src/jalview/jbgui/GPreferences.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   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.
  11  *
  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.
  16  *
  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.
  20  */
  21 package jalview.jbgui;
  22
  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;
  29
  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;
  35 import java.awt.Font;
  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;
  47
  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;
  73
  74 /**
  75  * Base class for the Preferences panel.
  76  *
  77  * @author $author$
  78  * @version $Revision$
  79  */
  80 public class GPreferences extends JPanel
  81 {
  82   private static final Font LABEL_FONT = JvSwingUtils.getLabelFont();
  83
  84   private static final Font LABEL_FONT_ITALIC = JvSwingUtils.getLabelFont(
  85           false, true);
  86
  87   /*
  88    * Visual tab components
  89    */
  90   protected JCheckBox fullScreen = new JCheckBox();
  91
  92   protected JCheckBox openoverv = new JCheckBox();
  93
  94   protected JCheckBox seqLimit = new JCheckBox();
  95
  96   protected JCheckBox rightAlign = new JCheckBox();
  97
  98   protected JComboBox<String> fontSizeCB = new JComboBox<>();
  99
 100   protected JComboBox<String> fontStyleCB = new JComboBox<>();
 101
 102   protected JComboBox<String> fontNameCB = new JComboBox<>();
 103
 104   protected JCheckBox showOccupancy = new JCheckBox();
 105
 106   protected JCheckBox showUnconserved = new JCheckBox();
 107
 108   protected JCheckBox idItalics = new JCheckBox();
 109
 110   protected JCheckBox smoothFont = new JCheckBox();
 111
 112   protected JCheckBox scaleProteinToCdna = new JCheckBox();
 113
 114   protected JComboBox<String> gapSymbolCB = new JComboBox<>();
 115
 116   protected JCheckBox wrap = new JCheckBox();
 117
 118   protected JComboBox<String> sortby = new JComboBox<>();
 119
 120   protected JComboBox<String> sortAnnBy = new JComboBox<>();
 121
 122   protected JComboBox<String> sortAutocalc = new JComboBox<>();
 123
 124   protected JCheckBox startupCheckbox = new JCheckBox();
 125
 126   protected JTextField startupFileTextfield = new JTextField();
 127
 128   // below are in the 'second column'
 129   protected JCheckBox annotations = new JCheckBox();
 130
 131   protected JCheckBox quality = new JCheckBox();
 132
 133   protected JCheckBox conservation = new JCheckBox();
 134
 135   protected JCheckBox identity = new JCheckBox();
 136
 137   protected JCheckBox showGroupConsensus = new JCheckBox();
 138
 139   protected JCheckBox showGroupConservation = new JCheckBox();
 140
 141   protected JCheckBox showConsensHistogram = new JCheckBox();
 142
 143   protected JCheckBox showConsensLogo = new JCheckBox();
 144
 145   protected JCheckBox showInformationHistogram = new JCheckBox();
 146
 147   protected JCheckBox showHMMLogo = new JCheckBox();
 148
 149   protected JCheckBox showDbRefTooltip = new JCheckBox();
 150
 151   protected JCheckBox showNpTooltip = new JCheckBox();
 152
 153
 154   /*
 155    * Structure tab and components
 156    */
 157   protected JPanel structureTab;
 158
 159   protected JCheckBox structFromPdb = new JCheckBox();
 160
 161   protected JCheckBox useRnaView = new JCheckBox();
 162
 163   protected JCheckBox addSecondaryStructure = new JCheckBox();
 164
 165   protected JCheckBox addTempFactor = new JCheckBox();
 166
 167   protected JComboBox<String> structViewer = new JComboBox<>();
 168
 169   protected JTextField chimeraPath = new JTextField();
 170
 171   protected ButtonGroup mappingMethod = new ButtonGroup();
 172
 173   protected JRadioButton siftsMapping = new JRadioButton();
 174
 175   protected JRadioButton nwMapping = new JRadioButton();
 176
 177   /*
 178    * Colours tab components
 179    */
 180   protected JPanel minColour = new JPanel();
 181
 182   protected JPanel maxColour = new JPanel();
 183
 184   protected JComboBox<String> protColour = new JComboBox<>();
 185
 186   protected JComboBox<String> nucColour = new JComboBox<>();
 187
 188   /*
 189    * Connections tab components
 190    */
 191   protected JTable linkUrlTable = new JTable();
 192
 193   protected JButton editLink = new JButton();
 194
 195   protected JButton deleteLink = new JButton();
 196
 197   protected JTextField filterTB = new JTextField();
 198
 199   protected JButton doReset = new JButton();
 200
 201   protected JButton userOnly = new JButton();
 202
 203   protected JLabel portLabel = new JLabel();
 204
 205   protected JLabel serverLabel = new JLabel();
 206
 207   protected JTextField proxyServerTB = new JTextField();
 208
 209   protected JTextField proxyPortTB = new JTextField();
 210
 211   protected JTextField defaultBrowser = new JTextField();
 212
 213   protected JCheckBox useProxy = new JCheckBox();
 214
 215   protected JCheckBox usagestats = new JCheckBox();
 216
 217   protected JCheckBox questionnaire = new JCheckBox();
 218
 219   protected JCheckBox versioncheck = new JCheckBox();
 220
 221   /*
 222    * Output tab components
 223    */
 224   protected JComboBox<Object> epsRendering = new JComboBox<>();
 225
 226   protected JLabel userIdWidthlabel = new JLabel();
 227
 228   protected JCheckBox autoIdWidth = new JCheckBox();
 229
 230   protected JTextField userIdWidth = new JTextField();
 231
 232   protected JCheckBox blcjv = new JCheckBox();
 233
 234   protected JCheckBox pileupjv = new JCheckBox();
 235
 236   protected JCheckBox clustaljv = new JCheckBox();
 237
 238   protected JCheckBox msfjv = new JCheckBox();
 239
 240   protected JCheckBox fastajv = new JCheckBox();
 241
 242   protected JCheckBox pfamjv = new JCheckBox();
 243
 244   protected JCheckBox pirjv = new JCheckBox();
 245
 246   protected JCheckBox modellerOutput = new JCheckBox();
 247
 248   protected JCheckBox embbedBioJSON = new JCheckBox();
 249
 250   /*
 251    * Editing tab components
 252    */
 253   protected JCheckBox autoCalculateConsCheck = new JCheckBox();
 254
 255   protected JCheckBox padGaps = new JCheckBox();
 256
 257   protected JCheckBox sortByTree = new JCheckBox();
 258
 259   /*
 260    * DAS Settings tab
 261    */
 262   protected JPanel dasTab = new JPanel();
 263
 264   /*
 265    * Web Services tab
 266    */
 267   protected JPanel wsTab = new JPanel();
 268
 269   /**
 270    * Creates a new GPreferences object.
 271    */
 272   public GPreferences()
 273   {
 274     try
 275     {
 276       jbInit();
 277     } catch (Exception ex)
 278     {
 279       ex.printStackTrace();
 280     }
 281   }
 282
 283   /**
 284    * Construct the panel and its tabbed sub-panels.
 285    *
 286    * @throws Exception
 287    */
 288   private void jbInit() throws Exception
 289   {
 290     final JTabbedPane tabbedPane = new JTabbedPane();
 291     this.setLayout(new BorderLayout());
 292     JPanel okCancelPanel = initOkCancelPanel();
 293     this.add(tabbedPane, BorderLayout.CENTER);
 294     this.add(okCancelPanel, BorderLayout.SOUTH);
 295
 296     tabbedPane.add(initVisualTab(),
 297             MessageManager.getString("label.visual"));
 298
 299     tabbedPane.add(initColoursTab(),
 300             MessageManager.getString("label.colours"));
 301
 302     tabbedPane.add(initStructureTab(),
 303             MessageManager.getString("label.structure"));
 304
 305     tabbedPane.add(initConnectionsTab(),
 306             MessageManager.getString("label.connections"));
 307
 308     tabbedPane.add(initLinksTab(),
 309             MessageManager.getString("label.urllinks"));
 310
 311     tabbedPane.add(initOutputTab(),
 312             MessageManager.getString("label.output"));
 313
 314     tabbedPane.add(initEditingTab(),
 315             MessageManager.getString("label.editing"));
 316
 317     /*
 318      * See DasSourceBrowser for the real work of configuring this tab.
 319      */
 320     dasTab.setLayout(new BorderLayout());
 321     tabbedPane.add(dasTab, MessageManager.getString("label.das_settings"));
 322
 323     /*
 324      * See WsPreferences for the real work of configuring this tab.
 325      */
 326     wsTab.setLayout(new BorderLayout());
 327     tabbedPane.add(wsTab, MessageManager.getString("label.web_services"));
 328
 329     /*
 330      * Handler to validate a tab before leaving it - currently only for
 331      * Structure.
 332      */
 333     tabbedPane.addChangeListener(new ChangeListener()
 334     {
 335       private Component lastTab;
 336
 337       @Override
 338       public void stateChanged(ChangeEvent e)
 339       {
 340         if (lastTab == structureTab
 341                 && tabbedPane.getSelectedComponent() != structureTab)
 342         {
 343           if (!validateStructure())
 344           {
 345             tabbedPane.setSelectedComponent(structureTab);
 346             return;
 347           }
 348         }
 349         lastTab = tabbedPane.getSelectedComponent();
 350       }
 351
 352     });
 353   }
 354
 355   /**
 356    * Initialises the Editing tabbed panel.
 357    *
 358    * @return
 359    */
 360   private JPanel initEditingTab()
 361   {
 362     JPanel editingTab = new JPanel();
 363     editingTab.setLayout(null);
 364     autoCalculateConsCheck.setFont(LABEL_FONT);
 365     autoCalculateConsCheck.setText(MessageManager
 366             .getString("label.autocalculate_consensus"));
 367     autoCalculateConsCheck.setBounds(new Rectangle(21, 52, 209, 23));
 368     padGaps.setFont(LABEL_FONT);
 369     padGaps.setText(MessageManager.getString("label.pad_gaps_when_editing"));
 370     padGaps.setBounds(new Rectangle(22, 94, 168, 23));
 371     sortByTree.setFont(LABEL_FONT);
 372     sortByTree
 373             .setText(MessageManager.getString("label.sort_with_new_tree"));
 374     sortByTree
 375             .setToolTipText(MessageManager
 376                     .getString("label.any_trees_calculated_or_loaded_alignment_automatically_sort"));
 377     sortByTree.setBounds(new Rectangle(22, 136, 168, 23));
 378     editingTab.add(autoCalculateConsCheck);
 379     editingTab.add(padGaps);
 380     editingTab.add(sortByTree);
 381     return editingTab;
 382   }
 383
 384   /**
 385    * Initialises the Output tabbed panel.
 386    *
 387    * @return
 388    */
 389   private JPanel initOutputTab()
 390   {
 391     JPanel outputTab = new JPanel();
 392     outputTab.setLayout(null);
 393     JLabel epsLabel = new JLabel();
 394     epsLabel.setFont(LABEL_FONT);
 395     epsLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 396     epsLabel.setText(MessageManager.getString("label.eps_rendering_style"));
 397     epsLabel.setBounds(new Rectangle(9, 31, 140, 24));
 398     epsRendering.setFont(LABEL_FONT);
 399     epsRendering.setBounds(new Rectangle(154, 34, 187, 21));
 400     JLabel jLabel1 = new JLabel();
 401     jLabel1.setFont(LABEL_FONT);
 402     jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
 403     jLabel1.setText(MessageManager.getString("label.append_start_end"));
 404     jLabel1.setFont(LABEL_FONT);
 405     fastajv.setFont(LABEL_FONT);
 406     fastajv.setHorizontalAlignment(SwingConstants.LEFT);
 407     clustaljv.setText(MessageManager.getString("label.clustal") + "     ");
 408     blcjv.setText(MessageManager.getString("label.blc") + "     ");
 409     fastajv.setText(MessageManager.getString("label.fasta") + "     ");
 410     msfjv.setText(MessageManager.getString("label.msf") + "     ");
 411     pfamjv.setText(MessageManager.getString("label.pfam") + "     ");
 412     pileupjv.setText(MessageManager.getString("label.pileup") + "     ");
 413     msfjv.setFont(LABEL_FONT);
 414     msfjv.setHorizontalAlignment(SwingConstants.LEFT);
 415     pirjv.setText(MessageManager.getString("label.pir") + "     ");
 416     JPanel jPanel11 = new JPanel();
 417     jPanel11.setFont(LABEL_FONT);
 418     TitledBorder titledBorder2 = new TitledBorder(
 419             MessageManager.getString("label.file_output"));
 420     jPanel11.setBorder(titledBorder2);
 421     jPanel11.setBounds(new Rectangle(30, 72, 196, 182));
 422     GridLayout gridLayout3 = new GridLayout();
 423     jPanel11.setLayout(gridLayout3);
 424     gridLayout3.setRows(8);
 425     blcjv.setFont(LABEL_FONT);
 426     blcjv.setHorizontalAlignment(SwingConstants.LEFT);
 427     clustaljv.setFont(LABEL_FONT);
 428     clustaljv.setHorizontalAlignment(SwingConstants.LEFT);
 429     pfamjv.setFont(LABEL_FONT);
 430     pfamjv.setHorizontalAlignment(SwingConstants.LEFT);
 431     pileupjv.setFont(LABEL_FONT);
 432     pileupjv.setHorizontalAlignment(SwingConstants.LEFT);
 433     pirjv.setFont(LABEL_FONT);
 434     pirjv.setHorizontalAlignment(SwingConstants.LEFT);
 435     autoIdWidth.setFont(LABEL_FONT);
 436     autoIdWidth.setText(MessageManager
 437             .getString("label.automatically_set_id_width"));
 438     autoIdWidth.setToolTipText(JvSwingUtils.wrapTooltip(true,
 439             MessageManager
 440                     .getString("label.adjusts_width_generated_eps_png")));
 441     autoIdWidth.setBounds(new Rectangle(228, 96, 188, 23));
 442     autoIdWidth.addActionListener(new ActionListener()
 443     {
 444
 445       @Override
 446       public void actionPerformed(ActionEvent e)
 447       {
 448         autoIdWidth_actionPerformed();
 449       }
 450     });
 451     userIdWidthlabel.setFont(LABEL_FONT);
 452     userIdWidthlabel.setText(MessageManager
 453             .getString("label.figure_id_column_width"));
 454     userIdWidth
 455             .setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager
 456                     .getString("label.manually_specify_width_left_column")));
 457     userIdWidthlabel
 458             .setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager
 459                     .getString("label.manually_specify_width_left_column")));
 460     userIdWidthlabel.setBounds(new Rectangle(236, 120, 168, 23));
 461     userIdWidth.setFont(JvSwingUtils.getTextAreaFont());
 462     userIdWidth.setText("");
 463     userIdWidth.setBounds(new Rectangle(232, 144, 84, 23));
 464     userIdWidth.addActionListener(new ActionListener()
 465     {
 466
 467       @Override
 468       public void actionPerformed(ActionEvent e)
 469       {
 470         userIdWidth_actionPerformed();
 471       }
 472     });
 473     modellerOutput.setFont(LABEL_FONT);
 474     modellerOutput.setText(MessageManager
 475             .getString("label.use_modeller_output"));
 476     modellerOutput.setBounds(new Rectangle(228, 226, 168, 23));
 477     embbedBioJSON.setFont(LABEL_FONT);
 478     embbedBioJSON.setText(MessageManager.getString("label.embbed_biojson"));
 479     embbedBioJSON.setBounds(new Rectangle(228, 200, 250, 23));
 480
 481     jPanel11.add(jLabel1);
 482     jPanel11.add(blcjv);
 483     jPanel11.add(clustaljv);
 484     jPanel11.add(fastajv);
 485     jPanel11.add(msfjv);
 486     jPanel11.add(pfamjv);
 487     jPanel11.add(pileupjv);
 488     jPanel11.add(pirjv);
 489     outputTab.add(autoIdWidth);
 490     outputTab.add(userIdWidth);
 491     outputTab.add(userIdWidthlabel);
 492     outputTab.add(modellerOutput);
 493     outputTab.add(embbedBioJSON);
 494     outputTab.add(epsLabel);
 495     outputTab.add(epsRendering);
 496     outputTab.add(jPanel11);
 497     return outputTab;
 498   }
 499
 500   /**
 501    * Initialises the Connections tabbed panel.
 502    *
 503    * @return
 504    */
 505   private JPanel initConnectionsTab()
 506   {
 507     JPanel connectTab = new JPanel();
 508     connectTab.setLayout(new GridBagLayout());
 509
 510     // Label for browser text box
 511     JLabel browserLabel = new JLabel();
 512     browserLabel.setFont(LABEL_FONT);
 513     browserLabel.setHorizontalAlignment(SwingConstants.TRAILING);
 514     browserLabel.setText(MessageManager
 515             .getString("label.default_browser_unix"));
 516     defaultBrowser.setFont(LABEL_FONT);
 517     defaultBrowser.setText("");
 518
 519     defaultBrowser.addMouseListener(new MouseAdapter()
 520     {
 521       @Override
 522       public void mouseClicked(MouseEvent e)
 523       {
 524         if (e.getClickCount() > 1)
 525         {
 526           defaultBrowser_mouseClicked(e);
 527         }
 528       }
 529     });
 530
 531     JPanel proxyPanel = initConnTabProxyPanel();
 532     initConnTabCheckboxes();
 533
 534     // Add default Browser text box
 535     connectTab.add(browserLabel, new GridBagConstraints(0, 0, 1, 1, 0.0,
 536             0.0, GridBagConstraints.WEST, GridBagConstraints.NONE,
 537             new Insets(10, 0, 5, 5), 5, 1));
 538     defaultBrowser.setFont(LABEL_FONT);
 539     defaultBrowser.setText("");
 540
 541     connectTab.add(defaultBrowser, new GridBagConstraints(1, 0, 1, 1, 1.0,
 542             0.0, GridBagConstraints.CENTER, GridBagConstraints.HORIZONTAL,
 543             new Insets(10, 0, 5, 10), 30, 1));
 544
 545     // Add proxy server panel
 546     connectTab.add(proxyPanel, new GridBagConstraints(0, 1, 2, 1, 1.0, 0.0,
 547             GridBagConstraints.CENTER, GridBagConstraints.HORIZONTAL,
 548             new Insets(10, 0, 5, 12), 4, 10));
 549
 550     // Add usage stats, version check and questionnaire checkboxes
 551     connectTab.add(usagestats, new GridBagConstraints(0, 2, 1, 1, 1.0, 0.0,
 552             GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 553             new Insets(0, 2, 5, 5), 70, 1));
 554     connectTab.add(questionnaire, new GridBagConstraints(1, 2, 1, 1, 1.0,
 555             0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 556             new Insets(0, 2, 5, 10), 70, 1));
 557     connectTab.add(versioncheck, new GridBagConstraints(0, 3, 1, 1, 1.0,
 558             0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 559             new Insets(0, 2, 5, 5), 70, 1));
 560
 561     // Add padding so the panel doesn't look ridiculous
 562     JPanel spacePanel = new JPanel();
 563     connectTab.add(spacePanel, new GridBagConstraints(0, 4, 1, 1, 1.0, 1.0,
 564             GridBagConstraints.WEST, GridBagConstraints.BOTH, new Insets(0,
 565                     0, 0, 5), 70, 1));
 566
 567     return connectTab;
 568   }
 569
 570   /**
 571    * Initialises the Links tabbed panel.
 572    *
 573    * @return
 574    */
 575   private JPanel initLinksTab()
 576   {
 577     JPanel linkTab = new JPanel();
 578     linkTab.setLayout(new GridBagLayout());
 579
 580     // Set up table for Url links
 581     linkUrlTable.setFillsViewportHeight(true);
 582     linkUrlTable.setAutoResizeMode(JTable.AUTO_RESIZE_ALL_COLUMNS);
 583     linkUrlTable.setAutoCreateRowSorter(true);
 584     linkUrlTable.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
 585
 586     // adjust row height so radio buttons actually fit
 587     // don't do this in the renderer, it causes the awt thread to activate
 588     // constantly
 589     JRadioButton temp = new JRadioButton();
 590     linkUrlTable.setRowHeight(temp.getMinimumSize().height);
 591
 592     // Table in scrollpane so that the table is given a scrollbar
 593     JScrollPane linkScrollPane = new JScrollPane(linkUrlTable);
 594     linkScrollPane.setBorder(null);
 595
 596     // Panel for links functionality
 597     JPanel linkPanel = new JPanel(new GridBagLayout());
 598     linkPanel.setBorder(new TitledBorder(MessageManager
 599             .getString("label.url_linkfrom_sequence_id")));
 600
 601     // Put the Url links panel together
 602
 603     // Buttons go at top right, resizing only resizes the blank space vertically
 604     JPanel buttonPanel = initLinkTabUrlButtons();
 605     GridBagConstraints linkConstraints1 = new GridBagConstraints();
 606     linkConstraints1.insets = new Insets(0, 0, 5, 0);
 607     linkConstraints1.gridx = 0;
 608     linkConstraints1.gridy = 0;
 609     linkConstraints1.weightx = 1.0;
 610     linkConstraints1.fill = GridBagConstraints.HORIZONTAL;
 611     linkTab.add(buttonPanel, linkConstraints1);
 612
 613     // Links table goes at top left, resizing resizes the table
 614     GridBagConstraints linkConstraints2 = new GridBagConstraints();
 615     linkConstraints2.insets = new Insets(0, 0, 5, 5);
 616     linkConstraints2.gridx = 0;
 617     linkConstraints2.gridy = 1;
 618     linkConstraints2.weightx = 1.0;
 619     linkConstraints2.weighty = 1.0;
 620     linkConstraints2.fill = GridBagConstraints.BOTH;
 621     linkTab.add(linkScrollPane, linkConstraints2);
 622
 623     // Filter box and buttons goes at bottom left, resizing resizes the text box
 624     JPanel filterPanel = initLinkTabFilterPanel();
 625     GridBagConstraints linkConstraints3 = new GridBagConstraints();
 626     linkConstraints3.insets = new Insets(0, 0, 0, 5);
 627     linkConstraints3.gridx = 0;
 628     linkConstraints3.gridy = 2;
 629     linkConstraints3.weightx = 1.0;
 630     linkConstraints3.fill = GridBagConstraints.HORIZONTAL;
 631     linkTab.add(filterPanel, linkConstraints3);
 632
 633     return linkTab;
 634   }
 635
 636   private JPanel initLinkTabFilterPanel()
 637   {
 638     // Filter textbox and reset button
 639     JLabel filterLabel = new JLabel(
 640             MessageManager.getString("label.filter"));
 641     filterLabel.setFont(LABEL_FONT);
 642     filterLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 643     filterLabel.setHorizontalTextPosition(SwingConstants.LEADING);
 644
 645     filterTB.setFont(LABEL_FONT);
 646     filterTB.setText("");
 647
 648     doReset.setText(MessageManager.getString("action.showall"));
 649     userOnly.setText(MessageManager.getString("action.customfilter"));
 650
 651     // Panel for filter functionality
 652     JPanel filterPanel = new JPanel(new GridBagLayout());
 653     filterPanel.setBorder(new TitledBorder("Filter"));
 654     GridBagConstraints gbc = new GridBagConstraints();
 655     gbc.gridx = 0;
 656     gbc.gridy = 0;
 657     gbc.fill = GridBagConstraints.NONE;
 658     gbc.anchor = GridBagConstraints.WEST;
 659
 660     filterPanel.add(filterLabel, gbc);
 661
 662     GridBagConstraints gbc1 = new GridBagConstraints();
 663     gbc1.gridx = 1;
 664     gbc1.gridwidth = 2;
 665     gbc1.fill = GridBagConstraints.HORIZONTAL;
 666     gbc1.anchor = GridBagConstraints.WEST;
 667     gbc1.weightx = 1.0;
 668     filterPanel.add(filterTB, gbc1);
 669
 670     GridBagConstraints gbc2 = new GridBagConstraints();
 671     gbc2.gridx = 3;
 672     gbc2.fill = GridBagConstraints.NONE;
 673     gbc2.anchor = GridBagConstraints.WEST;
 674     filterPanel.add(doReset, gbc2);
 675
 676     GridBagConstraints gbc3 = new GridBagConstraints();
 677     gbc3.gridx = 4;
 678     gbc3.fill = GridBagConstraints.NONE;
 679     gbc3.anchor = GridBagConstraints.WEST;
 680     filterPanel.add(userOnly, gbc3);
 681
 682     return filterPanel;
 683   }
 684
 685   private JPanel initLinkTabUrlButtons()
 686   {
 687     // Buttons for new / edit / delete Url links
 688     JButton newLink = new JButton();
 689     newLink.setText(MessageManager.getString("action.new"));
 690
 691     editLink.setText(MessageManager.getString("action.edit"));
 692
 693     deleteLink.setText(MessageManager.getString("action.delete"));
 694
 695     // no current selection, so initially disable delete/edit buttons
 696     editLink.setEnabled(false);
 697     deleteLink.setEnabled(false);
 698
 699     newLink.addActionListener(new java.awt.event.ActionListener()
 700     {
 701       @Override
 702       public void actionPerformed(ActionEvent e)
 703       {
 704         newLink_actionPerformed(e);
 705       }
 706     });
 707
 708     editLink.setText(MessageManager.getString("action.edit"));
 709     editLink.addActionListener(new java.awt.event.ActionListener()
 710     {
 711       @Override
 712       public void actionPerformed(ActionEvent e)
 713       {
 714         editLink_actionPerformed(e);
 715       }
 716     });
 717
 718     deleteLink.setText(MessageManager.getString("action.delete"));
 719     deleteLink.addActionListener(new java.awt.event.ActionListener()
 720     {
 721       @Override
 722       public void actionPerformed(ActionEvent e)
 723       {
 724         deleteLink_actionPerformed(e);
 725       }
 726     });
 727
 728     JPanel buttonPanel = new JPanel(new GridBagLayout());
 729     buttonPanel.setBorder(new TitledBorder("Edit links"));
 730     GridBagConstraints gbc = new GridBagConstraints();
 731     gbc.gridx = 0;
 732     gbc.gridy = 0;
 733     gbc.fill = GridBagConstraints.NONE;
 734     buttonPanel.add(newLink, gbc);
 735
 736     GridBagConstraints gbc1 = new GridBagConstraints();
 737     gbc1.gridx = 1;
 738     gbc1.gridy = 0;
 739     gbc1.fill = GridBagConstraints.NONE;
 740     buttonPanel.add(editLink, gbc1);
 741
 742     GridBagConstraints gbc2 = new GridBagConstraints();
 743     gbc2.gridx = 2;
 744     gbc2.gridy = 0;
 745     gbc2.fill = GridBagConstraints.NONE;
 746     buttonPanel.add(deleteLink, gbc2);
 747
 748     GridBagConstraints gbc3 = new GridBagConstraints();
 749     gbc3.gridx = 3;
 750     gbc3.gridy = 0;
 751     gbc3.fill = GridBagConstraints.HORIZONTAL;
 752     gbc3.weightx = 1.0;
 753     JPanel spacePanel = new JPanel();
 754     spacePanel.setBorder(null);
 755     buttonPanel.add(spacePanel, gbc3);
 756
 757     return buttonPanel;
 758   }
 759
 760   /**
 761    * Initialises the proxy server panel in the Connections tab
 762    *
 763    * @return the proxy server panel
 764    */
 765   private JPanel initConnTabProxyPanel()
 766   {
 767     // Label for server text box
 768     serverLabel.setText(MessageManager.getString("label.address"));
 769     serverLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 770     serverLabel.setFont(LABEL_FONT);
 771
 772     // Proxy server and port text boxes
 773     proxyServerTB.setFont(LABEL_FONT);
 774     proxyPortTB.setFont(LABEL_FONT);
 775
 776     // Label for Port text box
 777     portLabel.setFont(LABEL_FONT);
 778     portLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 779     portLabel.setText(MessageManager.getString("label.port"));
 780
 781     // Use proxy server checkbox
 782     useProxy.setFont(LABEL_FONT);
 783     useProxy.setHorizontalAlignment(SwingConstants.RIGHT);
 784     useProxy.setHorizontalTextPosition(SwingConstants.LEADING);
 785     useProxy.setText(MessageManager.getString("label.use_proxy_server"));
 786     useProxy.addActionListener(new ActionListener()
 787     {
 788       @Override
 789       public void actionPerformed(ActionEvent e)
 790       {
 791         useProxy_actionPerformed();
 792       }
 793     });
 794
 795     // Make proxy server panel
 796     JPanel proxyPanel = new JPanel();
 797     TitledBorder titledBorder1 = new TitledBorder(
 798             MessageManager.getString("label.proxy_server"));
 799     proxyPanel.setBorder(titledBorder1);
 800     proxyPanel.setLayout(new GridBagLayout());
 801     proxyPanel.add(serverLabel, new GridBagConstraints(0, 1, 1, 1, 0.0,
 802             0.0, GridBagConstraints.WEST, GridBagConstraints.NONE,
 803             new Insets(0, 2, 2, 0), 5, 0));
 804     proxyPanel.add(portLabel, new GridBagConstraints(2, 1, 1, 1, 0.0, 0.0,
 805             GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
 806                     0, 2, 0), 11, 0));
 807     proxyPanel.add(useProxy, new GridBagConstraints(0, 0, 2, 1, 0.0, 0.0,
 808             GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
 809                     2, 5, 185), 2, -4));
 810     proxyPanel.add(proxyPortTB, new GridBagConstraints(3, 1, 1, 1, 1.0,
 811             0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 812             new Insets(0, 2, 2, 2), 54, 1));
 813     proxyPanel.add(proxyServerTB, new GridBagConstraints(1, 1, 1, 1, 1.0,
 814             0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 815             new Insets(0, 2, 2, 0), 263, 1));
 816
 817     return proxyPanel;
 818   }
 819
 820   /**
 821    * Initialises the checkboxes in the Connections tab
 822    */
 823   private void initConnTabCheckboxes()
 824   {
 825     // Usage stats checkbox label
 826     usagestats.setText(MessageManager
 827             .getString("label.send_usage_statistics"));
 828     usagestats.setFont(LABEL_FONT);
 829     usagestats.setHorizontalAlignment(SwingConstants.RIGHT);
 830     usagestats.setHorizontalTextPosition(SwingConstants.LEADING);
 831
 832     // Questionnaire checkbox label
 833     questionnaire.setText(MessageManager
 834             .getString("label.check_for_questionnaires"));
 835     questionnaire.setFont(LABEL_FONT);
 836     questionnaire.setHorizontalAlignment(SwingConstants.RIGHT);
 837     questionnaire.setHorizontalTextPosition(SwingConstants.LEADING);
 838
 839     // Check for latest version checkbox label
 840     versioncheck.setText(MessageManager
 841             .getString("label.check_for_latest_version"));
 842     versioncheck.setFont(LABEL_FONT);
 843     versioncheck.setHorizontalAlignment(SwingConstants.RIGHT);
 844     versioncheck.setHorizontalTextPosition(SwingConstants.LEADING);
 845   }
 846
 847   /**
 848    * Initialises the parent panel which contains the tabbed sections.
 849    *
 850    * @return
 851    */
 852   private JPanel initOkCancelPanel()
 853   {
 854     JButton ok = new JButton();
 855     ok.setText(MessageManager.getString("action.ok"));
 856     ok.addActionListener(new ActionListener()
 857     {
 858       @Override
 859       public void actionPerformed(ActionEvent e)
 860       {
 861         ok_actionPerformed(e);
 862       }
 863     });
 864     JButton cancel = new JButton();
 865     cancel.setText(MessageManager.getString("action.cancel"));
 866     cancel.addActionListener(new ActionListener()
 867     {
 868       @Override
 869       public void actionPerformed(ActionEvent e)
 870       {
 871         cancel_actionPerformed(e);
 872       }
 873     });
 874     JPanel okCancelPanel = new JPanel();
 875     okCancelPanel.add(ok);
 876     okCancelPanel.add(cancel);
 877     return okCancelPanel;
 878   }
 879
 880   /**
 881    * Initialises the Colours tabbed panel.
 882    *
 883    * @return
 884    */
 885   private JPanel initColoursTab()
 886   {
 887     JPanel coloursTab = new JPanel();
 888     coloursTab.setBorder(new TitledBorder(MessageManager
 889             .getString("action.open_new_alignment")));
 890     coloursTab.setLayout(new FlowLayout());
 891     JLabel mincolourLabel = new JLabel();
 892     mincolourLabel.setFont(LABEL_FONT);
 893     mincolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 894     mincolourLabel.setText(MessageManager.getString("label.min_colour"));
 895     minColour.setFont(LABEL_FONT);
 896     minColour.setBorder(BorderFactory.createEtchedBorder());
 897     minColour.setPreferredSize(new Dimension(40, 20));
 898     minColour.addMouseListener(new MouseAdapter()
 899     {
 900       @Override
 901       public void mousePressed(MouseEvent e)
 902       {
 903         minColour_actionPerformed(minColour);
 904       }
 905     });
 906     JLabel maxcolourLabel = new JLabel();
 907     maxcolourLabel.setFont(LABEL_FONT);
 908     maxcolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 909     maxcolourLabel.setText(MessageManager.getString("label.max_colour"));
 910     maxColour.setFont(LABEL_FONT);
 911     maxColour.setBorder(BorderFactory.createEtchedBorder());
 912     maxColour.setPreferredSize(new Dimension(40, 20));
 913     maxColour.addMouseListener(new MouseAdapter()
 914     {
 915       @Override
 916       public void mousePressed(MouseEvent e)
 917       {
 918         maxColour_actionPerformed(maxColour);
 919       }
 920     });
 921
 922     protColour.setFont(LABEL_FONT);
 923     protColour.setBounds(new Rectangle(172, 225, 155, 21));
 924     JLabel protColourLabel = new JLabel();
 925     protColourLabel.setFont(LABEL_FONT);
 926     protColourLabel.setHorizontalAlignment(SwingConstants.LEFT);
 927     protColourLabel.setText(MessageManager
 928             .getString("label.prot_alignment_colour") + " ");
 929     JvSwingUtils.addtoLayout(coloursTab, MessageManager
 930             .getString("label.default_colour_scheme_for_alignment"),
 931             protColourLabel, protColour);
 932
 933     nucColour.setFont(LABEL_FONT);
 934     nucColour.setBounds(new Rectangle(172, 240, 155, 21));
 935     JLabel nucColourLabel = new JLabel();
 936     nucColourLabel.setFont(LABEL_FONT);
 937     nucColourLabel.setHorizontalAlignment(SwingConstants.LEFT);
 938     nucColourLabel.setText(MessageManager
 939             .getString("label.nuc_alignment_colour") + " ");
 940     JvSwingUtils.addtoLayout(coloursTab, MessageManager
 941             .getString("label.default_colour_scheme_for_alignment"),
 942             nucColourLabel, nucColour);
 943
 944     JPanel annotationShding = new JPanel();
 945     annotationShding.setBorder(new TitledBorder(MessageManager
 946             .getString("label.annotation_shading_default")));
 947     annotationShding.setLayout(new GridLayout(1, 2));
 948     JvSwingUtils.addtoLayout(annotationShding, MessageManager
 949             .getString("label.default_minimum_colour_annotation_shading"),
 950             mincolourLabel, minColour);
 951     JvSwingUtils.addtoLayout(annotationShding, MessageManager
 952             .getString("label.default_maximum_colour_annotation_shading"),
 953             maxcolourLabel, maxColour);
 954     coloursTab.add(annotationShding); // , FlowLayout.LEFT);
 955     return coloursTab;
 956   }
 957
 958   /**
 959    * Initialises the Structure tabbed panel.
 960    *
 961    * @return
 962    */
 963   private JPanel initStructureTab()
 964   {
 965     structureTab = new JPanel();
 966
 967     structureTab.setBorder(new TitledBorder(MessageManager
 968             .getString("label.structure_options")));
 969     structureTab.setLayout(null);
 970     final int width = 400;
 971     final int height = 22;
 972     final int lineSpacing = 25;
 973     int ypos = 15;
 974
 975     structFromPdb.setFont(LABEL_FONT);
 976     structFromPdb
 977             .setText(MessageManager.getString("label.struct_from_pdb"));
 978     structFromPdb.setBounds(new Rectangle(5, ypos, width, height));
 979     structFromPdb.addActionListener(new ActionListener()
 980     {
 981       @Override
 982       public void actionPerformed(ActionEvent e)
 983       {
 984         boolean selected = structFromPdb.isSelected();
 985         // enable other options only when the first is checked
 986         useRnaView.setEnabled(selected);
 987         addSecondaryStructure.setEnabled(selected);
 988         addTempFactor.setEnabled(selected);
 989       }
 990     });
 991     structureTab.add(structFromPdb);
 992
 993     // indent checkboxes that are conditional on the first one
 994     ypos += lineSpacing;
 995     useRnaView.setFont(LABEL_FONT);
 996     useRnaView.setText(MessageManager.getString("label.use_rnaview"));
 997     useRnaView.setBounds(new Rectangle(25, ypos, width, height));
 998     structureTab.add(useRnaView);
 999
1000     ypos += lineSpacing;
1001     addSecondaryStructure.setFont(LABEL_FONT);
1002     addSecondaryStructure.setText(MessageManager
1003             .getString("label.autoadd_secstr"));
1004     addSecondaryStructure.setBounds(new Rectangle(25, ypos, width, height));
1005     structureTab.add(addSecondaryStructure);
1006
1007     ypos += lineSpacing;
1008     addTempFactor.setFont(LABEL_FONT);
1009     addTempFactor.setText(MessageManager.getString("label.autoadd_temp"));
1010     addTempFactor.setBounds(new Rectangle(25, ypos, width, height));
1011     structureTab.add(addTempFactor);
1012
1013     ypos += lineSpacing;
1014     JLabel viewerLabel = new JLabel();
1015     viewerLabel.setFont(LABEL_FONT);
1016     viewerLabel.setHorizontalAlignment(SwingConstants.LEFT);
1017     viewerLabel.setText(MessageManager.getString("label.structure_viewer"));
1018     viewerLabel.setBounds(new Rectangle(10, ypos, 200, height));
1019     structureTab.add(viewerLabel);
1020
1021     structViewer.setFont(LABEL_FONT);
1022     structViewer.setBounds(new Rectangle(160, ypos, 120, height));
1023     structViewer.addItem(ViewerType.JMOL.name());
1024     structViewer.addItem(ViewerType.CHIMERA.name());
1025     structViewer.addActionListener(new ActionListener()
1026     {
1027       @Override
1028       public void actionPerformed(ActionEvent e)
1029       {
1030         structureViewer_actionPerformed((String) structViewer
1031                 .getSelectedItem());
1032       }
1033     });
1034     structureTab.add(structViewer);
1035
1036     ypos += lineSpacing;
1037     JLabel pathLabel = new JLabel();
1038     pathLabel.setFont(new java.awt.Font("SansSerif", 0, 11));
1039     pathLabel.setHorizontalAlignment(SwingConstants.LEFT);
1040     pathLabel.setText(MessageManager.getString("label.chimera_path"));
1041     final String tooltip = JvSwingUtils.wrapTooltip(true,
1042             MessageManager.getString("label.chimera_path_tip"));
1043     pathLabel.setToolTipText(tooltip);
1044     pathLabel.setBounds(new Rectangle(10, ypos, 140, height));
1045     structureTab.add(pathLabel);
1046
1047     chimeraPath.setFont(LABEL_FONT);
1048     chimeraPath.setText("");
1049     chimeraPath.setBounds(new Rectangle(160, ypos, 300, height));
1050     chimeraPath.addMouseListener(new MouseAdapter()
1051     {
1052       @Override
1053       public void mouseClicked(MouseEvent e)
1054       {
1055         if (e.getClickCount() == 2)
1056         {
1057           String chosen = openFileChooser();
1058           if (chosen != null)
1059           {
1060             chimeraPath.setText(chosen);
1061           }
1062         }
1063       }
1064     });
1065     structureTab.add(chimeraPath);
1066
1067     ypos += lineSpacing;
1068     nwMapping.setFont(LABEL_FONT);
1069     nwMapping.setText(MessageManager.getString("label.nw_mapping"));
1070     siftsMapping.setFont(LABEL_FONT);
1071     siftsMapping.setText(MessageManager.getString("label.sifts_mapping"));
1072     mappingMethod.add(nwMapping);
1073     mappingMethod.add(siftsMapping);
1074     JPanel mappingPanel = new JPanel();
1075     mappingPanel.setFont(LABEL_FONT);
1076     TitledBorder mmTitledBorder = new TitledBorder(
1077             MessageManager.getString("label.mapping_method"));
1078     mmTitledBorder.setTitleFont(LABEL_FONT);
1079     mappingPanel.setBorder(mmTitledBorder);
1080     mappingPanel.setBounds(new Rectangle(10, ypos, 452, 45));
1081     // GridLayout mappingLayout = new GridLayout();
1082     mappingPanel.setLayout(new GridLayout());
1083     mappingPanel.add(nwMapping);
1084     mappingPanel.add(siftsMapping);
1085     structureTab.add(mappingPanel);
1086
1087     ypos += lineSpacing;
1088     ypos += lineSpacing;
1089     FTSDataColumnPreferences docFieldPref = new FTSDataColumnPreferences(
1090             PreferenceSource.PREFERENCES, PDBFTSRestClient.getInstance());
1091     docFieldPref.setBounds(new Rectangle(10, ypos, 450, 120));
1092     structureTab.add(docFieldPref);
1093
1094     return structureTab;
1095   }
1096
1097   /**
1098    * Action on choosing a structure viewer from combobox options.
1099    *
1100    * @param selectedItem
1101    */
1102   protected void structureViewer_actionPerformed(String selectedItem)
1103   {
1104   }
1105
1106   /**
1107    * Show a dialog for the user to choose a file. Returns the chosen path, or
1108    * null on Cancel.
1109    *
1110    * @return
1111    */
1112   protected String openFileChooser()
1113   {
1114     String choice = null;
1115     JFileChooser chooser = new JFileChooser();
1116
1117     // chooser.setFileView(new JalviewFileView());
1118     chooser.setDialogTitle(MessageManager
1119             .getString("label.open_local_file"));
1120     chooser.setToolTipText(MessageManager.getString("action.open"));
1121
1122     int value = chooser.showOpenDialog(this);
1123
1124     if (value == JFileChooser.APPROVE_OPTION)
1125     {
1126       choice = chooser.getSelectedFile().getPath();
1127     }
1128     return choice;
1129   }
1130
1131   /**
1132    * Validate the structure tab preferences; if invalid, set focus on this tab.
1133    *
1134    * @param e
1135    */
1136   protected boolean validateStructure(FocusEvent e)
1137   {
1138     if (!validateStructure())
1139     {
1140       e.getComponent().requestFocusInWindow();
1141       return false;
1142     }
1143     return true;
1144   }
1145
1146   protected boolean validateStructure()
1147   {
1148     return false;
1149   }
1150
1151   /**
1152    * Initialises the Visual tabbed panel.
1153    *
1154    * @return
1155    */
1156   private JPanel initVisualTab()
1157   {
1158     JPanel visualTab = new JPanel();
1159     visualTab.setBorder(new TitledBorder(MessageManager
1160             .getString("action.open_new_alignment")));
1161     visualTab.setLayout(null);
1162     fullScreen.setFont(LABEL_FONT);
1163     fullScreen.setHorizontalAlignment(SwingConstants.RIGHT);
1164     fullScreen.setHorizontalTextPosition(SwingConstants.LEFT);
1165     fullScreen.setText(MessageManager.getString("label.maximize_window"));
1166     quality.setEnabled(false);
1167     quality.setFont(LABEL_FONT);
1168     quality.setHorizontalAlignment(SwingConstants.RIGHT);
1169     quality.setHorizontalTextPosition(SwingConstants.LEFT);
1170     quality.setSelected(true);
1171     quality.setText(MessageManager.getString("label.quality"));
1172     conservation.setEnabled(false);
1173     conservation.setFont(LABEL_FONT);
1174     conservation.setHorizontalAlignment(SwingConstants.RIGHT);
1175     conservation.setHorizontalTextPosition(SwingConstants.LEFT);
1176     conservation.setSelected(true);
1177     conservation.setText(MessageManager.getString("label.conservation"));
1178     identity.setEnabled(false);
1179     identity.setFont(LABEL_FONT);
1180     identity.setHorizontalAlignment(SwingConstants.RIGHT);
1181     identity.setHorizontalTextPosition(SwingConstants.LEFT);
1182     identity.setSelected(true);
1183     identity.setText(MessageManager.getString("label.consensus"));
1184     showOccupancy.setFont(LABEL_FONT);
1185     showOccupancy.setEnabled(false);
1186     showOccupancy.setHorizontalAlignment(SwingConstants.RIGHT);
1187     showOccupancy.setHorizontalTextPosition(SwingConstants.LEFT);
1188     showOccupancy.setSelected(true);
1189     showOccupancy.setText(MessageManager.getString("label.occupancy"));
1190
1191     JLabel showGroupbits = new JLabel();
1192     showGroupbits.setFont(LABEL_FONT);
1193     showGroupbits.setHorizontalAlignment(SwingConstants.RIGHT);
1194     showGroupbits.setHorizontalTextPosition(SwingConstants.LEFT);
1195     showGroupbits.setText(MessageManager.getString("action.show_group")
1196             + ":");
1197     JLabel showConsensbits = new JLabel();
1198     showConsensbits.setFont(LABEL_FONT);
1199     showConsensbits.setHorizontalAlignment(SwingConstants.RIGHT);
1200     showConsensbits.setHorizontalTextPosition(SwingConstants.LEFT);
1201     showConsensbits.setText(MessageManager.getString("label.consensus")
1202             + ":");
1203     showConsensHistogram.setEnabled(false);
1204     showConsensHistogram.setFont(LABEL_FONT);
1205     showConsensHistogram.setHorizontalAlignment(SwingConstants.RIGHT);
1206     showConsensHistogram.setHorizontalTextPosition(SwingConstants.LEFT);
1207     showConsensHistogram.setSelected(true);
1208     showConsensHistogram.setText(MessageManager
1209             .getString("label.histogram"));
1210     showConsensLogo.setEnabled(false);
1211     showConsensLogo.setFont(LABEL_FONT);
1212     showConsensLogo.setHorizontalAlignment(SwingConstants.RIGHT);
1213     showConsensLogo.setHorizontalTextPosition(SwingConstants.LEFT);
1214     showConsensLogo.setSelected(true);
1215     showConsensLogo.setText(MessageManager.getString("label.logo"));
1216     showGroupConsensus.setEnabled(false);
1217     showGroupConsensus.setFont(LABEL_FONT);
1218     showGroupConsensus.setHorizontalAlignment(SwingConstants.RIGHT);
1219     showGroupConsensus.setHorizontalTextPosition(SwingConstants.LEFT);
1220     showGroupConsensus.setSelected(true);
1221     showGroupConsensus.setText(MessageManager.getString("label.consensus"));
1222     showGroupConservation.setEnabled(false);
1223     showGroupConservation.setFont(LABEL_FONT);
1224     showGroupConservation.setHorizontalAlignment(SwingConstants.RIGHT);
1225     showGroupConservation.setHorizontalTextPosition(SwingConstants.LEFT);
1226     showGroupConservation.setSelected(true);
1227     showGroupConservation.setText(MessageManager
1228             .getString("label.conservation"));
1229     showNpTooltip.setEnabled(true);
1230     showNpTooltip.setFont(LABEL_FONT);
1231     showNpTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
1232     showNpTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
1233     showNpTooltip.setSelected(true);
1234     showNpTooltip.setText(MessageManager
1235             .getString("label.non_positional_features"));
1236     showDbRefTooltip.setEnabled(true);
1237     showDbRefTooltip.setFont(LABEL_FONT);
1238     showDbRefTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
1239     showDbRefTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
1240     showDbRefTooltip.setSelected(true);
1241     showDbRefTooltip.setText(MessageManager
1242             .getString("label.database_references"));
1243     annotations.setFont(LABEL_FONT);
1244     annotations.setHorizontalAlignment(SwingConstants.RIGHT);
1245     annotations.setHorizontalTextPosition(SwingConstants.LEFT);
1246     annotations.setSelected(true);
1247     annotations.setText(MessageManager.getString("label.show_annotations"));
1248     // annotations.setBounds(new Rectangle(169, 12, 200, 23));
1249     annotations.addActionListener(new ActionListener()
1250     {
1251       @Override
1252       public void actionPerformed(ActionEvent e)
1253       {
1254         annotations_actionPerformed(e);
1255       }
1256     });
1257     identity.addActionListener(new ActionListener()
1258     {
1259       @Override
1260       public void actionPerformed(ActionEvent e)
1261       {
1262         annotations_actionPerformed(e);
1263       }
1264     });
1265     showGroupConsensus.addActionListener(new ActionListener()
1266     {
1267       @Override
1268       public void actionPerformed(ActionEvent e)
1269       {
1270         annotations_actionPerformed(e);
1271       }
1272     });
1273     showUnconserved.setFont(LABEL_FONT);
1274     showUnconserved.setHorizontalAlignment(SwingConstants.RIGHT);
1275     showUnconserved.setHorizontalTextPosition(SwingConstants.LEFT);
1276     showUnconserved.setSelected(true);
1277     showUnconserved.setText(MessageManager
1278             .getString("action.show_unconserved"));
1279     showUnconserved.addActionListener(new ActionListener()
1280     {
1281       @Override
1282       public void actionPerformed(ActionEvent e)
1283       {
1284         showunconserved_actionPerformed(e);
1285       }
1286     });
1287
1288     // TODO these are not yet added to / action from Preferences
1289     // JCheckBox shareSelections = new JCheckBox();
1290     // shareSelections.setFont(verdana11);
1291     // shareSelections.setHorizontalAlignment(SwingConstants.RIGHT);
1292     // shareSelections.setHorizontalTextPosition(SwingConstants.LEFT);
1293     // shareSelections.setSelected(true);
1294     // shareSelections.setText(MessageManager
1295     // .getString("label.share_selection_across_views"));
1296     // JCheckBox followHighlight = new JCheckBox();
1297     // followHighlight.setFont(verdana11);
1298     // followHighlight.setHorizontalAlignment(SwingConstants.RIGHT);
1299     // followHighlight.setHorizontalTextPosition(SwingConstants.LEFT);
1300     // // showUnconserved.setBounds(new Rectangle(169, 40, 200, 23));
1301     // followHighlight.setSelected(true);
1302     // followHighlight.setText(MessageManager
1303     // .getString("label.scroll_highlighted_regions"));
1304
1305     seqLimit.setFont(LABEL_FONT);
1306     seqLimit.setHorizontalAlignment(SwingConstants.RIGHT);
1307     seqLimit.setHorizontalTextPosition(SwingConstants.LEFT);
1308     seqLimit.setText(MessageManager.getString("label.full_sequence_id"));
1309     smoothFont.setFont(LABEL_FONT);
1310     smoothFont.setHorizontalAlignment(SwingConstants.RIGHT);
1311     smoothFont.setHorizontalTextPosition(SwingConstants.LEADING);
1312     smoothFont.setText(MessageManager.getString("label.smooth_font"));
1313     scaleProteinToCdna.setFont(LABEL_FONT);
1314     scaleProteinToCdna.setHorizontalAlignment(SwingConstants.RIGHT);
1315     scaleProteinToCdna.setHorizontalTextPosition(SwingConstants.LEADING);
1316     scaleProteinToCdna.setText(MessageManager
1317             .getString("label.scale_protein_to_cdna"));
1318     scaleProteinToCdna.setToolTipText(MessageManager
1319             .getString("label.scale_protein_to_cdna_tip"));
1320     JLabel gapLabel = new JLabel();
1321     gapLabel.setFont(LABEL_FONT);
1322     gapLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1323     gapLabel.setText(MessageManager.getString("label.gap_symbol") + " ");
1324     JLabel fontLabel = new JLabel();
1325     fontLabel.setFont(LABEL_FONT);
1326     fontLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1327     fontLabel.setText(MessageManager.getString("label.font"));
1328     fontSizeCB.setFont(LABEL_FONT);
1329     fontSizeCB.setBounds(new Rectangle(320, 112, 65, 23));
1330     fontStyleCB.setFont(LABEL_FONT);
1331     fontStyleCB.setBounds(new Rectangle(382, 112, 80, 23));
1332     fontNameCB.setFont(LABEL_FONT);
1333     fontNameCB.setBounds(new Rectangle(172, 112, 147, 23));
1334     gapSymbolCB.setFont(LABEL_FONT);
1335     gapSymbolCB.setBounds(new Rectangle(172, 215, 69, 23));
1336     DefaultListCellRenderer dlcr = new DefaultListCellRenderer();
1337     dlcr.setHorizontalAlignment(DefaultListCellRenderer.CENTER);
1338     gapSymbolCB.setRenderer(dlcr);
1339
1340     startupCheckbox.setText(MessageManager.getString("action.open_file"));
1341     startupCheckbox.setFont(LABEL_FONT);
1342     startupCheckbox.setHorizontalAlignment(SwingConstants.RIGHT);
1343     startupCheckbox.setHorizontalTextPosition(SwingConstants.LEFT);
1344     startupCheckbox.setSelected(true);
1345     startupFileTextfield.setFont(LABEL_FONT);
1346     startupFileTextfield.setBounds(new Rectangle(172, 310, 330, 20));
1347     startupFileTextfield.addMouseListener(new MouseAdapter()
1348     {
1349       @Override
1350       public void mouseClicked(MouseEvent e)
1351       {
1352         if (e.getClickCount() > 1)
1353         {
1354           startupFileTextfield_mouseClicked();
1355         }
1356       }
1357     });
1358
1359     sortby.setFont(LABEL_FONT);
1360     sortby.setBounds(new Rectangle(172, 260, 155, 21));
1361     JLabel sortLabel = new JLabel();
1362     sortLabel.setFont(LABEL_FONT);
1363     sortLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1364     sortLabel.setText(MessageManager.getString("label.sort_by"));
1365     sortAnnBy.setFont(LABEL_FONT);
1366     sortAnnBy.setBounds(new Rectangle(172, 285, 110, 21));
1367     JLabel sortAnnLabel = new JLabel();
1368     sortAnnLabel.setFont(LABEL_FONT);
1369     sortAnnLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1370     sortAnnLabel.setText(MessageManager.getString("label.sort_ann_by"));
1371     sortAutocalc.setFont(LABEL_FONT);
1372     sortAutocalc.setBounds(new Rectangle(290, 285, 165, 21));
1373
1374     JPanel annsettingsPanel = new JPanel();
1375     annsettingsPanel.setBounds(new Rectangle(173, 13, 320, 96));
1376     annsettingsPanel.setLayout(new FlowLayout(FlowLayout.LEFT, 0, 0));
1377     annsettingsPanel.setBorder(new EtchedBorder());
1378     visualTab.add(annsettingsPanel);
1379     Border jb = new EmptyBorder(1, 1, 4, 5);
1380     annotations.setBorder(jb);
1381     showOccupancy.setBorder(jb);
1382     quality.setBorder(jb);
1383     conservation.setBorder(jb);
1384     identity.setBorder(jb);
1385     showConsensbits.setBorder(jb);
1386     showGroupbits.setBorder(jb);
1387     showGroupConsensus.setBorder(jb);
1388     showGroupConservation.setBorder(jb);
1389     showConsensHistogram.setBorder(jb);
1390     showConsensLogo.setBorder(jb);
1391
1392     JPanel autoAnnotSettings = new JPanel();
1393     annsettingsPanel.add(autoAnnotSettings);
1394     autoAnnotSettings.setLayout(new GridLayout(0, 2));
1395     autoAnnotSettings.add(annotations);
1396     autoAnnotSettings.add(quality);
1397     // second row of autoannotation box
1398     autoAnnotSettings = new JPanel();
1399     annsettingsPanel.add(autoAnnotSettings);
1400
1401     autoAnnotSettings.setLayout(new GridLayout(0, 3));
1402     autoAnnotSettings.add(conservation);
1403     autoAnnotSettings.add(identity);
1404     autoAnnotSettings.add(showOccupancy);
1405     autoAnnotSettings.add(showGroupbits);
1406     autoAnnotSettings.add(showGroupConservation);
1407     autoAnnotSettings.add(showGroupConsensus);
1408     autoAnnotSettings.add(showConsensbits);
1409     autoAnnotSettings.add(showConsensHistogram);
1410     autoAnnotSettings.add(showConsensLogo);
1411
1412
1413
1414     JPanel tooltipSettings = new JPanel();
1415     tooltipSettings.setBorder(new TitledBorder(MessageManager
1416             .getString("label.sequence_id_tooltip")));
1417     tooltipSettings.setBounds(173, 140, 220, 62);
1418     tooltipSettings.setLayout(new GridLayout(2, 1));
1419     tooltipSettings.add(showDbRefTooltip);
1420     tooltipSettings.add(showNpTooltip);
1421     visualTab.add(tooltipSettings);
1422
1423     wrap.setFont(LABEL_FONT);
1424     wrap.setHorizontalAlignment(SwingConstants.TRAILING);
1425     wrap.setHorizontalTextPosition(SwingConstants.LEADING);
1426     wrap.setText(MessageManager.getString("label.wrap_alignment"));
1427     rightAlign.setFont(LABEL_FONT);
1428     rightAlign.setForeground(Color.black);
1429     rightAlign.setHorizontalAlignment(SwingConstants.RIGHT);
1430     rightAlign.setHorizontalTextPosition(SwingConstants.LEFT);
1431     rightAlign.setText(MessageManager.getString("label.right_align_ids"));
1432     idItalics.setFont(LABEL_FONT_ITALIC);
1433     idItalics.setHorizontalAlignment(SwingConstants.RIGHT);
1434     idItalics.setHorizontalTextPosition(SwingConstants.LEADING);
1435     idItalics.setText(MessageManager
1436             .getString("label.sequence_name_italics"));
1437     openoverv.setFont(LABEL_FONT);
1438     openoverv.setActionCommand(MessageManager
1439             .getString("label.open_overview"));
1440     openoverv.setHorizontalAlignment(SwingConstants.RIGHT);
1441     openoverv.setHorizontalTextPosition(SwingConstants.LEFT);
1442     openoverv.setText(MessageManager.getString("label.open_overview"));
1443     JPanel jPanel2 = new JPanel();
1444     jPanel2.setBounds(new Rectangle(7, 17, 158, 310));
1445     jPanel2.setLayout(new GridLayout(14, 1));
1446     jPanel2.add(fullScreen);
1447     jPanel2.add(openoverv);
1448     jPanel2.add(seqLimit);
1449     jPanel2.add(rightAlign);
1450     jPanel2.add(fontLabel);
1451     jPanel2.add(showUnconserved);
1452     jPanel2.add(idItalics);
1453     jPanel2.add(smoothFont);
1454     jPanel2.add(scaleProteinToCdna);
1455     jPanel2.add(gapLabel);
1456     jPanel2.add(wrap);
1457     jPanel2.add(sortLabel);
1458     jPanel2.add(sortAnnLabel);
1459     jPanel2.add(startupCheckbox);
1460     visualTab.add(jPanel2);
1461     visualTab.add(startupFileTextfield);
1462     visualTab.add(sortby);
1463     visualTab.add(sortAnnBy);
1464     visualTab.add(sortAutocalc);
1465     visualTab.add(gapSymbolCB);
1466     visualTab.add(fontNameCB);
1467     visualTab.add(fontSizeCB);
1468     visualTab.add(fontStyleCB);
1469     return visualTab;
1470   }
1471
1472   protected void autoIdWidth_actionPerformed()
1473   {
1474     // TODO Auto-generated method stub
1475
1476   }
1477
1478   protected void userIdWidth_actionPerformed()
1479   {
1480     // TODO Auto-generated method stub
1481
1482   }
1483
1484   protected void maxColour_actionPerformed(JPanel panel)
1485   {
1486   }
1487
1488   protected void minColour_actionPerformed(JPanel panel)
1489   {
1490   }
1491
1492   protected void showunconserved_actionPerformed(ActionEvent e)
1493   {
1494     // TODO Auto-generated method stub
1495
1496   }
1497
1498   /**
1499    * DOCUMENT ME!
1500    *
1501    * @param e
1502    *          DOCUMENT ME!
1503    */
1504   public void ok_actionPerformed(ActionEvent e)
1505   {
1506   }
1507
1508   /**
1509    * DOCUMENT ME!
1510    *
1511    * @param e
1512    *          DOCUMENT ME!
1513    */
1514   public void cancel_actionPerformed(ActionEvent e)
1515   {
1516   }
1517
1518   /**
1519    * DOCUMENT ME!
1520    *
1521    * @param e
1522    *          DOCUMENT ME!
1523    */
1524   public void annotations_actionPerformed(ActionEvent e)
1525   {
1526   }
1527
1528   /**
1529    * DOCUMENT ME!
1530    */
1531   public void startupFileTextfield_mouseClicked()
1532   {
1533   }
1534
1535   public void newLink_actionPerformed(ActionEvent e)
1536   {
1537
1538   }
1539
1540   public void editLink_actionPerformed(ActionEvent e)
1541   {
1542
1543   }
1544
1545   public void deleteLink_actionPerformed(ActionEvent e)
1546   {
1547
1548   }
1549
1550   public void defaultBrowser_mouseClicked(MouseEvent e)
1551   {
1552
1553   }
1554
1555   public void linkURLList_keyTyped(KeyEvent e)
1556   {
1557
1558   }
1559
1560   public void useProxy_actionPerformed()
1561   {
1562     boolean enabled = useProxy.isSelected();
1563     portLabel.setEnabled(enabled);
1564     serverLabel.setEnabled(enabled);
1565     proxyServerTB.setEnabled(enabled);
1566     proxyPortTB.setEnabled(enabled);
1567   }
1568
1569   /**
1570    * Customer renderer for JTable: supports column of radio buttons
1571    */
1572   public class RadioButtonRenderer extends JRadioButton implements
1573           TableCellRenderer
1574   {
1575     public RadioButtonRenderer()
1576     {
1577       setHorizontalAlignment(CENTER);
1578       setToolTipText(MessageManager.getString("label.urltooltip"));
1579     }
1580
1581     @Override
1582     public Component getTableCellRendererComponent(JTable table,
1583             Object value, boolean isSelected, boolean hasFocus, int row,
1584             int column)
1585     {
1586       setSelected((boolean) value);
1587
1588       // set colours to match rest of table
1589       if (isSelected)
1590        {
1591          setBackground(table.getSelectionBackground());
1592          setForeground(table.getSelectionForeground());
1593        }
1594        else
1595        {
1596          setBackground(table.getBackground());
1597          setForeground(table.getForeground());
1598       }
1599       return this;
1600     }
1601   }
1602
1603   /**
1604    * Customer cell editor for JTable: supports column of radio buttons in
1605    * conjunction with renderer
1606    */
1607   public class RadioButtonEditor extends AbstractCellEditor implements
1608             TableCellEditor
1609     {
1610       private JRadioButton button = new JRadioButton();
1611
1612       public RadioButtonEditor()
1613       {
1614       button.setHorizontalAlignment(SwingConstants.CENTER);
1615       this.button.addActionListener(new ActionListener()
1616         {
1617           @Override
1618           public void actionPerformed(ActionEvent e)
1619           {
1620             fireEditingStopped();
1621           }
1622         });
1623       }
1624
1625       @Override
1626       public Component getTableCellEditorComponent(JTable table,
1627               Object value, boolean isSelected, int row, int column)
1628       {
1629       button.setSelected((boolean) value);
1630         return button;
1631       }
1632
1633       @Override
1634       public Object getCellEditorValue()
1635       {
1636       return button.isSelected();
1637       }
1638
1639   }
1640 }