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.TitledBorder;
  63 import javax.swing.event.ChangeEvent;
  64 import javax.swing.event.ChangeListener;
  65 import javax.swing.event.ListSelectionEvent;
  66 import javax.swing.event.ListSelectionListener;
  67
  68 /**
  69  * Base class for the Preferences panel.
  70  *
  71  * @author $author$
  72  * @version $Revision$
  73  */
  74 public class GPreferences extends JPanel
  75 {
  76   private static final Font verdana11 = JvSwingUtils.getLabelFont();
  77
  78   /*
  79    * Visual tab components
  80    */
  81   protected JCheckBox fullScreen = new JCheckBox();
  82
  83   protected JCheckBox openoverv = new JCheckBox();
  84
  85   protected JCheckBox seqLimit = new JCheckBox();
  86
  87   protected JCheckBox rightAlign = new JCheckBox();
  88
  89   protected JComboBox<String> fontSizeCB = new JComboBox<String>();
  90
  91   protected JComboBox<String> fontStyleCB = new JComboBox<String>();
  92
  93   protected JComboBox<String> fontNameCB = new JComboBox<String>();
  94
  95   protected JCheckBox showUnconserved = new JCheckBox();
  96
  97   protected JCheckBox idItalics = new JCheckBox();
  98
  99   protected JCheckBox smoothFont = new JCheckBox();
 100
 101   protected JComboBox<String> gapSymbolCB = new JComboBox<String>();
 102
 103   protected JCheckBox wrap = new JCheckBox();
 104
 105   protected JComboBox<String> sortby = new JComboBox<String>();
 106
 107   protected JComboBox<String> sortAnnBy = new JComboBox<String>();
 108
 109   protected JComboBox<String> sortAutocalc = new JComboBox<String>();
 110
 111   protected JCheckBox startupCheckbox = new JCheckBox();
 112
 113   protected JTextField startupFileTextfield = new JTextField();
 114
 115   // below are in the 'second column'
 116   protected JCheckBox annotations = new JCheckBox();
 117
 118   protected JCheckBox quality = new JCheckBox();
 119
 120   protected JCheckBox conservation = new JCheckBox();
 121
 122   protected JCheckBox identity = new JCheckBox();
 123
 124   protected JCheckBox showGroupConsensus = new JCheckBox();
 125
 126   protected JCheckBox showGroupConservation = new JCheckBox();
 127
 128   protected JCheckBox showConsensHistogram = new JCheckBox();
 129
 130   protected JCheckBox showConsensLogo = new JCheckBox();
 131
 132   protected JCheckBox showDbRefTooltip = new JCheckBox();
 133
 134   protected JCheckBox showNpTooltip = new JCheckBox();
 135
 136   /*
 137    * Structure tab and components
 138    */
 139   protected JPanel structureTab;
 140
 141   protected JCheckBox structFromPdb = new JCheckBox();
 142
 143   protected JCheckBox useRnaView = new JCheckBox();
 144
 145   protected JCheckBox addSecondaryStructure = new JCheckBox();
 146
 147   protected JCheckBox addTempFactor = new JCheckBox();
 148
 149   protected JComboBox<String> structViewer = new JComboBox<String>();
 150
 151   protected JTextField chimeraPath = new JTextField();
 152
 153
 154   /*
 155    * Colours tab components
 156    */
 157   protected JPanel minColour = new JPanel();
 158
 159   protected JPanel maxColour = new JPanel();
 160
 161   protected JComboBox<String> protColour = new JComboBox<String>();
 162
 163   protected JComboBox<String> nucColour = new JComboBox<String>();
 164
 165   /*
 166    * Connections tab components
 167    */
 168   protected JList linkURLList = new JList();
 169
 170   protected JTextField proxyServerTB = new JTextField();
 171
 172   protected JTextField proxyPortTB = new JTextField();
 173
 174   protected JTextField defaultBrowser = new JTextField();
 175
 176   protected JList linkNameList = new JList();
 177
 178   protected JCheckBox useProxy = new JCheckBox();
 179
 180   protected JCheckBox usagestats = new JCheckBox();
 181
 182   protected JCheckBox questionnaire = new JCheckBox();
 183
 184   protected JCheckBox versioncheck = new JCheckBox();
 185
 186   /*
 187    * Output tab components
 188    */
 189   protected JComboBox<String> epsRendering = new JComboBox<String>();
 190
 191   protected JLabel userIdWidthlabel = new JLabel();
 192
 193   protected JCheckBox autoIdWidth = new JCheckBox();
 194
 195   protected JTextField userIdWidth = new JTextField();
 196
 197   protected JCheckBox blcjv = new JCheckBox();
 198
 199   protected JCheckBox pileupjv = new JCheckBox();
 200
 201   protected JCheckBox clustaljv = new JCheckBox();
 202
 203   protected JCheckBox msfjv = new JCheckBox();
 204
 205   protected JCheckBox fastajv = new JCheckBox();
 206
 207   protected JCheckBox pfamjv = new JCheckBox();
 208
 209   protected JCheckBox pirjv = new JCheckBox();
 210
 211   protected JCheckBox modellerOutput = new JCheckBox();
 212
 213   /*
 214    * Editing tab components
 215    */
 216   protected JCheckBox autoCalculateConsCheck = new JCheckBox();
 217
 218   protected JCheckBox padGaps = new JCheckBox();
 219
 220   protected JCheckBox sortByTree = new JCheckBox();
 221
 222   /*
 223    * DAS Settings tab
 224    */
 225   protected JPanel dasTab = new JPanel();
 226
 227   /*
 228    * Web Services tab
 229    */
 230   protected JPanel wsTab = new JPanel();
 231
 232   /**
 233    * Creates a new GPreferences object.
 234    */
 235   public GPreferences()
 236   {
 237     try
 238     {
 239       jbInit();
 240     } catch (Exception ex)
 241     {
 242       ex.printStackTrace();
 243     }
 244   }
 245
 246   /**
 247    * Construct the panel and its tabbed sub-panels.
 248    *
 249    * @throws Exception
 250    */
 251   private void jbInit() throws Exception
 252   {
 253     final JTabbedPane tabbedPane = new JTabbedPane();
 254     this.setLayout(new BorderLayout());
 255     JPanel okCancelPanel = initOkCancelPanel();
 256     this.add(tabbedPane, BorderLayout.CENTER);
 257     this.add(okCancelPanel, BorderLayout.SOUTH);
 258
 259     tabbedPane.add(initVisualTab(),
 260             MessageManager.getString("label.visual"));
 261
 262     tabbedPane.add(initColoursTab(),
 263             MessageManager.getString("label.colours"));
 264
 265     tabbedPane.add(initStructureTab(),
 266             MessageManager.getString("label.structure"));
 267
 268     tabbedPane.add(initConnectionsTab(),
 269             MessageManager.getString("label.connections"));
 270
 271     tabbedPane.add(initOutputTab(), MessageManager.getString("label.output"));
 272
 273     tabbedPane.add(initEditingTab(), MessageManager.getString("label.editing"));
 274
 275     /*
 276      * See DasSourceBrowser for the real work of configuring this tab.
 277      */
 278     dasTab.setLayout(new BorderLayout());
 279     tabbedPane
 280             .add(dasTab, MessageManager.getString("label.das_settings"));
 281
 282     /*
 283      * See WsPreferences for the real work of configuring this tab.
 284      */
 285     wsTab.setLayout(new BorderLayout());
 286     tabbedPane.add(wsTab, MessageManager.getString("label.web_services"));
 287
 288     /*
 289      * Handler to validate a tab before leaving it - currently only for
 290      * Structure.
 291      */
 292     tabbedPane.addChangeListener(new ChangeListener()
 293     {
 294       private Component lastTab;
 295
 296       @Override
 297       public void stateChanged(ChangeEvent e)
 298       {
 299         if (lastTab == structureTab
 300                 && tabbedPane.getSelectedComponent() != structureTab)
 301         {
 302           if (!validateStructure())
 303           {
 304             tabbedPane.setSelectedComponent(structureTab);
 305             return;
 306           }
 307         }
 308         lastTab = tabbedPane.getSelectedComponent();
 309       }
 310
 311     });
 312   }
 313
 314   /**
 315    * Initialises the Editing tabbed panel.
 316    *
 317    * @return
 318    */
 319   private JPanel initEditingTab()
 320   {
 321     JPanel editingTab = new JPanel();
 322     editingTab.setLayout(null);
 323     autoCalculateConsCheck.setFont(verdana11);
 324     autoCalculateConsCheck.setText(MessageManager
 325             .getString("label.autocalculate_consensus"));
 326     autoCalculateConsCheck.setBounds(new Rectangle(21, 52, 209, 23));
 327     padGaps.setFont(verdana11);
 328     padGaps.setText(MessageManager.getString("label.pad_gaps_when_editing"));
 329     padGaps.setBounds(new Rectangle(22, 94, 168, 23));
 330     sortByTree.setFont(verdana11);
 331     sortByTree
 332             .setText(MessageManager.getString("label.sort_with_new_tree"));
 333     sortByTree
 334             .setToolTipText(MessageManager
 335                     .getString("label.any_trees_calculated_or_loaded_alignment_automatically_sort"));
 336     sortByTree.setBounds(new Rectangle(22, 136, 168, 23));
 337     editingTab.add(autoCalculateConsCheck);
 338     editingTab.add(padGaps);
 339     editingTab.add(sortByTree);
 340     return editingTab;
 341   }
 342
 343   /**
 344    * Initialises the Output tabbed panel.
 345    *
 346    * @return
 347    */
 348   private JPanel initOutputTab()
 349   {
 350     JPanel outputTab = new JPanel();
 351     outputTab.setLayout(null);
 352     JLabel epsLabel = new JLabel();
 353     epsLabel.setFont(verdana11);
 354     epsLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 355     epsLabel.setText(MessageManager.getString("label.eps_rendering_style"));
 356     epsLabel.setBounds(new Rectangle(9, 31, 140, 24));
 357     epsRendering.setFont(verdana11);
 358     epsRendering.setBounds(new Rectangle(154, 34, 187, 21));
 359     JLabel jLabel1 = new JLabel();
 360     jLabel1.setFont(verdana11);
 361     jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
 362     jLabel1.setText(MessageManager.getString("label.append_start_end"));
 363     jLabel1.setFont(verdana11);
 364     fastajv.setFont(verdana11);
 365     fastajv.setHorizontalAlignment(SwingConstants.LEFT);
 366     clustaljv.setText(MessageManager.getString("label.clustal") + "     ");
 367     blcjv.setText(MessageManager.getString("label.blc") + "     ");
 368     fastajv.setText(MessageManager.getString("label.fasta") + "     ");
 369     msfjv.setText(MessageManager.getString("label.msf") + "     ");
 370     pfamjv.setText(MessageManager.getString("label.pfam") + "     ");
 371     pileupjv.setText(MessageManager.getString("label.pileup") + "     ");
 372     msfjv.setFont(verdana11);
 373     msfjv.setHorizontalAlignment(SwingConstants.LEFT);
 374     pirjv.setText(MessageManager.getString("label.pir") + "     ");
 375     JPanel jPanel11 = new JPanel();
 376     jPanel11.setFont(verdana11);
 377     TitledBorder titledBorder2 = new TitledBorder(
 378             MessageManager.getString("label.file_output"));
 379     jPanel11.setBorder(titledBorder2);
 380     jPanel11.setBounds(new Rectangle(30, 72, 196, 182));
 381     GridLayout gridLayout3 = new GridLayout();
 382     jPanel11.setLayout(gridLayout3);
 383     gridLayout3.setRows(8);
 384     blcjv.setFont(verdana11);
 385     blcjv.setHorizontalAlignment(SwingConstants.LEFT);
 386     clustaljv.setFont(verdana11);
 387     clustaljv.setHorizontalAlignment(SwingConstants.LEFT);
 388     pfamjv.setFont(verdana11);
 389     pfamjv.setHorizontalAlignment(SwingConstants.LEFT);
 390     pileupjv.setFont(verdana11);
 391     pileupjv.setHorizontalAlignment(SwingConstants.LEFT);
 392     pirjv.setFont(verdana11);
 393     pirjv.setHorizontalAlignment(SwingConstants.LEFT);
 394     autoIdWidth.setFont(verdana11);
 395     autoIdWidth.setText(MessageManager
 396             .getString("label.automatically_set_id_width"));
 397     autoIdWidth
 398             .setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.getString("label.adjusts_width_generated_eps_png")));
 399     autoIdWidth.setBounds(new Rectangle(228, 96, 188, 23));
 400     autoIdWidth.addActionListener(new ActionListener()
 401     {
 402
 403       @Override
 404       public void actionPerformed(ActionEvent e)
 405       {
 406         autoIdWidth_actionPerformed();
 407       }
 408     });
 409     userIdWidthlabel.setFont(verdana11);
 410     userIdWidthlabel.setText(MessageManager
 411             .getString("label.figure_id_column_width"));
 412     userIdWidth
 413             .setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.getString("label.manually_specify_width_left_column")));
 414     userIdWidthlabel
 415             .setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.getString("label.manually_specify_width_left_column")));
 416     userIdWidthlabel.setBounds(new Rectangle(236, 120, 168, 23));
 417     userIdWidth.setFont(JvSwingUtils.getTextAreaFont());
 418     userIdWidth.setText("");
 419     userIdWidth.setBounds(new Rectangle(232, 144, 84, 23));
 420     userIdWidth.addActionListener(new ActionListener()
 421     {
 422
 423       @Override
 424       public void actionPerformed(ActionEvent e)
 425       {
 426         userIdWidth_actionPerformed();
 427       }
 428     });
 429     jPanel11.add(jLabel1);
 430     jPanel11.add(blcjv);
 431     jPanel11.add(clustaljv);
 432     jPanel11.add(fastajv);
 433     jPanel11.add(msfjv);
 434     jPanel11.add(pfamjv);
 435     jPanel11.add(pileupjv);
 436     jPanel11.add(pirjv);
 437     outputTab.add(autoIdWidth);
 438     outputTab.add(userIdWidth);
 439     outputTab.add(userIdWidthlabel);
 440     outputTab.add(modellerOutput);
 441     outputTab.add(epsLabel);
 442     outputTab.add(epsRendering);
 443     outputTab.add(jPanel11);
 444     modellerOutput.setFont(verdana11);
 445     modellerOutput.setText(MessageManager
 446             .getString("label.use_modeller_output"));
 447     modellerOutput.setBounds(new Rectangle(228, 226, 168, 23));
 448     return outputTab;
 449   }
 450
 451   /**
 452    * Initialises the Connections tabbed panel.
 453    *
 454    * @return
 455    */
 456   private JPanel initConnectionsTab()
 457   {
 458     JPanel connectTab = new JPanel();
 459     connectTab.setLayout(new GridBagLayout());
 460     JLabel serverLabel = new JLabel();
 461     serverLabel.setText(MessageManager.getString("label.address"));
 462     serverLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 463     serverLabel.setFont(verdana11);
 464     proxyServerTB.setFont(verdana11);
 465     proxyPortTB.setFont(verdana11);
 466     JLabel portLabel = new JLabel();
 467     portLabel.setFont(verdana11);
 468     portLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 469     portLabel.setText(MessageManager.getString("label.port"));
 470     JLabel browserLabel = new JLabel();
 471     browserLabel.setFont(new java.awt.Font("SansSerif", 0, 11));
 472     browserLabel.setHorizontalAlignment(SwingConstants.TRAILING);
 473     browserLabel.setText(MessageManager
 474             .getString("label.default_browser_unix"));
 475     defaultBrowser.setFont(verdana11);
 476     defaultBrowser.setText("");
 477     usagestats.setText(MessageManager
 478             .getString("label.send_usage_statistics"));
 479     usagestats.setFont(verdana11);
 480     usagestats.setHorizontalAlignment(SwingConstants.RIGHT);
 481     usagestats.setHorizontalTextPosition(SwingConstants.LEADING);
 482     questionnaire.setText(MessageManager
 483             .getString("label.check_for_questionnaires"));
 484     questionnaire.setFont(verdana11);
 485     questionnaire.setHorizontalAlignment(SwingConstants.RIGHT);
 486     questionnaire.setHorizontalTextPosition(SwingConstants.LEADING);
 487     versioncheck.setText(MessageManager
 488             .getString("label.check_for_latest_version"));
 489     versioncheck.setFont(verdana11);
 490     versioncheck.setHorizontalAlignment(SwingConstants.RIGHT);
 491     versioncheck.setHorizontalTextPosition(SwingConstants.LEADING);
 492     JButton newLink = new JButton();
 493     newLink.setText(MessageManager.getString("action.new"));
 494     newLink.addActionListener(new java.awt.event.ActionListener()
 495     {
 496       public void actionPerformed(ActionEvent e)
 497       {
 498         newLink_actionPerformed(e);
 499       }
 500     });
 501     JButton editLink = new JButton();
 502     editLink.setText(MessageManager.getString("action.edit"));
 503     editLink.addActionListener(new java.awt.event.ActionListener()
 504     {
 505       public void actionPerformed(ActionEvent e)
 506       {
 507         editLink_actionPerformed(e);
 508       }
 509     });
 510     JButton deleteLink = new JButton();
 511     deleteLink.setText(MessageManager.getString("action.delete"));
 512     deleteLink.addActionListener(new java.awt.event.ActionListener()
 513     {
 514       public void actionPerformed(ActionEvent e)
 515       {
 516         deleteLink_actionPerformed(e);
 517       }
 518     });
 519
 520     linkURLList.addListSelectionListener(new ListSelectionListener()
 521     {
 522       public void valueChanged(ListSelectionEvent e)
 523       {
 524         int index = linkURLList.getSelectedIndex();
 525         linkNameList.setSelectedIndex(index);
 526       }
 527     });
 528
 529     linkNameList.addListSelectionListener(new ListSelectionListener()
 530     {
 531       public void valueChanged(ListSelectionEvent e)
 532       {
 533         int index = linkNameList.getSelectedIndex();
 534         linkURLList.setSelectedIndex(index);
 535       }
 536     });
 537
 538     JScrollPane linkScrollPane = new JScrollPane();
 539     linkScrollPane.setBorder(null);
 540     JPanel linkPanel = new JPanel();
 541     linkPanel.setBorder(new TitledBorder(MessageManager
 542             .getString("label.url_linkfrom_sequence_id")));
 543     linkPanel.setLayout(new BorderLayout());
 544     GridLayout gridLayout1 = new GridLayout();
 545     JPanel editLinkButtons = new JPanel();
 546     editLinkButtons.setLayout(gridLayout1);
 547     gridLayout1.setRows(3);
 548     linkNameList.setFont(verdana11);
 549     linkNameList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
 550     BorderLayout borderLayout3 = new BorderLayout();
 551     JPanel linkPanel2 = new JPanel();
 552     linkPanel2.setLayout(borderLayout3);
 553     linkURLList.setFont(verdana11);
 554     linkURLList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
 555
 556     defaultBrowser.addMouseListener(new MouseAdapter()
 557     {
 558       public void mouseClicked(MouseEvent e)
 559       {
 560         if (e.getClickCount() > 1)
 561         {
 562           defaultBrowser_mouseClicked(e);
 563         }
 564       }
 565     });
 566     useProxy.setFont(verdana11);
 567     useProxy.setHorizontalAlignment(SwingConstants.RIGHT);
 568     useProxy.setHorizontalTextPosition(SwingConstants.LEADING);
 569     useProxy.setText(MessageManager.getString("label.use_proxy_server"));
 570     useProxy.addActionListener(new ActionListener()
 571     {
 572       public void actionPerformed(ActionEvent e)
 573       {
 574         useProxy_actionPerformed();
 575       }
 576     });
 577     linkPanel.add(editLinkButtons, BorderLayout.EAST);
 578     editLinkButtons.add(newLink, null);
 579     editLinkButtons.add(editLink, null);
 580     editLinkButtons.add(deleteLink, null);
 581     linkPanel.add(linkScrollPane, BorderLayout.CENTER);
 582     linkScrollPane.getViewport().add(linkPanel2, null);
 583     linkPanel2.add(linkURLList, BorderLayout.CENTER);
 584     linkPanel2.add(linkNameList, BorderLayout.WEST);
 585     JPanel jPanel1 = new JPanel();
 586     TitledBorder titledBorder1 = new TitledBorder(
 587             MessageManager.getString("label.proxy_server"));
 588     jPanel1.setBorder(titledBorder1);
 589     jPanel1.setLayout(new GridBagLayout());
 590     jPanel1.add(serverLabel, new GridBagConstraints(0, 1, 1, 1, 0.0, 0.0,
 591             GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
 592                     2, 4, 0), 5, 0));
 593     jPanel1.add(portLabel, new GridBagConstraints(2, 1, 1, 1, 0.0, 0.0,
 594             GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
 595                     0, 4, 0), 11, 6));
 596     connectTab.add(linkPanel, new GridBagConstraints(0, 0, 2, 1, 1.0, 1.0,
 597             GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(
 598                     16, 0, 0, 12), 359, -17));
 599     connectTab.add(jPanel1, new GridBagConstraints(0, 2, 2, 1, 1.0, 1.0,
 600             GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(
 601                     21, 0, 35, 12), 4, 6));
 602     connectTab.add(browserLabel, new GridBagConstraints(0, 1, 1, 1, 0.0,
 603             0.0, GridBagConstraints.WEST, GridBagConstraints.NONE,
 604             new Insets(16, 0, 0, 0), 5, 1));
 605     jPanel1.add(useProxy, new GridBagConstraints(0, 0, 2, 1, 0.0, 0.0,
 606             GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
 607                     2, 5, 185), 2, -4));
 608     jPanel1.add(proxyPortTB, new GridBagConstraints(3, 1, 1, 1, 1.0, 0.0,
 609             GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 610             new Insets(0, 2, 4, 2), 54, 1));
 611     jPanel1.add(proxyServerTB, new GridBagConstraints(1, 1, 1, 1, 1.0, 0.0,
 612             GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 613             new Insets(0, 2, 4, 0), 263, 1));
 614     connectTab.add(defaultBrowser, new GridBagConstraints(1, 1, 1, 1, 1.0,
 615             0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 616             new Insets(15, 0, 0, 15), 307, 1));
 617     connectTab.add(usagestats, new GridBagConstraints(0, 4, 1, 1, 1.0, 0.0,
 618             GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 619             new Insets(0, 2, 4, 2), 70, 1));
 620     connectTab.add(questionnaire, new GridBagConstraints(1, 4, 1, 1, 1.0,
 621             0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 622             new Insets(0, 2, 4, 2), 70, 1));
 623     connectTab.add(versioncheck, new GridBagConstraints(0, 5, 1, 1, 1.0,
 624             0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 625             new Insets(0, 2, 4, 2), 70, 1));
 626     return connectTab;
 627   }
 628
 629   /**
 630    * Initialises the parent panel which contains the tabbed sections.
 631    *
 632    * @return
 633    */
 634   private JPanel initOkCancelPanel()
 635   {
 636     JButton ok = new JButton();
 637     ok.setText(MessageManager.getString("action.ok"));
 638     ok.addActionListener(new ActionListener()
 639     {
 640       public void actionPerformed(ActionEvent e)
 641       {
 642         ok_actionPerformed(e);
 643       }
 644     });
 645     JButton cancel = new JButton();
 646     cancel.setText(MessageManager.getString("action.cancel"));
 647     cancel.addActionListener(new ActionListener()
 648     {
 649       public void actionPerformed(ActionEvent e)
 650       {
 651         cancel_actionPerformed(e);
 652       }
 653     });
 654     JPanel okCancelPanel = new JPanel();
 655     okCancelPanel.add(ok);
 656     okCancelPanel.add(cancel);
 657     return okCancelPanel;
 658   }
 659
 660   /**
 661    * Initialises the Colours tabbed panel.
 662    *
 663    * @return
 664    */
 665   private JPanel initColoursTab()
 666   {
 667     JPanel coloursTab = new JPanel();
 668     coloursTab.setBorder(new TitledBorder(MessageManager
 669             .getString("action.open_new_alignment")));
 670     coloursTab.setLayout(new FlowLayout());
 671     JLabel mincolourLabel = new JLabel();
 672     mincolourLabel.setFont(verdana11);
 673     mincolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 674     mincolourLabel.setText(MessageManager.getString("label.min_colour"));
 675     minColour.setFont(verdana11);
 676     minColour.setBorder(BorderFactory.createEtchedBorder());
 677     minColour.setPreferredSize(new Dimension(40, 20));
 678     minColour.addMouseListener(new MouseAdapter()
 679     {
 680       public void mousePressed(MouseEvent e)
 681       {
 682         minColour_actionPerformed(minColour);
 683       }
 684     });
 685     JLabel maxcolourLabel = new JLabel();
 686     maxcolourLabel.setFont(verdana11);
 687     maxcolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 688     maxcolourLabel.setText(MessageManager.getString("label.max_colour"));
 689     maxColour.setFont(verdana11);
 690     maxColour.setBorder(BorderFactory.createEtchedBorder());
 691     maxColour.setPreferredSize(new Dimension(40, 20));
 692     maxColour.addMouseListener(new MouseAdapter()
 693     {
 694       public void mousePressed(MouseEvent e)
 695       {
 696         maxColour_actionPerformed(maxColour);
 697       }
 698     });
 699
 700     protColour.setFont(verdana11);
 701     protColour.setBounds(new Rectangle(172, 225, 155, 21));
 702     JLabel protColourLabel = new JLabel();
 703     protColourLabel.setFont(verdana11);
 704     protColourLabel.setHorizontalAlignment(SwingConstants.LEFT);
 705     protColourLabel.setText(MessageManager
 706             .getString("label.prot_alignment_colour") + " ");
 707     JvSwingUtils.addtoLayout(coloursTab, MessageManager
 708             .getString("label.default_colour_scheme_for_alignment"),
 709             protColourLabel, protColour);
 710
 711     nucColour.setFont(verdana11);
 712     nucColour.setBounds(new Rectangle(172, 240, 155, 21));
 713     JLabel nucColourLabel = new JLabel();
 714     nucColourLabel.setFont(verdana11);
 715     nucColourLabel.setHorizontalAlignment(SwingConstants.LEFT);
 716     nucColourLabel.setText(MessageManager
 717             .getString("label.nuc_alignment_colour")
 718             + " ");
 719     JvSwingUtils.addtoLayout(coloursTab, MessageManager
 720             .getString("label.default_colour_scheme_for_alignment"),
 721             nucColourLabel, nucColour);
 722
 723     JPanel annotationShding = new JPanel();
 724     annotationShding.setBorder(new TitledBorder(MessageManager
 725             .getString("label.annotation_shading_default")));
 726     annotationShding.setLayout(new GridLayout(1, 2));
 727     JvSwingUtils.addtoLayout(annotationShding, MessageManager
 728             .getString("label.default_minimum_colour_annotation_shading"),
 729             mincolourLabel, minColour);
 730     JvSwingUtils.addtoLayout(annotationShding, MessageManager
 731             .getString("label.default_maximum_colour_annotation_shading"),
 732             maxcolourLabel, maxColour);
 733     coloursTab.add(annotationShding); // , FlowLayout.LEFT);
 734     return coloursTab;
 735   }
 736
 737   /**
 738    * Initialises the Structure tabbed panel.
 739    *
 740    * @return
 741    */
 742   private JPanel initStructureTab()
 743   {
 744     structureTab = new JPanel();
 745
 746     structureTab.setBorder(new TitledBorder(MessageManager
 747             .getString("label.structure_options")));
 748     structureTab.setLayout(null);
 749     final int width = 400;
 750     final int height = 22;
 751     final int lineSpacing = 25;
 752     int ypos = 30;
 753
 754     structFromPdb.setFont(verdana11);
 755     structFromPdb.setText(MessageManager.getString("label.struct_from_pdb"));
 756     structFromPdb.setBounds(new Rectangle(5, ypos, width, height));
 757     structFromPdb.addActionListener(new ActionListener()
 758     {
 759       @Override
 760       public void actionPerformed(ActionEvent e)
 761       {
 762         boolean selected = structFromPdb.isSelected();
 763         // enable other options only when the first is checked
 764         useRnaView.setEnabled(selected);
 765         addSecondaryStructure.setEnabled(selected);
 766         addTempFactor.setEnabled(selected);
 767       }
 768     });
 769     structureTab.add(structFromPdb);
 770
 771     // indent checkboxes that are conditional on the first one
 772     ypos += lineSpacing;
 773     useRnaView.setFont(verdana11);
 774     useRnaView.setText(MessageManager.getString("label.use_rnaview"));
 775     useRnaView.setBounds(new Rectangle(25, ypos, width, height));
 776     structureTab.add(useRnaView);
 777
 778     ypos += lineSpacing;
 779     addSecondaryStructure.setFont(verdana11);
 780     addSecondaryStructure.setText(MessageManager
 781             .getString("label.autoadd_secstr"));
 782     addSecondaryStructure.setBounds(new Rectangle(25, ypos, width, height));
 783     structureTab.add(addSecondaryStructure);
 784
 785     ypos += lineSpacing;
 786     addTempFactor.setFont(verdana11);
 787     addTempFactor.setText(MessageManager.getString("label.autoadd_temp"));
 788     addTempFactor.setBounds(new Rectangle(25, ypos, width, height));
 789     structureTab.add(addTempFactor);
 790
 791     ypos += lineSpacing;
 792     JLabel viewerLabel = new JLabel();
 793     viewerLabel.setFont(verdana11);
 794     viewerLabel.setHorizontalAlignment(SwingConstants.LEFT);
 795     viewerLabel.setText(MessageManager.getString("label.structure_viewer"));
 796     viewerLabel.setBounds(new Rectangle(10, ypos, 200, height));
 797     structureTab.add(viewerLabel);
 798
 799     structViewer.setFont(verdana11);
 800     structViewer.setBounds(new Rectangle(160, ypos, 120, height));
 801     structViewer.addItem(ViewerType.JMOL.name());
 802     structViewer.addItem(ViewerType.CHIMERA.name());
 803     structViewer.addActionListener(new ActionListener()
 804     {
 805       @Override
 806       public void actionPerformed(ActionEvent e)
 807       {
 808         structureViewer_actionPerformed((String) structViewer
 809                 .getSelectedItem());
 810       }
 811     });
 812     structureTab.add(structViewer);
 813
 814     ypos += lineSpacing;
 815     JLabel pathLabel = new JLabel();
 816     pathLabel.setFont(new java.awt.Font("SansSerif", 0, 11));
 817     pathLabel.setHorizontalAlignment(SwingConstants.LEFT);
 818     pathLabel.setText(MessageManager.getString("label.chimera_path"));
 819     final String tooltip = JvSwingUtils.wrapTooltip(true,
 820             MessageManager.getString("label.chimera_path_tip"));
 821     pathLabel.setToolTipText(tooltip);
 822     pathLabel.setBounds(new Rectangle(10, ypos, 140, height));
 823     structureTab.add(pathLabel);
 824
 825     chimeraPath.setFont(verdana11);
 826     chimeraPath.setText("");
 827     chimeraPath.setBounds(new Rectangle(160, ypos, 300, height));
 828     chimeraPath.addMouseListener(new MouseAdapter()
 829     {
 830       @Override
 831       public void mouseClicked(MouseEvent e)
 832       {
 833         if (e.getClickCount() == 2)
 834         {
 835           String chosen = openFileChooser();
 836           if (chosen != null)
 837           {
 838             chimeraPath.setText(chosen);
 839           }
 840         }
 841       }
 842     });
 843     structureTab.add(chimeraPath);
 844
 845     ypos += lineSpacing;
 846     // scrl_pdbDocFieldConfig.setPreferredSize(new Dimension(450, 100));
 847     // scrl_pdbDocFieldConfig
 848     // .setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_NEVER);
 849     // scrl_pdbDocFieldConfig.setBounds();
 850     PDBDocFieldPreferences docFieldPref = new PDBDocFieldPreferences(
 851             PreferenceSource.PREFERENCES);
 852     docFieldPref.setBounds(new Rectangle(10, ypos + 5, 450, 120));
 853     structureTab.add(docFieldPref);
 854
 855
 856
 857
 858     return structureTab;
 859   }
 860
 861
 862   /**
 863    * Action on choosing a structure viewer from combobox options.
 864    *
 865    * @param selectedItem
 866    */
 867   protected void structureViewer_actionPerformed(String selectedItem)
 868   {
 869   }
 870
 871   /**
 872    * Show a dialog for the user to choose a file. Returns the chosen path, or
 873    * null on Cancel.
 874    *
 875    * @return
 876    */
 877   protected String openFileChooser()
 878   {
 879     String choice = null;
 880     JFileChooser chooser = new JFileChooser();
 881
 882     // chooser.setFileView(new JalviewFileView());
 883     chooser.setDialogTitle(MessageManager
 884             .getString("label.open_local_file"));
 885     chooser.setToolTipText(MessageManager.getString("action.open"));
 886
 887     int value = chooser.showOpenDialog(this);
 888
 889     if (value == JFileChooser.APPROVE_OPTION)
 890     {
 891       choice = chooser.getSelectedFile().getPath();
 892     }
 893     return choice;
 894   }
 895
 896   /**
 897    * Validate the structure tab preferences; if invalid, set focus on this tab.
 898    *
 899    * @param e
 900    */
 901   protected boolean validateStructure(FocusEvent e)
 902   {
 903     if (!validateStructure())
 904     {
 905       e.getComponent().requestFocusInWindow();
 906       return false;
 907     }
 908     return true;
 909   }
 910
 911   protected boolean validateStructure()
 912   {
 913     return false;
 914   }
 915
 916   /**
 917    * Initialises the Visual tabbed panel.
 918    *
 919    * @return
 920    */
 921   private JPanel initVisualTab()
 922   {
 923     JPanel visualTab = new JPanel();
 924     visualTab.setBorder(new TitledBorder(MessageManager
 925             .getString("action.open_new_alignment")));
 926     visualTab.setLayout(null);
 927     fullScreen.setFont(verdana11);
 928     fullScreen.setHorizontalAlignment(SwingConstants.RIGHT);
 929     fullScreen.setHorizontalTextPosition(SwingConstants.LEFT);
 930     fullScreen.setText(MessageManager.getString("label.maximize_window"));
 931     quality.setEnabled(false);
 932     quality.setFont(verdana11);
 933     quality.setHorizontalAlignment(SwingConstants.RIGHT);
 934     quality.setHorizontalTextPosition(SwingConstants.LEFT);
 935     quality.setSelected(true);
 936     quality.setText(MessageManager.getString("label.quality"));
 937     conservation.setEnabled(false);
 938     conservation.setFont(verdana11);
 939     conservation.setHorizontalAlignment(SwingConstants.RIGHT);
 940     conservation.setHorizontalTextPosition(SwingConstants.LEFT);
 941     conservation.setSelected(true);
 942     conservation.setText(MessageManager.getString("label.conservation"));
 943     identity.setEnabled(false);
 944     identity.setFont(verdana11);
 945     identity.setHorizontalAlignment(SwingConstants.RIGHT);
 946     identity.setHorizontalTextPosition(SwingConstants.LEFT);
 947     identity.setSelected(true);
 948     identity.setText(MessageManager.getString("label.consensus"));
 949     JLabel showGroupbits = new JLabel();
 950     showGroupbits.setFont(verdana11);
 951     showGroupbits.setHorizontalAlignment(SwingConstants.RIGHT);
 952     showGroupbits.setHorizontalTextPosition(SwingConstants.LEFT);
 953     showGroupbits.setText(MessageManager.getString("action.show_group")
 954             + ":");
 955     JLabel showConsensbits = new JLabel();
 956     showConsensbits.setFont(verdana11);
 957     showConsensbits.setHorizontalAlignment(SwingConstants.RIGHT);
 958     showConsensbits.setHorizontalTextPosition(SwingConstants.LEFT);
 959     showConsensbits.setText(MessageManager.getString("label.consensus")
 960             + ":");
 961     showConsensHistogram.setEnabled(false);
 962     showConsensHistogram.setFont(verdana11);
 963     showConsensHistogram.setHorizontalAlignment(SwingConstants.RIGHT);
 964     showConsensHistogram.setHorizontalTextPosition(SwingConstants.LEFT);
 965     showConsensHistogram.setSelected(true);
 966     showConsensHistogram.setText(MessageManager
 967             .getString("label.histogram"));
 968     showConsensLogo.setEnabled(false);
 969     showConsensLogo.setFont(verdana11);
 970     showConsensLogo.setHorizontalAlignment(SwingConstants.RIGHT);
 971     showConsensLogo.setHorizontalTextPosition(SwingConstants.LEFT);
 972     showConsensLogo.setSelected(true);
 973     showConsensLogo.setText(MessageManager.getString("label.logo"));
 974     showGroupConsensus.setEnabled(false);
 975     showGroupConsensus.setFont(verdana11);
 976     showGroupConsensus.setHorizontalAlignment(SwingConstants.RIGHT);
 977     showGroupConsensus.setHorizontalTextPosition(SwingConstants.LEFT);
 978     showGroupConsensus.setSelected(true);
 979     showGroupConsensus.setText(MessageManager.getString("label.consensus"));
 980     showGroupConservation.setEnabled(false);
 981     showGroupConservation.setFont(verdana11);
 982     showGroupConservation.setHorizontalAlignment(SwingConstants.RIGHT);
 983     showGroupConservation.setHorizontalTextPosition(SwingConstants.LEFT);
 984     showGroupConservation.setSelected(true);
 985     showGroupConservation.setText(MessageManager
 986             .getString("label.conservation"));
 987     showNpTooltip.setEnabled(true);
 988     showNpTooltip.setFont(verdana11);
 989     showNpTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
 990     showNpTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
 991     showNpTooltip.setSelected(true);
 992     showNpTooltip.setText(MessageManager
 993             .getString("label.non_positional_features"));
 994     showDbRefTooltip.setEnabled(true);
 995     showDbRefTooltip.setFont(verdana11);
 996     showDbRefTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
 997     showDbRefTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
 998     showDbRefTooltip.setSelected(true);
 999     showDbRefTooltip.setText(MessageManager
1000             .getString("label.database_references"));
1001     annotations.setFont(verdana11);
1002     annotations.setHorizontalAlignment(SwingConstants.RIGHT);
1003     annotations.setHorizontalTextPosition(SwingConstants.LEADING);
1004     annotations.setSelected(true);
1005     annotations.setText(MessageManager.getString("label.show_annotations"));
1006     annotations.setBounds(new Rectangle(169, 12, 200, 23));
1007     annotations.addActionListener(new ActionListener()
1008     {
1009       public void actionPerformed(ActionEvent e)
1010       {
1011         annotations_actionPerformed(e);
1012       }
1013     });
1014     identity.addActionListener(new ActionListener()
1015     {
1016       public void actionPerformed(ActionEvent e)
1017       {
1018         annotations_actionPerformed(e);
1019       }
1020     });
1021     showGroupConsensus.addActionListener(new ActionListener()
1022     {
1023       public void actionPerformed(ActionEvent e)
1024       {
1025         annotations_actionPerformed(e);
1026       }
1027     });
1028     showUnconserved.setFont(verdana11);
1029     showUnconserved.setHorizontalAlignment(SwingConstants.RIGHT);
1030     showUnconserved.setHorizontalTextPosition(SwingConstants.LEFT);
1031     showUnconserved.setSelected(true);
1032     showUnconserved.setText(MessageManager
1033             .getString("action.show_unconserved"));
1034     showUnconserved.addActionListener(new ActionListener()
1035     {
1036       public void actionPerformed(ActionEvent e)
1037       {
1038         showunconserved_actionPerformed(e);
1039       }
1040     });
1041
1042     // TODO these are not yet added to / action from Preferences
1043     // JCheckBox shareSelections = new JCheckBox();
1044     // shareSelections.setFont(verdana11);
1045     // shareSelections.setHorizontalAlignment(SwingConstants.RIGHT);
1046     // shareSelections.setHorizontalTextPosition(SwingConstants.LEFT);
1047     // shareSelections.setSelected(true);
1048     // shareSelections.setText(MessageManager
1049     // .getString("label.share_selection_across_views"));
1050     // JCheckBox followHighlight = new JCheckBox();
1051     // followHighlight.setFont(verdana11);
1052     // followHighlight.setHorizontalAlignment(SwingConstants.RIGHT);
1053     // followHighlight.setHorizontalTextPosition(SwingConstants.LEFT);
1054     // // showUnconserved.setBounds(new Rectangle(169, 40, 200, 23));
1055     // followHighlight.setSelected(true);
1056     // followHighlight.setText(MessageManager
1057     // .getString("label.scroll_highlighted_regions"));
1058
1059     seqLimit.setFont(verdana11);
1060     seqLimit.setHorizontalAlignment(SwingConstants.RIGHT);
1061     seqLimit.setHorizontalTextPosition(SwingConstants.LEFT);
1062     seqLimit.setText(MessageManager.getString("label.full_sequence_id"));
1063     smoothFont.setFont(verdana11);
1064     smoothFont.setHorizontalAlignment(SwingConstants.RIGHT);
1065     smoothFont.setHorizontalTextPosition(SwingConstants.LEADING);
1066     smoothFont.setText(MessageManager.getString("label.smooth_font"));
1067     JLabel gapLabel = new JLabel();
1068     gapLabel.setFont(verdana11);
1069     gapLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1070     gapLabel.setText(MessageManager.getString("label.gap_symbol") + " ");
1071     JLabel fontLabel = new JLabel();
1072     fontLabel.setFont(verdana11);
1073     fontLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1074     fontLabel.setText(MessageManager.getString("label.font"));
1075     fontSizeCB.setFont(verdana11);
1076     fontSizeCB.setBounds(new Rectangle(320, 104, 65, 23));
1077     fontStyleCB.setFont(verdana11);
1078     fontStyleCB.setBounds(new Rectangle(382, 104, 80, 23));
1079     fontNameCB.setFont(verdana11);
1080     fontNameCB.setBounds(new Rectangle(172, 104, 147, 23));
1081     gapSymbolCB.setFont(verdana11);
1082     gapSymbolCB.setBounds(new Rectangle(172, 196, 69, 23));
1083     DefaultListCellRenderer dlcr = new DefaultListCellRenderer();
1084     dlcr.setHorizontalAlignment(DefaultListCellRenderer.CENTER);
1085     gapSymbolCB.setRenderer(dlcr);
1086
1087     startupCheckbox.setText(MessageManager.getString("action.open_file"));
1088     startupCheckbox.setFont(verdana11);
1089     startupCheckbox.setHorizontalAlignment(SwingConstants.RIGHT);
1090     startupCheckbox.setHorizontalTextPosition(SwingConstants.LEFT);
1091     startupCheckbox.setSelected(true);
1092     startupFileTextfield.setFont(verdana11);
1093     startupFileTextfield.setBounds(new Rectangle(172, 290, 270, 20));
1094     startupFileTextfield.addMouseListener(new MouseAdapter()
1095     {
1096       public void mouseClicked(MouseEvent e)
1097       {
1098         if (e.getClickCount() > 1)
1099         {
1100           startupFileTextfield_mouseClicked();
1101         }
1102       }
1103     });
1104
1105     sortby.setFont(verdana11);
1106     sortby.setBounds(new Rectangle(172, 240, 155, 21));
1107     JLabel sortLabel = new JLabel();
1108     sortLabel.setFont(verdana11);
1109     sortLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1110     sortLabel.setText(MessageManager.getString("label.sort_by"));
1111     sortAnnBy.setFont(verdana11);
1112     sortAnnBy.setBounds(new Rectangle(172, 265, 110, 21));
1113     JLabel sortAnnLabel = new JLabel();
1114     sortAnnLabel.setFont(verdana11);
1115     sortAnnLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1116     sortAnnLabel.setText(MessageManager.getString("label.sort_ann_by"));
1117     sortAutocalc.setFont(verdana11);
1118     sortAutocalc.setBounds(new Rectangle(290, 265, 165, 21));
1119     JPanel annsettingsPanel = new JPanel();
1120     annsettingsPanel.setBounds(new Rectangle(173, 34, 300, 61));
1121     annsettingsPanel.setLayout(new FlowLayout(FlowLayout.LEFT, 0, 0));
1122     JPanel autoAnnotSettings1 = new JPanel();
1123     autoAnnotSettings1.setLayout(new GridLayout(3, 1, 0, 0));
1124     annsettingsPanel.add(autoAnnotSettings1);
1125     JPanel autoAnnotSettings2 = new JPanel();
1126     autoAnnotSettings2.setLayout(new GridLayout(3, 1, 0, 0));
1127     annsettingsPanel.add(autoAnnotSettings2);
1128     JPanel autoAnnotSettings3 = new JPanel();
1129     autoAnnotSettings3.setLayout(new GridLayout(3, 1, 0, 0));
1130     annsettingsPanel.add(autoAnnotSettings3);
1131     visualTab.add(annsettingsPanel);
1132     Border jb = new EmptyBorder(1, 1, 4, 5);
1133     quality.setBorder(jb);
1134     conservation.setBorder(jb);
1135     identity.setBorder(jb);
1136     showConsensbits.setBorder(jb);
1137     showGroupbits.setBorder(jb);
1138     showGroupConsensus.setBorder(jb);
1139     showGroupConservation.setBorder(jb);
1140     showConsensHistogram.setBorder(jb);
1141     showConsensLogo.setBorder(jb);
1142
1143     autoAnnotSettings2.add(conservation);
1144     autoAnnotSettings1.add(quality);
1145     autoAnnotSettings3.add(identity);
1146     autoAnnotSettings1.add(showGroupbits);
1147     autoAnnotSettings3.add(showGroupConsensus);
1148     autoAnnotSettings2.add(showGroupConservation);
1149     autoAnnotSettings1.add(showConsensbits);
1150     autoAnnotSettings2.add(showConsensHistogram);
1151     autoAnnotSettings3.add(showConsensLogo);
1152
1153     JPanel tooltipSettings = new JPanel();
1154     tooltipSettings.setBorder(new TitledBorder(MessageManager
1155             .getString("label.sequence_id_tooltip")));
1156     tooltipSettings.setBounds(173, 130, 200, 62);
1157     tooltipSettings.setLayout(new GridLayout(2, 1));
1158     tooltipSettings.add(showDbRefTooltip);
1159     tooltipSettings.add(showNpTooltip);
1160     visualTab.add(tooltipSettings);
1161
1162     wrap.setFont(verdana11);
1163     wrap.setHorizontalAlignment(SwingConstants.TRAILING);
1164     wrap.setHorizontalTextPosition(SwingConstants.LEADING);
1165     wrap.setText(MessageManager.getString("label.wrap_alignment"));
1166     rightAlign.setFont(verdana11);
1167     rightAlign.setForeground(Color.black);
1168     rightAlign.setHorizontalAlignment(SwingConstants.RIGHT);
1169     rightAlign.setHorizontalTextPosition(SwingConstants.LEFT);
1170     rightAlign.setText(MessageManager.getString("label.right_align_ids"));
1171     idItalics.setFont(verdana11);
1172     idItalics.setHorizontalAlignment(SwingConstants.RIGHT);
1173     idItalics.setHorizontalTextPosition(SwingConstants.LEADING);
1174     idItalics.setText(MessageManager
1175             .getString("label.sequence_name_italics"));
1176     openoverv.setFont(verdana11);
1177     openoverv.setActionCommand(MessageManager
1178             .getString("label.open_overview"));
1179     openoverv.setHorizontalAlignment(SwingConstants.RIGHT);
1180     openoverv.setHorizontalTextPosition(SwingConstants.LEFT);
1181     openoverv.setText(MessageManager.getString(("label.open_overview")));
1182     JPanel jPanel2 = new JPanel();
1183     jPanel2.setBounds(new Rectangle(7, 17, 158, 297));
1184     GridLayout gridLayout2 = new GridLayout();
1185     jPanel2.setLayout(gridLayout2);
1186     gridLayout2.setRows(13);
1187     jPanel2.add(fullScreen);
1188     jPanel2.add(openoverv);
1189     jPanel2.add(seqLimit);
1190     jPanel2.add(rightAlign);
1191     jPanel2.add(fontLabel);
1192     jPanel2.add(showUnconserved);
1193     jPanel2.add(idItalics);
1194     jPanel2.add(smoothFont);
1195     jPanel2.add(gapLabel);
1196     jPanel2.add(wrap);
1197     jPanel2.add(sortLabel);
1198     jPanel2.add(sortAnnLabel);
1199     jPanel2.add(startupCheckbox);
1200     visualTab.add(jPanel2);
1201     visualTab.add(annotations);
1202     visualTab.add(startupFileTextfield);
1203     visualTab.add(sortby);
1204     visualTab.add(sortAnnBy);
1205     visualTab.add(sortAutocalc);
1206     visualTab.add(gapSymbolCB);
1207     visualTab.add(fontNameCB);
1208     visualTab.add(fontSizeCB);
1209     visualTab.add(fontStyleCB);
1210     return visualTab;
1211   }
1212
1213   protected void autoIdWidth_actionPerformed()
1214   {
1215     // TODO Auto-generated method stub
1216
1217   }
1218
1219   protected void userIdWidth_actionPerformed()
1220   {
1221     // TODO Auto-generated method stub
1222
1223   }
1224
1225   protected void maxColour_actionPerformed(JPanel panel)
1226   {
1227   }
1228
1229   protected void minColour_actionPerformed(JPanel panel)
1230   {
1231   }
1232
1233   protected void showunconserved_actionPerformed(ActionEvent e)
1234   {
1235     // TODO Auto-generated method stub
1236
1237   }
1238
1239   /**
1240    * DOCUMENT ME!
1241    *
1242    * @param e
1243    *          DOCUMENT ME!
1244    */
1245   public void ok_actionPerformed(ActionEvent e)
1246   {
1247   }
1248
1249   /**
1250    * DOCUMENT ME!
1251    *
1252    * @param e
1253    *          DOCUMENT ME!
1254    */
1255   public void cancel_actionPerformed(ActionEvent e)
1256   {
1257   }
1258
1259   /**
1260    * DOCUMENT ME!
1261    *
1262    * @param e
1263    *          DOCUMENT ME!
1264    */
1265   public void annotations_actionPerformed(ActionEvent e)
1266   {
1267   }
1268
1269   /**
1270    * DOCUMENT ME!
1271    */
1272   public void startupFileTextfield_mouseClicked()
1273   {
1274   }
1275
1276   public void newLink_actionPerformed(ActionEvent e)
1277   {
1278
1279   }
1280
1281   public void editLink_actionPerformed(ActionEvent e)
1282   {
1283
1284   }
1285
1286   public void deleteLink_actionPerformed(ActionEvent e)
1287   {
1288
1289   }
1290
1291   public void defaultBrowser_mouseClicked(MouseEvent e)
1292   {
1293
1294   }
1295
1296   public void linkURLList_keyTyped(KeyEvent e)
1297   {
1298
1299   }
1300
1301   public void useProxy_actionPerformed()
1302   {
1303     proxyServerTB.setEnabled(useProxy.isSelected());
1304     proxyPortTB.setEnabled(useProxy.isSelected());
1305   }
1306
1307 }