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.AbstractButton;
  49 import javax.swing.AbstractCellEditor;
  50 import javax.swing.BorderFactory;
  51 import javax.swing.ButtonGroup;
  52 import javax.swing.DefaultListCellRenderer;
  53 import javax.swing.JButton;
  54 import javax.swing.JCheckBox;
  55 import javax.swing.JComboBox;
  56 import javax.swing.JFileChooser;
  57 import javax.swing.JLabel;
  58 import javax.swing.JPanel;
  59 import javax.swing.JRadioButton;
  60 import javax.swing.JScrollPane;
  61 import javax.swing.JTabbedPane;
  62 import javax.swing.JTable;
  63 import javax.swing.JTextField;
  64 import javax.swing.ListSelectionModel;
  65 import javax.swing.SwingConstants;
  66 import javax.swing.border.Border;
  67 import javax.swing.border.EmptyBorder;
  68 import javax.swing.border.EtchedBorder;
  69 import javax.swing.border.TitledBorder;
  70 import javax.swing.event.ChangeEvent;
  71 import javax.swing.event.ChangeListener;
  72 import javax.swing.table.TableCellEditor;
  73 import javax.swing.table.TableCellRenderer;
  74
  75 /**
  76  * Base class for the Preferences panel.
  77  *
  78  * @author $author$
  79  * @version $Revision$
  80  */
  81 public class GPreferences extends JPanel
  82 {
  83   private static final Font LABEL_FONT = JvSwingUtils.getLabelFont();
  84
  85   private static final Font LABEL_FONT_ITALIC = JvSwingUtils.getLabelFont(
  86           false, true);
  87
  88   /*
  89    * Visual tab components
  90    */
  91   protected JCheckBox fullScreen = new JCheckBox();
  92
  93   protected JCheckBox openoverv = new JCheckBox();
  94
  95   protected JCheckBox seqLimit = new JCheckBox();
  96
  97   protected JCheckBox rightAlign = new JCheckBox();
  98
  99   protected JComboBox<String> fontSizeCB = new JComboBox<>();
 100
 101   protected JComboBox<String> fontStyleCB = new JComboBox<>();
 102
 103   protected JComboBox<String> fontNameCB = new JComboBox<>();
 104
 105   protected JCheckBox showOccupancy = new JCheckBox();
 106
 107   protected JCheckBox showUnconserved = new JCheckBox();
 108
 109   protected JCheckBox idItalics = new JCheckBox();
 110
 111   protected JCheckBox smoothFont = new JCheckBox();
 112
 113   protected JCheckBox scaleProteinToCdna = new JCheckBox();
 114
 115   protected JComboBox<String> gapSymbolCB = new JComboBox<>();
 116
 117   protected JCheckBox wrap = new JCheckBox();
 118
 119   protected JComboBox<String> sortby = new JComboBox<>();
 120
 121   protected JComboBox<String> sortAnnBy = new JComboBox<>();
 122
 123   protected JComboBox<String> sortAutocalc = new JComboBox<>();
 124
 125   protected JCheckBox startupCheckbox = new JCheckBox();
 126
 127   protected JTextField startupFileTextfield = new JTextField();
 128
 129   // below are in the 'second column'
 130   protected JCheckBox annotations = new JCheckBox();
 131
 132   protected JCheckBox quality = new JCheckBox();
 133
 134   protected JCheckBox conservation = new JCheckBox();
 135
 136   protected JCheckBox identity = new JCheckBox();
 137
 138   protected JCheckBox showGroupConsensus = new JCheckBox();
 139
 140   protected JCheckBox showGroupConservation = new JCheckBox();
 141
 142   protected JCheckBox showConsensHistogram = new JCheckBox();
 143
 144   protected JCheckBox showConsensLogo = new JCheckBox();
 145
 146   protected JCheckBox showInformationHistogram = new JCheckBox();
 147
 148   protected JCheckBox showHMMLogo = new JCheckBox();
 149
 150   protected JCheckBox showDbRefTooltip = new JCheckBox();
 151
 152   protected JCheckBox showNpTooltip = new JCheckBox();
 153
 154
 155   /*
 156    * Structure tab and components
 157    */
 158   protected JPanel structureTab;
 159
 160   protected JCheckBox structFromPdb = new JCheckBox();
 161
 162   protected JCheckBox useRnaView = new JCheckBox();
 163
 164   protected JCheckBox addSecondaryStructure = new JCheckBox();
 165
 166   protected JCheckBox addTempFactor = new JCheckBox();
 167
 168   protected JComboBox<String> structViewer = new JComboBox<>();
 169
 170   protected JTextField chimeraPath = new JTextField();
 171
 172   protected ButtonGroup mappingMethod = new ButtonGroup();
 173
 174   protected JRadioButton siftsMapping = new JRadioButton();
 175
 176   protected JRadioButton nwMapping = new JRadioButton();
 177
 178   /*
 179    * Colours tab components
 180    */
 181   protected JPanel minColour = new JPanel();
 182
 183   protected JPanel maxColour = new JPanel();
 184
 185   protected JComboBox<String> protColour = new JComboBox<>();
 186
 187   protected JComboBox<String> nucColour = new JComboBox<>();
 188
 189   /*
 190    * Connections tab components
 191    */
 192   protected JTable linkUrlTable = new JTable();
 193
 194   protected JButton editLink = new JButton();
 195
 196   protected JButton deleteLink = new JButton();
 197
 198   protected JTextField filterTB = new JTextField();
 199
 200   protected JButton doReset = new JButton();
 201
 202   protected JButton userOnly = new JButton();
 203
 204   protected JLabel portLabel = new JLabel();
 205
 206   protected JLabel serverLabel = new JLabel();
 207
 208   protected JTextField proxyServerTB = new JTextField();
 209
 210   protected JTextField proxyPortTB = new JTextField();
 211
 212   protected JTextField defaultBrowser = new JTextField();
 213
 214   protected JCheckBox useProxy = new JCheckBox();
 215
 216   protected JCheckBox usagestats = new JCheckBox();
 217
 218   protected JCheckBox questionnaire = new JCheckBox();
 219
 220   protected JCheckBox versioncheck = new JCheckBox();
 221
 222   /*
 223    * Output tab components
 224    */
 225   protected JComboBox<Object> epsRendering = new JComboBox<>();
 226
 227   protected JLabel userIdWidthlabel = new JLabel();
 228
 229   protected JCheckBox autoIdWidth = new JCheckBox();
 230
 231   protected JTextField userIdWidth = new JTextField();
 232
 233   protected JCheckBox blcjv = new JCheckBox();
 234
 235   protected JCheckBox pileupjv = new JCheckBox();
 236
 237   protected JCheckBox clustaljv = new JCheckBox();
 238
 239   protected JCheckBox msfjv = new JCheckBox();
 240
 241   protected JCheckBox fastajv = new JCheckBox();
 242
 243   protected JCheckBox pfamjv = new JCheckBox();
 244
 245   protected JCheckBox pirjv = new JCheckBox();
 246
 247   protected JCheckBox modellerOutput = new JCheckBox();
 248
 249   protected JCheckBox embbedBioJSON = new JCheckBox();
 250
 251   /*
 252    * Editing tab components
 253    */
 254   protected JCheckBox autoCalculateConsCheck = new JCheckBox();
 255
 256   protected JCheckBox padGaps = new JCheckBox();
 257
 258   protected JCheckBox sortByTree = new JCheckBox();
 259
 260   /*
 261    * hmmer tab and components
 262    */
 263   protected JPanel hmmerTab = new JPanel();
 264
 265   protected JCheckBox trimTermini = new JCheckBox();
 266
 267   protected ButtonGroup backgroundFreqSource = new ButtonGroup();
 268
 269   protected AbstractButton uniprot = new JCheckBox();
 270
 271   protected AbstractButton alignment = new JCheckBox();
 272
 273   protected JLabel sequencesToKeep = new JLabel();
 274
 275   protected JTextField numberOfSequencesToKeepField = new JTextField();
 276
 277   protected JLabel installationLocation = new JLabel();
 278
 279   protected JTextField installationLocationField = new JTextField();
 280
 281   protected JLabel hmmsearch = new JLabel();
 282
 283   protected JLabel hmmalign = new JLabel();
 284
 285   /*
 286    * DAS Settings tab
 287    */
 288   protected JPanel dasTab = new JPanel();
 289
 290   /*
 291    * Web Services tab
 292    */
 293   protected JPanel wsTab = new JPanel();
 294
 295
 296
 297   /**
 298    * Creates a new GPreferences object.
 299    */
 300   public GPreferences()
 301   {
 302     try
 303     {
 304       jbInit();
 305     } catch (Exception ex)
 306     {
 307       ex.printStackTrace();
 308     }
 309   }
 310
 311   /**
 312    * Construct the panel and its tabbed sub-panels.
 313    *
 314    * @throws Exception
 315    */
 316   private void jbInit() throws Exception
 317   {
 318     final JTabbedPane tabbedPane = new JTabbedPane();
 319     this.setLayout(new BorderLayout());
 320     JPanel okCancelPanel = initOkCancelPanel();
 321     this.add(tabbedPane, BorderLayout.CENTER);
 322     this.add(okCancelPanel, BorderLayout.SOUTH);
 323
 324     tabbedPane.add(initVisualTab(),
 325             MessageManager.getString("label.visual"));
 326
 327     tabbedPane.add(initColoursTab(),
 328             MessageManager.getString("label.colours"));
 329
 330     tabbedPane.add(initStructureTab(),
 331             MessageManager.getString("label.structure"));
 332
 333     tabbedPane.add(initConnectionsTab(),
 334             MessageManager.getString("label.connections"));
 335
 336     tabbedPane.add(initLinksTab(),
 337             MessageManager.getString("label.urllinks"));
 338
 339     tabbedPane.add(initOutputTab(),
 340             MessageManager.getString("label.output"));
 341
 342     tabbedPane.add(initEditingTab(),
 343             MessageManager.getString("label.editing"));
 344
 345     tabbedPane.add(initHMMERTab(), MessageManager.getString("label.hmmer"));
 346
 347     /*
 348      * See DasSourceBrowser for the real work of configuring this tab.
 349      */
 350     dasTab.setLayout(new BorderLayout());
 351     tabbedPane.add(dasTab, MessageManager.getString("label.das_settings"));
 352
 353     /*
 354      * See WsPreferences for the real work of configuring this tab.
 355      */
 356     wsTab.setLayout(new BorderLayout());
 357     tabbedPane.add(wsTab, MessageManager.getString("label.web_services"));
 358
 359     /*
 360      * Handler to validate a tab before leaving it - currently only for
 361      * Structure.
 362      */
 363     tabbedPane.addChangeListener(new ChangeListener()
 364     {
 365       private Component lastTab;
 366
 367       @Override
 368       public void stateChanged(ChangeEvent e)
 369       {
 370         if (lastTab == structureTab
 371                 && tabbedPane.getSelectedComponent() != structureTab)
 372         {
 373           if (!validateStructure())
 374           {
 375             tabbedPane.setSelectedComponent(structureTab);
 376             return;
 377           }
 378         }
 379         lastTab = tabbedPane.getSelectedComponent();
 380       }
 381
 382     });
 383   }
 384
 385   /**
 386    * Initialises the Editing tabbed panel.
 387    *
 388    * @return
 389    */
 390   private JPanel initEditingTab()
 391   {
 392     JPanel editingTab = new JPanel();
 393     editingTab.setLayout(null);
 394     autoCalculateConsCheck.setFont(LABEL_FONT);
 395     autoCalculateConsCheck.setText(MessageManager
 396             .getString("label.autocalculate_consensus"));
 397     autoCalculateConsCheck.setBounds(new Rectangle(21, 52, 209, 23));
 398     padGaps.setFont(LABEL_FONT);
 399     padGaps.setText(MessageManager.getString("label.pad_gaps_when_editing"));
 400     padGaps.setBounds(new Rectangle(22, 94, 168, 23));
 401     sortByTree.setFont(LABEL_FONT);
 402     sortByTree
 403             .setText(MessageManager.getString("label.sort_with_new_tree"));
 404     sortByTree
 405             .setToolTipText(MessageManager
 406                     .getString("label.any_trees_calculated_or_loaded_alignment_automatically_sort"));
 407     sortByTree.setBounds(new Rectangle(22, 136, 168, 23));
 408     editingTab.add(autoCalculateConsCheck);
 409     editingTab.add(padGaps);
 410     editingTab.add(sortByTree);
 411     return editingTab;
 412   }
 413
 414   /**
 415    * Initialises the hmmer tabbed panel.
 416    *
 417    * @return
 418    */
 419   private JPanel initHMMERTab()
 420   {
 421     JPanel hmmerTab = new JPanel();
 422     hmmerTab.setLayout(null);
 423
 424     hmmalign.setFont(LABEL_FONT);
 425     hmmalign.setText(MessageManager.getString("label.hmmalign_label"));
 426     hmmalign.setBounds(new Rectangle(22, 10, 200, 23));
 427
 428     trimTermini.setFont(LABEL_FONT);
 429     trimTermini.setText(MessageManager.getString("label.trim_termini"));
 430     trimTermini.setBounds(new Rectangle(22, 30, 200, 23));
 431
 432     hmmsearch.setFont(LABEL_FONT);
 433     hmmsearch.setText(MessageManager.getString("label.hmmsearch_label"));
 434     hmmsearch.setBounds(new Rectangle(250, 10, 200, 23));
 435
 436     sequencesToKeep.setFont(LABEL_FONT);
 437     sequencesToKeep
 438             .setText(MessageManager.getString("label.no_of_sequences"));
 439     sequencesToKeep.setBounds(new Rectangle(250, 30, 125, 23));
 440     numberOfSequencesToKeepField.setBounds(new Rectangle(375, 30, 40, 23));
 441
 442     installationLocation.setFont(LABEL_FONT);
 443     installationLocation.setText(
 444             MessageManager.getString("label.change_hmmer_location"));
 445     installationLocation.setBounds(new Rectangle(22, 200, 200, 23));
 446     installationLocationField.setBounds(new Rectangle(22, 220, 200, 23));
 447     installationLocationField.addMouseListener(new MouseAdapter()
 448     {
 449       @Override
 450       public void mouseClicked(MouseEvent e)
 451       {
 452         if (e.getClickCount() == 2)
 453         {
 454           String chosen = openFileChooser();
 455           if (chosen != null)
 456           {
 457             installationLocationField.setText(chosen);
 458           }
 459         }
 460       }
 461     });
 462
 463     backgroundFreqSource.add(uniprot);
 464     backgroundFreqSource.add(alignment);
 465     backgroundFreqSource.setSelected(uniprot.getModel(), true);
 466
 467     uniprot.setText(MessageManager.getString("label.freq_uniprot"));
 468     uniprot.setFont(LABEL_FONT);
 469     uniprot.setBounds(new Rectangle(22, 260, 255, 23));
 470
 471     alignment.setText(MessageManager.getString("label.freq_alignment"));
 472     alignment.setFont(LABEL_FONT);
 473     alignment.setBounds(new Rectangle(22, 280, 255, 23));
 474
 475     hmmerTab.add(uniprot);
 476     hmmerTab.add(alignment);
 477     hmmerTab.add(hmmalign);
 478     hmmerTab.add(hmmsearch);
 479     hmmerTab.add(installationLocation);
 480     hmmerTab.add(installationLocationField);
 481     hmmerTab.add(trimTermini);
 482     hmmerTab.add(sequencesToKeep);
 483     hmmerTab.add(sequencesToKeep);
 484     hmmerTab.add(numberOfSequencesToKeepField);
 485     return hmmerTab;
 486   }
 487
 488   /**
 489    * Initialises the Output tabbed panel.
 490    *
 491    * @return
 492    */
 493   private JPanel initOutputTab()
 494   {
 495     JPanel outputTab = new JPanel();
 496     outputTab.setLayout(null);
 497     JLabel epsLabel = new JLabel();
 498     epsLabel.setFont(LABEL_FONT);
 499     epsLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 500     epsLabel.setText(MessageManager.getString("label.eps_rendering_style"));
 501     epsLabel.setBounds(new Rectangle(9, 31, 140, 24));
 502     epsRendering.setFont(LABEL_FONT);
 503     epsRendering.setBounds(new Rectangle(154, 34, 187, 21));
 504     JLabel jLabel1 = new JLabel();
 505     jLabel1.setFont(LABEL_FONT);
 506     jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
 507     jLabel1.setText(MessageManager.getString("label.append_start_end"));
 508     jLabel1.setFont(LABEL_FONT);
 509     fastajv.setFont(LABEL_FONT);
 510     fastajv.setHorizontalAlignment(SwingConstants.LEFT);
 511     clustaljv.setText(MessageManager.getString("label.clustal") + "     ");
 512     blcjv.setText(MessageManager.getString("label.blc") + "     ");
 513     fastajv.setText(MessageManager.getString("label.fasta") + "     ");
 514     msfjv.setText(MessageManager.getString("label.msf") + "     ");
 515     pfamjv.setText(MessageManager.getString("label.pfam") + "     ");
 516     pileupjv.setText(MessageManager.getString("label.pileup") + "     ");
 517     msfjv.setFont(LABEL_FONT);
 518     msfjv.setHorizontalAlignment(SwingConstants.LEFT);
 519     pirjv.setText(MessageManager.getString("label.pir") + "     ");
 520     JPanel jPanel11 = new JPanel();
 521     jPanel11.setFont(LABEL_FONT);
 522     TitledBorder titledBorder2 = new TitledBorder(
 523             MessageManager.getString("label.file_output"));
 524     jPanel11.setBorder(titledBorder2);
 525     jPanel11.setBounds(new Rectangle(30, 72, 196, 182));
 526     GridLayout gridLayout3 = new GridLayout();
 527     jPanel11.setLayout(gridLayout3);
 528     gridLayout3.setRows(8);
 529     blcjv.setFont(LABEL_FONT);
 530     blcjv.setHorizontalAlignment(SwingConstants.LEFT);
 531     clustaljv.setFont(LABEL_FONT);
 532     clustaljv.setHorizontalAlignment(SwingConstants.LEFT);
 533     pfamjv.setFont(LABEL_FONT);
 534     pfamjv.setHorizontalAlignment(SwingConstants.LEFT);
 535     pileupjv.setFont(LABEL_FONT);
 536     pileupjv.setHorizontalAlignment(SwingConstants.LEFT);
 537     pirjv.setFont(LABEL_FONT);
 538     pirjv.setHorizontalAlignment(SwingConstants.LEFT);
 539     autoIdWidth.setFont(LABEL_FONT);
 540     autoIdWidth.setText(MessageManager
 541             .getString("label.automatically_set_id_width"));
 542     autoIdWidth.setToolTipText(JvSwingUtils.wrapTooltip(true,
 543             MessageManager
 544                     .getString("label.adjusts_width_generated_eps_png")));
 545     autoIdWidth.setBounds(new Rectangle(228, 96, 188, 23));
 546     autoIdWidth.addActionListener(new ActionListener()
 547     {
 548
 549       @Override
 550       public void actionPerformed(ActionEvent e)
 551       {
 552         autoIdWidth_actionPerformed();
 553       }
 554     });
 555     userIdWidthlabel.setFont(LABEL_FONT);
 556     userIdWidthlabel.setText(MessageManager
 557             .getString("label.figure_id_column_width"));
 558     userIdWidth
 559             .setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager
 560                     .getString("label.manually_specify_width_left_column")));
 561     userIdWidthlabel
 562             .setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager
 563                     .getString("label.manually_specify_width_left_column")));
 564     userIdWidthlabel.setBounds(new Rectangle(236, 120, 168, 23));
 565     userIdWidth.setFont(JvSwingUtils.getTextAreaFont());
 566     userIdWidth.setText("");
 567     userIdWidth.setBounds(new Rectangle(232, 144, 84, 23));
 568     userIdWidth.addActionListener(new ActionListener()
 569     {
 570
 571       @Override
 572       public void actionPerformed(ActionEvent e)
 573       {
 574         userIdWidth_actionPerformed();
 575       }
 576     });
 577     modellerOutput.setFont(LABEL_FONT);
 578     modellerOutput.setText(MessageManager
 579             .getString("label.use_modeller_output"));
 580     modellerOutput.setBounds(new Rectangle(228, 226, 168, 23));
 581     embbedBioJSON.setFont(LABEL_FONT);
 582     embbedBioJSON.setText(MessageManager.getString("label.embbed_biojson"));
 583     embbedBioJSON.setBounds(new Rectangle(228, 200, 250, 23));
 584
 585     jPanel11.add(jLabel1);
 586     jPanel11.add(blcjv);
 587     jPanel11.add(clustaljv);
 588     jPanel11.add(fastajv);
 589     jPanel11.add(msfjv);
 590     jPanel11.add(pfamjv);
 591     jPanel11.add(pileupjv);
 592     jPanel11.add(pirjv);
 593     outputTab.add(autoIdWidth);
 594     outputTab.add(userIdWidth);
 595     outputTab.add(userIdWidthlabel);
 596     outputTab.add(modellerOutput);
 597     outputTab.add(embbedBioJSON);
 598     outputTab.add(epsLabel);
 599     outputTab.add(epsRendering);
 600     outputTab.add(jPanel11);
 601     return outputTab;
 602   }
 603
 604   /**
 605    * Initialises the Connections tabbed panel.
 606    *
 607    * @return
 608    */
 609   private JPanel initConnectionsTab()
 610   {
 611     JPanel connectTab = new JPanel();
 612     connectTab.setLayout(new GridBagLayout());
 613
 614     // Label for browser text box
 615     JLabel browserLabel = new JLabel();
 616     browserLabel.setFont(LABEL_FONT);
 617     browserLabel.setHorizontalAlignment(SwingConstants.TRAILING);
 618     browserLabel.setText(MessageManager
 619             .getString("label.default_browser_unix"));
 620     defaultBrowser.setFont(LABEL_FONT);
 621     defaultBrowser.setText("");
 622
 623     defaultBrowser.addMouseListener(new MouseAdapter()
 624     {
 625       @Override
 626       public void mouseClicked(MouseEvent e)
 627       {
 628         if (e.getClickCount() > 1)
 629         {
 630           defaultBrowser_mouseClicked(e);
 631         }
 632       }
 633     });
 634
 635     JPanel proxyPanel = initConnTabProxyPanel();
 636     initConnTabCheckboxes();
 637
 638     // Add default Browser text box
 639     connectTab.add(browserLabel, new GridBagConstraints(0, 0, 1, 1, 0.0,
 640             0.0, GridBagConstraints.WEST, GridBagConstraints.NONE,
 641             new Insets(10, 0, 5, 5), 5, 1));
 642     defaultBrowser.setFont(LABEL_FONT);
 643     defaultBrowser.setText("");
 644
 645     connectTab.add(defaultBrowser, new GridBagConstraints(1, 0, 1, 1, 1.0,
 646             0.0, GridBagConstraints.CENTER, GridBagConstraints.HORIZONTAL,
 647             new Insets(10, 0, 5, 10), 30, 1));
 648
 649     // Add proxy server panel
 650     connectTab.add(proxyPanel, new GridBagConstraints(0, 1, 2, 1, 1.0, 0.0,
 651             GridBagConstraints.CENTER, GridBagConstraints.HORIZONTAL,
 652             new Insets(10, 0, 5, 12), 4, 10));
 653
 654     // Add usage stats, version check and questionnaire checkboxes
 655     connectTab.add(usagestats, new GridBagConstraints(0, 2, 1, 1, 1.0, 0.0,
 656             GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 657             new Insets(0, 2, 5, 5), 70, 1));
 658     connectTab.add(questionnaire, new GridBagConstraints(1, 2, 1, 1, 1.0,
 659             0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 660             new Insets(0, 2, 5, 10), 70, 1));
 661     connectTab.add(versioncheck, new GridBagConstraints(0, 3, 1, 1, 1.0,
 662             0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 663             new Insets(0, 2, 5, 5), 70, 1));
 664
 665     // Add padding so the panel doesn't look ridiculous
 666     JPanel spacePanel = new JPanel();
 667     connectTab.add(spacePanel, new GridBagConstraints(0, 4, 1, 1, 1.0, 1.0,
 668             GridBagConstraints.WEST, GridBagConstraints.BOTH, new Insets(0,
 669                     0, 0, 5), 70, 1));
 670
 671     return connectTab;
 672   }
 673
 674   /**
 675    * Initialises the Links tabbed panel.
 676    *
 677    * @return
 678    */
 679   private JPanel initLinksTab()
 680   {
 681     JPanel linkTab = new JPanel();
 682     linkTab.setLayout(new GridBagLayout());
 683
 684     // Set up table for Url links
 685     linkUrlTable.setFillsViewportHeight(true);
 686     linkUrlTable.setAutoResizeMode(JTable.AUTO_RESIZE_ALL_COLUMNS);
 687     linkUrlTable.setAutoCreateRowSorter(true);
 688     linkUrlTable.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
 689
 690     // adjust row height so radio buttons actually fit
 691     // don't do this in the renderer, it causes the awt thread to activate
 692     // constantly
 693     JRadioButton temp = new JRadioButton();
 694     linkUrlTable.setRowHeight(temp.getMinimumSize().height);
 695
 696     // Table in scrollpane so that the table is given a scrollbar
 697     JScrollPane linkScrollPane = new JScrollPane(linkUrlTable);
 698     linkScrollPane.setBorder(null);
 699
 700     // Panel for links functionality
 701     JPanel linkPanel = new JPanel(new GridBagLayout());
 702     linkPanel.setBorder(new TitledBorder(MessageManager
 703             .getString("label.url_linkfrom_sequence_id")));
 704
 705     // Put the Url links panel together
 706
 707     // Buttons go at top right, resizing only resizes the blank space vertically
 708     JPanel buttonPanel = initLinkTabUrlButtons();
 709     GridBagConstraints linkConstraints1 = new GridBagConstraints();
 710     linkConstraints1.insets = new Insets(0, 0, 5, 0);
 711     linkConstraints1.gridx = 0;
 712     linkConstraints1.gridy = 0;
 713     linkConstraints1.weightx = 1.0;
 714     linkConstraints1.fill = GridBagConstraints.HORIZONTAL;
 715     linkTab.add(buttonPanel, linkConstraints1);
 716
 717     // Links table goes at top left, resizing resizes the table
 718     GridBagConstraints linkConstraints2 = new GridBagConstraints();
 719     linkConstraints2.insets = new Insets(0, 0, 5, 5);
 720     linkConstraints2.gridx = 0;
 721     linkConstraints2.gridy = 1;
 722     linkConstraints2.weightx = 1.0;
 723     linkConstraints2.weighty = 1.0;
 724     linkConstraints2.fill = GridBagConstraints.BOTH;
 725     linkTab.add(linkScrollPane, linkConstraints2);
 726
 727     // Filter box and buttons goes at bottom left, resizing resizes the text box
 728     JPanel filterPanel = initLinkTabFilterPanel();
 729     GridBagConstraints linkConstraints3 = new GridBagConstraints();
 730     linkConstraints3.insets = new Insets(0, 0, 0, 5);
 731     linkConstraints3.gridx = 0;
 732     linkConstraints3.gridy = 2;
 733     linkConstraints3.weightx = 1.0;
 734     linkConstraints3.fill = GridBagConstraints.HORIZONTAL;
 735     linkTab.add(filterPanel, linkConstraints3);
 736
 737     return linkTab;
 738   }
 739
 740   private JPanel initLinkTabFilterPanel()
 741   {
 742     // Filter textbox and reset button
 743     JLabel filterLabel = new JLabel(
 744             MessageManager.getString("label.filter"));
 745     filterLabel.setFont(LABEL_FONT);
 746     filterLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 747     filterLabel.setHorizontalTextPosition(SwingConstants.LEADING);
 748
 749     filterTB.setFont(LABEL_FONT);
 750     filterTB.setText("");
 751
 752     doReset.setText(MessageManager.getString("action.showall"));
 753     userOnly.setText(MessageManager.getString("action.customfilter"));
 754
 755     // Panel for filter functionality
 756     JPanel filterPanel = new JPanel(new GridBagLayout());
 757     filterPanel.setBorder(new TitledBorder("Filter"));
 758     GridBagConstraints gbc = new GridBagConstraints();
 759     gbc.gridx = 0;
 760     gbc.gridy = 0;
 761     gbc.fill = GridBagConstraints.NONE;
 762     gbc.anchor = GridBagConstraints.WEST;
 763
 764     filterPanel.add(filterLabel, gbc);
 765
 766     GridBagConstraints gbc1 = new GridBagConstraints();
 767     gbc1.gridx = 1;
 768     gbc1.gridwidth = 2;
 769     gbc1.fill = GridBagConstraints.HORIZONTAL;
 770     gbc1.anchor = GridBagConstraints.WEST;
 771     gbc1.weightx = 1.0;
 772     filterPanel.add(filterTB, gbc1);
 773
 774     GridBagConstraints gbc2 = new GridBagConstraints();
 775     gbc2.gridx = 3;
 776     gbc2.fill = GridBagConstraints.NONE;
 777     gbc2.anchor = GridBagConstraints.WEST;
 778     filterPanel.add(doReset, gbc2);
 779
 780     GridBagConstraints gbc3 = new GridBagConstraints();
 781     gbc3.gridx = 4;
 782     gbc3.fill = GridBagConstraints.NONE;
 783     gbc3.anchor = GridBagConstraints.WEST;
 784     filterPanel.add(userOnly, gbc3);
 785
 786     return filterPanel;
 787   }
 788
 789   private JPanel initLinkTabUrlButtons()
 790   {
 791     // Buttons for new / edit / delete Url links
 792     JButton newLink = new JButton();
 793     newLink.setText(MessageManager.getString("action.new"));
 794
 795     editLink.setText(MessageManager.getString("action.edit"));
 796
 797     deleteLink.setText(MessageManager.getString("action.delete"));
 798
 799     // no current selection, so initially disable delete/edit buttons
 800     editLink.setEnabled(false);
 801     deleteLink.setEnabled(false);
 802
 803     newLink.addActionListener(new java.awt.event.ActionListener()
 804     {
 805       @Override
 806       public void actionPerformed(ActionEvent e)
 807       {
 808         newLink_actionPerformed(e);
 809       }
 810     });
 811
 812     editLink.setText(MessageManager.getString("action.edit"));
 813     editLink.addActionListener(new java.awt.event.ActionListener()
 814     {
 815       @Override
 816       public void actionPerformed(ActionEvent e)
 817       {
 818         editLink_actionPerformed(e);
 819       }
 820     });
 821
 822     deleteLink.setText(MessageManager.getString("action.delete"));
 823     deleteLink.addActionListener(new java.awt.event.ActionListener()
 824     {
 825       @Override
 826       public void actionPerformed(ActionEvent e)
 827       {
 828         deleteLink_actionPerformed(e);
 829       }
 830     });
 831
 832     JPanel buttonPanel = new JPanel(new GridBagLayout());
 833     buttonPanel.setBorder(new TitledBorder("Edit links"));
 834     GridBagConstraints gbc = new GridBagConstraints();
 835     gbc.gridx = 0;
 836     gbc.gridy = 0;
 837     gbc.fill = GridBagConstraints.NONE;
 838     buttonPanel.add(newLink, gbc);
 839
 840     GridBagConstraints gbc1 = new GridBagConstraints();
 841     gbc1.gridx = 1;
 842     gbc1.gridy = 0;
 843     gbc1.fill = GridBagConstraints.NONE;
 844     buttonPanel.add(editLink, gbc1);
 845
 846     GridBagConstraints gbc2 = new GridBagConstraints();
 847     gbc2.gridx = 2;
 848     gbc2.gridy = 0;
 849     gbc2.fill = GridBagConstraints.NONE;
 850     buttonPanel.add(deleteLink, gbc2);
 851
 852     GridBagConstraints gbc3 = new GridBagConstraints();
 853     gbc3.gridx = 3;
 854     gbc3.gridy = 0;
 855     gbc3.fill = GridBagConstraints.HORIZONTAL;
 856     gbc3.weightx = 1.0;
 857     JPanel spacePanel = new JPanel();
 858     spacePanel.setBorder(null);
 859     buttonPanel.add(spacePanel, gbc3);
 860
 861     return buttonPanel;
 862   }
 863
 864   /**
 865    * Initialises the proxy server panel in the Connections tab
 866    *
 867    * @return the proxy server panel
 868    */
 869   private JPanel initConnTabProxyPanel()
 870   {
 871     // Label for server text box
 872     serverLabel.setText(MessageManager.getString("label.address"));
 873     serverLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 874     serverLabel.setFont(LABEL_FONT);
 875
 876     // Proxy server and port text boxes
 877     proxyServerTB.setFont(LABEL_FONT);
 878     proxyPortTB.setFont(LABEL_FONT);
 879
 880     // Label for Port text box
 881     portLabel.setFont(LABEL_FONT);
 882     portLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 883     portLabel.setText(MessageManager.getString("label.port"));
 884
 885     // Use proxy server checkbox
 886     useProxy.setFont(LABEL_FONT);
 887     useProxy.setHorizontalAlignment(SwingConstants.RIGHT);
 888     useProxy.setHorizontalTextPosition(SwingConstants.LEADING);
 889     useProxy.setText(MessageManager.getString("label.use_proxy_server"));
 890     useProxy.addActionListener(new ActionListener()
 891     {
 892       @Override
 893       public void actionPerformed(ActionEvent e)
 894       {
 895         useProxy_actionPerformed();
 896       }
 897     });
 898
 899     // Make proxy server panel
 900     JPanel proxyPanel = new JPanel();
 901     TitledBorder titledBorder1 = new TitledBorder(
 902             MessageManager.getString("label.proxy_server"));
 903     proxyPanel.setBorder(titledBorder1);
 904     proxyPanel.setLayout(new GridBagLayout());
 905     proxyPanel.add(serverLabel, new GridBagConstraints(0, 1, 1, 1, 0.0,
 906             0.0, GridBagConstraints.WEST, GridBagConstraints.NONE,
 907             new Insets(0, 2, 2, 0), 5, 0));
 908     proxyPanel.add(portLabel, new GridBagConstraints(2, 1, 1, 1, 0.0, 0.0,
 909             GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
 910                     0, 2, 0), 11, 0));
 911     proxyPanel.add(useProxy, new GridBagConstraints(0, 0, 2, 1, 0.0, 0.0,
 912             GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
 913                     2, 5, 185), 2, -4));
 914     proxyPanel.add(proxyPortTB, new GridBagConstraints(3, 1, 1, 1, 1.0,
 915             0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 916             new Insets(0, 2, 2, 2), 54, 1));
 917     proxyPanel.add(proxyServerTB, new GridBagConstraints(1, 1, 1, 1, 1.0,
 918             0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 919             new Insets(0, 2, 2, 0), 263, 1));
 920
 921     return proxyPanel;
 922   }
 923
 924   /**
 925    * Initialises the checkboxes in the Connections tab
 926    */
 927   private void initConnTabCheckboxes()
 928   {
 929     // Usage stats checkbox label
 930     usagestats.setText(MessageManager
 931             .getString("label.send_usage_statistics"));
 932     usagestats.setFont(LABEL_FONT);
 933     usagestats.setHorizontalAlignment(SwingConstants.RIGHT);
 934     usagestats.setHorizontalTextPosition(SwingConstants.LEADING);
 935
 936     // Questionnaire checkbox label
 937     questionnaire.setText(MessageManager
 938             .getString("label.check_for_questionnaires"));
 939     questionnaire.setFont(LABEL_FONT);
 940     questionnaire.setHorizontalAlignment(SwingConstants.RIGHT);
 941     questionnaire.setHorizontalTextPosition(SwingConstants.LEADING);
 942
 943     // Check for latest version checkbox label
 944     versioncheck.setText(MessageManager
 945             .getString("label.check_for_latest_version"));
 946     versioncheck.setFont(LABEL_FONT);
 947     versioncheck.setHorizontalAlignment(SwingConstants.RIGHT);
 948     versioncheck.setHorizontalTextPosition(SwingConstants.LEADING);
 949   }
 950
 951   /**
 952    * Initialises the parent panel which contains the tabbed sections.
 953    *
 954    * @return
 955    */
 956   private JPanel initOkCancelPanel()
 957   {
 958     JButton ok = new JButton();
 959     ok.setText(MessageManager.getString("action.ok"));
 960     ok.addActionListener(new ActionListener()
 961     {
 962       @Override
 963       public void actionPerformed(ActionEvent e)
 964       {
 965         ok_actionPerformed(e);
 966       }
 967     });
 968     JButton cancel = new JButton();
 969     cancel.setText(MessageManager.getString("action.cancel"));
 970     cancel.addActionListener(new ActionListener()
 971     {
 972       @Override
 973       public void actionPerformed(ActionEvent e)
 974       {
 975         cancel_actionPerformed(e);
 976       }
 977     });
 978     JPanel okCancelPanel = new JPanel();
 979     okCancelPanel.add(ok);
 980     okCancelPanel.add(cancel);
 981     return okCancelPanel;
 982   }
 983
 984   /**
 985    * Initialises the Colours tabbed panel.
 986    *
 987    * @return
 988    */
 989   private JPanel initColoursTab()
 990   {
 991     JPanel coloursTab = new JPanel();
 992     coloursTab.setBorder(new TitledBorder(MessageManager
 993             .getString("action.open_new_alignment")));
 994     coloursTab.setLayout(new FlowLayout());
 995     JLabel mincolourLabel = new JLabel();
 996     mincolourLabel.setFont(LABEL_FONT);
 997     mincolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 998     mincolourLabel.setText(MessageManager.getString("label.min_colour"));
 999     minColour.setFont(LABEL_FONT);
1000     minColour.setBorder(BorderFactory.createEtchedBorder());
1001     minColour.setPreferredSize(new Dimension(40, 20));
1002     minColour.addMouseListener(new MouseAdapter()
1003     {
1004       @Override
1005       public void mousePressed(MouseEvent e)
1006       {
1007         minColour_actionPerformed(minColour);
1008       }
1009     });
1010     JLabel maxcolourLabel = new JLabel();
1011     maxcolourLabel.setFont(LABEL_FONT);
1012     maxcolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1013     maxcolourLabel.setText(MessageManager.getString("label.max_colour"));
1014     maxColour.setFont(LABEL_FONT);
1015     maxColour.setBorder(BorderFactory.createEtchedBorder());
1016     maxColour.setPreferredSize(new Dimension(40, 20));
1017     maxColour.addMouseListener(new MouseAdapter()
1018     {
1019       @Override
1020       public void mousePressed(MouseEvent e)
1021       {
1022         maxColour_actionPerformed(maxColour);
1023       }
1024     });
1025
1026     protColour.setFont(LABEL_FONT);
1027     protColour.setBounds(new Rectangle(172, 225, 155, 21));
1028     JLabel protColourLabel = new JLabel();
1029     protColourLabel.setFont(LABEL_FONT);
1030     protColourLabel.setHorizontalAlignment(SwingConstants.LEFT);
1031     protColourLabel.setText(MessageManager
1032             .getString("label.prot_alignment_colour") + " ");
1033     JvSwingUtils.addtoLayout(coloursTab, MessageManager
1034             .getString("label.default_colour_scheme_for_alignment"),
1035             protColourLabel, protColour);
1036
1037     nucColour.setFont(LABEL_FONT);
1038     nucColour.setBounds(new Rectangle(172, 240, 155, 21));
1039     JLabel nucColourLabel = new JLabel();
1040     nucColourLabel.setFont(LABEL_FONT);
1041     nucColourLabel.setHorizontalAlignment(SwingConstants.LEFT);
1042     nucColourLabel.setText(MessageManager
1043             .getString("label.nuc_alignment_colour") + " ");
1044     JvSwingUtils.addtoLayout(coloursTab, MessageManager
1045             .getString("label.default_colour_scheme_for_alignment"),
1046             nucColourLabel, nucColour);
1047
1048     JPanel annotationShding = new JPanel();
1049     annotationShding.setBorder(new TitledBorder(MessageManager
1050             .getString("label.annotation_shading_default")));
1051     annotationShding.setLayout(new GridLayout(1, 2));
1052     JvSwingUtils.addtoLayout(annotationShding, MessageManager
1053             .getString("label.default_minimum_colour_annotation_shading"),
1054             mincolourLabel, minColour);
1055     JvSwingUtils.addtoLayout(annotationShding, MessageManager
1056             .getString("label.default_maximum_colour_annotation_shading"),
1057             maxcolourLabel, maxColour);
1058     coloursTab.add(annotationShding); // , FlowLayout.LEFT);
1059     return coloursTab;
1060   }
1061
1062   /**
1063    * Initialises the Structure tabbed panel.
1064    *
1065    * @return
1066    */
1067   private JPanel initStructureTab()
1068   {
1069     structureTab = new JPanel();
1070
1071     structureTab.setBorder(new TitledBorder(MessageManager
1072             .getString("label.structure_options")));
1073     structureTab.setLayout(null);
1074     final int width = 400;
1075     final int height = 22;
1076     final int lineSpacing = 25;
1077     int ypos = 15;
1078
1079     structFromPdb.setFont(LABEL_FONT);
1080     structFromPdb
1081             .setText(MessageManager.getString("label.struct_from_pdb"));
1082     structFromPdb.setBounds(new Rectangle(5, ypos, width, height));
1083     structFromPdb.addActionListener(new ActionListener()
1084     {
1085       @Override
1086       public void actionPerformed(ActionEvent e)
1087       {
1088         boolean selected = structFromPdb.isSelected();
1089         // enable other options only when the first is checked
1090         useRnaView.setEnabled(selected);
1091         addSecondaryStructure.setEnabled(selected);
1092         addTempFactor.setEnabled(selected);
1093       }
1094     });
1095     structureTab.add(structFromPdb);
1096
1097     // indent checkboxes that are conditional on the first one
1098     ypos += lineSpacing;
1099     useRnaView.setFont(LABEL_FONT);
1100     useRnaView.setText(MessageManager.getString("label.use_rnaview"));
1101     useRnaView.setBounds(new Rectangle(25, ypos, width, height));
1102     structureTab.add(useRnaView);
1103
1104     ypos += lineSpacing;
1105     addSecondaryStructure.setFont(LABEL_FONT);
1106     addSecondaryStructure.setText(MessageManager
1107             .getString("label.autoadd_secstr"));
1108     addSecondaryStructure.setBounds(new Rectangle(25, ypos, width, height));
1109     structureTab.add(addSecondaryStructure);
1110
1111     ypos += lineSpacing;
1112     addTempFactor.setFont(LABEL_FONT);
1113     addTempFactor.setText(MessageManager.getString("label.autoadd_temp"));
1114     addTempFactor.setBounds(new Rectangle(25, ypos, width, height));
1115     structureTab.add(addTempFactor);
1116
1117     ypos += lineSpacing;
1118     JLabel viewerLabel = new JLabel();
1119     viewerLabel.setFont(LABEL_FONT);
1120     viewerLabel.setHorizontalAlignment(SwingConstants.LEFT);
1121     viewerLabel.setText(MessageManager.getString("label.structure_viewer"));
1122     viewerLabel.setBounds(new Rectangle(10, ypos, 200, height));
1123     structureTab.add(viewerLabel);
1124
1125     structViewer.setFont(LABEL_FONT);
1126     structViewer.setBounds(new Rectangle(160, ypos, 120, height));
1127     structViewer.addItem(ViewerType.JMOL.name());
1128     structViewer.addItem(ViewerType.CHIMERA.name());
1129     structViewer.addActionListener(new ActionListener()
1130     {
1131       @Override
1132       public void actionPerformed(ActionEvent e)
1133       {
1134         structureViewer_actionPerformed((String) structViewer
1135                 .getSelectedItem());
1136       }
1137     });
1138     structureTab.add(structViewer);
1139
1140     ypos += lineSpacing;
1141     JLabel pathLabel = new JLabel();
1142     pathLabel.setFont(new java.awt.Font("SansSerif", 0, 11));
1143     pathLabel.setHorizontalAlignment(SwingConstants.LEFT);
1144     pathLabel.setText(MessageManager.getString("label.chimera_path"));
1145     final String tooltip = JvSwingUtils.wrapTooltip(true,
1146             MessageManager.getString("label.chimera_path_tip"));
1147     pathLabel.setToolTipText(tooltip);
1148     pathLabel.setBounds(new Rectangle(10, ypos, 140, height));
1149     structureTab.add(pathLabel);
1150
1151     chimeraPath.setFont(LABEL_FONT);
1152     chimeraPath.setText("");
1153     chimeraPath.setBounds(new Rectangle(160, ypos, 300, height));
1154     chimeraPath.addMouseListener(new MouseAdapter()
1155     {
1156       @Override
1157       public void mouseClicked(MouseEvent e)
1158       {
1159         if (e.getClickCount() == 2)
1160         {
1161           String chosen = openFileChooser();
1162           if (chosen != null)
1163           {
1164             chimeraPath.setText(chosen);
1165           }
1166         }
1167       }
1168     });
1169     structureTab.add(chimeraPath);
1170
1171     ypos += lineSpacing;
1172     nwMapping.setFont(LABEL_FONT);
1173     nwMapping.setText(MessageManager.getString("label.nw_mapping"));
1174     siftsMapping.setFont(LABEL_FONT);
1175     siftsMapping.setText(MessageManager.getString("label.sifts_mapping"));
1176     mappingMethod.add(nwMapping);
1177     mappingMethod.add(siftsMapping);
1178     JPanel mappingPanel = new JPanel();
1179     mappingPanel.setFont(LABEL_FONT);
1180     TitledBorder mmTitledBorder = new TitledBorder(
1181             MessageManager.getString("label.mapping_method"));
1182     mmTitledBorder.setTitleFont(LABEL_FONT);
1183     mappingPanel.setBorder(mmTitledBorder);
1184     mappingPanel.setBounds(new Rectangle(10, ypos, 452, 45));
1185     // GridLayout mappingLayout = new GridLayout();
1186     mappingPanel.setLayout(new GridLayout());
1187     mappingPanel.add(nwMapping);
1188     mappingPanel.add(siftsMapping);
1189     structureTab.add(mappingPanel);
1190
1191     ypos += lineSpacing;
1192     ypos += lineSpacing;
1193     FTSDataColumnPreferences docFieldPref = new FTSDataColumnPreferences(
1194             PreferenceSource.PREFERENCES, PDBFTSRestClient.getInstance());
1195     docFieldPref.setBounds(new Rectangle(10, ypos, 450, 120));
1196     structureTab.add(docFieldPref);
1197
1198     return structureTab;
1199   }
1200
1201   /**
1202    * Action on choosing a structure viewer from combobox options.
1203    *
1204    * @param selectedItem
1205    */
1206   protected void structureViewer_actionPerformed(String selectedItem)
1207   {
1208   }
1209
1210   /**
1211    * Show a dialog for the user to choose a file. Returns the chosen path, or
1212    * null on Cancel.
1213    *
1214    * @return
1215    */
1216   protected String openFileChooser()
1217   {
1218     String choice = null;
1219     JFileChooser chooser = new JFileChooser();
1220
1221     // chooser.setFileView(new JalviewFileView());
1222     chooser.setDialogTitle(MessageManager
1223             .getString("label.open_local_file"));
1224     chooser.setToolTipText(MessageManager.getString("action.open"));
1225
1226     int value = chooser.showOpenDialog(this);
1227
1228     if (value == JFileChooser.APPROVE_OPTION)
1229     {
1230       choice = chooser.getSelectedFile().getPath();
1231     }
1232     return choice;
1233   }
1234
1235   /**
1236    * Validate the structure tab preferences; if invalid, set focus on this tab.
1237    *
1238    * @param e
1239    */
1240   protected boolean validateStructure(FocusEvent e)
1241   {
1242     if (!validateStructure())
1243     {
1244       e.getComponent().requestFocusInWindow();
1245       return false;
1246     }
1247     return true;
1248   }
1249
1250   protected boolean validateStructure()
1251   {
1252     return false;
1253   }
1254
1255   /**
1256    * Initialises the Visual tabbed panel.
1257    *
1258    * @return
1259    */
1260   private JPanel initVisualTab()
1261   {
1262     JPanel visualTab = new JPanel();
1263     visualTab.setBorder(new TitledBorder(MessageManager
1264             .getString("action.open_new_alignment")));
1265     visualTab.setLayout(null);
1266     fullScreen.setFont(LABEL_FONT);
1267     fullScreen.setHorizontalAlignment(SwingConstants.RIGHT);
1268     fullScreen.setHorizontalTextPosition(SwingConstants.LEFT);
1269     fullScreen.setText(MessageManager.getString("label.maximize_window"));
1270     quality.setEnabled(false);
1271     quality.setFont(LABEL_FONT);
1272     quality.setHorizontalAlignment(SwingConstants.RIGHT);
1273     quality.setHorizontalTextPosition(SwingConstants.LEFT);
1274     quality.setSelected(true);
1275     quality.setText(MessageManager.getString("label.quality"));
1276     conservation.setEnabled(false);
1277     conservation.setFont(LABEL_FONT);
1278     conservation.setHorizontalAlignment(SwingConstants.RIGHT);
1279     conservation.setHorizontalTextPosition(SwingConstants.LEFT);
1280     conservation.setSelected(true);
1281     conservation.setText(MessageManager.getString("label.conservation"));
1282     identity.setEnabled(false);
1283     identity.setFont(LABEL_FONT);
1284     identity.setHorizontalAlignment(SwingConstants.RIGHT);
1285     identity.setHorizontalTextPosition(SwingConstants.LEFT);
1286     identity.setSelected(true);
1287     identity.setText(MessageManager.getString("label.consensus"));
1288     showOccupancy.setFont(LABEL_FONT);
1289     showOccupancy.setEnabled(false);
1290     showOccupancy.setHorizontalAlignment(SwingConstants.RIGHT);
1291     showOccupancy.setHorizontalTextPosition(SwingConstants.LEFT);
1292     showOccupancy.setSelected(true);
1293     showOccupancy.setText(MessageManager.getString("label.occupancy"));
1294
1295     JLabel showGroupbits = new JLabel();
1296     showGroupbits.setFont(LABEL_FONT);
1297     showGroupbits.setHorizontalAlignment(SwingConstants.RIGHT);
1298     showGroupbits.setHorizontalTextPosition(SwingConstants.LEFT);
1299     showGroupbits.setText(MessageManager.getString("action.show_group")
1300             + ":");
1301     JLabel showConsensbits = new JLabel();
1302     showConsensbits.setFont(LABEL_FONT);
1303     showConsensbits.setHorizontalAlignment(SwingConstants.RIGHT);
1304     showConsensbits.setHorizontalTextPosition(SwingConstants.LEFT);
1305     showConsensbits.setText(MessageManager.getString("label.consensus")
1306             + ":");
1307     showConsensHistogram.setEnabled(false);
1308     showConsensHistogram.setFont(LABEL_FONT);
1309     showConsensHistogram.setHorizontalAlignment(SwingConstants.RIGHT);
1310     showConsensHistogram.setHorizontalTextPosition(SwingConstants.LEFT);
1311     showConsensHistogram.setSelected(true);
1312     showConsensHistogram.setText(MessageManager
1313             .getString("label.histogram"));
1314     showConsensLogo.setEnabled(false);
1315     showConsensLogo.setFont(LABEL_FONT);
1316     showConsensLogo.setHorizontalAlignment(SwingConstants.RIGHT);
1317     showConsensLogo.setHorizontalTextPosition(SwingConstants.LEFT);
1318     showConsensLogo.setSelected(true);
1319     showConsensLogo.setText(MessageManager.getString("label.logo"));
1320     showGroupConsensus.setEnabled(false);
1321     showGroupConsensus.setFont(LABEL_FONT);
1322     showGroupConsensus.setHorizontalAlignment(SwingConstants.RIGHT);
1323     showGroupConsensus.setHorizontalTextPosition(SwingConstants.LEFT);
1324     showGroupConsensus.setSelected(true);
1325     showGroupConsensus.setText(MessageManager.getString("label.consensus"));
1326     showGroupConservation.setEnabled(false);
1327     showGroupConservation.setFont(LABEL_FONT);
1328     showGroupConservation.setHorizontalAlignment(SwingConstants.RIGHT);
1329     showGroupConservation.setHorizontalTextPosition(SwingConstants.LEFT);
1330     showGroupConservation.setSelected(true);
1331     showGroupConservation.setText(MessageManager
1332             .getString("label.conservation"));
1333     showNpTooltip.setEnabled(true);
1334     showNpTooltip.setFont(LABEL_FONT);
1335     showNpTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
1336     showNpTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
1337     showNpTooltip.setSelected(true);
1338     showNpTooltip.setText(MessageManager
1339             .getString("label.non_positional_features"));
1340     showDbRefTooltip.setEnabled(true);
1341     showDbRefTooltip.setFont(LABEL_FONT);
1342     showDbRefTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
1343     showDbRefTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
1344     showDbRefTooltip.setSelected(true);
1345     showDbRefTooltip.setText(MessageManager
1346             .getString("label.database_references"));
1347     annotations.setFont(LABEL_FONT);
1348     annotations.setHorizontalAlignment(SwingConstants.RIGHT);
1349     annotations.setHorizontalTextPosition(SwingConstants.LEFT);
1350     annotations.setSelected(true);
1351     annotations.setText(MessageManager.getString("label.show_annotations"));
1352     // annotations.setBounds(new Rectangle(169, 12, 200, 23));
1353     annotations.addActionListener(new ActionListener()
1354     {
1355       @Override
1356       public void actionPerformed(ActionEvent e)
1357       {
1358         annotations_actionPerformed(e);
1359       }
1360     });
1361     identity.addActionListener(new ActionListener()
1362     {
1363       @Override
1364       public void actionPerformed(ActionEvent e)
1365       {
1366         annotations_actionPerformed(e);
1367       }
1368     });
1369     showGroupConsensus.addActionListener(new ActionListener()
1370     {
1371       @Override
1372       public void actionPerformed(ActionEvent e)
1373       {
1374         annotations_actionPerformed(e);
1375       }
1376     });
1377     showUnconserved.setFont(LABEL_FONT);
1378     showUnconserved.setHorizontalAlignment(SwingConstants.RIGHT);
1379     showUnconserved.setHorizontalTextPosition(SwingConstants.LEFT);
1380     showUnconserved.setSelected(true);
1381     showUnconserved.setText(MessageManager
1382             .getString("action.show_unconserved"));
1383     showUnconserved.addActionListener(new ActionListener()
1384     {
1385       @Override
1386       public void actionPerformed(ActionEvent e)
1387       {
1388         showunconserved_actionPerformed(e);
1389       }
1390     });
1391
1392     // TODO these are not yet added to / action from Preferences
1393     // JCheckBox shareSelections = new JCheckBox();
1394     // shareSelections.setFont(verdana11);
1395     // shareSelections.setHorizontalAlignment(SwingConstants.RIGHT);
1396     // shareSelections.setHorizontalTextPosition(SwingConstants.LEFT);
1397     // shareSelections.setSelected(true);
1398     // shareSelections.setText(MessageManager
1399     // .getString("label.share_selection_across_views"));
1400     // JCheckBox followHighlight = new JCheckBox();
1401     // followHighlight.setFont(verdana11);
1402     // followHighlight.setHorizontalAlignment(SwingConstants.RIGHT);
1403     // followHighlight.setHorizontalTextPosition(SwingConstants.LEFT);
1404     // // showUnconserved.setBounds(new Rectangle(169, 40, 200, 23));
1405     // followHighlight.setSelected(true);
1406     // followHighlight.setText(MessageManager
1407     // .getString("label.scroll_highlighted_regions"));
1408
1409     seqLimit.setFont(LABEL_FONT);
1410     seqLimit.setHorizontalAlignment(SwingConstants.RIGHT);
1411     seqLimit.setHorizontalTextPosition(SwingConstants.LEFT);
1412     seqLimit.setText(MessageManager.getString("label.full_sequence_id"));
1413     smoothFont.setFont(LABEL_FONT);
1414     smoothFont.setHorizontalAlignment(SwingConstants.RIGHT);
1415     smoothFont.setHorizontalTextPosition(SwingConstants.LEADING);
1416     smoothFont.setText(MessageManager.getString("label.smooth_font"));
1417     scaleProteinToCdna.setFont(LABEL_FONT);
1418     scaleProteinToCdna.setHorizontalAlignment(SwingConstants.RIGHT);
1419     scaleProteinToCdna.setHorizontalTextPosition(SwingConstants.LEADING);
1420     scaleProteinToCdna.setText(MessageManager
1421             .getString("label.scale_protein_to_cdna"));
1422     scaleProteinToCdna.setToolTipText(MessageManager
1423             .getString("label.scale_protein_to_cdna_tip"));
1424     JLabel gapLabel = new JLabel();
1425     gapLabel.setFont(LABEL_FONT);
1426     gapLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1427     gapLabel.setText(MessageManager.getString("label.gap_symbol") + " ");
1428     JLabel fontLabel = new JLabel();
1429     fontLabel.setFont(LABEL_FONT);
1430     fontLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1431     fontLabel.setText(MessageManager.getString("label.font"));
1432     fontSizeCB.setFont(LABEL_FONT);
1433     fontSizeCB.setBounds(new Rectangle(320, 112, 65, 23));
1434     fontStyleCB.setFont(LABEL_FONT);
1435     fontStyleCB.setBounds(new Rectangle(382, 112, 80, 23));
1436     fontNameCB.setFont(LABEL_FONT);
1437     fontNameCB.setBounds(new Rectangle(172, 112, 147, 23));
1438     gapSymbolCB.setFont(LABEL_FONT);
1439     gapSymbolCB.setBounds(new Rectangle(172, 215, 69, 23));
1440     DefaultListCellRenderer dlcr = new DefaultListCellRenderer();
1441     dlcr.setHorizontalAlignment(DefaultListCellRenderer.CENTER);
1442     gapSymbolCB.setRenderer(dlcr);
1443
1444     startupCheckbox.setText(MessageManager.getString("action.open_file"));
1445     startupCheckbox.setFont(LABEL_FONT);
1446     startupCheckbox.setHorizontalAlignment(SwingConstants.RIGHT);
1447     startupCheckbox.setHorizontalTextPosition(SwingConstants.LEFT);
1448     startupCheckbox.setSelected(true);
1449     startupFileTextfield.setFont(LABEL_FONT);
1450     startupFileTextfield.setBounds(new Rectangle(172, 310, 330, 20));
1451     startupFileTextfield.addMouseListener(new MouseAdapter()
1452     {
1453       @Override
1454       public void mouseClicked(MouseEvent e)
1455       {
1456         if (e.getClickCount() > 1)
1457         {
1458           startupFileTextfield_mouseClicked();
1459         }
1460       }
1461     });
1462
1463     sortby.setFont(LABEL_FONT);
1464     sortby.setBounds(new Rectangle(172, 260, 155, 21));
1465     JLabel sortLabel = new JLabel();
1466     sortLabel.setFont(LABEL_FONT);
1467     sortLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1468     sortLabel.setText(MessageManager.getString("label.sort_by"));
1469     sortAnnBy.setFont(LABEL_FONT);
1470     sortAnnBy.setBounds(new Rectangle(172, 285, 110, 21));
1471     JLabel sortAnnLabel = new JLabel();
1472     sortAnnLabel.setFont(LABEL_FONT);
1473     sortAnnLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1474     sortAnnLabel.setText(MessageManager.getString("label.sort_ann_by"));
1475     sortAutocalc.setFont(LABEL_FONT);
1476     sortAutocalc.setBounds(new Rectangle(290, 285, 165, 21));
1477
1478     JPanel annsettingsPanel = new JPanel();
1479     annsettingsPanel.setBounds(new Rectangle(173, 13, 320, 96));
1480     annsettingsPanel.setLayout(new FlowLayout(FlowLayout.LEFT, 0, 0));
1481     annsettingsPanel.setBorder(new EtchedBorder());
1482     visualTab.add(annsettingsPanel);
1483     Border jb = new EmptyBorder(1, 1, 4, 5);
1484     annotations.setBorder(jb);
1485     showOccupancy.setBorder(jb);
1486     quality.setBorder(jb);
1487     conservation.setBorder(jb);
1488     identity.setBorder(jb);
1489     showConsensbits.setBorder(jb);
1490     showGroupbits.setBorder(jb);
1491     showGroupConsensus.setBorder(jb);
1492     showGroupConservation.setBorder(jb);
1493     showConsensHistogram.setBorder(jb);
1494     showConsensLogo.setBorder(jb);
1495
1496     JPanel autoAnnotSettings = new JPanel();
1497     annsettingsPanel.add(autoAnnotSettings);
1498     autoAnnotSettings.setLayout(new GridLayout(0, 2));
1499     autoAnnotSettings.add(annotations);
1500     autoAnnotSettings.add(quality);
1501     // second row of autoannotation box
1502     autoAnnotSettings = new JPanel();
1503     annsettingsPanel.add(autoAnnotSettings);
1504
1505     autoAnnotSettings.setLayout(new GridLayout(0, 3));
1506     autoAnnotSettings.add(conservation);
1507     autoAnnotSettings.add(identity);
1508     autoAnnotSettings.add(showOccupancy);
1509     autoAnnotSettings.add(showGroupbits);
1510     autoAnnotSettings.add(showGroupConservation);
1511     autoAnnotSettings.add(showGroupConsensus);
1512     autoAnnotSettings.add(showConsensbits);
1513     autoAnnotSettings.add(showConsensHistogram);
1514     autoAnnotSettings.add(showConsensLogo);
1515
1516
1517
1518     JPanel tooltipSettings = new JPanel();
1519     tooltipSettings.setBorder(new TitledBorder(MessageManager
1520             .getString("label.sequence_id_tooltip")));
1521     tooltipSettings.setBounds(173, 140, 220, 62);
1522     tooltipSettings.setLayout(new GridLayout(2, 1));
1523     tooltipSettings.add(showDbRefTooltip);
1524     tooltipSettings.add(showNpTooltip);
1525     visualTab.add(tooltipSettings);
1526
1527     wrap.setFont(LABEL_FONT);
1528     wrap.setHorizontalAlignment(SwingConstants.TRAILING);
1529     wrap.setHorizontalTextPosition(SwingConstants.LEADING);
1530     wrap.setText(MessageManager.getString("label.wrap_alignment"));
1531     rightAlign.setFont(LABEL_FONT);
1532     rightAlign.setForeground(Color.black);
1533     rightAlign.setHorizontalAlignment(SwingConstants.RIGHT);
1534     rightAlign.setHorizontalTextPosition(SwingConstants.LEFT);
1535     rightAlign.setText(MessageManager.getString("label.right_align_ids"));
1536     idItalics.setFont(LABEL_FONT_ITALIC);
1537     idItalics.setHorizontalAlignment(SwingConstants.RIGHT);
1538     idItalics.setHorizontalTextPosition(SwingConstants.LEADING);
1539     idItalics.setText(MessageManager
1540             .getString("label.sequence_name_italics"));
1541     openoverv.setFont(LABEL_FONT);
1542     openoverv.setActionCommand(MessageManager
1543             .getString("label.open_overview"));
1544     openoverv.setHorizontalAlignment(SwingConstants.RIGHT);
1545     openoverv.setHorizontalTextPosition(SwingConstants.LEFT);
1546     openoverv.setText(MessageManager.getString("label.open_overview"));
1547     JPanel jPanel2 = new JPanel();
1548     jPanel2.setBounds(new Rectangle(7, 17, 158, 310));
1549     jPanel2.setLayout(new GridLayout(14, 1));
1550     jPanel2.add(fullScreen);
1551     jPanel2.add(openoverv);
1552     jPanel2.add(seqLimit);
1553     jPanel2.add(rightAlign);
1554     jPanel2.add(fontLabel);
1555     jPanel2.add(showUnconserved);
1556     jPanel2.add(idItalics);
1557     jPanel2.add(smoothFont);
1558     jPanel2.add(scaleProteinToCdna);
1559     jPanel2.add(gapLabel);
1560     jPanel2.add(wrap);
1561     jPanel2.add(sortLabel);
1562     jPanel2.add(sortAnnLabel);
1563     jPanel2.add(startupCheckbox);
1564     visualTab.add(jPanel2);
1565     visualTab.add(startupFileTextfield);
1566     visualTab.add(sortby);
1567     visualTab.add(sortAnnBy);
1568     visualTab.add(sortAutocalc);
1569     visualTab.add(gapSymbolCB);
1570     visualTab.add(fontNameCB);
1571     visualTab.add(fontSizeCB);
1572     visualTab.add(fontStyleCB);
1573     return visualTab;
1574   }
1575
1576   protected void autoIdWidth_actionPerformed()
1577   {
1578     // TODO Auto-generated method stub
1579
1580   }
1581
1582   protected void userIdWidth_actionPerformed()
1583   {
1584     // TODO Auto-generated method stub
1585
1586   }
1587
1588   protected void maxColour_actionPerformed(JPanel panel)
1589   {
1590   }
1591
1592   protected void minColour_actionPerformed(JPanel panel)
1593   {
1594   }
1595
1596   protected void showunconserved_actionPerformed(ActionEvent e)
1597   {
1598     // TODO Auto-generated method stub
1599
1600   }
1601
1602   /**
1603    * DOCUMENT ME!
1604    *
1605    * @param e
1606    *          DOCUMENT ME!
1607    */
1608   public void ok_actionPerformed(ActionEvent e)
1609   {
1610   }
1611
1612   /**
1613    * DOCUMENT ME!
1614    *
1615    * @param e
1616    *          DOCUMENT ME!
1617    */
1618   public void cancel_actionPerformed(ActionEvent e)
1619   {
1620   }
1621
1622   /**
1623    * DOCUMENT ME!
1624    *
1625    * @param e
1626    *          DOCUMENT ME!
1627    */
1628   public void annotations_actionPerformed(ActionEvent e)
1629   {
1630   }
1631
1632   /**
1633    * DOCUMENT ME!
1634    */
1635   public void startupFileTextfield_mouseClicked()
1636   {
1637   }
1638
1639   public void newLink_actionPerformed(ActionEvent e)
1640   {
1641
1642   }
1643
1644   public void editLink_actionPerformed(ActionEvent e)
1645   {
1646
1647   }
1648
1649   public void deleteLink_actionPerformed(ActionEvent e)
1650   {
1651
1652   }
1653
1654   public void defaultBrowser_mouseClicked(MouseEvent e)
1655   {
1656
1657   }
1658
1659   public void linkURLList_keyTyped(KeyEvent e)
1660   {
1661
1662   }
1663
1664   public void useProxy_actionPerformed()
1665   {
1666     boolean enabled = useProxy.isSelected();
1667     portLabel.setEnabled(enabled);
1668     serverLabel.setEnabled(enabled);
1669     proxyServerTB.setEnabled(enabled);
1670     proxyPortTB.setEnabled(enabled);
1671   }
1672
1673   /**
1674    * Customer renderer for JTable: supports column of radio buttons
1675    */
1676   public class RadioButtonRenderer extends JRadioButton implements
1677           TableCellRenderer
1678   {
1679     public RadioButtonRenderer()
1680     {
1681       setHorizontalAlignment(CENTER);
1682       setToolTipText(MessageManager.getString("label.urltooltip"));
1683     }
1684
1685     @Override
1686     public Component getTableCellRendererComponent(JTable table,
1687             Object value, boolean isSelected, boolean hasFocus, int row,
1688             int column)
1689     {
1690       setSelected((boolean) value);
1691
1692       // set colours to match rest of table
1693       if (isSelected)
1694        {
1695          setBackground(table.getSelectionBackground());
1696          setForeground(table.getSelectionForeground());
1697        }
1698        else
1699        {
1700          setBackground(table.getBackground());
1701          setForeground(table.getForeground());
1702       }
1703       return this;
1704     }
1705   }
1706
1707   /**
1708    * Customer cell editor for JTable: supports column of radio buttons in
1709    * conjunction with renderer
1710    */
1711   public class RadioButtonEditor extends AbstractCellEditor implements
1712             TableCellEditor
1713     {
1714       private JRadioButton button = new JRadioButton();
1715
1716       public RadioButtonEditor()
1717       {
1718       button.setHorizontalAlignment(SwingConstants.CENTER);
1719       this.button.addActionListener(new ActionListener()
1720         {
1721           @Override
1722           public void actionPerformed(ActionEvent e)
1723           {
1724             fireEditingStopped();
1725           }
1726         });
1727       }
1728
1729       @Override
1730       public Component getTableCellEditorComponent(JTable table,
1731               Object value, boolean isSelected, int row, int column)
1732       {
1733       button.setSelected((boolean) value);
1734         return button;
1735       }
1736
1737       @Override
1738       public Object getCellEditorValue()
1739       {
1740       return button.isSelected();
1741       }
1742
1743   }
1744 }