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.gui.JvSwingUtils;
  24 import jalview.gui.StructureViewer.ViewerType;
  25 import jalview.jbgui.PDBDocFieldPreferences.PreferenceSource;
  26 import jalview.util.MessageManager;
  27
  28 import java.awt.BorderLayout;
  29 import java.awt.Color;
  30 import java.awt.Component;
  31 import java.awt.Dimension;
  32 import java.awt.FlowLayout;
  33 import java.awt.Font;
  34 import java.awt.GridBagConstraints;
  35 import java.awt.GridBagLayout;
  36 import java.awt.GridLayout;
  37 import java.awt.Insets;
  38 import java.awt.Rectangle;
  39 import java.awt.event.ActionEvent;
  40 import java.awt.event.ActionListener;
  41 import java.awt.event.FocusEvent;
  42 import java.awt.event.KeyEvent;
  43 import java.awt.event.MouseAdapter;
  44 import java.awt.event.MouseEvent;
  45
  46 import javax.swing.BorderFactory;
  47 import javax.swing.DefaultListCellRenderer;
  48 import javax.swing.JButton;
  49 import javax.swing.JCheckBox;
  50 import javax.swing.JComboBox;
  51 import javax.swing.JFileChooser;
  52 import javax.swing.JLabel;
  53 import javax.swing.JList;
  54 import javax.swing.JPanel;
  55 import javax.swing.JScrollPane;
  56 import javax.swing.JTabbedPane;
  57 import javax.swing.JTextField;
  58 import javax.swing.ListSelectionModel;
  59 import javax.swing.SwingConstants;
  60 import javax.swing.border.Border;
  61 import javax.swing.border.EmptyBorder;
  62 import javax.swing.border.EtchedBorder;
  63 import javax.swing.border.TitledBorder;
  64 import javax.swing.event.ChangeEvent;
  65 import javax.swing.event.ChangeListener;
  66 import javax.swing.event.ListSelectionEvent;
  67 import javax.swing.event.ListSelectionListener;
  68
  69 /**
  70  * Base class for the Preferences panel.
  71  *
  72  * @author $author$
  73  * @version $Revision$
  74  */
  75 public class GPreferences extends JPanel
  76 {
  77   private static final Font LABEL_FONT = JvSwingUtils.getLabelFont();
  78
  79   private static final Font LABEL_FONT_ITALIC = JvSwingUtils.getLabelFont(
  80           false, true);
  81
  82   /*
  83    * Visual tab components
  84    */
  85   protected JCheckBox fullScreen = new JCheckBox();
  86
  87   protected JCheckBox openoverv = new JCheckBox();
  88
  89   protected JCheckBox seqLimit = new JCheckBox();
  90
  91   protected JCheckBox rightAlign = new JCheckBox();
  92
  93   protected JComboBox<String> fontSizeCB = new JComboBox<String>();
  94
  95   protected JComboBox<String> fontStyleCB = new JComboBox<String>();
  96
  97   protected JComboBox<String> fontNameCB = new JComboBox<String>();
  98
  99   protected JCheckBox showUnconserved = new JCheckBox();
 100
 101   protected JCheckBox idItalics = new JCheckBox();
 102
 103   protected JCheckBox smoothFont = new JCheckBox();
 104
 105   protected JCheckBox scaleProteinToCdna = new JCheckBox();
 106
 107   protected JComboBox<String> gapSymbolCB = new JComboBox<String>();
 108
 109   protected JCheckBox wrap = new JCheckBox();
 110
 111   protected JComboBox<String> sortby = new JComboBox<String>();
 112
 113   protected JComboBox<String> sortAnnBy = new JComboBox<String>();
 114
 115   protected JComboBox<String> sortAutocalc = new JComboBox<String>();
 116
 117   protected JCheckBox startupCheckbox = new JCheckBox();
 118
 119   protected JTextField startupFileTextfield = new JTextField();
 120
 121   // below are in the 'second column'
 122   protected JCheckBox annotations = new JCheckBox();
 123
 124   protected JCheckBox quality = new JCheckBox();
 125
 126   protected JCheckBox conservation = new JCheckBox();
 127
 128   protected JCheckBox identity = new JCheckBox();
 129
 130   protected JCheckBox showGroupConsensus = new JCheckBox();
 131
 132   protected JCheckBox showGroupConservation = new JCheckBox();
 133
 134   protected JCheckBox showConsensHistogram = new JCheckBox();
 135
 136   protected JCheckBox showConsensLogo = new JCheckBox();
 137
 138   protected JCheckBox showDbRefTooltip = new JCheckBox();
 139
 140   protected JCheckBox showNpTooltip = new JCheckBox();
 141
 142   /*
 143    * Structure tab and components
 144    */
 145   protected JPanel structureTab;
 146
 147   protected JCheckBox structFromPdb = new JCheckBox();
 148
 149   protected JCheckBox useRnaView = new JCheckBox();
 150
 151   protected JCheckBox addSecondaryStructure = new JCheckBox();
 152
 153   protected JCheckBox addTempFactor = new JCheckBox();
 154
 155   protected JComboBox<String> structViewer = new JComboBox<String>();
 156
 157   protected JTextField chimeraPath = new JTextField();
 158
 159   /*
 160    * Colours tab components
 161    */
 162   protected JPanel minColour = new JPanel();
 163
 164   protected JPanel maxColour = new JPanel();
 165
 166   protected JComboBox<String> protColour = new JComboBox<String>();
 167
 168   protected JComboBox<String> nucColour = new JComboBox<String>();
 169
 170   /*
 171    * Connections tab components
 172    */
 173   protected JList linkURLList = new JList();
 174
 175   protected JTextField proxyServerTB = new JTextField();
 176
 177   protected JTextField proxyPortTB = new JTextField();
 178
 179   protected JTextField defaultBrowser = new JTextField();
 180
 181   protected JList linkNameList = new JList();
 182
 183   protected JCheckBox useProxy = new JCheckBox();
 184
 185   protected JCheckBox usagestats = new JCheckBox();
 186
 187   protected JCheckBox questionnaire = new JCheckBox();
 188
 189   protected JCheckBox versioncheck = new JCheckBox();
 190
 191   /*
 192    * Output tab components
 193    */
 194   protected JComboBox<String> epsRendering = new JComboBox<String>();
 195
 196   protected JLabel userIdWidthlabel = new JLabel();
 197
 198   protected JCheckBox autoIdWidth = new JCheckBox();
 199
 200   protected JTextField userIdWidth = new JTextField();
 201
 202   protected JCheckBox blcjv = new JCheckBox();
 203
 204   protected JCheckBox pileupjv = new JCheckBox();
 205
 206   protected JCheckBox clustaljv = new JCheckBox();
 207
 208   protected JCheckBox msfjv = new JCheckBox();
 209
 210   protected JCheckBox fastajv = new JCheckBox();
 211
 212   protected JCheckBox pfamjv = new JCheckBox();
 213
 214   protected JCheckBox pirjv = new JCheckBox();
 215
 216   protected JCheckBox modellerOutput = new JCheckBox();
 217
 218   protected JCheckBox embbedBioJSON = new JCheckBox();
 219
 220   /*
 221    * Editing tab components
 222    */
 223   protected JCheckBox autoCalculateConsCheck = new JCheckBox();
 224
 225   protected JCheckBox padGaps = new JCheckBox();
 226
 227   protected JCheckBox sortByTree = new JCheckBox();
 228
 229   /*
 230    * DAS Settings tab
 231    */
 232   protected JPanel dasTab = new JPanel();
 233
 234   /*
 235    * Web Services tab
 236    */
 237   protected JPanel wsTab = new JPanel();
 238
 239   /**
 240    * Creates a new GPreferences object.
 241    */
 242   public GPreferences()
 243   {
 244     try
 245     {
 246       jbInit();
 247     } catch (Exception ex)
 248     {
 249       ex.printStackTrace();
 250     }
 251   }
 252
 253   /**
 254    * Construct the panel and its tabbed sub-panels.
 255    *
 256    * @throws Exception
 257    */
 258   private void jbInit() throws Exception
 259   {
 260     final JTabbedPane tabbedPane = new JTabbedPane();
 261     this.setLayout(new BorderLayout());
 262     JPanel okCancelPanel = initOkCancelPanel();
 263     this.add(tabbedPane, BorderLayout.CENTER);
 264     this.add(okCancelPanel, BorderLayout.SOUTH);
 265
 266     tabbedPane.add(initVisualTab(),
 267             MessageManager.getString("label.visual"));
 268
 269     tabbedPane.add(initColoursTab(),
 270             MessageManager.getString("label.colours"));
 271
 272     tabbedPane.add(initStructureTab(),
 273             MessageManager.getString("label.structure"));
 274
 275     tabbedPane.add(initConnectionsTab(),
 276             MessageManager.getString("label.connections"));
 277
 278     tabbedPane.add(initOutputTab(),
 279             MessageManager.getString("label.output"));
 280
 281     tabbedPane.add(initEditingTab(),
 282             MessageManager.getString("label.editing"));
 283
 284     /*
 285      * See DasSourceBrowser for the real work of configuring this tab.
 286      */
 287     dasTab.setLayout(new BorderLayout());
 288     tabbedPane.add(dasTab, MessageManager.getString("label.das_settings"));
 289
 290     /*
 291      * See WsPreferences for the real work of configuring this tab.
 292      */
 293     wsTab.setLayout(new BorderLayout());
 294     tabbedPane.add(wsTab, MessageManager.getString("label.web_services"));
 295
 296     /*
 297      * Handler to validate a tab before leaving it - currently only for
 298      * Structure.
 299      */
 300     tabbedPane.addChangeListener(new ChangeListener()
 301     {
 302       private Component lastTab;
 303
 304       @Override
 305       public void stateChanged(ChangeEvent e)
 306       {
 307         if (lastTab == structureTab
 308                 && tabbedPane.getSelectedComponent() != structureTab)
 309         {
 310           if (!validateStructure())
 311           {
 312             tabbedPane.setSelectedComponent(structureTab);
 313             return;
 314           }
 315         }
 316         lastTab = tabbedPane.getSelectedComponent();
 317       }
 318
 319     });
 320   }
 321
 322   /**
 323    * Initialises the Editing tabbed panel.
 324    *
 325    * @return
 326    */
 327   private JPanel initEditingTab()
 328   {
 329     JPanel editingTab = new JPanel();
 330     editingTab.setLayout(null);
 331     autoCalculateConsCheck.setFont(LABEL_FONT);
 332     autoCalculateConsCheck.setText(MessageManager
 333             .getString("label.autocalculate_consensus"));
 334     autoCalculateConsCheck.setBounds(new Rectangle(21, 52, 209, 23));
 335     padGaps.setFont(LABEL_FONT);
 336     padGaps.setText(MessageManager.getString("label.pad_gaps_when_editing"));
 337     padGaps.setBounds(new Rectangle(22, 94, 168, 23));
 338     sortByTree.setFont(LABEL_FONT);
 339     sortByTree
 340             .setText(MessageManager.getString("label.sort_with_new_tree"));
 341     sortByTree
 342             .setToolTipText(MessageManager
 343                     .getString("label.any_trees_calculated_or_loaded_alignment_automatically_sort"));
 344     sortByTree.setBounds(new Rectangle(22, 136, 168, 23));
 345     editingTab.add(autoCalculateConsCheck);
 346     editingTab.add(padGaps);
 347     editingTab.add(sortByTree);
 348     return editingTab;
 349   }
 350
 351   /**
 352    * Initialises the Output tabbed panel.
 353    *
 354    * @return
 355    */
 356   private JPanel initOutputTab()
 357   {
 358     JPanel outputTab = new JPanel();
 359     outputTab.setLayout(null);
 360     JLabel epsLabel = new JLabel();
 361     epsLabel.setFont(LABEL_FONT);
 362     epsLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 363     epsLabel.setText(MessageManager.getString("label.eps_rendering_style"));
 364     epsLabel.setBounds(new Rectangle(9, 31, 140, 24));
 365     epsRendering.setFont(LABEL_FONT);
 366     epsRendering.setBounds(new Rectangle(154, 34, 187, 21));
 367     JLabel jLabel1 = new JLabel();
 368     jLabel1.setFont(LABEL_FONT);
 369     jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
 370     jLabel1.setText(MessageManager.getString("label.append_start_end"));
 371     jLabel1.setFont(LABEL_FONT);
 372     fastajv.setFont(LABEL_FONT);
 373     fastajv.setHorizontalAlignment(SwingConstants.LEFT);
 374     clustaljv.setText(MessageManager.getString("label.clustal") + "     ");
 375     blcjv.setText(MessageManager.getString("label.blc") + "     ");
 376     fastajv.setText(MessageManager.getString("label.fasta") + "     ");
 377     msfjv.setText(MessageManager.getString("label.msf") + "     ");
 378     pfamjv.setText(MessageManager.getString("label.pfam") + "     ");
 379     pileupjv.setText(MessageManager.getString("label.pileup") + "     ");
 380     msfjv.setFont(LABEL_FONT);
 381     msfjv.setHorizontalAlignment(SwingConstants.LEFT);
 382     pirjv.setText(MessageManager.getString("label.pir") + "     ");
 383     JPanel jPanel11 = new JPanel();
 384     jPanel11.setFont(LABEL_FONT);
 385     TitledBorder titledBorder2 = new TitledBorder(
 386             MessageManager.getString("label.file_output"));
 387     jPanel11.setBorder(titledBorder2);
 388     jPanel11.setBounds(new Rectangle(30, 72, 196, 182));
 389     GridLayout gridLayout3 = new GridLayout();
 390     jPanel11.setLayout(gridLayout3);
 391     gridLayout3.setRows(8);
 392     blcjv.setFont(LABEL_FONT);
 393     blcjv.setHorizontalAlignment(SwingConstants.LEFT);
 394     clustaljv.setFont(LABEL_FONT);
 395     clustaljv.setHorizontalAlignment(SwingConstants.LEFT);
 396     pfamjv.setFont(LABEL_FONT);
 397     pfamjv.setHorizontalAlignment(SwingConstants.LEFT);
 398     pileupjv.setFont(LABEL_FONT);
 399     pileupjv.setHorizontalAlignment(SwingConstants.LEFT);
 400     pirjv.setFont(LABEL_FONT);
 401     pirjv.setHorizontalAlignment(SwingConstants.LEFT);
 402     autoIdWidth.setFont(LABEL_FONT);
 403     autoIdWidth.setText(MessageManager
 404             .getString("label.automatically_set_id_width"));
 405     autoIdWidth.setToolTipText(JvSwingUtils.wrapTooltip(true,
 406             MessageManager
 407                     .getString("label.adjusts_width_generated_eps_png")));
 408     autoIdWidth.setBounds(new Rectangle(228, 96, 188, 23));
 409     autoIdWidth.addActionListener(new ActionListener()
 410     {
 411
 412       @Override
 413       public void actionPerformed(ActionEvent e)
 414       {
 415         autoIdWidth_actionPerformed();
 416       }
 417     });
 418     userIdWidthlabel.setFont(LABEL_FONT);
 419     userIdWidthlabel.setText(MessageManager
 420             .getString("label.figure_id_column_width"));
 421     userIdWidth
 422             .setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager
 423                     .getString("label.manually_specify_width_left_column")));
 424     userIdWidthlabel
 425             .setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager
 426                     .getString("label.manually_specify_width_left_column")));
 427     userIdWidthlabel.setBounds(new Rectangle(236, 120, 168, 23));
 428     userIdWidth.setFont(JvSwingUtils.getTextAreaFont());
 429     userIdWidth.setText("");
 430     userIdWidth.setBounds(new Rectangle(232, 144, 84, 23));
 431     userIdWidth.addActionListener(new ActionListener()
 432     {
 433
 434       @Override
 435       public void actionPerformed(ActionEvent e)
 436       {
 437         userIdWidth_actionPerformed();
 438       }
 439     });
 440     modellerOutput.setFont(LABEL_FONT);
 441     modellerOutput.setText(MessageManager
 442             .getString("label.use_modeller_output"));
 443     modellerOutput.setBounds(new Rectangle(228, 226, 168, 23));
 444     embbedBioJSON.setFont(LABEL_FONT);
 445     embbedBioJSON.setText(MessageManager.getString("label.embbed_biojson"));
 446     embbedBioJSON.setBounds(new Rectangle(228, 200, 250, 23));
 447
 448     jPanel11.add(jLabel1);
 449     jPanel11.add(blcjv);
 450     jPanel11.add(clustaljv);
 451     jPanel11.add(fastajv);
 452     jPanel11.add(msfjv);
 453     jPanel11.add(pfamjv);
 454     jPanel11.add(pileupjv);
 455     jPanel11.add(pirjv);
 456     outputTab.add(autoIdWidth);
 457     outputTab.add(userIdWidth);
 458     outputTab.add(userIdWidthlabel);
 459     outputTab.add(modellerOutput);
 460     outputTab.add(embbedBioJSON);
 461     outputTab.add(epsLabel);
 462     outputTab.add(epsRendering);
 463     outputTab.add(jPanel11);
 464     return outputTab;
 465   }
 466
 467   /**
 468    * Initialises the Connections tabbed panel.
 469    *
 470    * @return
 471    */
 472   private JPanel initConnectionsTab()
 473   {
 474     JPanel connectTab = new JPanel();
 475     connectTab.setLayout(new GridBagLayout());
 476     JLabel serverLabel = new JLabel();
 477     serverLabel.setText(MessageManager.getString("label.address"));
 478     serverLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 479     serverLabel.setFont(LABEL_FONT);
 480     proxyServerTB.setFont(LABEL_FONT);
 481     proxyPortTB.setFont(LABEL_FONT);
 482     JLabel portLabel = new JLabel();
 483     portLabel.setFont(LABEL_FONT);
 484     portLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 485     portLabel.setText(MessageManager.getString("label.port"));
 486     JLabel browserLabel = new JLabel();
 487     browserLabel.setFont(new java.awt.Font("SansSerif", 0, 11));
 488     browserLabel.setHorizontalAlignment(SwingConstants.TRAILING);
 489     browserLabel.setText(MessageManager
 490             .getString("label.default_browser_unix"));
 491     defaultBrowser.setFont(LABEL_FONT);
 492     defaultBrowser.setText("");
 493     usagestats.setText(MessageManager
 494             .getString("label.send_usage_statistics"));
 495     usagestats.setFont(LABEL_FONT);
 496     usagestats.setHorizontalAlignment(SwingConstants.RIGHT);
 497     usagestats.setHorizontalTextPosition(SwingConstants.LEADING);
 498     questionnaire.setText(MessageManager
 499             .getString("label.check_for_questionnaires"));
 500     questionnaire.setFont(LABEL_FONT);
 501     questionnaire.setHorizontalAlignment(SwingConstants.RIGHT);
 502     questionnaire.setHorizontalTextPosition(SwingConstants.LEADING);
 503     versioncheck.setText(MessageManager
 504             .getString("label.check_for_latest_version"));
 505     versioncheck.setFont(LABEL_FONT);
 506     versioncheck.setHorizontalAlignment(SwingConstants.RIGHT);
 507     versioncheck.setHorizontalTextPosition(SwingConstants.LEADING);
 508     JButton newLink = new JButton();
 509     newLink.setText(MessageManager.getString("action.new"));
 510     newLink.addActionListener(new java.awt.event.ActionListener()
 511     {
 512       public void actionPerformed(ActionEvent e)
 513       {
 514         newLink_actionPerformed(e);
 515       }
 516     });
 517     JButton editLink = new JButton();
 518     editLink.setText(MessageManager.getString("action.edit"));
 519     editLink.addActionListener(new java.awt.event.ActionListener()
 520     {
 521       public void actionPerformed(ActionEvent e)
 522       {
 523         editLink_actionPerformed(e);
 524       }
 525     });
 526     JButton deleteLink = new JButton();
 527     deleteLink.setText(MessageManager.getString("action.delete"));
 528     deleteLink.addActionListener(new java.awt.event.ActionListener()
 529     {
 530       public void actionPerformed(ActionEvent e)
 531       {
 532         deleteLink_actionPerformed(e);
 533       }
 534     });
 535
 536     linkURLList.addListSelectionListener(new ListSelectionListener()
 537     {
 538       public void valueChanged(ListSelectionEvent e)
 539       {
 540         int index = linkURLList.getSelectedIndex();
 541         linkNameList.setSelectedIndex(index);
 542       }
 543     });
 544
 545     linkNameList.addListSelectionListener(new ListSelectionListener()
 546     {
 547       public void valueChanged(ListSelectionEvent e)
 548       {
 549         int index = linkNameList.getSelectedIndex();
 550         linkURLList.setSelectedIndex(index);
 551       }
 552     });
 553
 554     JScrollPane linkScrollPane = new JScrollPane();
 555     linkScrollPane.setBorder(null);
 556     JPanel linkPanel = new JPanel();
 557     linkPanel.setBorder(new TitledBorder(MessageManager
 558             .getString("label.url_linkfrom_sequence_id")));
 559     linkPanel.setLayout(new BorderLayout());
 560     GridLayout gridLayout1 = new GridLayout();
 561     JPanel editLinkButtons = new JPanel();
 562     editLinkButtons.setLayout(gridLayout1);
 563     gridLayout1.setRows(3);
 564     linkNameList.setFont(LABEL_FONT);
 565     linkNameList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
 566     BorderLayout borderLayout3 = new BorderLayout();
 567     JPanel linkPanel2 = new JPanel();
 568     linkPanel2.setLayout(borderLayout3);
 569     linkURLList.setFont(LABEL_FONT);
 570     linkURLList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
 571
 572     defaultBrowser.addMouseListener(new MouseAdapter()
 573     {
 574       public void mouseClicked(MouseEvent e)
 575       {
 576         if (e.getClickCount() > 1)
 577         {
 578           defaultBrowser_mouseClicked(e);
 579         }
 580       }
 581     });
 582     useProxy.setFont(LABEL_FONT);
 583     useProxy.setHorizontalAlignment(SwingConstants.RIGHT);
 584     useProxy.setHorizontalTextPosition(SwingConstants.LEADING);
 585     useProxy.setText(MessageManager.getString("label.use_proxy_server"));
 586     useProxy.addActionListener(new ActionListener()
 587     {
 588       public void actionPerformed(ActionEvent e)
 589       {
 590         useProxy_actionPerformed();
 591       }
 592     });
 593     linkPanel.add(editLinkButtons, BorderLayout.EAST);
 594     editLinkButtons.add(newLink, null);
 595     editLinkButtons.add(editLink, null);
 596     editLinkButtons.add(deleteLink, null);
 597     linkPanel.add(linkScrollPane, BorderLayout.CENTER);
 598     linkScrollPane.getViewport().add(linkPanel2, null);
 599     linkPanel2.add(linkURLList, BorderLayout.CENTER);
 600     linkPanel2.add(linkNameList, BorderLayout.WEST);
 601     JPanel jPanel1 = new JPanel();
 602     TitledBorder titledBorder1 = new TitledBorder(
 603             MessageManager.getString("label.proxy_server"));
 604     jPanel1.setBorder(titledBorder1);
 605     jPanel1.setLayout(new GridBagLayout());
 606     jPanel1.add(serverLabel, new GridBagConstraints(0, 1, 1, 1, 0.0, 0.0,
 607             GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
 608                     2, 4, 0), 5, 0));
 609     jPanel1.add(portLabel, new GridBagConstraints(2, 1, 1, 1, 0.0, 0.0,
 610             GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
 611                     0, 4, 0), 11, 6));
 612     connectTab.add(linkPanel, new GridBagConstraints(0, 0, 2, 1, 1.0, 1.0,
 613             GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(
 614                     16, 0, 0, 12), 359, -17));
 615     connectTab.add(jPanel1, new GridBagConstraints(0, 2, 2, 1, 1.0, 1.0,
 616             GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(
 617                     21, 0, 35, 12), 4, 6));
 618     connectTab.add(browserLabel, new GridBagConstraints(0, 1, 1, 1, 0.0,
 619             0.0, GridBagConstraints.WEST, GridBagConstraints.NONE,
 620             new Insets(16, 0, 0, 0), 5, 1));
 621     jPanel1.add(useProxy, new GridBagConstraints(0, 0, 2, 1, 0.0, 0.0,
 622             GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
 623                     2, 5, 185), 2, -4));
 624     jPanel1.add(proxyPortTB, new GridBagConstraints(3, 1, 1, 1, 1.0, 0.0,
 625             GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 626             new Insets(0, 2, 4, 2), 54, 1));
 627     jPanel1.add(proxyServerTB, new GridBagConstraints(1, 1, 1, 1, 1.0, 0.0,
 628             GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 629             new Insets(0, 2, 4, 0), 263, 1));
 630     connectTab.add(defaultBrowser, new GridBagConstraints(1, 1, 1, 1, 1.0,
 631             0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 632             new Insets(15, 0, 0, 15), 307, 1));
 633     connectTab.add(usagestats, new GridBagConstraints(0, 4, 1, 1, 1.0, 0.0,
 634             GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 635             new Insets(0, 2, 4, 2), 70, 1));
 636     connectTab.add(questionnaire, new GridBagConstraints(1, 4, 1, 1, 1.0,
 637             0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 638             new Insets(0, 2, 4, 2), 70, 1));
 639     connectTab.add(versioncheck, new GridBagConstraints(0, 5, 1, 1, 1.0,
 640             0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 641             new Insets(0, 2, 4, 2), 70, 1));
 642     return connectTab;
 643   }
 644
 645   /**
 646    * Initialises the parent panel which contains the tabbed sections.
 647    *
 648    * @return
 649    */
 650   private JPanel initOkCancelPanel()
 651   {
 652     JButton ok = new JButton();
 653     ok.setText(MessageManager.getString("action.ok"));
 654     ok.addActionListener(new ActionListener()
 655     {
 656       public void actionPerformed(ActionEvent e)
 657       {
 658         ok_actionPerformed(e);
 659       }
 660     });
 661     JButton cancel = new JButton();
 662     cancel.setText(MessageManager.getString("action.cancel"));
 663     cancel.addActionListener(new ActionListener()
 664     {
 665       public void actionPerformed(ActionEvent e)
 666       {
 667         cancel_actionPerformed(e);
 668       }
 669     });
 670     JPanel okCancelPanel = new JPanel();
 671     okCancelPanel.add(ok);
 672     okCancelPanel.add(cancel);
 673     return okCancelPanel;
 674   }
 675
 676   /**
 677    * Initialises the Colours tabbed panel.
 678    *
 679    * @return
 680    */
 681   private JPanel initColoursTab()
 682   {
 683     JPanel coloursTab = new JPanel();
 684     coloursTab.setBorder(new TitledBorder(MessageManager
 685             .getString("action.open_new_alignment")));
 686     coloursTab.setLayout(new FlowLayout());
 687     JLabel mincolourLabel = new JLabel();
 688     mincolourLabel.setFont(LABEL_FONT);
 689     mincolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 690     mincolourLabel.setText(MessageManager.getString("label.min_colour"));
 691     minColour.setFont(LABEL_FONT);
 692     minColour.setBorder(BorderFactory.createEtchedBorder());
 693     minColour.setPreferredSize(new Dimension(40, 20));
 694     minColour.addMouseListener(new MouseAdapter()
 695     {
 696       public void mousePressed(MouseEvent e)
 697       {
 698         minColour_actionPerformed(minColour);
 699       }
 700     });
 701     JLabel maxcolourLabel = new JLabel();
 702     maxcolourLabel.setFont(LABEL_FONT);
 703     maxcolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 704     maxcolourLabel.setText(MessageManager.getString("label.max_colour"));
 705     maxColour.setFont(LABEL_FONT);
 706     maxColour.setBorder(BorderFactory.createEtchedBorder());
 707     maxColour.setPreferredSize(new Dimension(40, 20));
 708     maxColour.addMouseListener(new MouseAdapter()
 709     {
 710       public void mousePressed(MouseEvent e)
 711       {
 712         maxColour_actionPerformed(maxColour);
 713       }
 714     });
 715
 716     protColour.setFont(LABEL_FONT);
 717     protColour.setBounds(new Rectangle(172, 225, 155, 21));
 718     JLabel protColourLabel = new JLabel();
 719     protColourLabel.setFont(LABEL_FONT);
 720     protColourLabel.setHorizontalAlignment(SwingConstants.LEFT);
 721     protColourLabel.setText(MessageManager
 722             .getString("label.prot_alignment_colour") + " ");
 723     JvSwingUtils.addtoLayout(coloursTab, MessageManager
 724             .getString("label.default_colour_scheme_for_alignment"),
 725             protColourLabel, protColour);
 726
 727     nucColour.setFont(LABEL_FONT);
 728     nucColour.setBounds(new Rectangle(172, 240, 155, 21));
 729     JLabel nucColourLabel = new JLabel();
 730     nucColourLabel.setFont(LABEL_FONT);
 731     nucColourLabel.setHorizontalAlignment(SwingConstants.LEFT);
 732     nucColourLabel.setText(MessageManager
 733             .getString("label.nuc_alignment_colour") + " ");
 734     JvSwingUtils.addtoLayout(coloursTab, MessageManager
 735             .getString("label.default_colour_scheme_for_alignment"),
 736             nucColourLabel, nucColour);
 737
 738     JPanel annotationShding = new JPanel();
 739     annotationShding.setBorder(new TitledBorder(MessageManager
 740             .getString("label.annotation_shading_default")));
 741     annotationShding.setLayout(new GridLayout(1, 2));
 742     JvSwingUtils.addtoLayout(annotationShding, MessageManager
 743             .getString("label.default_minimum_colour_annotation_shading"),
 744             mincolourLabel, minColour);
 745     JvSwingUtils.addtoLayout(annotationShding, MessageManager
 746             .getString("label.default_maximum_colour_annotation_shading"),
 747             maxcolourLabel, maxColour);
 748     coloursTab.add(annotationShding); // , FlowLayout.LEFT);
 749     return coloursTab;
 750   }
 751
 752   /**
 753    * Initialises the Structure tabbed panel.
 754    *
 755    * @return
 756    */
 757   private JPanel initStructureTab()
 758   {
 759     structureTab = new JPanel();
 760
 761     structureTab.setBorder(new TitledBorder(MessageManager
 762             .getString("label.structure_options")));
 763     structureTab.setLayout(null);
 764     final int width = 400;
 765     final int height = 22;
 766     final int lineSpacing = 25;
 767     int ypos = 30;
 768
 769     structFromPdb.setFont(LABEL_FONT);
 770     structFromPdb
 771             .setText(MessageManager.getString("label.struct_from_pdb"));
 772     structFromPdb.setBounds(new Rectangle(5, ypos, width, height));
 773     structFromPdb.addActionListener(new ActionListener()
 774     {
 775       @Override
 776       public void actionPerformed(ActionEvent e)
 777       {
 778         boolean selected = structFromPdb.isSelected();
 779         // enable other options only when the first is checked
 780         useRnaView.setEnabled(selected);
 781         addSecondaryStructure.setEnabled(selected);
 782         addTempFactor.setEnabled(selected);
 783       }
 784     });
 785     structureTab.add(structFromPdb);
 786
 787     // indent checkboxes that are conditional on the first one
 788     ypos += lineSpacing;
 789     useRnaView.setFont(LABEL_FONT);
 790     useRnaView.setText(MessageManager.getString("label.use_rnaview"));
 791     useRnaView.setBounds(new Rectangle(25, ypos, width, height));
 792     structureTab.add(useRnaView);
 793
 794     ypos += lineSpacing;
 795     addSecondaryStructure.setFont(LABEL_FONT);
 796     addSecondaryStructure.setText(MessageManager
 797             .getString("label.autoadd_secstr"));
 798     addSecondaryStructure.setBounds(new Rectangle(25, ypos, width, height));
 799     structureTab.add(addSecondaryStructure);
 800
 801     ypos += lineSpacing;
 802     addTempFactor.setFont(LABEL_FONT);
 803     addTempFactor.setText(MessageManager.getString("label.autoadd_temp"));
 804     addTempFactor.setBounds(new Rectangle(25, ypos, width, height));
 805     structureTab.add(addTempFactor);
 806
 807     ypos += lineSpacing;
 808     JLabel viewerLabel = new JLabel();
 809     viewerLabel.setFont(LABEL_FONT);
 810     viewerLabel.setHorizontalAlignment(SwingConstants.LEFT);
 811     viewerLabel.setText(MessageManager.getString("label.structure_viewer"));
 812     viewerLabel.setBounds(new Rectangle(10, ypos, 200, height));
 813     structureTab.add(viewerLabel);
 814
 815     structViewer.setFont(LABEL_FONT);
 816     structViewer.setBounds(new Rectangle(160, ypos, 120, height));
 817     structViewer.addItem(ViewerType.JMOL.name());
 818     structViewer.addItem(ViewerType.CHIMERA.name());
 819     structViewer.addActionListener(new ActionListener()
 820     {
 821       @Override
 822       public void actionPerformed(ActionEvent e)
 823       {
 824         structureViewer_actionPerformed((String) structViewer
 825                 .getSelectedItem());
 826       }
 827     });
 828     structureTab.add(structViewer);
 829
 830     ypos += lineSpacing;
 831     JLabel pathLabel = new JLabel();
 832     pathLabel.setFont(new java.awt.Font("SansSerif", 0, 11));
 833     pathLabel.setHorizontalAlignment(SwingConstants.LEFT);
 834     pathLabel.setText(MessageManager.getString("label.chimera_path"));
 835     final String tooltip = JvSwingUtils.wrapTooltip(true,
 836             MessageManager.getString("label.chimera_path_tip"));
 837     pathLabel.setToolTipText(tooltip);
 838     pathLabel.setBounds(new Rectangle(10, ypos, 140, height));
 839     structureTab.add(pathLabel);
 840
 841     chimeraPath.setFont(LABEL_FONT);
 842     chimeraPath.setText("");
 843     chimeraPath.setBounds(new Rectangle(160, ypos, 300, height));
 844     chimeraPath.addMouseListener(new MouseAdapter()
 845     {
 846       @Override
 847       public void mouseClicked(MouseEvent e)
 848       {
 849         if (e.getClickCount() == 2)
 850         {
 851           String chosen = openFileChooser();
 852           if (chosen != null)
 853           {
 854             chimeraPath.setText(chosen);
 855           }
 856         }
 857       }
 858     });
 859     structureTab.add(chimeraPath);
 860
 861     ypos += lineSpacing;
 862     // scrl_pdbDocFieldConfig.setPreferredSize(new Dimension(450, 100));
 863     // scrl_pdbDocFieldConfig
 864     // .setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_NEVER);
 865     // scrl_pdbDocFieldConfig.setBounds();
 866     PDBDocFieldPreferences docFieldPref = new PDBDocFieldPreferences(
 867             PreferenceSource.PREFERENCES);
 868     docFieldPref.setBounds(new Rectangle(10, ypos + 5, 450, 120));
 869     structureTab.add(docFieldPref);
 870
 871     return structureTab;
 872   }
 873
 874   /**
 875    * Action on choosing a structure viewer from combobox options.
 876    *
 877    * @param selectedItem
 878    */
 879   protected void structureViewer_actionPerformed(String selectedItem)
 880   {
 881   }
 882
 883   /**
 884    * Show a dialog for the user to choose a file. Returns the chosen path, or
 885    * null on Cancel.
 886    *
 887    * @return
 888    */
 889   protected String openFileChooser()
 890   {
 891     String choice = null;
 892     JFileChooser chooser = new JFileChooser();
 893
 894     // chooser.setFileView(new JalviewFileView());
 895     chooser.setDialogTitle(MessageManager
 896             .getString("label.open_local_file"));
 897     chooser.setToolTipText(MessageManager.getString("action.open"));
 898
 899     int value = chooser.showOpenDialog(this);
 900
 901     if (value == JFileChooser.APPROVE_OPTION)
 902     {
 903       choice = chooser.getSelectedFile().getPath();
 904     }
 905     return choice;
 906   }
 907
 908   /**
 909    * Validate the structure tab preferences; if invalid, set focus on this tab.
 910    *
 911    * @param e
 912    */
 913   protected boolean validateStructure(FocusEvent e)
 914   {
 915     if (!validateStructure())
 916     {
 917       e.getComponent().requestFocusInWindow();
 918       return false;
 919     }
 920     return true;
 921   }
 922
 923   protected boolean validateStructure()
 924   {
 925     return false;
 926   }
 927
 928   /**
 929    * Initialises the Visual tabbed panel.
 930    *
 931    * @return
 932    */
 933   private JPanel initVisualTab()
 934   {
 935     JPanel visualTab = new JPanel();
 936     visualTab.setBorder(new TitledBorder(MessageManager
 937             .getString("action.open_new_alignment")));
 938     visualTab.setLayout(null);
 939     fullScreen.setFont(LABEL_FONT);
 940     fullScreen.setHorizontalAlignment(SwingConstants.RIGHT);
 941     fullScreen.setHorizontalTextPosition(SwingConstants.LEFT);
 942     fullScreen.setText(MessageManager.getString("label.maximize_window"));
 943     quality.setEnabled(false);
 944     quality.setFont(LABEL_FONT);
 945     quality.setHorizontalAlignment(SwingConstants.RIGHT);
 946     quality.setHorizontalTextPosition(SwingConstants.LEFT);
 947     quality.setSelected(true);
 948     quality.setText(MessageManager.getString("label.quality"));
 949     conservation.setEnabled(false);
 950     conservation.setFont(LABEL_FONT);
 951     conservation.setHorizontalAlignment(SwingConstants.RIGHT);
 952     conservation.setHorizontalTextPosition(SwingConstants.LEFT);
 953     conservation.setSelected(true);
 954     conservation.setText(MessageManager.getString("label.conservation"));
 955     identity.setEnabled(false);
 956     identity.setFont(LABEL_FONT);
 957     identity.setHorizontalAlignment(SwingConstants.RIGHT);
 958     identity.setHorizontalTextPosition(SwingConstants.LEFT);
 959     identity.setSelected(true);
 960     identity.setText(MessageManager.getString("label.consensus"));
 961     JLabel showGroupbits = new JLabel();
 962     showGroupbits.setFont(LABEL_FONT);
 963     showGroupbits.setHorizontalAlignment(SwingConstants.RIGHT);
 964     showGroupbits.setHorizontalTextPosition(SwingConstants.LEFT);
 965     showGroupbits.setText(MessageManager.getString("action.show_group")
 966             + ":");
 967     JLabel showConsensbits = new JLabel();
 968     showConsensbits.setFont(LABEL_FONT);
 969     showConsensbits.setHorizontalAlignment(SwingConstants.RIGHT);
 970     showConsensbits.setHorizontalTextPosition(SwingConstants.LEFT);
 971     showConsensbits.setText(MessageManager.getString("label.consensus")
 972             + ":");
 973     showConsensHistogram.setEnabled(false);
 974     showConsensHistogram.setFont(LABEL_FONT);
 975     showConsensHistogram.setHorizontalAlignment(SwingConstants.RIGHT);
 976     showConsensHistogram.setHorizontalTextPosition(SwingConstants.LEFT);
 977     showConsensHistogram.setSelected(true);
 978     showConsensHistogram.setText(MessageManager
 979             .getString("label.histogram"));
 980     showConsensLogo.setEnabled(false);
 981     showConsensLogo.setFont(LABEL_FONT);
 982     showConsensLogo.setHorizontalAlignment(SwingConstants.RIGHT);
 983     showConsensLogo.setHorizontalTextPosition(SwingConstants.LEFT);
 984     showConsensLogo.setSelected(true);
 985     showConsensLogo.setText(MessageManager.getString("label.logo"));
 986     showGroupConsensus.setEnabled(false);
 987     showGroupConsensus.setFont(LABEL_FONT);
 988     showGroupConsensus.setHorizontalAlignment(SwingConstants.RIGHT);
 989     showGroupConsensus.setHorizontalTextPosition(SwingConstants.LEFT);
 990     showGroupConsensus.setSelected(true);
 991     showGroupConsensus.setText(MessageManager.getString("label.consensus"));
 992     showGroupConservation.setEnabled(false);
 993     showGroupConservation.setFont(LABEL_FONT);
 994     showGroupConservation.setHorizontalAlignment(SwingConstants.RIGHT);
 995     showGroupConservation.setHorizontalTextPosition(SwingConstants.LEFT);
 996     showGroupConservation.setSelected(true);
 997     showGroupConservation.setText(MessageManager
 998             .getString("label.conservation"));
 999     showNpTooltip.setEnabled(true);
1000     showNpTooltip.setFont(LABEL_FONT);
1001     showNpTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
1002     showNpTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
1003     showNpTooltip.setSelected(true);
1004     showNpTooltip.setText(MessageManager
1005             .getString("label.non_positional_features"));
1006     showDbRefTooltip.setEnabled(true);
1007     showDbRefTooltip.setFont(LABEL_FONT);
1008     showDbRefTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
1009     showDbRefTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
1010     showDbRefTooltip.setSelected(true);
1011     showDbRefTooltip.setText(MessageManager
1012             .getString("label.database_references"));
1013     annotations.setFont(LABEL_FONT);
1014     annotations.setHorizontalAlignment(SwingConstants.RIGHT);
1015     annotations.setHorizontalTextPosition(SwingConstants.LEADING);
1016     annotations.setSelected(true);
1017     annotations.setText(MessageManager.getString("label.show_annotations"));
1018     annotations.setBounds(new Rectangle(169, 12, 200, 23));
1019     annotations.addActionListener(new ActionListener()
1020     {
1021       public void actionPerformed(ActionEvent e)
1022       {
1023         annotations_actionPerformed(e);
1024       }
1025     });
1026     identity.addActionListener(new ActionListener()
1027     {
1028       public void actionPerformed(ActionEvent e)
1029       {
1030         annotations_actionPerformed(e);
1031       }
1032     });
1033     showGroupConsensus.addActionListener(new ActionListener()
1034     {
1035       public void actionPerformed(ActionEvent e)
1036       {
1037         annotations_actionPerformed(e);
1038       }
1039     });
1040     showUnconserved.setFont(LABEL_FONT);
1041     showUnconserved.setHorizontalAlignment(SwingConstants.RIGHT);
1042     showUnconserved.setHorizontalTextPosition(SwingConstants.LEFT);
1043     showUnconserved.setSelected(true);
1044     showUnconserved.setText(MessageManager
1045             .getString("action.show_unconserved"));
1046     showUnconserved.addActionListener(new ActionListener()
1047     {
1048       public void actionPerformed(ActionEvent e)
1049       {
1050         showunconserved_actionPerformed(e);
1051       }
1052     });
1053
1054     // TODO these are not yet added to / action from Preferences
1055     // JCheckBox shareSelections = new JCheckBox();
1056     // shareSelections.setFont(verdana11);
1057     // shareSelections.setHorizontalAlignment(SwingConstants.RIGHT);
1058     // shareSelections.setHorizontalTextPosition(SwingConstants.LEFT);
1059     // shareSelections.setSelected(true);
1060     // shareSelections.setText(MessageManager
1061     // .getString("label.share_selection_across_views"));
1062     // JCheckBox followHighlight = new JCheckBox();
1063     // followHighlight.setFont(verdana11);
1064     // followHighlight.setHorizontalAlignment(SwingConstants.RIGHT);
1065     // followHighlight.setHorizontalTextPosition(SwingConstants.LEFT);
1066     // // showUnconserved.setBounds(new Rectangle(169, 40, 200, 23));
1067     // followHighlight.setSelected(true);
1068     // followHighlight.setText(MessageManager
1069     // .getString("label.scroll_highlighted_regions"));
1070
1071     seqLimit.setFont(LABEL_FONT);
1072     seqLimit.setHorizontalAlignment(SwingConstants.RIGHT);
1073     seqLimit.setHorizontalTextPosition(SwingConstants.LEFT);
1074     seqLimit.setText(MessageManager.getString("label.full_sequence_id"));
1075     smoothFont.setFont(LABEL_FONT);
1076     smoothFont.setHorizontalAlignment(SwingConstants.RIGHT);
1077     smoothFont.setHorizontalTextPosition(SwingConstants.LEADING);
1078     smoothFont.setText(MessageManager.getString("label.smooth_font"));
1079     scaleProteinToCdna.setFont(LABEL_FONT);
1080     scaleProteinToCdna.setHorizontalAlignment(SwingConstants.RIGHT);
1081     scaleProteinToCdna.setHorizontalTextPosition(SwingConstants.LEADING);
1082     scaleProteinToCdna.setText(MessageManager
1083             .getString("label.scale_protein_to_cdna"));
1084     scaleProteinToCdna.setToolTipText(MessageManager
1085             .getString("label.scale_protein_to_cdna_tip"));
1086     JLabel gapLabel = new JLabel();
1087     gapLabel.setFont(LABEL_FONT);
1088     gapLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1089     gapLabel.setText(MessageManager.getString("label.gap_symbol") + " ");
1090     JLabel fontLabel = new JLabel();
1091     fontLabel.setFont(LABEL_FONT);
1092     fontLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1093     fontLabel.setText(MessageManager.getString("label.font"));
1094     fontSizeCB.setFont(LABEL_FONT);
1095     fontSizeCB.setBounds(new Rectangle(320, 112, 65, 23));
1096     fontStyleCB.setFont(LABEL_FONT);
1097     fontStyleCB.setBounds(new Rectangle(382, 112, 80, 23));
1098     fontNameCB.setFont(LABEL_FONT);
1099     fontNameCB.setBounds(new Rectangle(172, 112, 147, 23));
1100     gapSymbolCB.setFont(LABEL_FONT);
1101     gapSymbolCB.setBounds(new Rectangle(172, 215, 69, 23));
1102     DefaultListCellRenderer dlcr = new DefaultListCellRenderer();
1103     dlcr.setHorizontalAlignment(DefaultListCellRenderer.CENTER);
1104     gapSymbolCB.setRenderer(dlcr);
1105
1106     startupCheckbox.setText(MessageManager.getString("action.open_file"));
1107     startupCheckbox.setFont(LABEL_FONT);
1108     startupCheckbox.setHorizontalAlignment(SwingConstants.RIGHT);
1109     startupCheckbox.setHorizontalTextPosition(SwingConstants.LEFT);
1110     startupCheckbox.setSelected(true);
1111     startupFileTextfield.setFont(LABEL_FONT);
1112     startupFileTextfield.setBounds(new Rectangle(172, 310, 330, 20));
1113     startupFileTextfield.addMouseListener(new MouseAdapter()
1114     {
1115       public void mouseClicked(MouseEvent e)
1116       {
1117         if (e.getClickCount() > 1)
1118         {
1119           startupFileTextfield_mouseClicked();
1120         }
1121       }
1122     });
1123
1124     sortby.setFont(LABEL_FONT);
1125     sortby.setBounds(new Rectangle(172, 260, 155, 21));
1126     JLabel sortLabel = new JLabel();
1127     sortLabel.setFont(LABEL_FONT);
1128     sortLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1129     sortLabel.setText(MessageManager.getString("label.sort_by"));
1130     sortAnnBy.setFont(LABEL_FONT);
1131     sortAnnBy.setBounds(new Rectangle(172, 285, 110, 21));
1132     JLabel sortAnnLabel = new JLabel();
1133     sortAnnLabel.setFont(LABEL_FONT);
1134     sortAnnLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1135     sortAnnLabel.setText(MessageManager.getString("label.sort_ann_by"));
1136     sortAutocalc.setFont(LABEL_FONT);
1137     sortAutocalc.setBounds(new Rectangle(290, 285, 165, 21));
1138
1139     JPanel annsettingsPanel = new JPanel();
1140     annsettingsPanel.setBounds(new Rectangle(173, 34, 320, 75));
1141     annsettingsPanel.setLayout(new FlowLayout(FlowLayout.LEFT, 0, 0));
1142     annsettingsPanel.setBorder(new EtchedBorder());
1143     visualTab.add(annsettingsPanel);
1144     Border jb = new EmptyBorder(1, 1, 4, 5);
1145     quality.setBorder(jb);
1146     conservation.setBorder(jb);
1147     identity.setBorder(jb);
1148     showConsensbits.setBorder(jb);
1149     showGroupbits.setBorder(jb);
1150     showGroupConsensus.setBorder(jb);
1151     showGroupConservation.setBorder(jb);
1152     showConsensHistogram.setBorder(jb);
1153     showConsensLogo.setBorder(jb);
1154
1155     JPanel autoAnnotSettings = new JPanel();
1156     autoAnnotSettings.setLayout(new GridLayout(3, 3));
1157     annsettingsPanel.add(autoAnnotSettings);
1158     autoAnnotSettings.add(quality);
1159     autoAnnotSettings.add(conservation);
1160     autoAnnotSettings.add(identity);
1161     autoAnnotSettings.add(showGroupbits);
1162     autoAnnotSettings.add(showGroupConservation);
1163     autoAnnotSettings.add(showGroupConsensus);
1164     autoAnnotSettings.add(showConsensbits);
1165     autoAnnotSettings.add(showConsensHistogram);
1166     autoAnnotSettings.add(showConsensLogo);
1167
1168     JPanel tooltipSettings = new JPanel();
1169     tooltipSettings.setBorder(new TitledBorder(MessageManager
1170             .getString("label.sequence_id_tooltip")));
1171     tooltipSettings.setBounds(173, 140, 220, 62);
1172     tooltipSettings.setLayout(new GridLayout(2, 1));
1173     tooltipSettings.add(showDbRefTooltip);
1174     tooltipSettings.add(showNpTooltip);
1175     visualTab.add(tooltipSettings);
1176
1177     wrap.setFont(LABEL_FONT);
1178     wrap.setHorizontalAlignment(SwingConstants.TRAILING);
1179     wrap.setHorizontalTextPosition(SwingConstants.LEADING);
1180     wrap.setText(MessageManager.getString("label.wrap_alignment"));
1181     rightAlign.setFont(LABEL_FONT);
1182     rightAlign.setForeground(Color.black);
1183     rightAlign.setHorizontalAlignment(SwingConstants.RIGHT);
1184     rightAlign.setHorizontalTextPosition(SwingConstants.LEFT);
1185     rightAlign.setText(MessageManager.getString("label.right_align_ids"));
1186     idItalics.setFont(LABEL_FONT_ITALIC);
1187     idItalics.setHorizontalAlignment(SwingConstants.RIGHT);
1188     idItalics.setHorizontalTextPosition(SwingConstants.LEADING);
1189     idItalics.setText(MessageManager
1190             .getString("label.sequence_name_italics"));
1191     openoverv.setFont(LABEL_FONT);
1192     openoverv.setActionCommand(MessageManager
1193             .getString("label.open_overview"));
1194     openoverv.setHorizontalAlignment(SwingConstants.RIGHT);
1195     openoverv.setHorizontalTextPosition(SwingConstants.LEFT);
1196     openoverv.setText(MessageManager.getString(("label.open_overview")));
1197     JPanel jPanel2 = new JPanel();
1198     jPanel2.setBounds(new Rectangle(7, 17, 158, 310));
1199     jPanel2.setLayout(new GridLayout(14, 1));
1200     jPanel2.add(fullScreen);
1201     jPanel2.add(openoverv);
1202     jPanel2.add(seqLimit);
1203     jPanel2.add(rightAlign);
1204     jPanel2.add(fontLabel);
1205     jPanel2.add(showUnconserved);
1206     jPanel2.add(idItalics);
1207     jPanel2.add(smoothFont);
1208     jPanel2.add(scaleProteinToCdna);
1209     jPanel2.add(gapLabel);
1210     jPanel2.add(wrap);
1211     jPanel2.add(sortLabel);
1212     jPanel2.add(sortAnnLabel);
1213     jPanel2.add(startupCheckbox);
1214     visualTab.add(jPanel2);
1215     visualTab.add(annotations);
1216     visualTab.add(startupFileTextfield);
1217     visualTab.add(sortby);
1218     visualTab.add(sortAnnBy);
1219     visualTab.add(sortAutocalc);
1220     visualTab.add(gapSymbolCB);
1221     visualTab.add(fontNameCB);
1222     visualTab.add(fontSizeCB);
1223     visualTab.add(fontStyleCB);
1224     return visualTab;
1225   }
1226
1227   protected void autoIdWidth_actionPerformed()
1228   {
1229     // TODO Auto-generated method stub
1230
1231   }
1232
1233   protected void userIdWidth_actionPerformed()
1234   {
1235     // TODO Auto-generated method stub
1236
1237   }
1238
1239   protected void maxColour_actionPerformed(JPanel panel)
1240   {
1241   }
1242
1243   protected void minColour_actionPerformed(JPanel panel)
1244   {
1245   }
1246
1247   protected void showunconserved_actionPerformed(ActionEvent e)
1248   {
1249     // TODO Auto-generated method stub
1250
1251   }
1252
1253   /**
1254    * DOCUMENT ME!
1255    *
1256    * @param e
1257    *          DOCUMENT ME!
1258    */
1259   public void ok_actionPerformed(ActionEvent e)
1260   {
1261   }
1262
1263   /**
1264    * DOCUMENT ME!
1265    *
1266    * @param e
1267    *          DOCUMENT ME!
1268    */
1269   public void cancel_actionPerformed(ActionEvent e)
1270   {
1271   }
1272
1273   /**
1274    * DOCUMENT ME!
1275    *
1276    * @param e
1277    *          DOCUMENT ME!
1278    */
1279   public void annotations_actionPerformed(ActionEvent e)
1280   {
1281   }
1282
1283   /**
1284    * DOCUMENT ME!
1285    */
1286   public void startupFileTextfield_mouseClicked()
1287   {
1288   }
1289
1290   public void newLink_actionPerformed(ActionEvent e)
1291   {
1292
1293   }
1294
1295   public void editLink_actionPerformed(ActionEvent e)
1296   {
1297
1298   }
1299
1300   public void deleteLink_actionPerformed(ActionEvent e)
1301   {
1302
1303   }
1304
1305   public void defaultBrowser_mouseClicked(MouseEvent e)
1306   {
1307
1308   }
1309
1310   public void linkURLList_keyTyped(KeyEvent e)
1311   {
1312
1313   }
1314
1315   public void useProxy_actionPerformed()
1316   {
1317     proxyServerTB.setEnabled(useProxy.isSelected());
1318     proxyPortTB.setEnabled(useProxy.isSelected());
1319   }
1320
1321 }