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
  80           .getLabelFont(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   /*
 161    * Colours tab components
 162    */
 163   protected JPanel minColour = new JPanel();
 164
 165   protected JPanel maxColour = new JPanel();
 166
 167   protected JComboBox<String> protColour = new JComboBox<String>();
 168
 169   protected JComboBox<String> nucColour = new JComboBox<String>();
 170
 171   /*
 172    * Connections tab components
 173    */
 174   protected JList linkURLList = new JList();
 175
 176   protected JTextField proxyServerTB = new JTextField();
 177
 178   protected JTextField proxyPortTB = new JTextField();
 179
 180   protected JTextField defaultBrowser = new JTextField();
 181
 182   protected JList linkNameList = new JList();
 183
 184   protected JCheckBox useProxy = new JCheckBox();
 185
 186   protected JCheckBox usagestats = new JCheckBox();
 187
 188   protected JCheckBox questionnaire = new JCheckBox();
 189
 190   protected JCheckBox versioncheck = new JCheckBox();
 191
 192   /*
 193    * Output tab components
 194    */
 195   protected JComboBox<String> epsRendering = new JComboBox<String>();
 196
 197   protected JLabel userIdWidthlabel = new JLabel();
 198
 199   protected JCheckBox autoIdWidth = new JCheckBox();
 200
 201   protected JTextField userIdWidth = new JTextField();
 202
 203   protected JCheckBox blcjv = new JCheckBox();
 204
 205   protected JCheckBox pileupjv = new JCheckBox();
 206
 207   protected JCheckBox clustaljv = new JCheckBox();
 208
 209   protected JCheckBox msfjv = new JCheckBox();
 210
 211   protected JCheckBox fastajv = new JCheckBox();
 212
 213   protected JCheckBox pfamjv = new JCheckBox();
 214
 215   protected JCheckBox pirjv = new JCheckBox();
 216
 217   protected JCheckBox modellerOutput = new JCheckBox();
 218
 219   protected JCheckBox embbedBioJSON = new JCheckBox();
 220
 221   /*
 222    * Editing tab components
 223    */
 224   protected JCheckBox autoCalculateConsCheck = new JCheckBox();
 225
 226   protected JCheckBox padGaps = new JCheckBox();
 227
 228   protected JCheckBox sortByTree = new JCheckBox();
 229
 230   /*
 231    * DAS Settings tab
 232    */
 233   protected JPanel dasTab = new JPanel();
 234
 235   /*
 236    * Web Services tab
 237    */
 238   protected JPanel wsTab = new JPanel();
 239
 240   /**
 241    * Creates a new GPreferences object.
 242    */
 243   public GPreferences()
 244   {
 245     try
 246     {
 247       jbInit();
 248     } catch (Exception ex)
 249     {
 250       ex.printStackTrace();
 251     }
 252   }
 253
 254   /**
 255    * Construct the panel and its tabbed sub-panels.
 256    *
 257    * @throws Exception
 258    */
 259   private void jbInit() throws Exception
 260   {
 261     final JTabbedPane tabbedPane = new JTabbedPane();
 262     this.setLayout(new BorderLayout());
 263     JPanel okCancelPanel = initOkCancelPanel();
 264     this.add(tabbedPane, BorderLayout.CENTER);
 265     this.add(okCancelPanel, BorderLayout.SOUTH);
 266
 267     tabbedPane.add(initVisualTab(),
 268             MessageManager.getString("label.visual"));
 269
 270     tabbedPane.add(initColoursTab(),
 271             MessageManager.getString("label.colours"));
 272
 273     tabbedPane.add(initStructureTab(),
 274             MessageManager.getString("label.structure"));
 275
 276     tabbedPane.add(initConnectionsTab(),
 277             MessageManager.getString("label.connections"));
 278
 279     tabbedPane.add(initOutputTab(), MessageManager.getString("label.output"));
 280
 281     tabbedPane.add(initEditingTab(), MessageManager.getString("label.editing"));
 282
 283     /*
 284      * See DasSourceBrowser for the real work of configuring this tab.
 285      */
 286     dasTab.setLayout(new BorderLayout());
 287     tabbedPane
 288             .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
 406             .setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.getString("label.adjusts_width_generated_eps_png")));
 407     autoIdWidth.setBounds(new Rectangle(228, 96, 188, 23));
 408     autoIdWidth.addActionListener(new ActionListener()
 409     {
 410
 411       @Override
 412       public void actionPerformed(ActionEvent e)
 413       {
 414         autoIdWidth_actionPerformed();
 415       }
 416     });
 417     userIdWidthlabel.setFont(LABEL_FONT);
 418     userIdWidthlabel.setText(MessageManager
 419             .getString("label.figure_id_column_width"));
 420     userIdWidth
 421             .setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.getString("label.manually_specify_width_left_column")));
 422     userIdWidthlabel
 423             .setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.getString("label.manually_specify_width_left_column")));
 424     userIdWidthlabel.setBounds(new Rectangle(236, 120, 168, 23));
 425     userIdWidth.setFont(JvSwingUtils.getTextAreaFont());
 426     userIdWidth.setText("");
 427     userIdWidth.setBounds(new Rectangle(232, 144, 84, 23));
 428     userIdWidth.addActionListener(new ActionListener()
 429     {
 430
 431       @Override
 432       public void actionPerformed(ActionEvent e)
 433       {
 434         userIdWidth_actionPerformed();
 435       }
 436     });
 437     modellerOutput.setFont(LABEL_FONT);
 438     modellerOutput.setText(MessageManager
 439             .getString("label.use_modeller_output"));
 440     modellerOutput.setBounds(new Rectangle(228, 226, 168, 23));
 441     embbedBioJSON.setFont(LABEL_FONT);
 442     embbedBioJSON.setText(MessageManager.getString("label.embbed_biojson"));
 443     embbedBioJSON.setBounds(new Rectangle(228, 200, 250, 23));
 444
 445     jPanel11.add(jLabel1);
 446     jPanel11.add(blcjv);
 447     jPanel11.add(clustaljv);
 448     jPanel11.add(fastajv);
 449     jPanel11.add(msfjv);
 450     jPanel11.add(pfamjv);
 451     jPanel11.add(pileupjv);
 452     jPanel11.add(pirjv);
 453     outputTab.add(autoIdWidth);
 454     outputTab.add(userIdWidth);
 455     outputTab.add(userIdWidthlabel);
 456     outputTab.add(modellerOutput);
 457     outputTab.add(embbedBioJSON);
 458     outputTab.add(epsLabel);
 459     outputTab.add(epsRendering);
 460     outputTab.add(jPanel11);
 461     return outputTab;
 462   }
 463
 464   /**
 465    * Initialises the Connections tabbed panel.
 466    *
 467    * @return
 468    */
 469   private JPanel initConnectionsTab()
 470   {
 471     JPanel connectTab = new JPanel();
 472     connectTab.setLayout(new GridBagLayout());
 473     JLabel serverLabel = new JLabel();
 474     serverLabel.setText(MessageManager.getString("label.address"));
 475     serverLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 476     serverLabel.setFont(LABEL_FONT);
 477     proxyServerTB.setFont(LABEL_FONT);
 478     proxyPortTB.setFont(LABEL_FONT);
 479     JLabel portLabel = new JLabel();
 480     portLabel.setFont(LABEL_FONT);
 481     portLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 482     portLabel.setText(MessageManager.getString("label.port"));
 483     JLabel browserLabel = new JLabel();
 484     browserLabel.setFont(new java.awt.Font("SansSerif", 0, 11));
 485     browserLabel.setHorizontalAlignment(SwingConstants.TRAILING);
 486     browserLabel.setText(MessageManager
 487             .getString("label.default_browser_unix"));
 488     defaultBrowser.setFont(LABEL_FONT);
 489     defaultBrowser.setText("");
 490     usagestats.setText(MessageManager
 491             .getString("label.send_usage_statistics"));
 492     usagestats.setFont(LABEL_FONT);
 493     usagestats.setHorizontalAlignment(SwingConstants.RIGHT);
 494     usagestats.setHorizontalTextPosition(SwingConstants.LEADING);
 495     questionnaire.setText(MessageManager
 496             .getString("label.check_for_questionnaires"));
 497     questionnaire.setFont(LABEL_FONT);
 498     questionnaire.setHorizontalAlignment(SwingConstants.RIGHT);
 499     questionnaire.setHorizontalTextPosition(SwingConstants.LEADING);
 500     versioncheck.setText(MessageManager
 501             .getString("label.check_for_latest_version"));
 502     versioncheck.setFont(LABEL_FONT);
 503     versioncheck.setHorizontalAlignment(SwingConstants.RIGHT);
 504     versioncheck.setHorizontalTextPosition(SwingConstants.LEADING);
 505     JButton newLink = new JButton();
 506     newLink.setText(MessageManager.getString("action.new"));
 507     newLink.addActionListener(new java.awt.event.ActionListener()
 508     {
 509       public void actionPerformed(ActionEvent e)
 510       {
 511         newLink_actionPerformed(e);
 512       }
 513     });
 514     JButton editLink = new JButton();
 515     editLink.setText(MessageManager.getString("action.edit"));
 516     editLink.addActionListener(new java.awt.event.ActionListener()
 517     {
 518       public void actionPerformed(ActionEvent e)
 519       {
 520         editLink_actionPerformed(e);
 521       }
 522     });
 523     JButton deleteLink = new JButton();
 524     deleteLink.setText(MessageManager.getString("action.delete"));
 525     deleteLink.addActionListener(new java.awt.event.ActionListener()
 526     {
 527       public void actionPerformed(ActionEvent e)
 528       {
 529         deleteLink_actionPerformed(e);
 530       }
 531     });
 532
 533     linkURLList.addListSelectionListener(new ListSelectionListener()
 534     {
 535       public void valueChanged(ListSelectionEvent e)
 536       {
 537         int index = linkURLList.getSelectedIndex();
 538         linkNameList.setSelectedIndex(index);
 539       }
 540     });
 541
 542     linkNameList.addListSelectionListener(new ListSelectionListener()
 543     {
 544       public void valueChanged(ListSelectionEvent e)
 545       {
 546         int index = linkNameList.getSelectedIndex();
 547         linkURLList.setSelectedIndex(index);
 548       }
 549     });
 550
 551     JScrollPane linkScrollPane = new JScrollPane();
 552     linkScrollPane.setBorder(null);
 553     JPanel linkPanel = new JPanel();
 554     linkPanel.setBorder(new TitledBorder(MessageManager
 555             .getString("label.url_linkfrom_sequence_id")));
 556     linkPanel.setLayout(new BorderLayout());
 557     GridLayout gridLayout1 = new GridLayout();
 558     JPanel editLinkButtons = new JPanel();
 559     editLinkButtons.setLayout(gridLayout1);
 560     gridLayout1.setRows(3);
 561     linkNameList.setFont(LABEL_FONT);
 562     linkNameList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
 563     BorderLayout borderLayout3 = new BorderLayout();
 564     JPanel linkPanel2 = new JPanel();
 565     linkPanel2.setLayout(borderLayout3);
 566     linkURLList.setFont(LABEL_FONT);
 567     linkURLList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
 568
 569     defaultBrowser.addMouseListener(new MouseAdapter()
 570     {
 571       public void mouseClicked(MouseEvent e)
 572       {
 573         if (e.getClickCount() > 1)
 574         {
 575           defaultBrowser_mouseClicked(e);
 576         }
 577       }
 578     });
 579     useProxy.setFont(LABEL_FONT);
 580     useProxy.setHorizontalAlignment(SwingConstants.RIGHT);
 581     useProxy.setHorizontalTextPosition(SwingConstants.LEADING);
 582     useProxy.setText(MessageManager.getString("label.use_proxy_server"));
 583     useProxy.addActionListener(new ActionListener()
 584     {
 585       public void actionPerformed(ActionEvent e)
 586       {
 587         useProxy_actionPerformed();
 588       }
 589     });
 590     linkPanel.add(editLinkButtons, BorderLayout.EAST);
 591     editLinkButtons.add(newLink, null);
 592     editLinkButtons.add(editLink, null);
 593     editLinkButtons.add(deleteLink, null);
 594     linkPanel.add(linkScrollPane, BorderLayout.CENTER);
 595     linkScrollPane.getViewport().add(linkPanel2, null);
 596     linkPanel2.add(linkURLList, BorderLayout.CENTER);
 597     linkPanel2.add(linkNameList, BorderLayout.WEST);
 598     JPanel jPanel1 = new JPanel();
 599     TitledBorder titledBorder1 = new TitledBorder(
 600             MessageManager.getString("label.proxy_server"));
 601     jPanel1.setBorder(titledBorder1);
 602     jPanel1.setLayout(new GridBagLayout());
 603     jPanel1.add(serverLabel, new GridBagConstraints(0, 1, 1, 1, 0.0, 0.0,
 604             GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
 605                     2, 4, 0), 5, 0));
 606     jPanel1.add(portLabel, new GridBagConstraints(2, 1, 1, 1, 0.0, 0.0,
 607             GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
 608                     0, 4, 0), 11, 6));
 609     connectTab.add(linkPanel, new GridBagConstraints(0, 0, 2, 1, 1.0, 1.0,
 610             GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(
 611                     16, 0, 0, 12), 359, -17));
 612     connectTab.add(jPanel1, new GridBagConstraints(0, 2, 2, 1, 1.0, 1.0,
 613             GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(
 614                     21, 0, 35, 12), 4, 6));
 615     connectTab.add(browserLabel, new GridBagConstraints(0, 1, 1, 1, 0.0,
 616             0.0, GridBagConstraints.WEST, GridBagConstraints.NONE,
 617             new Insets(16, 0, 0, 0), 5, 1));
 618     jPanel1.add(useProxy, new GridBagConstraints(0, 0, 2, 1, 0.0, 0.0,
 619             GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
 620                     2, 5, 185), 2, -4));
 621     jPanel1.add(proxyPortTB, new GridBagConstraints(3, 1, 1, 1, 1.0, 0.0,
 622             GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 623             new Insets(0, 2, 4, 2), 54, 1));
 624     jPanel1.add(proxyServerTB, new GridBagConstraints(1, 1, 1, 1, 1.0, 0.0,
 625             GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 626             new Insets(0, 2, 4, 0), 263, 1));
 627     connectTab.add(defaultBrowser, new GridBagConstraints(1, 1, 1, 1, 1.0,
 628             0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 629             new Insets(15, 0, 0, 15), 307, 1));
 630     connectTab.add(usagestats, new GridBagConstraints(0, 4, 1, 1, 1.0, 0.0,
 631             GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 632             new Insets(0, 2, 4, 2), 70, 1));
 633     connectTab.add(questionnaire, new GridBagConstraints(1, 4, 1, 1, 1.0,
 634             0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 635             new Insets(0, 2, 4, 2), 70, 1));
 636     connectTab.add(versioncheck, new GridBagConstraints(0, 5, 1, 1, 1.0,
 637             0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 638             new Insets(0, 2, 4, 2), 70, 1));
 639     return connectTab;
 640   }
 641
 642   /**
 643    * Initialises the parent panel which contains the tabbed sections.
 644    *
 645    * @return
 646    */
 647   private JPanel initOkCancelPanel()
 648   {
 649     JButton ok = new JButton();
 650     ok.setText(MessageManager.getString("action.ok"));
 651     ok.addActionListener(new ActionListener()
 652     {
 653       public void actionPerformed(ActionEvent e)
 654       {
 655         ok_actionPerformed(e);
 656       }
 657     });
 658     JButton cancel = new JButton();
 659     cancel.setText(MessageManager.getString("action.cancel"));
 660     cancel.addActionListener(new ActionListener()
 661     {
 662       public void actionPerformed(ActionEvent e)
 663       {
 664         cancel_actionPerformed(e);
 665       }
 666     });
 667     JPanel okCancelPanel = new JPanel();
 668     okCancelPanel.add(ok);
 669     okCancelPanel.add(cancel);
 670     return okCancelPanel;
 671   }
 672
 673   /**
 674    * Initialises the Colours tabbed panel.
 675    *
 676    * @return
 677    */
 678   private JPanel initColoursTab()
 679   {
 680     JPanel coloursTab = new JPanel();
 681     coloursTab.setBorder(new TitledBorder(MessageManager
 682             .getString("action.open_new_alignment")));
 683     coloursTab.setLayout(new FlowLayout());
 684     JLabel mincolourLabel = new JLabel();
 685     mincolourLabel.setFont(LABEL_FONT);
 686     mincolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 687     mincolourLabel.setText(MessageManager.getString("label.min_colour"));
 688     minColour.setFont(LABEL_FONT);
 689     minColour.setBorder(BorderFactory.createEtchedBorder());
 690     minColour.setPreferredSize(new Dimension(40, 20));
 691     minColour.addMouseListener(new MouseAdapter()
 692     {
 693       public void mousePressed(MouseEvent e)
 694       {
 695         minColour_actionPerformed(minColour);
 696       }
 697     });
 698     JLabel maxcolourLabel = new JLabel();
 699     maxcolourLabel.setFont(LABEL_FONT);
 700     maxcolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 701     maxcolourLabel.setText(MessageManager.getString("label.max_colour"));
 702     maxColour.setFont(LABEL_FONT);
 703     maxColour.setBorder(BorderFactory.createEtchedBorder());
 704     maxColour.setPreferredSize(new Dimension(40, 20));
 705     maxColour.addMouseListener(new MouseAdapter()
 706     {
 707       public void mousePressed(MouseEvent e)
 708       {
 709         maxColour_actionPerformed(maxColour);
 710       }
 711     });
 712
 713     protColour.setFont(LABEL_FONT);
 714     protColour.setBounds(new Rectangle(172, 225, 155, 21));
 715     JLabel protColourLabel = new JLabel();
 716     protColourLabel.setFont(LABEL_FONT);
 717     protColourLabel.setHorizontalAlignment(SwingConstants.LEFT);
 718     protColourLabel.setText(MessageManager
 719             .getString("label.prot_alignment_colour") + " ");
 720     JvSwingUtils.addtoLayout(coloursTab, MessageManager
 721             .getString("label.default_colour_scheme_for_alignment"),
 722             protColourLabel, protColour);
 723
 724     nucColour.setFont(LABEL_FONT);
 725     nucColour.setBounds(new Rectangle(172, 240, 155, 21));
 726     JLabel nucColourLabel = new JLabel();
 727     nucColourLabel.setFont(LABEL_FONT);
 728     nucColourLabel.setHorizontalAlignment(SwingConstants.LEFT);
 729     nucColourLabel.setText(MessageManager
 730             .getString("label.nuc_alignment_colour")
 731             + " ");
 732     JvSwingUtils.addtoLayout(coloursTab, MessageManager
 733             .getString("label.default_colour_scheme_for_alignment"),
 734             nucColourLabel, nucColour);
 735
 736     JPanel annotationShding = new JPanel();
 737     annotationShding.setBorder(new TitledBorder(MessageManager
 738             .getString("label.annotation_shading_default")));
 739     annotationShding.setLayout(new GridLayout(1, 2));
 740     JvSwingUtils.addtoLayout(annotationShding, MessageManager
 741             .getString("label.default_minimum_colour_annotation_shading"),
 742             mincolourLabel, minColour);
 743     JvSwingUtils.addtoLayout(annotationShding, MessageManager
 744             .getString("label.default_maximum_colour_annotation_shading"),
 745             maxcolourLabel, maxColour);
 746     coloursTab.add(annotationShding); // , FlowLayout.LEFT);
 747     return coloursTab;
 748   }
 749
 750   /**
 751    * Initialises the Structure tabbed panel.
 752    *
 753    * @return
 754    */
 755   private JPanel initStructureTab()
 756   {
 757     structureTab = new JPanel();
 758
 759     structureTab.setBorder(new TitledBorder(MessageManager
 760             .getString("label.structure_options")));
 761     structureTab.setLayout(null);
 762     final int width = 400;
 763     final int height = 22;
 764     final int lineSpacing = 25;
 765     int ypos = 30;
 766
 767     structFromPdb.setFont(LABEL_FONT);
 768     structFromPdb.setText(MessageManager.getString("label.struct_from_pdb"));
 769     structFromPdb.setBounds(new Rectangle(5, ypos, width, height));
 770     structFromPdb.addActionListener(new ActionListener()
 771     {
 772       @Override
 773       public void actionPerformed(ActionEvent e)
 774       {
 775         boolean selected = structFromPdb.isSelected();
 776         // enable other options only when the first is checked
 777         useRnaView.setEnabled(selected);
 778         addSecondaryStructure.setEnabled(selected);
 779         addTempFactor.setEnabled(selected);
 780       }
 781     });
 782     structureTab.add(structFromPdb);
 783
 784     // indent checkboxes that are conditional on the first one
 785     ypos += lineSpacing;
 786     useRnaView.setFont(LABEL_FONT);
 787     useRnaView.setText(MessageManager.getString("label.use_rnaview"));
 788     useRnaView.setBounds(new Rectangle(25, ypos, width, height));
 789     structureTab.add(useRnaView);
 790
 791     ypos += lineSpacing;
 792     addSecondaryStructure.setFont(LABEL_FONT);
 793     addSecondaryStructure.setText(MessageManager
 794             .getString("label.autoadd_secstr"));
 795     addSecondaryStructure.setBounds(new Rectangle(25, ypos, width, height));
 796     structureTab.add(addSecondaryStructure);
 797
 798     ypos += lineSpacing;
 799     addTempFactor.setFont(LABEL_FONT);
 800     addTempFactor.setText(MessageManager.getString("label.autoadd_temp"));
 801     addTempFactor.setBounds(new Rectangle(25, ypos, width, height));
 802     structureTab.add(addTempFactor);
 803
 804     ypos += lineSpacing;
 805     JLabel viewerLabel = new JLabel();
 806     viewerLabel.setFont(LABEL_FONT);
 807     viewerLabel.setHorizontalAlignment(SwingConstants.LEFT);
 808     viewerLabel.setText(MessageManager.getString("label.structure_viewer"));
 809     viewerLabel.setBounds(new Rectangle(10, ypos, 200, height));
 810     structureTab.add(viewerLabel);
 811
 812     structViewer.setFont(LABEL_FONT);
 813     structViewer.setBounds(new Rectangle(160, ypos, 120, height));
 814     structViewer.addItem(ViewerType.JMOL.name());
 815     structViewer.addItem(ViewerType.CHIMERA.name());
 816     structViewer.addActionListener(new ActionListener()
 817     {
 818       @Override
 819       public void actionPerformed(ActionEvent e)
 820       {
 821         structureViewer_actionPerformed((String) structViewer
 822                 .getSelectedItem());
 823       }
 824     });
 825     structureTab.add(structViewer);
 826
 827     ypos += lineSpacing;
 828     JLabel pathLabel = new JLabel();
 829     pathLabel.setFont(new java.awt.Font("SansSerif", 0, 11));
 830     pathLabel.setHorizontalAlignment(SwingConstants.LEFT);
 831     pathLabel.setText(MessageManager.getString("label.chimera_path"));
 832     final String tooltip = JvSwingUtils.wrapTooltip(true,
 833             MessageManager.getString("label.chimera_path_tip"));
 834     pathLabel.setToolTipText(tooltip);
 835     pathLabel.setBounds(new Rectangle(10, ypos, 140, height));
 836     structureTab.add(pathLabel);
 837
 838     chimeraPath.setFont(LABEL_FONT);
 839     chimeraPath.setText("");
 840     chimeraPath.setBounds(new Rectangle(160, ypos, 300, height));
 841     chimeraPath.addMouseListener(new MouseAdapter()
 842     {
 843       @Override
 844       public void mouseClicked(MouseEvent e)
 845       {
 846         if (e.getClickCount() == 2)
 847         {
 848           String chosen = openFileChooser();
 849           if (chosen != null)
 850           {
 851             chimeraPath.setText(chosen);
 852           }
 853         }
 854       }
 855     });
 856     structureTab.add(chimeraPath);
 857
 858     ypos += lineSpacing;
 859     // scrl_pdbDocFieldConfig.setPreferredSize(new Dimension(450, 100));
 860     // scrl_pdbDocFieldConfig
 861     // .setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_NEVER);
 862     // scrl_pdbDocFieldConfig.setBounds();
 863     PDBDocFieldPreferences docFieldPref = new PDBDocFieldPreferences(
 864             PreferenceSource.PREFERENCES);
 865     docFieldPref.setBounds(new Rectangle(10, ypos + 5, 450, 120));
 866     structureTab.add(docFieldPref);
 867
 868
 869
 870
 871     return structureTab;
 872   }
 873
 874
 875   /**
 876    * Action on choosing a structure viewer from combobox options.
 877    *
 878    * @param selectedItem
 879    */
 880   protected void structureViewer_actionPerformed(String selectedItem)
 881   {
 882   }
 883
 884   /**
 885    * Show a dialog for the user to choose a file. Returns the chosen path, or
 886    * null on Cancel.
 887    *
 888    * @return
 889    */
 890   protected String openFileChooser()
 891   {
 892     String choice = null;
 893     JFileChooser chooser = new JFileChooser();
 894
 895     // chooser.setFileView(new JalviewFileView());
 896     chooser.setDialogTitle(MessageManager
 897             .getString("label.open_local_file"));
 898     chooser.setToolTipText(MessageManager.getString("action.open"));
 899
 900     int value = chooser.showOpenDialog(this);
 901
 902     if (value == JFileChooser.APPROVE_OPTION)
 903     {
 904       choice = chooser.getSelectedFile().getPath();
 905     }
 906     return choice;
 907   }
 908
 909   /**
 910    * Validate the structure tab preferences; if invalid, set focus on this tab.
 911    *
 912    * @param e
 913    */
 914   protected boolean validateStructure(FocusEvent e)
 915   {
 916     if (!validateStructure())
 917     {
 918       e.getComponent().requestFocusInWindow();
 919       return false;
 920     }
 921     return true;
 922   }
 923
 924   protected boolean validateStructure()
 925   {
 926     return false;
 927   }
 928
 929   /**
 930    * Initialises the Visual tabbed panel.
 931    *
 932    * @return
 933    */
 934   private JPanel initVisualTab()
 935   {
 936     JPanel visualTab = new JPanel();
 937     visualTab.setBorder(new TitledBorder(MessageManager
 938             .getString("action.open_new_alignment")));
 939     visualTab.setLayout(null);
 940     fullScreen.setFont(LABEL_FONT);
 941     fullScreen.setHorizontalAlignment(SwingConstants.RIGHT);
 942     fullScreen.setHorizontalTextPosition(SwingConstants.LEFT);
 943     fullScreen.setText(MessageManager.getString("label.maximize_window"));
 944     quality.setEnabled(false);
 945     quality.setFont(LABEL_FONT);
 946     quality.setHorizontalAlignment(SwingConstants.RIGHT);
 947     quality.setHorizontalTextPosition(SwingConstants.LEFT);
 948     quality.setSelected(true);
 949     quality.setText(MessageManager.getString("label.quality"));
 950     conservation.setEnabled(false);
 951     conservation.setFont(LABEL_FONT);
 952     conservation.setHorizontalAlignment(SwingConstants.RIGHT);
 953     conservation.setHorizontalTextPosition(SwingConstants.LEFT);
 954     conservation.setSelected(true);
 955     conservation.setText(MessageManager.getString("label.conservation"));
 956     identity.setEnabled(false);
 957     identity.setFont(LABEL_FONT);
 958     identity.setHorizontalAlignment(SwingConstants.RIGHT);
 959     identity.setHorizontalTextPosition(SwingConstants.LEFT);
 960     identity.setSelected(true);
 961     identity.setText(MessageManager.getString("label.consensus"));
 962     JLabel showGroupbits = new JLabel();
 963     showGroupbits.setFont(LABEL_FONT);
 964     showGroupbits.setHorizontalAlignment(SwingConstants.RIGHT);
 965     showGroupbits.setHorizontalTextPosition(SwingConstants.LEFT);
 966     showGroupbits.setText(MessageManager.getString("action.show_group")
 967             + ":");
 968     JLabel showConsensbits = new JLabel();
 969     showConsensbits.setFont(LABEL_FONT);
 970     showConsensbits.setHorizontalAlignment(SwingConstants.RIGHT);
 971     showConsensbits.setHorizontalTextPosition(SwingConstants.LEFT);
 972     showConsensbits.setText(MessageManager.getString("label.consensus")
 973             + ":");
 974     showConsensHistogram.setEnabled(false);
 975     showConsensHistogram.setFont(LABEL_FONT);
 976     showConsensHistogram.setHorizontalAlignment(SwingConstants.RIGHT);
 977     showConsensHistogram.setHorizontalTextPosition(SwingConstants.LEFT);
 978     showConsensHistogram.setSelected(true);
 979     showConsensHistogram.setText(MessageManager
 980             .getString("label.histogram"));
 981     showConsensLogo.setEnabled(false);
 982     showConsensLogo.setFont(LABEL_FONT);
 983     showConsensLogo.setHorizontalAlignment(SwingConstants.RIGHT);
 984     showConsensLogo.setHorizontalTextPosition(SwingConstants.LEFT);
 985     showConsensLogo.setSelected(true);
 986     showConsensLogo.setText(MessageManager.getString("label.logo"));
 987     showGroupConsensus.setEnabled(false);
 988     showGroupConsensus.setFont(LABEL_FONT);
 989     showGroupConsensus.setHorizontalAlignment(SwingConstants.RIGHT);
 990     showGroupConsensus.setHorizontalTextPosition(SwingConstants.LEFT);
 991     showGroupConsensus.setSelected(true);
 992     showGroupConsensus.setText(MessageManager.getString("label.consensus"));
 993     showGroupConservation.setEnabled(false);
 994     showGroupConservation.setFont(LABEL_FONT);
 995     showGroupConservation.setHorizontalAlignment(SwingConstants.RIGHT);
 996     showGroupConservation.setHorizontalTextPosition(SwingConstants.LEFT);
 997     showGroupConservation.setSelected(true);
 998     showGroupConservation.setText(MessageManager
 999             .getString("label.conservation"));
1000     showNpTooltip.setEnabled(true);
1001     showNpTooltip.setFont(LABEL_FONT);
1002     showNpTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
1003     showNpTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
1004     showNpTooltip.setSelected(true);
1005     showNpTooltip.setText(MessageManager
1006             .getString("label.non_positional_features"));
1007     showDbRefTooltip.setEnabled(true);
1008     showDbRefTooltip.setFont(LABEL_FONT);
1009     showDbRefTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
1010     showDbRefTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
1011     showDbRefTooltip.setSelected(true);
1012     showDbRefTooltip.setText(MessageManager
1013             .getString("label.database_references"));
1014     annotations.setFont(LABEL_FONT);
1015     annotations.setHorizontalAlignment(SwingConstants.RIGHT);
1016     annotations.setHorizontalTextPosition(SwingConstants.LEADING);
1017     annotations.setSelected(true);
1018     annotations.setText(MessageManager.getString("label.show_annotations"));
1019     annotations.setBounds(new Rectangle(169, 12, 200, 23));
1020     annotations.addActionListener(new ActionListener()
1021     {
1022       public void actionPerformed(ActionEvent e)
1023       {
1024         annotations_actionPerformed(e);
1025       }
1026     });
1027     identity.addActionListener(new ActionListener()
1028     {
1029       public void actionPerformed(ActionEvent e)
1030       {
1031         annotations_actionPerformed(e);
1032       }
1033     });
1034     showGroupConsensus.addActionListener(new ActionListener()
1035     {
1036       public void actionPerformed(ActionEvent e)
1037       {
1038         annotations_actionPerformed(e);
1039       }
1040     });
1041     showUnconserved.setFont(LABEL_FONT);
1042     showUnconserved.setHorizontalAlignment(SwingConstants.RIGHT);
1043     showUnconserved.setHorizontalTextPosition(SwingConstants.LEFT);
1044     showUnconserved.setSelected(true);
1045     showUnconserved.setText(MessageManager
1046             .getString("action.show_unconserved"));
1047     showUnconserved.addActionListener(new ActionListener()
1048     {
1049       public void actionPerformed(ActionEvent e)
1050       {
1051         showunconserved_actionPerformed(e);
1052       }
1053     });
1054
1055     // TODO these are not yet added to / action from Preferences
1056     // JCheckBox shareSelections = new JCheckBox();
1057     // shareSelections.setFont(verdana11);
1058     // shareSelections.setHorizontalAlignment(SwingConstants.RIGHT);
1059     // shareSelections.setHorizontalTextPosition(SwingConstants.LEFT);
1060     // shareSelections.setSelected(true);
1061     // shareSelections.setText(MessageManager
1062     // .getString("label.share_selection_across_views"));
1063     // JCheckBox followHighlight = new JCheckBox();
1064     // followHighlight.setFont(verdana11);
1065     // followHighlight.setHorizontalAlignment(SwingConstants.RIGHT);
1066     // followHighlight.setHorizontalTextPosition(SwingConstants.LEFT);
1067     // // showUnconserved.setBounds(new Rectangle(169, 40, 200, 23));
1068     // followHighlight.setSelected(true);
1069     // followHighlight.setText(MessageManager
1070     // .getString("label.scroll_highlighted_regions"));
1071
1072     seqLimit.setFont(LABEL_FONT);
1073     seqLimit.setHorizontalAlignment(SwingConstants.RIGHT);
1074     seqLimit.setHorizontalTextPosition(SwingConstants.LEFT);
1075     seqLimit.setText(MessageManager.getString("label.full_sequence_id"));
1076     smoothFont.setFont(LABEL_FONT);
1077     smoothFont.setHorizontalAlignment(SwingConstants.RIGHT);
1078     smoothFont.setHorizontalTextPosition(SwingConstants.LEADING);
1079     smoothFont.setText(MessageManager.getString("label.smooth_font"));
1080     scaleProteinToCdna.setFont(LABEL_FONT);
1081     scaleProteinToCdna.setHorizontalAlignment(SwingConstants.RIGHT);
1082     scaleProteinToCdna.setHorizontalTextPosition(SwingConstants.LEADING);
1083     scaleProteinToCdna.setText(MessageManager
1084             .getString("label.scale_protein_to_cdna"));
1085     scaleProteinToCdna.setToolTipText(MessageManager
1086             .getString("label.scale_protein_to_cdna_tip"));
1087     JLabel gapLabel = new JLabel();
1088     gapLabel.setFont(LABEL_FONT);
1089     gapLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1090     gapLabel.setText(MessageManager.getString("label.gap_symbol") + " ");
1091     JLabel fontLabel = new JLabel();
1092     fontLabel.setFont(LABEL_FONT);
1093     fontLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1094     fontLabel.setText(MessageManager.getString("label.font"));
1095     fontSizeCB.setFont(LABEL_FONT);
1096     fontSizeCB.setBounds(new Rectangle(320, 112, 65, 23));
1097     fontStyleCB.setFont(LABEL_FONT);
1098     fontStyleCB.setBounds(new Rectangle(382, 112, 80, 23));
1099     fontNameCB.setFont(LABEL_FONT);
1100     fontNameCB.setBounds(new Rectangle(172, 112, 147, 23));
1101     gapSymbolCB.setFont(LABEL_FONT);
1102     gapSymbolCB.setBounds(new Rectangle(172, 215, 69, 23));
1103     DefaultListCellRenderer dlcr = new DefaultListCellRenderer();
1104     dlcr.setHorizontalAlignment(DefaultListCellRenderer.CENTER);
1105     gapSymbolCB.setRenderer(dlcr);
1106
1107     startupCheckbox.setText(MessageManager.getString("action.open_file"));
1108     startupCheckbox.setFont(LABEL_FONT);
1109     startupCheckbox.setHorizontalAlignment(SwingConstants.RIGHT);
1110     startupCheckbox.setHorizontalTextPosition(SwingConstants.LEFT);
1111     startupCheckbox.setSelected(true);
1112     startupFileTextfield.setFont(LABEL_FONT);
1113     startupFileTextfield.setBounds(new Rectangle(172, 310, 330, 20));
1114     startupFileTextfield.addMouseListener(new MouseAdapter()
1115     {
1116       public void mouseClicked(MouseEvent e)
1117       {
1118         if (e.getClickCount() > 1)
1119         {
1120           startupFileTextfield_mouseClicked();
1121         }
1122       }
1123     });
1124
1125     sortby.setFont(LABEL_FONT);
1126     sortby.setBounds(new Rectangle(172, 260, 155, 21));
1127     JLabel sortLabel = new JLabel();
1128     sortLabel.setFont(LABEL_FONT);
1129     sortLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1130     sortLabel.setText(MessageManager.getString("label.sort_by"));
1131     sortAnnBy.setFont(LABEL_FONT);
1132     sortAnnBy.setBounds(new Rectangle(172, 285, 110, 21));
1133     JLabel sortAnnLabel = new JLabel();
1134     sortAnnLabel.setFont(LABEL_FONT);
1135     sortAnnLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1136     sortAnnLabel.setText(MessageManager.getString("label.sort_ann_by"));
1137     sortAutocalc.setFont(LABEL_FONT);
1138     sortAutocalc.setBounds(new Rectangle(290, 285, 165, 21));
1139
1140     JPanel annsettingsPanel = new JPanel();
1141     annsettingsPanel.setBounds(new Rectangle(173, 34, 320, 75));
1142     annsettingsPanel.setLayout(new FlowLayout(FlowLayout.LEFT, 0, 0));
1143     annsettingsPanel.setBorder(new EtchedBorder());
1144     visualTab.add(annsettingsPanel);
1145     Border jb = new EmptyBorder(1, 1, 4, 5);
1146     quality.setBorder(jb);
1147     conservation.setBorder(jb);
1148     identity.setBorder(jb);
1149     showConsensbits.setBorder(jb);
1150     showGroupbits.setBorder(jb);
1151     showGroupConsensus.setBorder(jb);
1152     showGroupConservation.setBorder(jb);
1153     showConsensHistogram.setBorder(jb);
1154     showConsensLogo.setBorder(jb);
1155
1156     JPanel autoAnnotSettings = new JPanel();
1157     autoAnnotSettings.setLayout(new GridLayout(3, 3));
1158     annsettingsPanel.add(autoAnnotSettings);
1159     autoAnnotSettings.add(quality);
1160     autoAnnotSettings.add(conservation);
1161     autoAnnotSettings.add(identity);
1162     autoAnnotSettings.add(showGroupbits);
1163     autoAnnotSettings.add(showGroupConservation);
1164     autoAnnotSettings.add(showGroupConsensus);
1165     autoAnnotSettings.add(showConsensbits);
1166     autoAnnotSettings.add(showConsensHistogram);
1167     autoAnnotSettings.add(showConsensLogo);
1168
1169     JPanel tooltipSettings = new JPanel();
1170     tooltipSettings.setBorder(new TitledBorder(MessageManager
1171             .getString("label.sequence_id_tooltip")));
1172     tooltipSettings.setBounds(173, 140, 220, 62);
1173     tooltipSettings.setLayout(new GridLayout(2, 1));
1174     tooltipSettings.add(showDbRefTooltip);
1175     tooltipSettings.add(showNpTooltip);
1176     visualTab.add(tooltipSettings);
1177
1178     wrap.setFont(LABEL_FONT);
1179     wrap.setHorizontalAlignment(SwingConstants.TRAILING);
1180     wrap.setHorizontalTextPosition(SwingConstants.LEADING);
1181     wrap.setText(MessageManager.getString("label.wrap_alignment"));
1182     rightAlign.setFont(LABEL_FONT);
1183     rightAlign.setForeground(Color.black);
1184     rightAlign.setHorizontalAlignment(SwingConstants.RIGHT);
1185     rightAlign.setHorizontalTextPosition(SwingConstants.LEFT);
1186     rightAlign.setText(MessageManager.getString("label.right_align_ids"));
1187     idItalics.setFont(LABEL_FONT_ITALIC);
1188     idItalics.setHorizontalAlignment(SwingConstants.RIGHT);
1189     idItalics.setHorizontalTextPosition(SwingConstants.LEADING);
1190     idItalics.setText(MessageManager
1191             .getString("label.sequence_name_italics"));
1192     openoverv.setFont(LABEL_FONT);
1193     openoverv.setActionCommand(MessageManager
1194             .getString("label.open_overview"));
1195     openoverv.setHorizontalAlignment(SwingConstants.RIGHT);
1196     openoverv.setHorizontalTextPosition(SwingConstants.LEFT);
1197     openoverv.setText(MessageManager.getString(("label.open_overview")));
1198     JPanel jPanel2 = new JPanel();
1199     jPanel2.setBounds(new Rectangle(7, 17, 158, 310));
1200     jPanel2.setLayout(new GridLayout(14, 1));
1201     jPanel2.add(fullScreen);
1202     jPanel2.add(openoverv);
1203     jPanel2.add(seqLimit);
1204     jPanel2.add(rightAlign);
1205     jPanel2.add(fontLabel);
1206     jPanel2.add(showUnconserved);
1207     jPanel2.add(idItalics);
1208     jPanel2.add(smoothFont);
1209     jPanel2.add(scaleProteinToCdna);
1210     jPanel2.add(gapLabel);
1211     jPanel2.add(wrap);
1212     jPanel2.add(sortLabel);
1213     jPanel2.add(sortAnnLabel);
1214     jPanel2.add(startupCheckbox);
1215     visualTab.add(jPanel2);
1216     visualTab.add(annotations);
1217     visualTab.add(startupFileTextfield);
1218     visualTab.add(sortby);
1219     visualTab.add(sortAnnBy);
1220     visualTab.add(sortAutocalc);
1221     visualTab.add(gapSymbolCB);
1222     visualTab.add(fontNameCB);
1223     visualTab.add(fontSizeCB);
1224     visualTab.add(fontStyleCB);
1225     return visualTab;
1226   }
1227
1228   protected void autoIdWidth_actionPerformed()
1229   {
1230     // TODO Auto-generated method stub
1231
1232   }
1233
1234   protected void userIdWidth_actionPerformed()
1235   {
1236     // TODO Auto-generated method stub
1237
1238   }
1239
1240   protected void maxColour_actionPerformed(JPanel panel)
1241   {
1242   }
1243
1244   protected void minColour_actionPerformed(JPanel panel)
1245   {
1246   }
1247
1248   protected void showunconserved_actionPerformed(ActionEvent e)
1249   {
1250     // TODO Auto-generated method stub
1251
1252   }
1253
1254   /**
1255    * DOCUMENT ME!
1256    *
1257    * @param e
1258    *          DOCUMENT ME!
1259    */
1260   public void ok_actionPerformed(ActionEvent e)
1261   {
1262   }
1263
1264   /**
1265    * DOCUMENT ME!
1266    *
1267    * @param e
1268    *          DOCUMENT ME!
1269    */
1270   public void cancel_actionPerformed(ActionEvent e)
1271   {
1272   }
1273
1274   /**
1275    * DOCUMENT ME!
1276    *
1277    * @param e
1278    *          DOCUMENT ME!
1279    */
1280   public void annotations_actionPerformed(ActionEvent e)
1281   {
1282   }
1283
1284   /**
1285    * DOCUMENT ME!
1286    */
1287   public void startupFileTextfield_mouseClicked()
1288   {
1289   }
1290
1291   public void newLink_actionPerformed(ActionEvent e)
1292   {
1293
1294   }
1295
1296   public void editLink_actionPerformed(ActionEvent e)
1297   {
1298
1299   }
1300
1301   public void deleteLink_actionPerformed(ActionEvent e)
1302   {
1303
1304   }
1305
1306   public void defaultBrowser_mouseClicked(MouseEvent e)
1307   {
1308
1309   }
1310
1311   public void linkURLList_keyTyped(KeyEvent e)
1312   {
1313
1314   }
1315
1316   public void useProxy_actionPerformed()
1317   {
1318     proxyServerTB.setEnabled(useProxy.isSelected());
1319     proxyPortTB.setEnabled(useProxy.isSelected());
1320   }
1321
1322 }