
57 import javax.swing.JPanel;
58 import javax.swing.JRadioButton;
59 import javax.swing.JScrollPane;
60 import javax.swing.JTabbedPane;
61 import javax.swing.JTable;
62 import javax.swing.JTextField;
63 import javax.swing.ListSelectionModel;
64 import javax.swing.SwingConstants;
65 import javax.swing.border.Border;
66 import javax.swing.border.EmptyBorder;
67 import javax.swing.border.EtchedBorder;
68 import javax.swing.border.TitledBorder;
69 import javax.swing.event.ChangeEvent;
70 import javax.swing.event.ChangeListener;
71 import javax.swing.table.TableCellEditor;
72 import javax.swing.table.TableCellRenderer;
75 * Base class for the Preferences panel.
80 public class GPreferences extends JPanel
82 private static final Font LABEL_FONT = JvSwingUtils.getLabelFont();
84 private static final Font LABEL_FONT_ITALIC = JvSwingUtils
85 .getLabelFont(false, true);
88 * Visual tab components
90 protected JCheckBox fullScreen = new JCheckBox();
92 protected JCheckBox openoverv = new JCheckBox();
94 protected JCheckBox seqLimit = new JCheckBox();
96 protected JCheckBox rightAlign = new JCheckBox();
98 protected JComboBox<String> fontSizeCB = new JComboBox<>();
100 protected JComboBox<String> fontStyleCB = new JComboBox<>();
102 protected JComboBox<String> fontNameCB = new JComboBox<>();
104 protected JCheckBox showOccupancy = new JCheckBox();
106 protected JCheckBox showUnconserved = new JCheckBox();
108 protected JCheckBox idItalics = new JCheckBox();
110 protected JCheckBox smoothFont = new JCheckBox();
112 protected JCheckBox scaleProteinToCdna = new JCheckBox();
114 protected JComboBox<String> gapSymbolCB = new JComboBox<>();
116 protected JCheckBox wrap = new JCheckBox();
118 protected JComboBox<String> sortby = new JComboBox<>();
120 protected JComboBox<String> sortAnnBy = new JComboBox<>();
122 protected JComboBox<String> sortAutocalc = new JComboBox<>();
124 protected JCheckBox startupCheckbox = new JCheckBox();
126 protected JTextField startupFileTextfield = new JTextField();
128 // below are in the 'second column'
129 protected JCheckBox annotations = new JCheckBox();
131 protected JCheckBox quality = new JCheckBox();
133 protected JCheckBox conservation = new JCheckBox();
135 protected JCheckBox identity = new JCheckBox();
137 protected JCheckBox showGroupConsensus = new JCheckBox();
139 protected JCheckBox showGroupConservation = new JCheckBox();
141 protected JCheckBox showConsensHistogram = new JCheckBox();
143 protected JCheckBox showConsensLogo = new JCheckBox();
145 protected JCheckBox showDbRefTooltip = new JCheckBox();
147 protected JCheckBox showNpTooltip = new JCheckBox();
150 * Structure tab and components
152 protected JPanel structureTab;
154 protected JCheckBox structFromPdb = new JCheckBox();
156 protected JCheckBox useRnaView = new JCheckBox();
158 protected JCheckBox addSecondaryStructure = new JCheckBox();
160 protected JCheckBox addTempFactor = new JCheckBox();
162 protected JComboBox<String> structViewer = new JComboBox<>();
164 protected JTextField chimeraPath = new JTextField();
166 protected ButtonGroup mappingMethod = new ButtonGroup();
168 protected JRadioButton siftsMapping = new JRadioButton();
170 protected JRadioButton nwMapping = new JRadioButton();
173 * Colours tab components
175 protected JPanel minColour = new JPanel();
177 protected JPanel maxColour = new JPanel();
179 protected JComboBox<String> protColour = new JComboBox<>();
181 protected JComboBox<String> nucColour = new JComboBox<>();
184 * Overview tab components
186 protected JPanel gapColour = new JPanel();
188 protected JPanel hiddenColour = new JPanel();
190 protected JCheckBox useLegacyGap;
192 protected JCheckBox showHiddenAtStart;
194 protected JLabel gapLabel;
197 * Connections tab components
199 protected JTable linkUrlTable = new JTable();
201 protected JButton editLink = new JButton();
203 protected JButton deleteLink = new JButton();
205 protected JTextField filterTB = new JTextField();
207 protected JButton doReset = new JButton();
209 protected JButton userOnly = new JButton();
211 protected JLabel portLabel = new JLabel();
213 protected JLabel serverLabel = new JLabel();
215 protected JTextField proxyServerTB = new JTextField();
217 protected JTextField proxyPortTB = new JTextField();
219 protected JTextField defaultBrowser = new JTextField();
221 protected JCheckBox useProxy = new JCheckBox();
223 protected JCheckBox usagestats = new JCheckBox();
225 protected JCheckBox questionnaire = new JCheckBox();
227 protected JCheckBox versioncheck = new JCheckBox();
230 * Output tab components
232 protected JComboBox<Object> epsRendering = new JComboBox<>();
234 protected JLabel userIdWidthlabel = new JLabel();
236 protected JCheckBox autoIdWidth = new JCheckBox();
238 protected JTextField userIdWidth = new JTextField();
240 protected JCheckBox blcjv = new JCheckBox();
242 protected JCheckBox pileupjv = new JCheckBox();
244 protected JCheckBox clustaljv = new JCheckBox();
246 protected JCheckBox msfjv = new JCheckBox();
248 protected JCheckBox fastajv = new JCheckBox();
250 protected JCheckBox pfamjv = new JCheckBox();
252 protected JCheckBox pirjv = new JCheckBox();
254 protected JCheckBox modellerOutput = new JCheckBox();
256 protected JCheckBox embbedBioJSON = new JCheckBox();
259 * Editing tab components
261 protected JCheckBox autoCalculateConsCheck = new JCheckBox();
263 protected JCheckBox padGaps = new JCheckBox();
265 protected JCheckBox sortByTree = new JCheckBox();
270 protected JPanel dasTab = new JPanel();
275 protected JPanel wsTab = new JPanel();
278 * Creates a new GPreferences object.
280 public GPreferences()
285 } catch (Exception ex)
287 ex.printStackTrace();
292 * Construct the panel and its tabbed sub-panels.
296 private void jbInit() throws Exception
298 final JTabbedPane tabbedPane = new JTabbedPane();
299 this.setLayout(new BorderLayout());
300 JPanel okCancelPanel = initOkCancelPanel();
301 this.add(tabbedPane, BorderLayout.CENTER);
302 this.add(okCancelPanel, BorderLayout.SOUTH);
304 tabbedPane.add(initVisualTab(),
305 MessageManager.getString("label.visual"));
307 tabbedPane.add(initColoursTab(),
308 MessageManager.getString("label.colours"));
310 tabbedPane.add(initOverviewTab(),
311 MessageManager.getString("label.overview"));
313 tabbedPane.add(initStructureTab(),
314 MessageManager.getString("label.structure"));
316 tabbedPane.add(initConnectionsTab(),
317 MessageManager.getString("label.connections"));
319 tabbedPane.add(initLinksTab(),
320 MessageManager.getString("label.urllinks"));
322 tabbedPane.add(initOutputTab(),
323 MessageManager.getString("label.output"));
325 tabbedPane.add(initEditingTab(),
326 MessageManager.getString("label.editing"));
329 * See DasSourceBrowser for the real work of configuring this tab.
331 dasTab.setLayout(new BorderLayout());
332 tabbedPane.add(dasTab, MessageManager.getString("label.das_settings"));
335 * See WsPreferences for the real work of configuring this tab.
337 wsTab.setLayout(new BorderLayout());
338 tabbedPane.add(wsTab, MessageManager.getString("label.web_services"));
341 * Handler to validate a tab before leaving it - currently only for
344 tabbedPane.addChangeListener(new ChangeListener()
346 private Component lastTab;
349 public void stateChanged(ChangeEvent e)
351 if (lastTab == structureTab
352 && tabbedPane.getSelectedComponent() != structureTab)
354 if (!validateStructure())
356 tabbedPane.setSelectedComponent(structureTab);
360 lastTab = tabbedPane.getSelectedComponent();
367 * Initialises the Editing tabbed panel.
371 private JPanel initEditingTab()
373 JPanel editingTab = new JPanel();
374 editingTab.setLayout(null);
375 autoCalculateConsCheck.setFont(LABEL_FONT);
376 autoCalculateConsCheck.setText(
377 MessageManager.getString("label.autocalculate_consensus"));
378 autoCalculateConsCheck.setBounds(new Rectangle(21, 52, 209, 23));
379 padGaps.setFont(LABEL_FONT);
381 MessageManager.getString("label.pad_gaps_when_editing"));
382 padGaps.setBounds(new Rectangle(22, 94, 168, 23));
383 sortByTree.setFont(LABEL_FONT);
385 .setText(MessageManager.getString("label.sort_with_new_tree"));
386 sortByTree.setToolTipText(MessageManager.getString(
387 "label.any_trees_calculated_or_loaded_alignment_automatically_sort"));
388 sortByTree.setBounds(new Rectangle(22, 136, 168, 23));
389 editingTab.add(autoCalculateConsCheck);
390 editingTab.add(padGaps);
391 editingTab.add(sortByTree);
396 * Initialises the Output tabbed panel.
400 private JPanel initOutputTab()
402 JPanel outputTab = new JPanel();
403 outputTab.setLayout(null);
404 JLabel epsLabel = new JLabel();
405 epsLabel.setFont(LABEL_FONT);
406 epsLabel.setHorizontalAlignment(SwingConstants.RIGHT);
407 epsLabel.setText(MessageManager.getString("label.eps_rendering_style"));
408 epsLabel.setBounds(new Rectangle(9, 31, 140, 24));
409 epsRendering.setFont(LABEL_FONT);
410 epsRendering.setBounds(new Rectangle(154, 34, 187, 21));
411 JLabel jLabel1 = new JLabel();
412 jLabel1.setFont(LABEL_FONT);
413 jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
414 jLabel1.setText(MessageManager.getString("label.append_start_end"));
415 jLabel1.setFont(LABEL_FONT);
416 fastajv.setFont(LABEL_FONT);
417 fastajv.setHorizontalAlignment(SwingConstants.LEFT);
418 clustaljv.setText(MessageManager.getString("label.clustal") + " ");
419 blcjv.setText(MessageManager.getString("label.blc") + " ");
420 fastajv.setText(MessageManager.getString("label.fasta") + " ");
421 msfjv.setText(MessageManager.getString("label.msf") + " ");
422 pfamjv.setText(MessageManager.getString("label.pfam") + " ");
423 pileupjv.setText(MessageManager.getString("label.pileup") + " ");
424 msfjv.setFont(LABEL_FONT);
425 msfjv.setHorizontalAlignment(SwingConstants.LEFT);
426 pirjv.setText(MessageManager.getString("label.pir") + " ");
427 JPanel jPanel11 = new JPanel();
428 jPanel11.setFont(LABEL_FONT);
429 TitledBorder titledBorder2 = new TitledBorder(
430 MessageManager.getString("label.file_output"));
431 jPanel11.setBorder(titledBorder2);
432 jPanel11.setBounds(new Rectangle(30, 72, 196, 182));
433 GridLayout gridLayout3 = new GridLayout();
434 jPanel11.setLayout(gridLayout3);
435 gridLayout3.setRows(8);
436 blcjv.setFont(LABEL_FONT);
437 blcjv.setHorizontalAlignment(SwingConstants.LEFT);
438 clustaljv.setFont(LABEL_FONT);
439 clustaljv.setHorizontalAlignment(SwingConstants.LEFT);
440 pfamjv.setFont(LABEL_FONT);
441 pfamjv.setHorizontalAlignment(SwingConstants.LEFT);
442 pileupjv.setFont(LABEL_FONT);
443 pileupjv.setHorizontalAlignment(SwingConstants.LEFT);
444 pirjv.setFont(LABEL_FONT);
445 pirjv.setHorizontalAlignment(SwingConstants.LEFT);
446 autoIdWidth.setFont(LABEL_FONT);
448 MessageManager.getString("label.automatically_set_id_width"));
449 autoIdWidth.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager
450 .getString("label.adjusts_width_generated_eps_png")));
451 autoIdWidth.setBounds(new Rectangle(228, 96, 188, 23));
452 autoIdWidth.addActionListener(new ActionListener()
456 public void actionPerformed(ActionEvent e)
458 autoIdWidth_actionPerformed();
461 userIdWidthlabel.setFont(LABEL_FONT);
462 userIdWidthlabel.setText(
463 MessageManager.getString("label.figure_id_column_width"));
464 userIdWidth.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager
465 .getString("label.manually_specify_width_left_column")));
466 userIdWidthlabel.setToolTipText(
467 JvSwingUtils.wrapTooltip(true, MessageManager.getString(
468 "label.manually_specify_width_left_column")));
469 userIdWidthlabel.setBounds(new Rectangle(236, 120, 168, 23));
470 userIdWidth.setFont(JvSwingUtils.getTextAreaFont());
471 userIdWidth.setText("");
472 userIdWidth.setBounds(new Rectangle(232, 144, 84, 23));
473 userIdWidth.addActionListener(new ActionListener()
477 public void actionPerformed(ActionEvent e)
479 userIdWidth_actionPerformed();
482 modellerOutput.setFont(LABEL_FONT);
484 .setText(MessageManager.getString("label.use_modeller_output"));
485 modellerOutput.setBounds(new Rectangle(228, 226, 168, 23));
486 embbedBioJSON.setFont(LABEL_FONT);
487 embbedBioJSON.setText(MessageManager.getString("label.embbed_biojson"));
488 embbedBioJSON.setBounds(new Rectangle(228, 200, 250, 23));
490 jPanel11.add(jLabel1);
492 jPanel11.add(clustaljv);
493 jPanel11.add(fastajv);
495 jPanel11.add(pfamjv);
496 jPanel11.add(pileupjv);
498 outputTab.add(autoIdWidth);
499 outputTab.add(userIdWidth);
500 outputTab.add(userIdWidthlabel);
501 outputTab.add(modellerOutput);
502 outputTab.add(embbedBioJSON);
503 outputTab.add(epsLabel);
504 outputTab.add(epsRendering);
505 outputTab.add(jPanel11);
510 * Initialises the Connections tabbed panel.
514 private JPanel initConnectionsTab()
516 JPanel connectTab = new JPanel();
517 connectTab.setLayout(new GridBagLayout());
519 // Label for browser text box
520 JLabel browserLabel = new JLabel();
521 browserLabel.setFont(LABEL_FONT);
522 browserLabel.setHorizontalAlignment(SwingConstants.TRAILING);
523 browserLabel.setText(
524 MessageManager.getString("label.default_browser_unix"));
525 defaultBrowser.setFont(LABEL_FONT);
526 defaultBrowser.setText("");
528 defaultBrowser.addMouseListener(new MouseAdapter()
531 public void mouseClicked(MouseEvent e)
533 if (e.getClickCount() > 1)
535 defaultBrowser_mouseClicked(e);
540 JPanel proxyPanel = initConnTabProxyPanel();
541 initConnTabCheckboxes();
543 // Add default Browser text box
544 connectTab.add(browserLabel,
545 new GridBagConstraints(0, 0, 1, 1, 0.0, 0.0,
546 GridBagConstraints.WEST, GridBagConstraints.NONE,
547 new Insets(10, 0, 5, 5), 5, 1));
548 defaultBrowser.setFont(LABEL_FONT);
549 defaultBrowser.setText("");
551 connectTab.add(defaultBrowser, new GridBagConstraints(1, 0, 1, 1, 1.0,
552 0.0, GridBagConstraints.CENTER, GridBagConstraints.HORIZONTAL,
553 new Insets(10, 0, 5, 10), 30, 1));
555 // Add proxy server panel
556 connectTab.add(proxyPanel, new GridBagConstraints(0, 1, 2, 1, 1.0, 0.0,
557 GridBagConstraints.CENTER, GridBagConstraints.HORIZONTAL,
558 new Insets(10, 0, 5, 12), 4, 10));
560 // Add usage stats, version check and questionnaire checkboxes
561 connectTab.add(usagestats,
562 new GridBagConstraints(0, 2, 1, 1, 1.0, 0.0,
563 GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
564 new Insets(0, 2, 5, 5), 70, 1));
565 connectTab.add(questionnaire,
566 new GridBagConstraints(1, 2, 1, 1, 1.0, 0.0,
567 GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
568 new Insets(0, 2, 5, 10), 70, 1));
569 connectTab.add(versioncheck,
570 new GridBagConstraints(0, 3, 1, 1, 1.0, 0.0,
571 GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
572 new Insets(0, 2, 5, 5), 70, 1));
574 // Add padding so the panel doesn't look ridiculous
575 JPanel spacePanel = new JPanel();
576 connectTab.add(spacePanel,
577 new GridBagConstraints(0, 4, 1, 1, 1.0, 1.0,
578 GridBagConstraints.WEST, GridBagConstraints.BOTH,
579 new Insets(0, 0, 0, 5), 70, 1));
585 * Initialises the Links tabbed panel.
589 private JPanel initLinksTab()
591 JPanel linkTab = new JPanel();
592 linkTab.setLayout(new GridBagLayout());
594 // Set up table for Url links
595 linkUrlTable.setFillsViewportHeight(true);
596 linkUrlTable.setAutoResizeMode(JTable.AUTO_RESIZE_ALL_COLUMNS);
597 linkUrlTable.setAutoCreateRowSorter(true);
598 linkUrlTable.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
600 // adjust row height so radio buttons actually fit
601 // don't do this in the renderer, it causes the awt thread to activate
603 JRadioButton temp = new JRadioButton();
604 linkUrlTable.setRowHeight(temp.getMinimumSize().height);
606 // Table in scrollpane so that the table is given a scrollbar
607 JScrollPane linkScrollPane = new JScrollPane(linkUrlTable);
608 linkScrollPane.setBorder(null);
610 // Panel for links functionality
611 JPanel linkPanel = new JPanel(new GridBagLayout());
612 linkPanel.setBorder(new TitledBorder(
613 MessageManager.getString("label.url_linkfrom_sequence_id")));
615 // Put the Url links panel together
617 // Buttons go at top right, resizing only resizes the blank space vertically
618 JPanel buttonPanel = initLinkTabUrlButtons();
619 GridBagConstraints linkConstraints1 = new GridBagConstraints();
620 linkConstraints1.insets = new Insets(0, 0, 5, 0);
621 linkConstraints1.gridx = 0;
622 linkConstraints1.gridy = 0;
623 linkConstraints1.weightx = 1.0;
624 linkConstraints1.fill = GridBagConstraints.HORIZONTAL;
625 linkTab.add(buttonPanel, linkConstraints1);
627 // Links table goes at top left, resizing resizes the table
628 GridBagConstraints linkConstraints2 = new GridBagConstraints();
629 linkConstraints2.insets = new Insets(0, 0, 5, 5);
630 linkConstraints2.gridx = 0;
631 linkConstraints2.gridy = 1;
632 linkConstraints2.weightx = 1.0;
633 linkConstraints2.weighty = 1.0;
634 linkConstraints2.fill = GridBagConstraints.BOTH;
635 linkTab.add(linkScrollPane, linkConstraints2);
637 // Filter box and buttons goes at bottom left, resizing resizes the text box
638 JPanel filterPanel = initLinkTabFilterPanel();
639 GridBagConstraints linkConstraints3 = new GridBagConstraints();
640 linkConstraints3.insets = new Insets(0, 0, 0, 5);
641 linkConstraints3.gridx = 0;
642 linkConstraints3.gridy = 2;
643 linkConstraints3.weightx = 1.0;
644 linkConstraints3.fill = GridBagConstraints.HORIZONTAL;
645 linkTab.add(filterPanel, linkConstraints3);
650 private JPanel initLinkTabFilterPanel()
652 // Filter textbox and reset button
653 JLabel filterLabel = new JLabel(
654 MessageManager.getString("label.filter"));
655 filterLabel.setFont(LABEL_FONT);
656 filterLabel.setHorizontalAlignment(SwingConstants.RIGHT);
657 filterLabel.setHorizontalTextPosition(SwingConstants.LEADING);
659 filterTB.setFont(LABEL_FONT);
660 filterTB.setText("");
662 doReset.setText(MessageManager.getString("action.showall"));
663 userOnly.setText(MessageManager.getString("action.customfilter"));
665 // Panel for filter functionality
666 JPanel filterPanel = new JPanel(new GridBagLayout());
667 filterPanel.setBorder(new TitledBorder("Filter"));
668 GridBagConstraints gbc = new GridBagConstraints();
671 gbc.fill = GridBagConstraints.NONE;
672 gbc.anchor = GridBagConstraints.WEST;
674 filterPanel.add(filterLabel, gbc);
676 GridBagConstraints gbc1 = new GridBagConstraints();
679 gbc1.fill = GridBagConstraints.HORIZONTAL;
680 gbc1.anchor = GridBagConstraints.WEST;
682 filterPanel.add(filterTB, gbc1);
684 GridBagConstraints gbc2 = new GridBagConstraints();
686 gbc2.fill = GridBagConstraints.NONE;
687 gbc2.anchor = GridBagConstraints.WEST;
688 filterPanel.add(doReset, gbc2);
690 GridBagConstraints gbc3 = new GridBagConstraints();
692 gbc3.fill = GridBagConstraints.NONE;
693 gbc3.anchor = GridBagConstraints.WEST;
694 filterPanel.add(userOnly, gbc3);
699 private JPanel initLinkTabUrlButtons()
701 // Buttons for new / edit / delete Url links
702 JButton newLink = new JButton();
703 newLink.setText(MessageManager.getString("action.new"));
705 editLink.setText(MessageManager.getString("action.edit"));
707 deleteLink.setText(MessageManager.getString("action.delete"));
709 // no current selection, so initially disable delete/edit buttons
710 editLink.setEnabled(false);
711 deleteLink.setEnabled(false);
713 newLink.addActionListener(new java.awt.event.ActionListener()
716 public void actionPerformed(ActionEvent e)
718 newLink_actionPerformed(e);
722 editLink.setText(MessageManager.getString("action.edit"));
723 editLink.addActionListener(new java.awt.event.ActionListener()
726 public void actionPerformed(ActionEvent e)
728 editLink_actionPerformed(e);
732 deleteLink.setText(MessageManager.getString("action.delete"));
733 deleteLink.addActionListener(new java.awt.event.ActionListener()
736 public void actionPerformed(ActionEvent e)
738 deleteLink_actionPerformed(e);
742 JPanel buttonPanel = new JPanel(new GridBagLayout());
743 buttonPanel.setBorder(new TitledBorder("Edit links"));
744 GridBagConstraints gbc = new GridBagConstraints();
747 gbc.fill = GridBagConstraints.NONE;
748 buttonPanel.add(newLink, gbc);
750 GridBagConstraints gbc1 = new GridBagConstraints();
753 gbc1.fill = GridBagConstraints.NONE;
754 buttonPanel.add(editLink, gbc1);
756 GridBagConstraints gbc2 = new GridBagConstraints();
759 gbc2.fill = GridBagConstraints.NONE;
760 buttonPanel.add(deleteLink, gbc2);
762 GridBagConstraints gbc3 = new GridBagConstraints();
765 gbc3.fill = GridBagConstraints.HORIZONTAL;
767 JPanel spacePanel = new JPanel();
768 spacePanel.setBorder(null);
769 buttonPanel.add(spacePanel, gbc3);
775 * Initialises the proxy server panel in the Connections tab
777 * @return the proxy server panel
779 private JPanel initConnTabProxyPanel()
781 // Label for server text box
782 serverLabel.setText(MessageManager.getString("label.address"));
783 serverLabel.setHorizontalAlignment(SwingConstants.RIGHT);
784 serverLabel.setFont(LABEL_FONT);
786 // Proxy server and port text boxes
787 proxyServerTB.setFont(LABEL_FONT);
788 proxyPortTB.setFont(LABEL_FONT);
790 // Label for Port text box
791 portLabel.setFont(LABEL_FONT);
792 portLabel.setHorizontalAlignment(SwingConstants.RIGHT);
793 portLabel.setText(MessageManager.getString("label.port"));
795 // Use proxy server checkbox
796 useProxy.setFont(LABEL_FONT);
797 useProxy.setHorizontalAlignment(SwingConstants.RIGHT);
798 useProxy.setHorizontalTextPosition(SwingConstants.LEADING);
799 useProxy.setText(MessageManager.getString("label.use_proxy_server"));
800 useProxy.addActionListener(new ActionListener()
803 public void actionPerformed(ActionEvent e)
805 useProxy_actionPerformed();
809 // Make proxy server panel
810 JPanel proxyPanel = new JPanel();
811 TitledBorder titledBorder1 = new TitledBorder(
812 MessageManager.getString("label.proxy_server"));
813 proxyPanel.setBorder(titledBorder1);
814 proxyPanel.setLayout(new GridBagLayout());
815 proxyPanel.add(serverLabel,
816 new GridBagConstraints(0, 1, 1, 1, 0.0, 0.0,
817 GridBagConstraints.WEST, GridBagConstraints.NONE,
818 new Insets(0, 2, 2, 0), 5, 0));
819 proxyPanel.add(portLabel,
820 new GridBagConstraints(2, 1, 1, 1, 0.0, 0.0,
821 GridBagConstraints.WEST, GridBagConstraints.NONE,
822 new Insets(0, 0, 2, 0), 11, 0));
823 proxyPanel.add(useProxy,
824 new GridBagConstraints(0, 0, 2, 1, 0.0, 0.0,
825 GridBagConstraints.WEST, GridBagConstraints.NONE,
826 new Insets(0, 2, 5, 185), 2, -4));
827 proxyPanel.add(proxyPortTB,
828 new GridBagConstraints(3, 1, 1, 1, 1.0, 0.0,
829 GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
830 new Insets(0, 2, 2, 2), 54, 1));
831 proxyPanel.add(proxyServerTB,
832 new GridBagConstraints(1, 1, 1, 1, 1.0, 0.0,
833 GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
834 new Insets(0, 2, 2, 0), 263, 1));
840 * Initialises the checkboxes in the Connections tab
842 private void initConnTabCheckboxes()
844 // Usage stats checkbox label
846 MessageManager.getString("label.send_usage_statistics"));
847 usagestats.setFont(LABEL_FONT);
848 usagestats.setHorizontalAlignment(SwingConstants.RIGHT);
849 usagestats.setHorizontalTextPosition(SwingConstants.LEADING);
851 // Questionnaire checkbox label
852 questionnaire.setText(
853 MessageManager.getString("label.check_for_questionnaires"));
854 questionnaire.setFont(LABEL_FONT);
855 questionnaire.setHorizontalAlignment(SwingConstants.RIGHT);
856 questionnaire.setHorizontalTextPosition(SwingConstants.LEADING);
858 // Check for latest version checkbox label
859 versioncheck.setText(
860 MessageManager.getString("label.check_for_latest_version"));
861 versioncheck.setFont(LABEL_FONT);
862 versioncheck.setHorizontalAlignment(SwingConstants.RIGHT);
863 versioncheck.setHorizontalTextPosition(SwingConstants.LEADING);
867 * Initialises the parent panel which contains the tabbed sections.
871 private JPanel initOkCancelPanel()
873 JButton ok = new JButton();
874 ok.setText(MessageManager.getString("action.ok"));
875 ok.addActionListener(new ActionListener()
878 public void actionPerformed(ActionEvent e)
880 ok_actionPerformed(e);
883 JButton cancel = new JButton();
884 cancel.setText(MessageManager.getString("action.cancel"));
885 cancel.addActionListener(new ActionListener()
888 public void actionPerformed(ActionEvent e)
890 cancel_actionPerformed(e);
893 JPanel okCancelPanel = new JPanel();
894 okCancelPanel.add(ok);
895 okCancelPanel.add(cancel);
896 return okCancelPanel;
900 * Initialises the Colours tabbed panel.
904 private JPanel initColoursTab()
906 JPanel coloursTab = new JPanel();
907 coloursTab.setBorder(new TitledBorder(
908 MessageManager.getString("action.open_new_alignment")));
909 coloursTab.setLayout(new FlowLayout());
910 JLabel mincolourLabel = new JLabel();
911 mincolourLabel.setFont(LABEL_FONT);
912 mincolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
913 mincolourLabel.setText(MessageManager.getString("label.min_colour"));
914 minColour.setFont(LABEL_FONT);
915 minColour.setBorder(BorderFactory.createEtchedBorder());
916 minColour.setPreferredSize(new Dimension(40, 20));
917 minColour.addMouseListener(new MouseAdapter()
920 public void mousePressed(MouseEvent e)
922 minColour_actionPerformed(minColour);
925 JLabel maxcolourLabel = new JLabel();
926 maxcolourLabel.setFont(LABEL_FONT);
927 maxcolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
928 maxcolourLabel.setText(MessageManager.getString("label.max_colour"));
929 maxColour.setFont(LABEL_FONT);
930 maxColour.setBorder(BorderFactory.createEtchedBorder());
931 maxColour.setPreferredSize(new Dimension(40, 20));
932 maxColour.addMouseListener(new MouseAdapter()
935 public void mousePressed(MouseEvent e)
937 maxColour_actionPerformed(maxColour);
941 protColour.setFont(LABEL_FONT);
942 protColour.setBounds(new Rectangle(172, 225, 155, 21));
943 JLabel protColourLabel = new JLabel();
944 protColourLabel.setFont(LABEL_FONT);
945 protColourLabel.setHorizontalAlignment(SwingConstants.LEFT);
946 protColourLabel.setText(
947 MessageManager.getString("label.prot_alignment_colour") + " ");
948 JvSwingUtils.addtoLayout(coloursTab,
950 .getString("label.default_colour_scheme_for_alignment"),
951 protColourLabel, protColour);
953 nucColour.setFont(LABEL_FONT);
954 nucColour.setBounds(new Rectangle(172, 240, 155, 21));
955 JLabel nucColourLabel = new JLabel();
956 nucColourLabel.setFont(LABEL_FONT);
957 nucColourLabel.setHorizontalAlignment(SwingConstants.LEFT);
958 nucColourLabel.setText(
959 MessageManager.getString("label.nuc_alignment_colour") + " ");
960 JvSwingUtils.addtoLayout(coloursTab,
962 .getString("label.default_colour_scheme_for_alignment"),
963 nucColourLabel, nucColour);
965 JPanel annotationShding = new JPanel();
966 annotationShding.setBorder(new TitledBorder(
967 MessageManager.getString("label.annotation_shading_default")));
968 annotationShding.setLayout(new GridLayout(1, 2));
969 JvSwingUtils.addtoLayout(annotationShding,
970 MessageManager.getString(
971 "label.default_minimum_colour_annotation_shading"),
972 mincolourLabel, minColour);
973 JvSwingUtils.addtoLayout(annotationShding,
974 MessageManager.getString(
975 "label.default_maximum_colour_annotation_shading"),
976 maxcolourLabel, maxColour);
977 coloursTab.add(annotationShding); // , FlowLayout.LEFT);
982 * Initialises the Overview tabbed panel.
986 private JPanel initOverviewTab()
988 JPanel overviewPanel = new JPanel();
989 overviewPanel.setBorder(new TitledBorder(
990 MessageManager.getString("label.overview_settings")));
992 gapColour.setFont(LABEL_FONT);
993 // fixing the border colours stops apparent colour bleed from the panel
995 BorderFactory.createEtchedBorder(Color.white, Color.lightGray));
996 gapColour.setPreferredSize(new Dimension(40, 20));
997 gapColour.addMouseListener(new MouseAdapter()
1000 public void mousePressed(MouseEvent e)
1002 gapColour_actionPerformed(gapColour);
1006 hiddenColour.setFont(LABEL_FONT);
1007 // fixing the border colours stops apparent colour bleed from the panel
1008 hiddenColour.setBorder(
1009 BorderFactory.createEtchedBorder(Color.white, Color.lightGray));
1010 hiddenColour.setPreferredSize(new Dimension(40, 20));
1011 hiddenColour.addMouseListener(new MouseAdapter()
1014 public void mousePressed(MouseEvent e)
1016 hiddenColour_actionPerformed(hiddenColour);
1020 useLegacyGap = new JCheckBox(
1021 MessageManager.getString("label.ov_legacy_gap"));
1022 useLegacyGap.setFont(LABEL_FONT);
1023 useLegacyGap.setHorizontalAlignment(SwingConstants.LEFT);
1024 gapLabel = new JLabel(
1025 MessageManager.getString("label.gap_colour"));
1026 gapLabel.setFont(LABEL_FONT);
1027 gapLabel.setHorizontalAlignment(SwingConstants.LEFT);
1028 showHiddenAtStart = new JCheckBox(
1029 MessageManager.getString("label.ov_show_hide_default"));
1030 showHiddenAtStart.setFont(LABEL_FONT);
1031 showHiddenAtStart.setHorizontalAlignment(SwingConstants.LEFT);
1032 JLabel hiddenLabel = new JLabel(
1033 MessageManager.getString("label.hidden_colour"));
1034 hiddenLabel.setFont(LABEL_FONT);
1035 hiddenLabel.setHorizontalAlignment(SwingConstants.LEFT);
1037 useLegacyGap.addActionListener(new ActionListener()
1040 public void actionPerformed(ActionEvent e)
1042 useLegacyGaps_actionPerformed(e);
1046 overviewPanel.setLayout(new GridBagLayout());
1047 GridBagConstraints c1 = new GridBagConstraints();
1049 c1.fill = GridBagConstraints.HORIZONTAL;
1054 c1.anchor = GridBagConstraints.FIRST_LINE_START;
1055 overviewPanel.add(useLegacyGap, c1);
1057 GridBagConstraints c2 = new GridBagConstraints();
1058 c2.fill = GridBagConstraints.HORIZONTAL;
1061 c2.insets = new Insets(0, 15, 0, 10);
1062 overviewPanel.add(gapLabel, c2);
1064 GridBagConstraints c3 = new GridBagConstraints();
1065 c3.fill = GridBagConstraints.HORIZONTAL;
1068 c3.insets = new Insets(0, 0, 0, 15);
1069 overviewPanel.add(gapColour, c3);
1071 GridBagConstraints c4 = new GridBagConstraints();
1072 c4.fill = GridBagConstraints.HORIZONTAL;
1076 overviewPanel.add(showHiddenAtStart, c4);
1078 GridBagConstraints c5 = new GridBagConstraints();
1079 c5.fill = GridBagConstraints.HORIZONTAL;
1082 c5.insets = new Insets(0, 15, 0, 10);
1083 overviewPanel.add(hiddenLabel, c5);
1085 GridBagConstraints c6 = new GridBagConstraints();
1086 c6.fill = GridBagConstraints.HORIZONTAL;
1089 c6.insets = new Insets(0, 0, 0, 15);
1090 overviewPanel.add(hiddenColour, c6);
1092 JButton resetButton = new JButton(
1093 MessageManager.getString("label.reset_to_defaults"));
1095 resetButton.addActionListener(new ActionListener()
1098 public void actionPerformed(ActionEvent e)
1100 resetOvDefaults_actionPerformed(e);
1104 GridBagConstraints c7 = new GridBagConstraints();
1105 c7.fill = GridBagConstraints.NONE;
1108 c7.insets = new Insets(10, 0, 0, 0);
1109 c7.anchor = GridBagConstraints.WEST;
1110 overviewPanel.add(resetButton, c7);
1112 // Add padding so the panel doesn't look ridiculous
1113 JPanel spacePanel = new JPanel();
1114 overviewPanel.add(spacePanel,
1115 new GridBagConstraints(0, 3, 1, 1, 1.0, 1.0,
1116 GridBagConstraints.WEST, GridBagConstraints.BOTH,
1117 new Insets(0, 0, 0, 5), 0, 0));
1119 return overviewPanel;
1123 * Initialises the Structure tabbed panel.
1127 private JPanel initStructureTab()
1129 structureTab = new JPanel();
1131 structureTab.setBorder(new TitledBorder(
1132 MessageManager.getString("label.structure_options")));
1133 structureTab.setLayout(null);
1134 final int width = 400;
1135 final int height = 22;
1136 final int lineSpacing = 25;
1139 structFromPdb.setFont(LABEL_FONT);
1141 .setText(MessageManager.getString("label.struct_from_pdb"));
1142 structFromPdb.setBounds(new Rectangle(5, ypos, width, height));
1143 structFromPdb.addActionListener(new ActionListener()
1146 public void actionPerformed(ActionEvent e)
1148 boolean selected = structFromPdb.isSelected();
1149 // enable other options only when the first is checked
1150 useRnaView.setEnabled(selected);
1151 addSecondaryStructure.setEnabled(selected);
1152 addTempFactor.setEnabled(selected);
1155 structureTab.add(structFromPdb);
1157 // indent checkboxes that are conditional on the first one
1158 ypos += lineSpacing;
1159 useRnaView.setFont(LABEL_FONT);
1160 useRnaView.setText(MessageManager.getString("label.use_rnaview"));
1161 useRnaView.setBounds(new Rectangle(25, ypos, width, height));
1162 structureTab.add(useRnaView);
1164 ypos += lineSpacing;
1165 addSecondaryStructure.setFont(LABEL_FONT);
1166 addSecondaryStructure
1167 .setText(MessageManager.getString("label.autoadd_secstr"));
1168 addSecondaryStructure.setBounds(new Rectangle(25, ypos, width, height));
1169 structureTab.add(addSecondaryStructure);
1171 ypos += lineSpacing;
1172 addTempFactor.setFont(LABEL_FONT);
1173 addTempFactor.setText(MessageManager.getString("label.autoadd_temp"));
1174 addTempFactor.setBounds(new Rectangle(25, ypos, width, height));
1175 structureTab.add(addTempFactor);
1177 ypos += lineSpacing;
1178 JLabel viewerLabel = new JLabel();
1179 viewerLabel.setFont(LABEL_FONT);
1180 viewerLabel.setHorizontalAlignment(SwingConstants.LEFT);
1181 viewerLabel.setText(MessageManager.getString("label.structure_viewer"));
1182 viewerLabel.setBounds(new Rectangle(10, ypos, 200, height));
1183 structureTab.add(viewerLabel);
1185 structViewer.setFont(LABEL_FONT);
1186 structViewer.setBounds(new Rectangle(160, ypos, 120, height));
1187 structViewer.addItem(ViewerType.JMOL.name());
1188 structViewer.addItem(ViewerType.CHIMERA.name());
1189 structViewer.addActionListener(new ActionListener()
1192 public void actionPerformed(ActionEvent e)
1194 structureViewer_actionPerformed(
1195 (String) structViewer.getSelectedItem());
1198 structureTab.add(structViewer);
1200 ypos += lineSpacing;
1201 JLabel pathLabel = new JLabel();
1202 pathLabel.setFont(new java.awt.Font("SansSerif", 0, 11));
1203 pathLabel.setHorizontalAlignment(SwingConstants.LEFT);
1204 pathLabel.setText(MessageManager.getString("label.chimera_path"));
1205 final String tooltip = JvSwingUtils.wrapTooltip(true,
1206 MessageManager.getString("label.chimera_path_tip"));
1207 pathLabel.setToolTipText(tooltip);
1208 pathLabel.setBounds(new Rectangle(10, ypos, 140, height));
1209 structureTab.add(pathLabel);
1211 chimeraPath.setFont(LABEL_FONT);
1212 chimeraPath.setText("");
1213 chimeraPath.setBounds(new Rectangle(160, ypos, 300, height));
1214 chimeraPath.addMouseListener(new MouseAdapter()
1217 public void mouseClicked(MouseEvent e)
1219 if (e.getClickCount() == 2)
1221 String chosen = openFileChooser();
1224 chimeraPath.setText(chosen);
1229 structureTab.add(chimeraPath);
1231 ypos += lineSpacing;
1232 nwMapping.setFont(LABEL_FONT);
1233 nwMapping.setText(MessageManager.getString("label.nw_mapping"));
1234 siftsMapping.setFont(LABEL_FONT);
1235 siftsMapping.setText(MessageManager.getString("label.sifts_mapping"));
1236 mappingMethod.add(nwMapping);
1237 mappingMethod.add(siftsMapping);
1238 JPanel mappingPanel = new JPanel();
1239 mappingPanel.setFont(LABEL_FONT);
1240 TitledBorder mmTitledBorder = new TitledBorder(
1241 MessageManager.getString("label.mapping_method"));
1242 mmTitledBorder.setTitleFont(LABEL_FONT);
1243 mappingPanel.setBorder(mmTitledBorder);
1244 mappingPanel.setBounds(new Rectangle(10, ypos, 452, 45));
1245 // GridLayout mappingLayout = new GridLayout();
1246 mappingPanel.setLayout(new GridLayout());
1247 mappingPanel.add(nwMapping);
1248 mappingPanel.add(siftsMapping);
1249 structureTab.add(mappingPanel);
1251 ypos += lineSpacing;
1252 ypos += lineSpacing;
1253 FTSDataColumnPreferences docFieldPref = new FTSDataColumnPreferences(
1254 PreferenceSource.PREFERENCES, PDBFTSRestClient.getInstance());
1255 docFieldPref.setBounds(new Rectangle(10, ypos, 450, 120));
1256 structureTab.add(docFieldPref);
1258 return structureTab;
1262 * Action on choosing a structure viewer from combobox options.
1264 * @param selectedItem
1266 protected void structureViewer_actionPerformed(String selectedItem)
1271 * Show a dialog for the user to choose a file. Returns the chosen path, or
1276 protected String openFileChooser()
1278 String choice = null;
1279 JFileChooser chooser = new JFileChooser();
1281 // chooser.setFileView(new JalviewFileView());
1282 chooser.setDialogTitle(
1283 MessageManager.getString("label.open_local_file"));
1284 chooser.setToolTipText(MessageManager.getString("action.open"));
1286 int value = chooser.showOpenDialog(this);
1288 if (value == JFileChooser.APPROVE_OPTION)
1290 choice = chooser.getSelectedFile().getPath();
1296 * Validate the structure tab preferences; if invalid, set focus on this tab.
1300 protected boolean validateStructure(FocusEvent e)
1302 if (!validateStructure())
1304 e.getComponent().requestFocusInWindow();
1310 protected boolean validateStructure()
1316 * Initialises the Visual tabbed panel.
1320 private JPanel initVisualTab()
1322 JPanel visualTab = new JPanel();
1323 visualTab.setBorder(new TitledBorder(
1324 MessageManager.getString("action.open_new_alignment")));
1325 visualTab.setLayout(null);
1326 fullScreen.setFont(LABEL_FONT);
1327 fullScreen.setHorizontalAlignment(SwingConstants.RIGHT);
1328 fullScreen.setHorizontalTextPosition(SwingConstants.LEFT);
1329 fullScreen.setText(MessageManager.getString("label.maximize_window"));
1330 quality.setEnabled(false);
1331 quality.setFont(LABEL_FONT);
1332 quality.setHorizontalAlignment(SwingConstants.RIGHT);
1333 quality.setHorizontalTextPosition(SwingConstants.LEFT);
1334 quality.setSelected(true);
1335 quality.setText(MessageManager.getString("label.quality"));
1336 conservation.setEnabled(false);
1337 conservation.setFont(LABEL_FONT);
1338 conservation.setHorizontalAlignment(SwingConstants.RIGHT);
1339 conservation.setHorizontalTextPosition(SwingConstants.LEFT);
1340 conservation.setSelected(true);
1341 conservation.setText(MessageManager.getString("label.conservation"));
1342 identity.setEnabled(false);
1343 identity.setFont(LABEL_FONT);
1344 identity.setHorizontalAlignment(SwingConstants.RIGHT);
1345 identity.setHorizontalTextPosition(SwingConstants.LEFT);
1346 identity.setSelected(true);
1347 identity.setText(MessageManager.getString("label.consensus"));
1348 showOccupancy.setFont(LABEL_FONT);
1349 showOccupancy.setEnabled(false);
1350 showOccupancy.setHorizontalAlignment(SwingConstants.RIGHT);
1351 showOccupancy.setHorizontalTextPosition(SwingConstants.LEFT);
1352 showOccupancy.setSelected(true);
1353 showOccupancy.setText(MessageManager.getString("label.occupancy"));
1355 JLabel showGroupbits = new JLabel();
1356 showGroupbits.setFont(LABEL_FONT);
1357 showGroupbits.setHorizontalAlignment(SwingConstants.RIGHT);
1358 showGroupbits.setHorizontalTextPosition(SwingConstants.LEFT);
1360 .setText(MessageManager.getString("action.show_group") + ":");
1361 JLabel showConsensbits = new JLabel();
1362 showConsensbits.setFont(LABEL_FONT);
1363 showConsensbits.setHorizontalAlignment(SwingConstants.RIGHT);
1364 showConsensbits.setHorizontalTextPosition(SwingConstants.LEFT);
1366 .setText(MessageManager.getString("label.consensus") + ":");
1367 showConsensHistogram.setEnabled(false);
1368 showConsensHistogram.setFont(LABEL_FONT);
1369 showConsensHistogram.setHorizontalAlignment(SwingConstants.RIGHT);
1370 showConsensHistogram.setHorizontalTextPosition(SwingConstants.LEFT);
1371 showConsensHistogram.setSelected(true);
1372 showConsensHistogram
1373 .setText(MessageManager.getString("label.histogram"));
1374 showConsensLogo.setEnabled(false);
1375 showConsensLogo.setFont(LABEL_FONT);
1376 showConsensLogo.setHorizontalAlignment(SwingConstants.RIGHT);
1377 showConsensLogo.setHorizontalTextPosition(SwingConstants.LEFT);
1378 showConsensLogo.setSelected(true);
1379 showConsensLogo.setText(MessageManager.getString("label.logo"));
1380 showGroupConsensus.setEnabled(false);
1381 showGroupConsensus.setFont(LABEL_FONT);
1382 showGroupConsensus.setHorizontalAlignment(SwingConstants.RIGHT);
1383 showGroupConsensus.setHorizontalTextPosition(SwingConstants.LEFT);
1384 showGroupConsensus.setSelected(true);
1385 showGroupConsensus.setText(MessageManager.getString("label.consensus"));
1386 showGroupConservation.setEnabled(false);
1387 showGroupConservation.setFont(LABEL_FONT);
1388 showGroupConservation.setHorizontalAlignment(SwingConstants.RIGHT);
1389 showGroupConservation.setHorizontalTextPosition(SwingConstants.LEFT);
1390 showGroupConservation.setSelected(true);
1391 showGroupConservation
1392 .setText(MessageManager.getString("label.conservation"));
1393 showNpTooltip.setEnabled(true);
1394 showNpTooltip.setFont(LABEL_FONT);
1395 showNpTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
1396 showNpTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
1397 showNpTooltip.setSelected(true);
1398 showNpTooltip.setText(
1399 MessageManager.getString("label.non_positional_features"));
1400 showDbRefTooltip.setEnabled(true);
1401 showDbRefTooltip.setFont(LABEL_FONT);
1402 showDbRefTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
1403 showDbRefTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
1404 showDbRefTooltip.setSelected(true);
1406 .setText(MessageManager.getString("label.database_references"));
1407 annotations.setFont(LABEL_FONT);
1408 annotations.setHorizontalAlignment(SwingConstants.RIGHT);
1409 annotations.setHorizontalTextPosition(SwingConstants.LEFT);
1410 annotations.setSelected(true);
1411 annotations.setText(MessageManager.getString("label.show_annotations"));
1412 // annotations.setBounds(new Rectangle(169, 12, 200, 23));
1413 annotations.addActionListener(new ActionListener()
1416 public void actionPerformed(ActionEvent e)
1418 annotations_actionPerformed(e);
1421 identity.addActionListener(new ActionListener()
1424 public void actionPerformed(ActionEvent e)
1426 annotations_actionPerformed(e);
1429 showGroupConsensus.addActionListener(new ActionListener()
1432 public void actionPerformed(ActionEvent e)
1434 annotations_actionPerformed(e);
1437 showUnconserved.setFont(LABEL_FONT);
1438 showUnconserved.setHorizontalAlignment(SwingConstants.RIGHT);
1439 showUnconserved.setHorizontalTextPosition(SwingConstants.LEFT);
1440 showUnconserved.setSelected(true);
1442 .setText(MessageManager.getString("action.show_unconserved"));
1443 showUnconserved.addActionListener(new ActionListener()
1446 public void actionPerformed(ActionEvent e)
1448 showunconserved_actionPerformed(e);
1452 // TODO these are not yet added to / action from Preferences
1453 // JCheckBox shareSelections = new JCheckBox();
1454 // shareSelections.setFont(verdana11);
1455 // shareSelections.setHorizontalAlignment(SwingConstants.RIGHT);
1456 // shareSelections.setHorizontalTextPosition(SwingConstants.LEFT);
1457 // shareSelections.setSelected(true);
1458 // shareSelections.setText(MessageManager
1459 // .getString("label.share_selection_across_views"));
1460 // JCheckBox followHighlight = new JCheckBox();
1461 // followHighlight.setFont(verdana11);
1462 // followHighlight.setHorizontalAlignment(SwingConstants.RIGHT);
1463 // followHighlight.setHorizontalTextPosition(SwingConstants.LEFT);
1464 // // showUnconserved.setBounds(new Rectangle(169, 40, 200, 23));
1465 // followHighlight.setSelected(true);
1466 // followHighlight.setText(MessageManager
1467 // .getString("label.scroll_highlighted_regions"));
1469 seqLimit.setFont(LABEL_FONT);
1470 seqLimit.setHorizontalAlignment(SwingConstants.RIGHT);
1471 seqLimit.setHorizontalTextPosition(SwingConstants.LEFT);
1472 seqLimit.setText(MessageManager.getString("label.full_sequence_id"));
1473 smoothFont.setFont(LABEL_FONT);
1474 smoothFont.setHorizontalAlignment(SwingConstants.RIGHT);
1475 smoothFont.setHorizontalTextPosition(SwingConstants.LEADING);
1476 smoothFont.setText(MessageManager.getString("label.smooth_font"));
1477 scaleProteinToCdna.setFont(LABEL_FONT);
1478 scaleProteinToCdna.setHorizontalAlignment(SwingConstants.RIGHT);
1479 scaleProteinToCdna.setHorizontalTextPosition(SwingConstants.LEADING);
1480 scaleProteinToCdna.setText(
1481 MessageManager.getString("label.scale_protein_to_cdna"));
1482 scaleProteinToCdna.setToolTipText(
1483 MessageManager.getString("label.scale_protein_to_cdna_tip"));
1484 JLabel gapLabel = new JLabel();
1485 gapLabel.setFont(LABEL_FONT);
1486 gapLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1487 gapLabel.setText(MessageManager.getString("label.gap_symbol") + " ");
1488 JLabel fontLabel = new JLabel();
1489 fontLabel.setFont(LABEL_FONT);
1490 fontLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1491 fontLabel.setText(MessageManager.getString("label.font"));
1492 fontSizeCB.setFont(LABEL_FONT);
1493 fontSizeCB.setBounds(new Rectangle(320, 112, 65, 23));
1494 fontStyleCB.setFont(LABEL_FONT);
1495 fontStyleCB.setBounds(new Rectangle(382, 112, 80, 23));
1496 fontNameCB.setFont(LABEL_FONT);
1497 fontNameCB.setBounds(new Rectangle(172, 112, 147, 23));
1498 gapSymbolCB.setFont(LABEL_FONT);
1499 gapSymbolCB.setBounds(new Rectangle(172, 215, 69, 23));
1500 DefaultListCellRenderer dlcr = new DefaultListCellRenderer();
1501 dlcr.setHorizontalAlignment(DefaultListCellRenderer.CENTER);
1502 gapSymbolCB.setRenderer(dlcr);
1504 startupCheckbox.setText(MessageManager.getString("action.open_file"));
1505 startupCheckbox.setFont(LABEL_FONT);
1506 startupCheckbox.setHorizontalAlignment(SwingConstants.RIGHT);
1507 startupCheckbox.setHorizontalTextPosition(SwingConstants.LEFT);
1508 startupCheckbox.setSelected(true);
1509 startupFileTextfield.setFont(LABEL_FONT);
1510 startupFileTextfield.setBounds(new Rectangle(172, 310, 330, 20));
1511 startupFileTextfield.addMouseListener(new MouseAdapter()
1514 public void mouseClicked(MouseEvent e)
1516 if (e.getClickCount() > 1)
1518 startupFileTextfield_mouseClicked();
1523 sortby.setFont(LABEL_FONT);
1524 sortby.setBounds(new Rectangle(172, 260, 155, 21));
1525 JLabel sortLabel = new JLabel();
1526 sortLabel.setFont(LABEL_FONT);
1527 sortLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1528 sortLabel.setText(MessageManager.getString("label.sort_by"));
1529 sortAnnBy.setFont(LABEL_FONT);
1530 sortAnnBy.setBounds(new Rectangle(172, 285, 110, 21));
1531 JLabel sortAnnLabel = new JLabel();
1532 sortAnnLabel.setFont(LABEL_FONT);
1533 sortAnnLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1534 sortAnnLabel.setText(MessageManager.getString("label.sort_ann_by"));
1535 sortAutocalc.setFont(LABEL_FONT);
1536 sortAutocalc.setBounds(new Rectangle(290, 285, 165, 21));
1538 JPanel annsettingsPanel = new JPanel();
1539 annsettingsPanel.setBounds(new Rectangle(173, 13, 320, 96));
1540 annsettingsPanel.setLayout(new FlowLayout(FlowLayout.LEFT, 0, 0));
1541 annsettingsPanel.setBorder(new EtchedBorder());
1542 visualTab.add(annsettingsPanel);
1543 Border jb = new EmptyBorder(1, 1, 4, 5);
1544 annotations.setBorder(jb);
1545 showOccupancy.setBorder(jb);
1546 quality.setBorder(jb);
1547 conservation.setBorder(jb);
1548 identity.setBorder(jb);
1549 showConsensbits.setBorder(jb);
1550 showGroupbits.setBorder(jb);
1551 showGroupConsensus.setBorder(jb);
1552 showGroupConservation.setBorder(jb);
1553 showConsensHistogram.setBorder(jb);
1554 showConsensLogo.setBorder(jb);
1556 JPanel autoAnnotSettings = new JPanel();
1557 annsettingsPanel.add(autoAnnotSettings);
1558 autoAnnotSettings.setLayout(new GridLayout(0, 2));
1559 autoAnnotSettings.add(annotations);
1560 autoAnnotSettings.add(quality);
1561 // second row of autoannotation box
1562 autoAnnotSettings = new JPanel();
1563 annsettingsPanel.add(autoAnnotSettings);
1565 autoAnnotSettings.setLayout(new GridLayout(0, 3));
1566 autoAnnotSettings.add(conservation);
1567 autoAnnotSettings.add(identity);
1568 autoAnnotSettings.add(showOccupancy);
1569 autoAnnotSettings.add(showGroupbits);
1570 autoAnnotSettings.add(showGroupConservation);
1571 autoAnnotSettings.add(showGroupConsensus);
1572 autoAnnotSettings.add(showConsensbits);
1573 autoAnnotSettings.add(showConsensHistogram);
1574 autoAnnotSettings.add(showConsensLogo);
1576 JPanel tooltipSettings = new JPanel();
1577 tooltipSettings.setBorder(new TitledBorder(
1578 MessageManager.getString("label.sequence_id_tooltip")));
1579 tooltipSettings.setBounds(173, 140, 220, 62);
1580 tooltipSettings.setLayout(new GridLayout(2, 1));
1581 tooltipSettings.add(showDbRefTooltip);
1582 tooltipSettings.add(showNpTooltip);
1583 visualTab.add(tooltipSettings);
1585 wrap.setFont(LABEL_FONT);
1586 wrap.setHorizontalAlignment(SwingConstants.TRAILING);
1587 wrap.setHorizontalTextPosition(SwingConstants.LEADING);
1588 wrap.setText(MessageManager.getString("label.wrap_alignment"));
1589 rightAlign.setFont(LABEL_FONT);
1590 rightAlign.setForeground(Color.black);
1591 rightAlign.setHorizontalAlignment(SwingConstants.RIGHT);
1592 rightAlign.setHorizontalTextPosition(SwingConstants.LEFT);
1593 rightAlign.setText(MessageManager.getString("label.right_align_ids"));
1594 idItalics.setFont(LABEL_FONT_ITALIC);
1595 idItalics.setHorizontalAlignment(SwingConstants.RIGHT);
1596 idItalics.setHorizontalTextPosition(SwingConstants.LEADING);
1598 MessageManager.getString("label.sequence_name_italics"));
1599 openoverv.setFont(LABEL_FONT);
1600 openoverv.setActionCommand(
1601 MessageManager.getString("label.open_overview"));
1602 openoverv.setHorizontalAlignment(SwingConstants.RIGHT);
1603 openoverv.setHorizontalTextPosition(SwingConstants.LEFT);
1604 openoverv.setText(MessageManager.getString("label.open_overview"));
1605 JPanel jPanel2 = new JPanel();
1606 jPanel2.setBounds(new Rectangle(7, 17, 158, 310));
1607 jPanel2.setLayout(new GridLayout(14, 1));
1608 jPanel2.add(fullScreen);
1609 jPanel2.add(openoverv);
1610 jPanel2.add(seqLimit);
1611 jPanel2.add(rightAlign);
1612 jPanel2.add(fontLabel);
1613 jPanel2.add(showUnconserved);
1614 jPanel2.add(idItalics);
1615 jPanel2.add(smoothFont);
1616 jPanel2.add(scaleProteinToCdna);
1617 jPanel2.add(gapLabel);
1619 jPanel2.add(sortLabel);
1620 jPanel2.add(sortAnnLabel);
1621 jPanel2.add(startupCheckbox);
1622 visualTab.add(jPanel2);
1623 visualTab.add(startupFileTextfield);
1624 visualTab.add(sortby);
1625 visualTab.add(sortAnnBy);
1626 visualTab.add(sortAutocalc);
1627 visualTab.add(gapSymbolCB);
1628 visualTab.add(fontNameCB);
1629 visualTab.add(fontSizeCB);
1630 visualTab.add(fontStyleCB);
1634 protected void autoIdWidth_actionPerformed()
1636 // TODO Auto-generated method stub
1640 protected void userIdWidth_actionPerformed()
1642 // TODO Auto-generated method stub
1646 protected void maxColour_actionPerformed(JPanel panel)
1650 protected void minColour_actionPerformed(JPanel panel)
1654 protected void gapColour_actionPerformed(JPanel panel)
1658 protected void hiddenColour_actionPerformed(JPanel panel)
1662 protected void showunconserved_actionPerformed(ActionEvent e)
1664 // TODO Auto-generated method stub
1668 protected void useLegacyGaps_actionPerformed(ActionEvent e)
1672 protected void resetOvDefaults_actionPerformed(ActionEvent e)
1682 public void ok_actionPerformed(ActionEvent e)
1692 public void cancel_actionPerformed(ActionEvent e)
1702 public void annotations_actionPerformed(ActionEvent e)
1709 public void startupFileTextfield_mouseClicked()
1713 public void newLink_actionPerformed(ActionEvent e)
1718 public void editLink_actionPerformed(ActionEvent e)
1723 public void deleteLink_actionPerformed(ActionEvent e)
1728 public void defaultBrowser_mouseClicked(MouseEvent e)
1733 public void linkURLList_keyTyped(KeyEvent e)
1738 public void useProxy_actionPerformed()
1740 boolean enabled = useProxy.isSelected();
1741 portLabel.setEnabled(enabled);
1742 serverLabel.setEnabled(enabled);
1743 proxyServerTB.setEnabled(enabled);
1744 proxyPortTB.setEnabled(enabled);
1748 * Customer renderer for JTable: supports column of radio buttons
1750 public class RadioButtonRenderer extends JRadioButton
1751 implements TableCellRenderer
1753 public RadioButtonRenderer()
1755 setHorizontalAlignment(CENTER);
1756 setToolTipText(MessageManager.getString("label.urltooltip"));
1760 public Component getTableCellRendererComponent(JTable table,
1761 Object value, boolean isSelected, boolean hasFocus, int row,
1764 setSelected((boolean) value);
1766 // set colours to match rest of table
1769 setBackground(table.getSelectionBackground());
1770 setForeground(table.getSelectionForeground());
1774 setBackground(table.getBackground());
1775 setForeground(table.getForeground());
1782 * Customer cell editor for JTable: supports column of radio buttons in
1783 * conjunction with renderer
1785 public class RadioButtonEditor extends AbstractCellEditor
1786 implements TableCellEditor
1788 private JRadioButton button = new JRadioButton();
1790 public RadioButtonEditor()
1792 button.setHorizontalAlignment(SwingConstants.CENTER);
1793 this.button.addActionListener(new ActionListener()
1796 public void actionPerformed(ActionEvent e)
1798 fireEditingStopped();
1804 public Component getTableCellEditorComponent(JTable table, Object value,
1805 boolean isSelected, int row, int column)
1807 button.setSelected((boolean) value);
1812 public Object getCellEditorValue()
1814 return button.isSelected();