src/jalview/jbgui/GPreferences.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
   3  * Copyright (C) 2014 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.util.MessageManager;
  26
  27 import java.awt.BorderLayout;
  28 import java.awt.Color;
  29 import java.awt.Component;
  30 import java.awt.Dimension;
  31 import java.awt.FlowLayout;
  32 import java.awt.Font;
  33 import java.awt.GridBagConstraints;
  34 import java.awt.GridBagLayout;
  35 import java.awt.GridLayout;
  36 import java.awt.Insets;
  37 import java.awt.Rectangle;
  38 import java.awt.event.ActionEvent;
  39 import java.awt.event.ActionListener;
  40 import java.awt.event.FocusEvent;
  41 import java.awt.event.KeyEvent;
  42 import java.awt.event.MouseAdapter;
  43 import java.awt.event.MouseEvent;
  44
  45 import javax.swing.BorderFactory;
  46 import javax.swing.DefaultListCellRenderer;
  47 import javax.swing.JButton;
  48 import javax.swing.JCheckBox;
  49 import javax.swing.JComboBox;
  50 import javax.swing.JFileChooser;
  51 import javax.swing.JLabel;
  52 import javax.swing.JList;
  53 import javax.swing.JPanel;
  54 import javax.swing.JScrollPane;
  55 import javax.swing.JTabbedPane;
  56 import javax.swing.JTextField;
  57 import javax.swing.ListSelectionModel;
  58 import javax.swing.SwingConstants;
  59 import javax.swing.border.Border;
  60 import javax.swing.border.EmptyBorder;
  61 import javax.swing.border.TitledBorder;
  62 import javax.swing.event.ChangeEvent;
  63 import javax.swing.event.ChangeListener;
  64 import javax.swing.event.ListSelectionEvent;
  65 import javax.swing.event.ListSelectionListener;
  66
  67 /**
  68  * Base class for the Preferences panel.
  69  *
  70  * @author $author$
  71  * @version $Revision$
  72  */
  73 public class GPreferences extends JPanel
  74 {
  75   private static final Font verdana11 = JvSwingUtils.getLabelFont();
  76
  77   /*
  78    * Visual tab components
  79    */
  80   protected JCheckBox fullScreen = new JCheckBox();
  81
  82   protected JCheckBox openoverv = new JCheckBox();
  83
  84   protected JCheckBox seqLimit = new JCheckBox();
  85
  86   protected JCheckBox rightAlign = new JCheckBox();
  87
  88   protected JComboBox<String> fontSizeCB = new JComboBox<String>();
  89
  90   protected JComboBox<String> fontStyleCB = new JComboBox<String>();
  91
  92   protected JComboBox<String> fontNameCB = new JComboBox<String>();
  93
  94   protected JCheckBox showUnconserved = new JCheckBox();
  95
  96   protected JCheckBox idItalics = new JCheckBox();
  97
  98   protected JCheckBox smoothFont = new JCheckBox();
  99
 100   protected JComboBox<String> gapSymbolCB = new JComboBox<String>();
 101
 102   protected JCheckBox wrap = new JCheckBox();
 103
 104   protected JComboBox<String> sortby = new JComboBox<String>();
 105
 106   protected JComboBox<String> sortAnnBy = new JComboBox<String>();
 107
 108   protected JComboBox<String> sortAutocalc = new JComboBox<String>();
 109
 110   protected JCheckBox startupCheckbox = new JCheckBox();
 111
 112   protected JTextField startupFileTextfield = new JTextField();
 113
 114   // below are in the 'second column'
 115   protected JCheckBox annotations = new JCheckBox();
 116
 117   protected JCheckBox quality = new JCheckBox();
 118
 119   protected JCheckBox conservation = new JCheckBox();
 120
 121   protected JCheckBox identity = new JCheckBox();
 122
 123   protected JCheckBox showGroupConsensus = new JCheckBox();
 124
 125   protected JCheckBox showGroupConservation = new JCheckBox();
 126
 127   protected JCheckBox showConsensHistogram = new JCheckBox();
 128
 129   protected JCheckBox showConsensLogo = new JCheckBox();
 130
 131   protected JCheckBox showDbRefTooltip = new JCheckBox();
 132
 133   protected JCheckBox showNpTooltip = new JCheckBox();
 134
 135   /*
 136    * Structure tab and components
 137    */
 138   protected JPanel structureTab;
 139
 140   protected JCheckBox structFromPdb = new JCheckBox();
 141
 142   protected JCheckBox useRnaView = new JCheckBox();
 143
 144   protected JCheckBox addSecondaryStructure = new JCheckBox();
 145
 146   protected JCheckBox addTempFactor = new JCheckBox();
 147
 148   protected JComboBox<String> structViewer = new JComboBox<String>();
 149
 150   protected JTextField chimeraPath = new JTextField();
 151
 152
 153   /*
 154    * Colours tab components
 155    */
 156   protected JPanel minColour = new JPanel();
 157
 158   protected JPanel maxColour = new JPanel();
 159
 160   protected JComboBox<String> colour = new JComboBox<String>();
 161
 162   /*
 163    * Connections tab components
 164    */
 165   protected JList linkURLList = new JList();
 166
 167   protected JTextField proxyServerTB = new JTextField();
 168
 169   protected JTextField proxyPortTB = new JTextField();
 170
 171   protected JTextField defaultBrowser = new JTextField();
 172
 173   protected JList linkNameList = new JList();
 174
 175   protected JCheckBox useProxy = new JCheckBox();
 176
 177   protected JCheckBox usagestats = new JCheckBox();
 178
 179   protected JCheckBox questionnaire = new JCheckBox();
 180
 181   protected JCheckBox versioncheck = new JCheckBox();
 182
 183   /*
 184    * Output tab components
 185    */
 186   protected JComboBox<String> epsRendering = new JComboBox<String>();
 187
 188   protected JLabel userIdWidthlabel = new JLabel();
 189
 190   protected JCheckBox autoIdWidth = new JCheckBox();
 191
 192   protected JTextField userIdWidth = new JTextField();
 193
 194   protected JCheckBox blcjv = new JCheckBox();
 195
 196   protected JCheckBox pileupjv = new JCheckBox();
 197
 198   protected JCheckBox clustaljv = new JCheckBox();
 199
 200   protected JCheckBox msfjv = new JCheckBox();
 201
 202   protected JCheckBox fastajv = new JCheckBox();
 203
 204   protected JCheckBox pfamjv = new JCheckBox();
 205
 206   protected JCheckBox pirjv = new JCheckBox();
 207
 208   protected JCheckBox modellerOutput = new JCheckBox();
 209
 210   /*
 211    * Editing tab components
 212    */
 213   protected JCheckBox autoCalculateConsCheck = new JCheckBox();
 214
 215   protected JCheckBox padGaps = new JCheckBox();
 216
 217   protected JCheckBox sortByTree = new JCheckBox();
 218
 219   /*
 220    * DAS Settings tab
 221    */
 222   protected JPanel dasTab = new JPanel();
 223
 224   /*
 225    * Web Services tab
 226    */
 227   protected JPanel wsTab = new JPanel();
 228
 229   /**
 230    * Creates a new GPreferences object.
 231    */
 232   public GPreferences()
 233   {
 234     try
 235     {
 236       jbInit();
 237     } catch (Exception ex)
 238     {
 239       ex.printStackTrace();
 240     }
 241   }
 242
 243   /**
 244    * Construct the panel and its tabbed sub-panels.
 245    *
 246    * @throws Exception
 247    */
 248   private void jbInit() throws Exception
 249   {
 250     final JTabbedPane tabbedPane = new JTabbedPane();
 251     this.setLayout(new BorderLayout());
 252     JPanel okCancelPanel = initOkCancelPanel();
 253     this.add(tabbedPane, BorderLayout.CENTER);
 254     this.add(okCancelPanel, BorderLayout.SOUTH);
 255
 256     tabbedPane.add(initVisualTab(),
 257             MessageManager.getString("label.visual"));
 258
 259     tabbedPane.add(initColoursTab(),
 260             MessageManager.getString("label.colours"));
 261
 262     tabbedPane.add(initStructureTab(),
 263             MessageManager.getString("label.structure"));
 264
 265     tabbedPane.add(initConnectionsTab(),
 266             MessageManager.getString("label.connections"));
 267
 268     tabbedPane.add(initOutputTab(), MessageManager.getString("label.output"));
 269
 270     tabbedPane.add(initEditingTab(), MessageManager.getString("label.editing"));
 271
 272     /*
 273      * See DasSourceBrowser for the real work of configuring this tab.
 274      */
 275     dasTab.setLayout(new BorderLayout());
 276     tabbedPane
 277             .add(dasTab, MessageManager.getString("label.das_settings"));
 278
 279     /*
 280      * See WsPreferences for the real work of configuring this tab.
 281      */
 282     wsTab.setLayout(new BorderLayout());
 283     tabbedPane.add(wsTab, MessageManager.getString("label.web_services"));
 284
 285     /*
 286      * Handler to validate a tab before leaving it - currently only for
 287      * Structure.
 288      */
 289     tabbedPane.addChangeListener(new ChangeListener()
 290     {
 291       private Component lastTab;
 292
 293       @Override
 294       public void stateChanged(ChangeEvent e)
 295       {
 296         if (lastTab == structureTab
 297                 && tabbedPane.getSelectedComponent() != structureTab)
 298         {
 299           if (!validateStructure())
 300           {
 301             tabbedPane.setSelectedComponent(structureTab);
 302             return;
 303           }
 304         }
 305         lastTab = tabbedPane.getSelectedComponent();
 306       }
 307
 308     });
 309   }
 310
 311   /**
 312    * Initialises the Editing tabbed panel.
 313    *
 314    * @return
 315    */
 316   private JPanel initEditingTab()
 317   {
 318     JPanel editingTab = new JPanel();
 319     editingTab.setLayout(null);
 320     autoCalculateConsCheck.setFont(verdana11);
 321     autoCalculateConsCheck.setText(MessageManager
 322             .getString("label.autocalculate_consensus"));
 323     autoCalculateConsCheck.setBounds(new Rectangle(21, 52, 209, 23));
 324     padGaps.setFont(verdana11);
 325     padGaps.setText(MessageManager.getString("label.pad_gaps_when_editing"));
 326     padGaps.setBounds(new Rectangle(22, 94, 168, 23));
 327     sortByTree.setFont(verdana11);
 328     sortByTree
 329             .setText(MessageManager.getString("label.sort_with_new_tree"));
 330     sortByTree
 331             .setToolTipText(MessageManager
 332                     .getString("label.any_trees_calculated_or_loaded_alignment_automatically_sort"));
 333     sortByTree.setBounds(new Rectangle(22, 136, 168, 23));
 334     editingTab.add(autoCalculateConsCheck);
 335     editingTab.add(padGaps);
 336     editingTab.add(sortByTree);
 337     return editingTab;
 338   }
 339
 340   /**
 341    * Initialises the Output tabbed panel.
 342    *
 343    * @return
 344    */
 345   private JPanel initOutputTab()
 346   {
 347     JPanel outputTab = new JPanel();
 348     outputTab.setLayout(null);
 349     JLabel epsLabel = new JLabel();
 350     epsLabel.setFont(verdana11);
 351     epsLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 352     epsLabel.setText(MessageManager.getString("label.eps_rendering_style"));
 353     epsLabel.setBounds(new Rectangle(9, 31, 140, 24));
 354     epsRendering.setFont(verdana11);
 355     epsRendering.setBounds(new Rectangle(154, 34, 187, 21));
 356     JLabel jLabel1 = new JLabel();
 357     jLabel1.setFont(verdana11);
 358     jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
 359     jLabel1.setText(MessageManager.getString("label.append_start_end"));
 360     jLabel1.setFont(verdana11);
 361     fastajv.setFont(verdana11);
 362     fastajv.setHorizontalAlignment(SwingConstants.LEFT);
 363     clustaljv.setText(MessageManager.getString("label.clustal") + "     ");
 364     blcjv.setText(MessageManager.getString("label.blc") + "     ");
 365     fastajv.setText(MessageManager.getString("label.fasta") + "     ");
 366     msfjv.setText(MessageManager.getString("label.msf") + "     ");
 367     pfamjv.setText(MessageManager.getString("label.pfam") + "     ");
 368     pileupjv.setText(MessageManager.getString("label.pileup") + "     ");
 369     msfjv.setFont(verdana11);
 370     msfjv.setHorizontalAlignment(SwingConstants.LEFT);
 371     pirjv.setText(MessageManager.getString("label.pir") + "     ");
 372     JPanel jPanel11 = new JPanel();
 373     jPanel11.setFont(verdana11);
 374     TitledBorder titledBorder2 = new TitledBorder(
 375             MessageManager.getString("label.file_output"));
 376     jPanel11.setBorder(titledBorder2);
 377     jPanel11.setBounds(new Rectangle(30, 72, 196, 182));
 378     GridLayout gridLayout3 = new GridLayout();
 379     jPanel11.setLayout(gridLayout3);
 380     gridLayout3.setRows(8);
 381     blcjv.setFont(verdana11);
 382     blcjv.setHorizontalAlignment(SwingConstants.LEFT);
 383     clustaljv.setFont(verdana11);
 384     clustaljv.setHorizontalAlignment(SwingConstants.LEFT);
 385     pfamjv.setFont(verdana11);
 386     pfamjv.setHorizontalAlignment(SwingConstants.LEFT);
 387     pileupjv.setFont(verdana11);
 388     pileupjv.setHorizontalAlignment(SwingConstants.LEFT);
 389     pirjv.setFont(verdana11);
 390     pirjv.setHorizontalAlignment(SwingConstants.LEFT);
 391     autoIdWidth.setFont(verdana11);
 392     autoIdWidth.setText(MessageManager
 393             .getString("label.automatically_set_id_width"));
 394     autoIdWidth
 395             .setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.getString("label.adjusts_width_generated_eps_png")));
 396     autoIdWidth.setBounds(new Rectangle(228, 96, 188, 23));
 397     autoIdWidth.addActionListener(new ActionListener()
 398     {
 399
 400       @Override
 401       public void actionPerformed(ActionEvent e)
 402       {
 403         autoIdWidth_actionPerformed();
 404       }
 405     });
 406     userIdWidthlabel.setFont(verdana11);
 407     userIdWidthlabel.setText(MessageManager
 408             .getString("label.figure_id_column_width"));
 409     userIdWidth
 410             .setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.getString("label.manually_specify_width_left_column")));
 411     userIdWidthlabel
 412             .setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.getString("label.manually_specify_width_left_column")));
 413     userIdWidthlabel.setBounds(new Rectangle(236, 120, 168, 23));
 414     userIdWidth.setFont(JvSwingUtils.getTextAreaFont());
 415     userIdWidth.setText("");
 416     userIdWidth.setBounds(new Rectangle(232, 144, 84, 23));
 417     userIdWidth.addActionListener(new ActionListener()
 418     {
 419
 420       @Override
 421       public void actionPerformed(ActionEvent e)
 422       {
 423         userIdWidth_actionPerformed();
 424       }
 425     });
 426     jPanel11.add(jLabel1);
 427     jPanel11.add(blcjv);
 428     jPanel11.add(clustaljv);
 429     jPanel11.add(fastajv);
 430     jPanel11.add(msfjv);
 431     jPanel11.add(pfamjv);
 432     jPanel11.add(pileupjv);
 433     jPanel11.add(pirjv);
 434     outputTab.add(autoIdWidth);
 435     outputTab.add(userIdWidth);
 436     outputTab.add(userIdWidthlabel);
 437     outputTab.add(modellerOutput);
 438     outputTab.add(epsLabel);
 439     outputTab.add(epsRendering);
 440     outputTab.add(jPanel11);
 441     modellerOutput.setFont(verdana11);
 442     modellerOutput.setText(MessageManager
 443             .getString("label.use_modeller_output"));
 444     modellerOutput.setBounds(new Rectangle(228, 226, 168, 23));
 445     return outputTab;
 446   }
 447
 448   /**
 449    * Initialises the Connections tabbed panel.
 450    *
 451    * @return
 452    */
 453   private JPanel initConnectionsTab()
 454   {
 455     JPanel connectTab = new JPanel();
 456     connectTab.setLayout(new GridBagLayout());
 457     JLabel serverLabel = new JLabel();
 458     serverLabel.setText(MessageManager.getString("label.address"));
 459     serverLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 460     serverLabel.setFont(verdana11);
 461     proxyServerTB.setFont(verdana11);
 462     proxyPortTB.setFont(verdana11);
 463     JLabel portLabel = new JLabel();
 464     portLabel.setFont(verdana11);
 465     portLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 466     portLabel.setText(MessageManager.getString("label.port"));
 467     JLabel browserLabel = new JLabel();
 468     browserLabel.setFont(new java.awt.Font("SansSerif", 0, 11));
 469     browserLabel.setHorizontalAlignment(SwingConstants.TRAILING);
 470     browserLabel.setText(MessageManager
 471             .getString("label.default_browser_unix"));
 472     defaultBrowser.setFont(verdana11);
 473     defaultBrowser.setText("");
 474     usagestats.setText(MessageManager
 475             .getString("label.send_usage_statistics"));
 476     usagestats.setFont(verdana11);
 477     usagestats.setHorizontalAlignment(SwingConstants.RIGHT);
 478     usagestats.setHorizontalTextPosition(SwingConstants.LEADING);
 479     questionnaire.setText(MessageManager
 480             .getString("label.check_for_questionnaires"));
 481     questionnaire.setFont(verdana11);
 482     questionnaire.setHorizontalAlignment(SwingConstants.RIGHT);
 483     questionnaire.setHorizontalTextPosition(SwingConstants.LEADING);
 484     versioncheck.setText(MessageManager
 485             .getString("label.check_for_latest_version"));
 486     versioncheck.setFont(verdana11);
 487     versioncheck.setHorizontalAlignment(SwingConstants.RIGHT);
 488     versioncheck.setHorizontalTextPosition(SwingConstants.LEADING);
 489     JButton newLink = new JButton();
 490     newLink.setText(MessageManager.getString("action.new"));
 491     newLink.addActionListener(new java.awt.event.ActionListener()
 492     {
 493       public void actionPerformed(ActionEvent e)
 494       {
 495         newLink_actionPerformed(e);
 496       }
 497     });
 498     JButton editLink = new JButton();
 499     editLink.setText(MessageManager.getString("action.edit"));
 500     editLink.addActionListener(new java.awt.event.ActionListener()
 501     {
 502       public void actionPerformed(ActionEvent e)
 503       {
 504         editLink_actionPerformed(e);
 505       }
 506     });
 507     JButton deleteLink = new JButton();
 508     deleteLink.setText(MessageManager.getString("action.delete"));
 509     deleteLink.addActionListener(new java.awt.event.ActionListener()
 510     {
 511       public void actionPerformed(ActionEvent e)
 512       {
 513         deleteLink_actionPerformed(e);
 514       }
 515     });
 516
 517     linkURLList.addListSelectionListener(new ListSelectionListener()
 518     {
 519       public void valueChanged(ListSelectionEvent e)
 520       {
 521         int index = linkURLList.getSelectedIndex();
 522         linkNameList.setSelectedIndex(index);
 523       }
 524     });
 525
 526     linkNameList.addListSelectionListener(new ListSelectionListener()
 527     {
 528       public void valueChanged(ListSelectionEvent e)
 529       {
 530         int index = linkNameList.getSelectedIndex();
 531         linkURLList.setSelectedIndex(index);
 532       }
 533     });
 534
 535     JScrollPane linkScrollPane = new JScrollPane();
 536     linkScrollPane.setBorder(null);
 537     JPanel linkPanel = new JPanel();
 538     linkPanel.setBorder(new TitledBorder(MessageManager
 539             .getString("label.url_linkfrom_sequence_id")));
 540     linkPanel.setLayout(new BorderLayout());
 541     GridLayout gridLayout1 = new GridLayout();
 542     JPanel editLinkButtons = new JPanel();
 543     editLinkButtons.setLayout(gridLayout1);
 544     gridLayout1.setRows(3);
 545     linkNameList.setFont(verdana11);
 546     linkNameList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
 547     BorderLayout borderLayout3 = new BorderLayout();
 548     JPanel linkPanel2 = new JPanel();
 549     linkPanel2.setLayout(borderLayout3);
 550     linkURLList.setFont(verdana11);
 551     linkURLList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
 552
 553     defaultBrowser.addMouseListener(new MouseAdapter()
 554     {
 555       public void mouseClicked(MouseEvent e)
 556       {
 557         if (e.getClickCount() > 1)
 558         {
 559           defaultBrowser_mouseClicked(e);
 560         }
 561       }
 562     });
 563     useProxy.setFont(verdana11);
 564     useProxy.setHorizontalAlignment(SwingConstants.RIGHT);
 565     useProxy.setHorizontalTextPosition(SwingConstants.LEADING);
 566     useProxy.setText(MessageManager.getString("label.use_proxy_server"));
 567     useProxy.addActionListener(new ActionListener()
 568     {
 569       public void actionPerformed(ActionEvent e)
 570       {
 571         useProxy_actionPerformed();
 572       }
 573     });
 574     linkPanel.add(editLinkButtons, BorderLayout.EAST);
 575     editLinkButtons.add(newLink, null);
 576     editLinkButtons.add(editLink, null);
 577     editLinkButtons.add(deleteLink, null);
 578     linkPanel.add(linkScrollPane, BorderLayout.CENTER);
 579     linkScrollPane.getViewport().add(linkPanel2, null);
 580     linkPanel2.add(linkURLList, BorderLayout.CENTER);
 581     linkPanel2.add(linkNameList, BorderLayout.WEST);
 582     JPanel jPanel1 = new JPanel();
 583     TitledBorder titledBorder1 = new TitledBorder(
 584             MessageManager.getString("label.proxy_server"));
 585     jPanel1.setBorder(titledBorder1);
 586     jPanel1.setLayout(new GridBagLayout());
 587     jPanel1.add(serverLabel, new GridBagConstraints(0, 1, 1, 1, 0.0, 0.0,
 588             GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
 589                     2, 4, 0), 5, 0));
 590     jPanel1.add(portLabel, new GridBagConstraints(2, 1, 1, 1, 0.0, 0.0,
 591             GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
 592                     0, 4, 0), 11, 6));
 593     connectTab.add(linkPanel, new GridBagConstraints(0, 0, 2, 1, 1.0, 1.0,
 594             GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(
 595                     16, 0, 0, 12), 359, -17));
 596     connectTab.add(jPanel1, new GridBagConstraints(0, 2, 2, 1, 1.0, 1.0,
 597             GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(
 598                     21, 0, 35, 12), 4, 6));
 599     connectTab.add(browserLabel, new GridBagConstraints(0, 1, 1, 1, 0.0,
 600             0.0, GridBagConstraints.WEST, GridBagConstraints.NONE,
 601             new Insets(16, 0, 0, 0), 5, 1));
 602     jPanel1.add(useProxy, new GridBagConstraints(0, 0, 2, 1, 0.0, 0.0,
 603             GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
 604                     2, 5, 185), 2, -4));
 605     jPanel1.add(proxyPortTB, new GridBagConstraints(3, 1, 1, 1, 1.0, 0.0,
 606             GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 607             new Insets(0, 2, 4, 2), 54, 1));
 608     jPanel1.add(proxyServerTB, new GridBagConstraints(1, 1, 1, 1, 1.0, 0.0,
 609             GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 610             new Insets(0, 2, 4, 0), 263, 1));
 611     connectTab.add(defaultBrowser, new GridBagConstraints(1, 1, 1, 1, 1.0,
 612             0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 613             new Insets(15, 0, 0, 15), 307, 1));
 614     connectTab.add(usagestats, new GridBagConstraints(0, 4, 1, 1, 1.0, 0.0,
 615             GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 616             new Insets(0, 2, 4, 2), 70, 1));
 617     connectTab.add(questionnaire, new GridBagConstraints(1, 4, 1, 1, 1.0,
 618             0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 619             new Insets(0, 2, 4, 2), 70, 1));
 620     connectTab.add(versioncheck, new GridBagConstraints(0, 5, 1, 1, 1.0,
 621             0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 622             new Insets(0, 2, 4, 2), 70, 1));
 623     return connectTab;
 624   }
 625
 626   /**
 627    * Initialises the parent panel which contains the tabbed sections.
 628    *
 629    * @return
 630    */
 631   private JPanel initOkCancelPanel()
 632   {
 633     JButton ok = new JButton();
 634     ok.setText(MessageManager.getString("action.ok"));
 635     ok.addActionListener(new ActionListener()
 636     {
 637       public void actionPerformed(ActionEvent e)
 638       {
 639         ok_actionPerformed(e);
 640       }
 641     });
 642     JButton cancel = new JButton();
 643     cancel.setText(MessageManager.getString("action.cancel"));
 644     cancel.addActionListener(new ActionListener()
 645     {
 646       public void actionPerformed(ActionEvent e)
 647       {
 648         cancel_actionPerformed(e);
 649       }
 650     });
 651     JPanel okCancelPanel = new JPanel();
 652     okCancelPanel.add(ok);
 653     okCancelPanel.add(cancel);
 654     return okCancelPanel;
 655   }
 656
 657   /**
 658    * Initialises the Colours tabbed panel.
 659    *
 660    * @return
 661    */
 662   private JPanel initColoursTab()
 663   {
 664     JPanel coloursTab = new JPanel();
 665     coloursTab.setBorder(new TitledBorder(MessageManager
 666             .getString("action.open_new_alignment")));
 667     coloursTab.setLayout(new FlowLayout());
 668     JLabel mincolourLabel = new JLabel();
 669     mincolourLabel.setFont(verdana11);
 670     mincolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 671     mincolourLabel.setText(MessageManager.getString("label.min_colour"));
 672     minColour.setFont(verdana11);
 673     minColour.setBorder(BorderFactory.createEtchedBorder());
 674     minColour.setPreferredSize(new Dimension(40, 20));
 675     minColour.addMouseListener(new MouseAdapter()
 676     {
 677       public void mousePressed(MouseEvent e)
 678       {
 679         minColour_actionPerformed(minColour);
 680       }
 681     });
 682     JLabel maxcolourLabel = new JLabel();
 683     maxcolourLabel.setFont(verdana11);
 684     maxcolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 685     maxcolourLabel.setText(MessageManager.getString("label.max_colour"));
 686     maxColour.setFont(verdana11);
 687     maxColour.setBorder(BorderFactory.createEtchedBorder());
 688     maxColour.setPreferredSize(new Dimension(40, 20));
 689     maxColour.addMouseListener(new MouseAdapter()
 690     {
 691       public void mousePressed(MouseEvent e)
 692       {
 693         maxColour_actionPerformed(maxColour);
 694       }
 695     });
 696     colour.setFont(verdana11);
 697     colour.setBounds(new Rectangle(172, 225, 155, 21));
 698     JLabel colourLabel = new JLabel();
 699     colourLabel.setFont(verdana11);
 700     colourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 701     colourLabel.setText(MessageManager.getString("label.alignment_colour")
 702             + " ");
 703     JvSwingUtils.addtoLayout(coloursTab, MessageManager
 704             .getString("label.default_colour_scheme_for_alignment"),
 705             colourLabel, colour);
 706     JPanel annotationShding = new JPanel();
 707     annotationShding.setBorder(new TitledBorder(MessageManager
 708             .getString("label.annotation_shading_default")));
 709     annotationShding.setLayout(new GridLayout(1, 2));
 710     JvSwingUtils.addtoLayout(annotationShding, MessageManager
 711             .getString("label.default_minimum_colour_annotation_shading"),
 712             mincolourLabel, minColour);
 713     JvSwingUtils.addtoLayout(annotationShding, MessageManager
 714             .getString("label.default_maximum_colour_annotation_shading"),
 715             maxcolourLabel, maxColour);
 716     coloursTab.add(annotationShding); // , FlowLayout.LEFT);
 717     return coloursTab;
 718   }
 719
 720   /**
 721    * Initialises the Structure tabbed panel.
 722    *
 723    * @return
 724    */
 725   private JPanel initStructureTab()
 726   {
 727     structureTab = new JPanel();
 728
 729     structureTab.setBorder(new TitledBorder(MessageManager
 730             .getString("label.structure_options")));
 731     structureTab.setLayout(null);
 732     final int width = 400;
 733     final int height = 22;
 734     final int lineSpacing = 25;
 735     int ypos = 30;
 736
 737     structFromPdb.setFont(verdana11);
 738     structFromPdb.setText(MessageManager.getString("label.struct_from_pdb"));
 739     structFromPdb.setBounds(new Rectangle(5, ypos, width, height));
 740     structFromPdb.addActionListener(new ActionListener()
 741     {
 742       @Override
 743       public void actionPerformed(ActionEvent e)
 744       {
 745         boolean selected = structFromPdb.isSelected();
 746         // enable other options only when the first is checked
 747         useRnaView.setEnabled(selected);
 748         addSecondaryStructure.setEnabled(selected);
 749         addTempFactor.setEnabled(selected);
 750       }
 751     });
 752     structureTab.add(structFromPdb);
 753
 754     // indent checkboxes that are conditional on the first one
 755     ypos += lineSpacing;
 756     useRnaView.setFont(verdana11);
 757     useRnaView.setText(MessageManager.getString("label.use_rnaview"));
 758     useRnaView.setBounds(new Rectangle(25, ypos, width, height));
 759     structureTab.add(useRnaView);
 760
 761     ypos += lineSpacing;
 762     addSecondaryStructure.setFont(verdana11);
 763     addSecondaryStructure.setText(MessageManager
 764             .getString("label.autoadd_secstr"));
 765     addSecondaryStructure.setBounds(new Rectangle(25, ypos, width, height));
 766     structureTab.add(addSecondaryStructure);
 767
 768     ypos += lineSpacing;
 769     addTempFactor.setFont(verdana11);
 770     addTempFactor.setText(MessageManager.getString("label.autoadd_temp"));
 771     addTempFactor.setBounds(new Rectangle(25, ypos, width, height));
 772     structureTab.add(addTempFactor);
 773
 774     ypos += lineSpacing;
 775     JLabel viewerLabel = new JLabel();
 776     viewerLabel.setFont(verdana11);
 777     viewerLabel.setHorizontalAlignment(SwingConstants.LEFT);
 778     viewerLabel.setText(MessageManager.getString("label.structure_viewer"));
 779     viewerLabel.setBounds(new Rectangle(10, ypos, 200, height));
 780     structureTab.add(viewerLabel);
 781
 782     structViewer.setFont(verdana11);
 783     structViewer.setBounds(new Rectangle(160, ypos, 120, height));
 784     structViewer.addItem(ViewerType.JMOL.name());
 785     structViewer.addItem(ViewerType.CHIMERA.name());
 786     structViewer.addActionListener(new ActionListener()
 787     {
 788       @Override
 789       public void actionPerformed(ActionEvent e)
 790       {
 791         structureViewer_actionPerformed((String) structViewer
 792                 .getSelectedItem());
 793       }
 794     });
 795     structureTab.add(structViewer);
 796
 797     ypos += lineSpacing;
 798     JLabel pathLabel = new JLabel();
 799     pathLabel.setFont(new java.awt.Font("SansSerif", 0, 11));
 800     pathLabel.setHorizontalAlignment(SwingConstants.LEFT);
 801     pathLabel.setText(MessageManager.getString("label.chimera_path"));
 802     final String tooltip = JvSwingUtils.wrapTooltip(true,
 803             MessageManager.getString("label.chimera_path_tip"));
 804     pathLabel.setToolTipText(tooltip);
 805     pathLabel.setBounds(new Rectangle(10, ypos, 140, height));
 806     structureTab.add(pathLabel);
 807
 808     chimeraPath.setFont(verdana11);
 809     chimeraPath.setText("");
 810     chimeraPath.setBounds(new Rectangle(160, ypos, 300, height));
 811     chimeraPath.addMouseListener(new MouseAdapter()
 812     {
 813       @Override
 814       public void mouseClicked(MouseEvent e)
 815       {
 816         if (e.getClickCount() == 2)
 817         {
 818           String chosen = openFileChooser();
 819           if (chosen != null)
 820           {
 821             chimeraPath.setText(chosen);
 822           }
 823         }
 824       }
 825     });
 826     structureTab.add(chimeraPath);
 827
 828     ypos += lineSpacing;
 829     // scrl_pdbDocFieldConfig.setPreferredSize(new Dimension(450, 100));
 830     // scrl_pdbDocFieldConfig
 831     // .setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_NEVER);
 832     // scrl_pdbDocFieldConfig.setBounds();
 833     PDBDocFieldPreferences docFieldPref = new PDBDocFieldPreferences(
 834             new Rectangle(10, ypos + 5, 450, 120));
 835     structureTab.add(docFieldPref);
 836
 837
 838
 839
 840     return structureTab;
 841   }
 842
 843
 844   /**
 845    * Action on choosing a structure viewer from combobox options.
 846    *
 847    * @param selectedItem
 848    */
 849   protected void structureViewer_actionPerformed(String selectedItem)
 850   {
 851   }
 852
 853   /**
 854    * Show a dialog for the user to choose a file. Returns the chosen path, or
 855    * null on Cancel.
 856    *
 857    * @return
 858    */
 859   protected String openFileChooser()
 860   {
 861     String choice = null;
 862     JFileChooser chooser = new JFileChooser();
 863
 864     // chooser.setFileView(new JalviewFileView());
 865     chooser.setDialogTitle(MessageManager
 866             .getString("label.open_local_file"));
 867     chooser.setToolTipText(MessageManager.getString("action.open"));
 868
 869     int value = chooser.showOpenDialog(this);
 870
 871     if (value == JFileChooser.APPROVE_OPTION)
 872     {
 873       choice = chooser.getSelectedFile().getPath();
 874     }
 875     return choice;
 876   }
 877
 878   /**
 879    * Validate the structure tab preferences; if invalid, set focus on this tab.
 880    *
 881    * @param e
 882    */
 883   protected boolean validateStructure(FocusEvent e)
 884   {
 885     if (!validateStructure())
 886     {
 887       e.getComponent().requestFocusInWindow();
 888       return false;
 889     }
 890     return true;
 891   }
 892
 893   protected boolean validateStructure()
 894   {
 895     return false;
 896   }
 897
 898   /**
 899    * Initialises the Visual tabbed panel.
 900    *
 901    * @return
 902    */
 903   private JPanel initVisualTab()
 904   {
 905     JPanel visualTab = new JPanel();
 906     visualTab.setBorder(new TitledBorder(MessageManager
 907             .getString("action.open_new_alignment")));
 908     visualTab.setLayout(null);
 909     fullScreen.setFont(verdana11);
 910     fullScreen.setHorizontalAlignment(SwingConstants.RIGHT);
 911     fullScreen.setHorizontalTextPosition(SwingConstants.LEFT);
 912     fullScreen.setText(MessageManager.getString("label.maximize_window"));
 913     quality.setEnabled(false);
 914     quality.setFont(verdana11);
 915     quality.setHorizontalAlignment(SwingConstants.RIGHT);
 916     quality.setHorizontalTextPosition(SwingConstants.LEFT);
 917     quality.setSelected(true);
 918     quality.setText(MessageManager.getString("label.quality"));
 919     conservation.setEnabled(false);
 920     conservation.setFont(verdana11);
 921     conservation.setHorizontalAlignment(SwingConstants.RIGHT);
 922     conservation.setHorizontalTextPosition(SwingConstants.LEFT);
 923     conservation.setSelected(true);
 924     conservation.setText(MessageManager.getString("label.conservation"));
 925     identity.setEnabled(false);
 926     identity.setFont(verdana11);
 927     identity.setHorizontalAlignment(SwingConstants.RIGHT);
 928     identity.setHorizontalTextPosition(SwingConstants.LEFT);
 929     identity.setSelected(true);
 930     identity.setText(MessageManager.getString("label.consensus"));
 931     JLabel showGroupbits = new JLabel();
 932     showGroupbits.setFont(verdana11);
 933     showGroupbits.setHorizontalAlignment(SwingConstants.RIGHT);
 934     showGroupbits.setHorizontalTextPosition(SwingConstants.LEFT);
 935     showGroupbits.setText(MessageManager.getString("action.show_group")
 936             + ":");
 937     JLabel showConsensbits = new JLabel();
 938     showConsensbits.setFont(verdana11);
 939     showConsensbits.setHorizontalAlignment(SwingConstants.RIGHT);
 940     showConsensbits.setHorizontalTextPosition(SwingConstants.LEFT);
 941     showConsensbits.setText(MessageManager.getString("label.consensus")
 942             + ":");
 943     showConsensHistogram.setEnabled(false);
 944     showConsensHistogram.setFont(verdana11);
 945     showConsensHistogram.setHorizontalAlignment(SwingConstants.RIGHT);
 946     showConsensHistogram.setHorizontalTextPosition(SwingConstants.LEFT);
 947     showConsensHistogram.setSelected(true);
 948     showConsensHistogram.setText(MessageManager
 949             .getString("label.histogram"));
 950     showConsensLogo.setEnabled(false);
 951     showConsensLogo.setFont(verdana11);
 952     showConsensLogo.setHorizontalAlignment(SwingConstants.RIGHT);
 953     showConsensLogo.setHorizontalTextPosition(SwingConstants.LEFT);
 954     showConsensLogo.setSelected(true);
 955     showConsensLogo.setText(MessageManager.getString("label.logo"));
 956     showGroupConsensus.setEnabled(false);
 957     showGroupConsensus.setFont(verdana11);
 958     showGroupConsensus.setHorizontalAlignment(SwingConstants.RIGHT);
 959     showGroupConsensus.setHorizontalTextPosition(SwingConstants.LEFT);
 960     showGroupConsensus.setSelected(true);
 961     showGroupConsensus.setText(MessageManager.getString("label.consensus"));
 962     showGroupConservation.setEnabled(false);
 963     showGroupConservation.setFont(verdana11);
 964     showGroupConservation.setHorizontalAlignment(SwingConstants.RIGHT);
 965     showGroupConservation.setHorizontalTextPosition(SwingConstants.LEFT);
 966     showGroupConservation.setSelected(true);
 967     showGroupConservation.setText(MessageManager
 968             .getString("label.conservation"));
 969     showNpTooltip.setEnabled(true);
 970     showNpTooltip.setFont(verdana11);
 971     showNpTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
 972     showNpTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
 973     showNpTooltip.setSelected(true);
 974     showNpTooltip.setText(MessageManager
 975             .getString("label.non_positional_features"));
 976     showDbRefTooltip.setEnabled(true);
 977     showDbRefTooltip.setFont(verdana11);
 978     showDbRefTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
 979     showDbRefTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
 980     showDbRefTooltip.setSelected(true);
 981     showDbRefTooltip.setText(MessageManager
 982             .getString("label.database_references"));
 983     annotations.setFont(verdana11);
 984     annotations.setHorizontalAlignment(SwingConstants.RIGHT);
 985     annotations.setHorizontalTextPosition(SwingConstants.LEADING);
 986     annotations.setSelected(true);
 987     annotations.setText(MessageManager.getString("label.show_annotations"));
 988     annotations.setBounds(new Rectangle(169, 12, 200, 23));
 989     annotations.addActionListener(new ActionListener()
 990     {
 991       public void actionPerformed(ActionEvent e)
 992       {
 993         annotations_actionPerformed(e);
 994       }
 995     });
 996     identity.addActionListener(new ActionListener()
 997     {
 998       public void actionPerformed(ActionEvent e)
 999       {
1000         annotations_actionPerformed(e);
1001       }
1002     });
1003     showGroupConsensus.addActionListener(new ActionListener()
1004     {
1005       public void actionPerformed(ActionEvent e)
1006       {
1007         annotations_actionPerformed(e);
1008       }
1009     });
1010     showUnconserved.setFont(verdana11);
1011     showUnconserved.setHorizontalAlignment(SwingConstants.RIGHT);
1012     showUnconserved.setHorizontalTextPosition(SwingConstants.LEFT);
1013     showUnconserved.setSelected(true);
1014     showUnconserved.setText(MessageManager
1015             .getString("action.show_unconserved"));
1016     showUnconserved.addActionListener(new ActionListener()
1017     {
1018       public void actionPerformed(ActionEvent e)
1019       {
1020         showunconserved_actionPerformed(e);
1021       }
1022     });
1023
1024     // TODO these are not yet added to / action from Preferences
1025     // JCheckBox shareSelections = new JCheckBox();
1026     // shareSelections.setFont(verdana11);
1027     // shareSelections.setHorizontalAlignment(SwingConstants.RIGHT);
1028     // shareSelections.setHorizontalTextPosition(SwingConstants.LEFT);
1029     // shareSelections.setSelected(true);
1030     // shareSelections.setText(MessageManager
1031     // .getString("label.share_selection_across_views"));
1032     // JCheckBox followHighlight = new JCheckBox();
1033     // followHighlight.setFont(verdana11);
1034     // followHighlight.setHorizontalAlignment(SwingConstants.RIGHT);
1035     // followHighlight.setHorizontalTextPosition(SwingConstants.LEFT);
1036     // // showUnconserved.setBounds(new Rectangle(169, 40, 200, 23));
1037     // followHighlight.setSelected(true);
1038     // followHighlight.setText(MessageManager
1039     // .getString("label.scroll_highlighted_regions"));
1040
1041     seqLimit.setFont(verdana11);
1042     seqLimit.setHorizontalAlignment(SwingConstants.RIGHT);
1043     seqLimit.setHorizontalTextPosition(SwingConstants.LEFT);
1044     seqLimit.setText(MessageManager.getString("label.full_sequence_id"));
1045     smoothFont.setFont(verdana11);
1046     smoothFont.setHorizontalAlignment(SwingConstants.RIGHT);
1047     smoothFont.setHorizontalTextPosition(SwingConstants.LEADING);
1048     smoothFont.setText(MessageManager.getString("label.smooth_font"));
1049     JLabel gapLabel = new JLabel();
1050     gapLabel.setFont(verdana11);
1051     gapLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1052     gapLabel.setText(MessageManager.getString("label.gap_symbol") + " ");
1053     JLabel fontLabel = new JLabel();
1054     fontLabel.setFont(verdana11);
1055     fontLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1056     fontLabel.setText(MessageManager.getString("label.font"));
1057     fontSizeCB.setFont(verdana11);
1058     fontSizeCB.setBounds(new Rectangle(320, 104, 65, 23));
1059     fontStyleCB.setFont(verdana11);
1060     fontStyleCB.setBounds(new Rectangle(382, 104, 80, 23));
1061     fontNameCB.setFont(verdana11);
1062     fontNameCB.setBounds(new Rectangle(172, 104, 147, 23));
1063     gapSymbolCB.setFont(verdana11);
1064     gapSymbolCB.setBounds(new Rectangle(172, 196, 69, 23));
1065     DefaultListCellRenderer dlcr = new DefaultListCellRenderer();
1066     dlcr.setHorizontalAlignment(DefaultListCellRenderer.CENTER);
1067     gapSymbolCB.setRenderer(dlcr);
1068
1069     startupCheckbox.setText(MessageManager.getString("action.open_file"));
1070     startupCheckbox.setFont(verdana11);
1071     startupCheckbox.setHorizontalAlignment(SwingConstants.RIGHT);
1072     startupCheckbox.setHorizontalTextPosition(SwingConstants.LEFT);
1073     startupCheckbox.setSelected(true);
1074     startupFileTextfield.setFont(verdana11);
1075     startupFileTextfield.setBounds(new Rectangle(172, 290, 270, 20));
1076     startupFileTextfield.addMouseListener(new MouseAdapter()
1077     {
1078       public void mouseClicked(MouseEvent e)
1079       {
1080         if (e.getClickCount() > 1)
1081         {
1082           startupFileTextfield_mouseClicked();
1083         }
1084       }
1085     });
1086
1087     sortby.setFont(verdana11);
1088     sortby.setBounds(new Rectangle(172, 240, 155, 21));
1089     JLabel sortLabel = new JLabel();
1090     sortLabel.setFont(verdana11);
1091     sortLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1092     sortLabel.setText(MessageManager.getString("label.sort_by"));
1093     sortAnnBy.setFont(verdana11);
1094     sortAnnBy.setBounds(new Rectangle(172, 265, 110, 21));
1095     JLabel sortAnnLabel = new JLabel();
1096     sortAnnLabel.setFont(verdana11);
1097     sortAnnLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1098     sortAnnLabel.setText(MessageManager.getString("label.sort_ann_by"));
1099     sortAutocalc.setFont(verdana11);
1100     sortAutocalc.setBounds(new Rectangle(290, 265, 165, 21));
1101     JPanel annsettingsPanel = new JPanel();
1102     annsettingsPanel.setBounds(new Rectangle(173, 34, 300, 61));
1103     annsettingsPanel.setLayout(new FlowLayout(FlowLayout.LEFT, 0, 0));
1104     JPanel autoAnnotSettings1 = new JPanel();
1105     autoAnnotSettings1.setLayout(new GridLayout(3, 1, 0, 0));
1106     annsettingsPanel.add(autoAnnotSettings1);
1107     JPanel autoAnnotSettings2 = new JPanel();
1108     autoAnnotSettings2.setLayout(new GridLayout(3, 1, 0, 0));
1109     annsettingsPanel.add(autoAnnotSettings2);
1110     JPanel autoAnnotSettings3 = new JPanel();
1111     autoAnnotSettings3.setLayout(new GridLayout(3, 1, 0, 0));
1112     annsettingsPanel.add(autoAnnotSettings3);
1113     visualTab.add(annsettingsPanel);
1114     Border jb = new EmptyBorder(1, 1, 4, 5);
1115     quality.setBorder(jb);
1116     conservation.setBorder(jb);
1117     identity.setBorder(jb);
1118     showConsensbits.setBorder(jb);
1119     showGroupbits.setBorder(jb);
1120     showGroupConsensus.setBorder(jb);
1121     showGroupConservation.setBorder(jb);
1122     showConsensHistogram.setBorder(jb);
1123     showConsensLogo.setBorder(jb);
1124
1125     autoAnnotSettings2.add(conservation);
1126     autoAnnotSettings1.add(quality);
1127     autoAnnotSettings3.add(identity);
1128     autoAnnotSettings1.add(showGroupbits);
1129     autoAnnotSettings3.add(showGroupConsensus);
1130     autoAnnotSettings2.add(showGroupConservation);
1131     autoAnnotSettings1.add(showConsensbits);
1132     autoAnnotSettings2.add(showConsensHistogram);
1133     autoAnnotSettings3.add(showConsensLogo);
1134
1135     JPanel tooltipSettings = new JPanel();
1136     tooltipSettings.setBorder(new TitledBorder(MessageManager
1137             .getString("label.sequence_id_tooltip")));
1138     tooltipSettings.setBounds(173, 130, 200, 62);
1139     tooltipSettings.setLayout(new GridLayout(2, 1));
1140     tooltipSettings.add(showDbRefTooltip);
1141     tooltipSettings.add(showNpTooltip);
1142     visualTab.add(tooltipSettings);
1143
1144     wrap.setFont(verdana11);
1145     wrap.setHorizontalAlignment(SwingConstants.TRAILING);
1146     wrap.setHorizontalTextPosition(SwingConstants.LEADING);
1147     wrap.setText(MessageManager.getString("label.wrap_alignment"));
1148     rightAlign.setFont(verdana11);
1149     rightAlign.setForeground(Color.black);
1150     rightAlign.setHorizontalAlignment(SwingConstants.RIGHT);
1151     rightAlign.setHorizontalTextPosition(SwingConstants.LEFT);
1152     rightAlign.setText(MessageManager.getString("label.right_align_ids"));
1153     idItalics.setFont(verdana11);
1154     idItalics.setHorizontalAlignment(SwingConstants.RIGHT);
1155     idItalics.setHorizontalTextPosition(SwingConstants.LEADING);
1156     idItalics.setText(MessageManager
1157             .getString("label.sequence_name_italics"));
1158     openoverv.setFont(verdana11);
1159     openoverv.setActionCommand(MessageManager
1160             .getString("label.open_overview"));
1161     openoverv.setHorizontalAlignment(SwingConstants.RIGHT);
1162     openoverv.setHorizontalTextPosition(SwingConstants.LEFT);
1163     openoverv.setText(MessageManager.getString(("label.open_overview")));
1164     JPanel jPanel2 = new JPanel();
1165     jPanel2.setBounds(new Rectangle(7, 17, 158, 297));
1166     GridLayout gridLayout2 = new GridLayout();
1167     jPanel2.setLayout(gridLayout2);
1168     gridLayout2.setRows(13);
1169     jPanel2.add(fullScreen);
1170     jPanel2.add(openoverv);
1171     jPanel2.add(seqLimit);
1172     jPanel2.add(rightAlign);
1173     jPanel2.add(fontLabel);
1174     jPanel2.add(showUnconserved);
1175     jPanel2.add(idItalics);
1176     jPanel2.add(smoothFont);
1177     jPanel2.add(gapLabel);
1178     jPanel2.add(wrap);
1179     jPanel2.add(sortLabel);
1180     jPanel2.add(sortAnnLabel);
1181     jPanel2.add(startupCheckbox);
1182     visualTab.add(jPanel2);
1183     visualTab.add(annotations);
1184     visualTab.add(startupFileTextfield);
1185     visualTab.add(sortby);
1186     visualTab.add(sortAnnBy);
1187     visualTab.add(sortAutocalc);
1188     visualTab.add(gapSymbolCB);
1189     visualTab.add(fontNameCB);
1190     visualTab.add(fontSizeCB);
1191     visualTab.add(fontStyleCB);
1192     return visualTab;
1193   }
1194
1195   protected void autoIdWidth_actionPerformed()
1196   {
1197     // TODO Auto-generated method stub
1198
1199   }
1200
1201   protected void userIdWidth_actionPerformed()
1202   {
1203     // TODO Auto-generated method stub
1204
1205   }
1206
1207   protected void maxColour_actionPerformed(JPanel panel)
1208   {
1209   }
1210
1211   protected void minColour_actionPerformed(JPanel panel)
1212   {
1213   }
1214
1215   protected void showunconserved_actionPerformed(ActionEvent e)
1216   {
1217     // TODO Auto-generated method stub
1218
1219   }
1220
1221   /**
1222    * DOCUMENT ME!
1223    *
1224    * @param e
1225    *          DOCUMENT ME!
1226    */
1227   public void ok_actionPerformed(ActionEvent e)
1228   {
1229   }
1230
1231   /**
1232    * DOCUMENT ME!
1233    *
1234    * @param e
1235    *          DOCUMENT ME!
1236    */
1237   public void cancel_actionPerformed(ActionEvent e)
1238   {
1239   }
1240
1241   /**
1242    * DOCUMENT ME!
1243    *
1244    * @param e
1245    *          DOCUMENT ME!
1246    */
1247   public void annotations_actionPerformed(ActionEvent e)
1248   {
1249   }
1250
1251   /**
1252    * DOCUMENT ME!
1253    */
1254   public void startupFileTextfield_mouseClicked()
1255   {
1256   }
1257
1258   public void newLink_actionPerformed(ActionEvent e)
1259   {
1260
1261   }
1262
1263   public void editLink_actionPerformed(ActionEvent e)
1264   {
1265
1266   }
1267
1268   public void deleteLink_actionPerformed(ActionEvent e)
1269   {
1270
1271   }
1272
1273   public void defaultBrowser_mouseClicked(MouseEvent e)
1274   {
1275
1276   }
1277
1278   public void linkURLList_keyTyped(KeyEvent e)
1279   {
1280
1281   }
1282
1283   public void useProxy_actionPerformed()
1284   {
1285     proxyServerTB.setEnabled(useProxy.isSelected());
1286     proxyPortTB.setEnabled(useProxy.isSelected());
1287   }
1288
1289 }