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.Viewer;
  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.FocusAdapter;
  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    * 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 = 23;
 734     final int lineSpacing = 30;
 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(Viewer.JMOL.name());
 785     structViewer.addItem(Viewer.CHIMERA.name());
 786     structureTab.add(structViewer);
 787
 788     ypos += lineSpacing;
 789     JLabel pathLabel = new JLabel();
 790     pathLabel.setFont(new java.awt.Font("SansSerif", 0, 11));
 791     pathLabel.setHorizontalAlignment(SwingConstants.LEFT);
 792     pathLabel.setText(MessageManager.getString("label.chimera_path"));
 793     pathLabel.setToolTipText(MessageManager
 794             .getString("label.chimera_path_tip"));
 795     pathLabel.setBounds(new Rectangle(10, ypos, 140, height));
 796     structureTab.add(pathLabel);
 797
 798     chimeraPath.setFont(verdana11);
 799     chimeraPath.setText("");
 800     chimeraPath.setBounds(new Rectangle(160, ypos, 300, height));
 801     chimeraPath.addMouseListener(new MouseAdapter()
 802     {
 803       @Override
 804       public void mouseClicked(MouseEvent e)
 805       {
 806         if (e.getClickCount() == 2)
 807         {
 808           String chosen = openFileChooser();
 809           if (chosen != null)
 810           {
 811             chimeraPath.setText(chosen);
 812           }
 813         }
 814       }
 815     });
 816     structureTab.add(chimeraPath);
 817
 818     structureTab.addFocusListener(new FocusAdapter()
 819     {
 820       @Override
 821       public void focusLost(FocusEvent e)
 822       {
 823         validateStructure(e);
 824       }
 825
 826     });
 827     return structureTab;
 828   }
 829
 830   /**
 831    * Show a dialog for the user to choose a file. Returns the chosen path, or
 832    * null on Cancel.
 833    *
 834    * @return
 835    */
 836   protected String openFileChooser()
 837   {
 838     String choice = null;
 839     JFileChooser chooser = new JFileChooser();
 840
 841     // chooser.setFileView(new JalviewFileView());
 842     chooser.setDialogTitle(MessageManager
 843             .getString("label.open_local_file"));
 844     chooser.setToolTipText(MessageManager.getString("action.open"));
 845
 846     int value = chooser.showOpenDialog(this);
 847
 848     if (value == JFileChooser.APPROVE_OPTION)
 849     {
 850       choice = chooser.getSelectedFile().getPath();
 851     }
 852     return choice;
 853   }
 854
 855   /**
 856    * Validate the structure tab preferences; if invalid, set focus on this tab.
 857    *
 858    * @param e
 859    */
 860   protected boolean validateStructure(FocusEvent e)
 861   {
 862     if (!validateStructure())
 863     {
 864       e.getComponent().requestFocusInWindow();
 865       return false;
 866     }
 867     return true;
 868   }
 869
 870   protected boolean validateStructure()
 871   {
 872     return false;
 873   }
 874
 875   /**
 876    * Initialises the Visual tabbed panel.
 877    *
 878    * @return
 879    */
 880   private JPanel initVisualTab()
 881   {
 882     JPanel visualTab = new JPanel();
 883     visualTab.setBorder(new TitledBorder(MessageManager
 884             .getString("action.open_new_alignment")));
 885     visualTab.setLayout(null);
 886     fullScreen.setFont(verdana11);
 887     fullScreen.setHorizontalAlignment(SwingConstants.RIGHT);
 888     fullScreen.setHorizontalTextPosition(SwingConstants.LEFT);
 889     fullScreen.setText(MessageManager.getString("label.maximize_window"));
 890     quality.setEnabled(false);
 891     quality.setFont(verdana11);
 892     quality.setHorizontalAlignment(SwingConstants.RIGHT);
 893     quality.setHorizontalTextPosition(SwingConstants.LEFT);
 894     quality.setSelected(true);
 895     quality.setText(MessageManager.getString("label.quality"));
 896     conservation.setEnabled(false);
 897     conservation.setFont(verdana11);
 898     conservation.setHorizontalAlignment(SwingConstants.RIGHT);
 899     conservation.setHorizontalTextPosition(SwingConstants.LEFT);
 900     conservation.setSelected(true);
 901     conservation.setText(MessageManager.getString("label.conservation"));
 902     identity.setEnabled(false);
 903     identity.setFont(verdana11);
 904     identity.setHorizontalAlignment(SwingConstants.RIGHT);
 905     identity.setHorizontalTextPosition(SwingConstants.LEFT);
 906     identity.setSelected(true);
 907     identity.setText(MessageManager.getString("label.consensus"));
 908     JLabel showGroupbits = new JLabel();
 909     showGroupbits.setFont(verdana11);
 910     showGroupbits.setHorizontalAlignment(SwingConstants.RIGHT);
 911     showGroupbits.setHorizontalTextPosition(SwingConstants.LEFT);
 912     showGroupbits.setText(MessageManager.getString("action.show_group")
 913             + ":");
 914     JLabel showConsensbits = new JLabel();
 915     showConsensbits.setFont(verdana11);
 916     showConsensbits.setHorizontalAlignment(SwingConstants.RIGHT);
 917     showConsensbits.setHorizontalTextPosition(SwingConstants.LEFT);
 918     showConsensbits.setText(MessageManager.getString("label.consensus")
 919             + ":");
 920     showConsensHistogram.setEnabled(false);
 921     showConsensHistogram.setFont(verdana11);
 922     showConsensHistogram.setHorizontalAlignment(SwingConstants.RIGHT);
 923     showConsensHistogram.setHorizontalTextPosition(SwingConstants.LEFT);
 924     showConsensHistogram.setSelected(true);
 925     showConsensHistogram.setText(MessageManager
 926             .getString("label.histogram"));
 927     showConsensLogo.setEnabled(false);
 928     showConsensLogo.setFont(verdana11);
 929     showConsensLogo.setHorizontalAlignment(SwingConstants.RIGHT);
 930     showConsensLogo.setHorizontalTextPosition(SwingConstants.LEFT);
 931     showConsensLogo.setSelected(true);
 932     showConsensLogo.setText(MessageManager.getString("label.logo"));
 933     showGroupConsensus.setEnabled(false);
 934     showGroupConsensus.setFont(verdana11);
 935     showGroupConsensus.setHorizontalAlignment(SwingConstants.RIGHT);
 936     showGroupConsensus.setHorizontalTextPosition(SwingConstants.LEFT);
 937     showGroupConsensus.setSelected(true);
 938     showGroupConsensus.setText(MessageManager.getString("label.consensus"));
 939     showGroupConservation.setEnabled(false);
 940     showGroupConservation.setFont(verdana11);
 941     showGroupConservation.setHorizontalAlignment(SwingConstants.RIGHT);
 942     showGroupConservation.setHorizontalTextPosition(SwingConstants.LEFT);
 943     showGroupConservation.setSelected(true);
 944     showGroupConservation.setText(MessageManager
 945             .getString("label.conservation"));
 946     showNpTooltip.setEnabled(true);
 947     showNpTooltip.setFont(verdana11);
 948     showNpTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
 949     showNpTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
 950     showNpTooltip.setSelected(true);
 951     showNpTooltip.setText(MessageManager
 952             .getString("label.non_positional_features"));
 953     showDbRefTooltip.setEnabled(true);
 954     showDbRefTooltip.setFont(verdana11);
 955     showDbRefTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
 956     showDbRefTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
 957     showDbRefTooltip.setSelected(true);
 958     showDbRefTooltip.setText(MessageManager
 959             .getString("label.database_references"));
 960     annotations.setFont(verdana11);
 961     annotations.setHorizontalAlignment(SwingConstants.RIGHT);
 962     annotations.setHorizontalTextPosition(SwingConstants.LEADING);
 963     annotations.setSelected(true);
 964     annotations.setText(MessageManager.getString("label.show_annotations"));
 965     annotations.setBounds(new Rectangle(169, 12, 200, 23));
 966     annotations.addActionListener(new ActionListener()
 967     {
 968       public void actionPerformed(ActionEvent e)
 969       {
 970         annotations_actionPerformed(e);
 971       }
 972     });
 973     identity.addActionListener(new ActionListener()
 974     {
 975       public void actionPerformed(ActionEvent e)
 976       {
 977         annotations_actionPerformed(e);
 978       }
 979     });
 980     showGroupConsensus.addActionListener(new ActionListener()
 981     {
 982       public void actionPerformed(ActionEvent e)
 983       {
 984         annotations_actionPerformed(e);
 985       }
 986     });
 987     showUnconserved.setFont(verdana11);
 988     showUnconserved.setHorizontalAlignment(SwingConstants.RIGHT);
 989     showUnconserved.setHorizontalTextPosition(SwingConstants.LEFT);
 990     showUnconserved.setSelected(true);
 991     showUnconserved.setText(MessageManager
 992             .getString("action.show_unconserved"));
 993     showUnconserved.addActionListener(new ActionListener()
 994     {
 995       public void actionPerformed(ActionEvent e)
 996       {
 997         showunconserved_actionPerformed(e);
 998       }
 999     });
1000
1001     // TODO these are not yet added to / action from Preferences
1002     // JCheckBox shareSelections = new JCheckBox();
1003     // shareSelections.setFont(verdana11);
1004     // shareSelections.setHorizontalAlignment(SwingConstants.RIGHT);
1005     // shareSelections.setHorizontalTextPosition(SwingConstants.LEFT);
1006     // shareSelections.setSelected(true);
1007     // shareSelections.setText(MessageManager
1008     // .getString("label.share_selection_across_views"));
1009     // JCheckBox followHighlight = new JCheckBox();
1010     // followHighlight.setFont(verdana11);
1011     // followHighlight.setHorizontalAlignment(SwingConstants.RIGHT);
1012     // followHighlight.setHorizontalTextPosition(SwingConstants.LEFT);
1013     // // showUnconserved.setBounds(new Rectangle(169, 40, 200, 23));
1014     // followHighlight.setSelected(true);
1015     // followHighlight.setText(MessageManager
1016     // .getString("label.scroll_highlighted_regions"));
1017
1018     seqLimit.setFont(verdana11);
1019     seqLimit.setHorizontalAlignment(SwingConstants.RIGHT);
1020     seqLimit.setHorizontalTextPosition(SwingConstants.LEFT);
1021     seqLimit.setText(MessageManager.getString("label.full_sequence_id"));
1022     smoothFont.setFont(verdana11);
1023     smoothFont.setHorizontalAlignment(SwingConstants.RIGHT);
1024     smoothFont.setHorizontalTextPosition(SwingConstants.LEADING);
1025     smoothFont.setText(MessageManager.getString("label.smooth_font"));
1026     JLabel gapLabel = new JLabel();
1027     gapLabel.setFont(verdana11);
1028     gapLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1029     gapLabel.setText(MessageManager.getString("label.gap_symbol") + " ");
1030     JLabel fontLabel = new JLabel();
1031     fontLabel.setFont(verdana11);
1032     fontLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1033     fontLabel.setText(MessageManager.getString("label.font"));
1034     fontSizeCB.setFont(verdana11);
1035     fontSizeCB.setBounds(new Rectangle(320, 104, 65, 23));
1036     fontStyleCB.setFont(verdana11);
1037     fontStyleCB.setBounds(new Rectangle(382, 104, 80, 23));
1038     fontNameCB.setFont(verdana11);
1039     fontNameCB.setBounds(new Rectangle(172, 104, 147, 23));
1040     gapSymbolCB.setFont(verdana11);
1041     gapSymbolCB.setBounds(new Rectangle(172, 196, 69, 23));
1042     DefaultListCellRenderer dlcr = new DefaultListCellRenderer();
1043     dlcr.setHorizontalAlignment(DefaultListCellRenderer.CENTER);
1044     gapSymbolCB.setRenderer(dlcr);
1045
1046     startupCheckbox.setText(MessageManager.getString("action.open_file"));
1047     startupCheckbox.setFont(verdana11);
1048     startupCheckbox.setHorizontalAlignment(SwingConstants.RIGHT);
1049     startupCheckbox.setHorizontalTextPosition(SwingConstants.LEFT);
1050     startupCheckbox.setSelected(true);
1051     startupFileTextfield.setFont(verdana11);
1052     startupFileTextfield.setBounds(new Rectangle(172, 290, 270, 20));
1053     startupFileTextfield.addMouseListener(new MouseAdapter()
1054     {
1055       public void mouseClicked(MouseEvent e)
1056       {
1057         if (e.getClickCount() > 1)
1058         {
1059           startupFileTextfield_mouseClicked();
1060         }
1061       }
1062     });
1063
1064     sortby.setFont(verdana11);
1065     sortby.setBounds(new Rectangle(172, 240, 155, 21));
1066     JLabel sortLabel = new JLabel();
1067     sortLabel.setFont(verdana11);
1068     sortLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1069     sortLabel.setText(MessageManager.getString("label.sort_by"));
1070     sortAnnBy.setFont(verdana11);
1071     sortAnnBy.setBounds(new Rectangle(172, 265, 110, 21));
1072     JLabel sortAnnLabel = new JLabel();
1073     sortAnnLabel.setFont(verdana11);
1074     sortAnnLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1075     sortAnnLabel.setText(MessageManager.getString("label.sort_ann_by"));
1076     sortAutocalc.setFont(verdana11);
1077     sortAutocalc.setBounds(new Rectangle(290, 265, 165, 21));
1078     JPanel annsettingsPanel = new JPanel();
1079     annsettingsPanel.setBounds(new Rectangle(173, 34, 300, 61));
1080     annsettingsPanel.setLayout(new FlowLayout(FlowLayout.LEFT, 0, 0));
1081     JPanel autoAnnotSettings1 = new JPanel();
1082     autoAnnotSettings1.setLayout(new GridLayout(3, 1, 0, 0));
1083     annsettingsPanel.add(autoAnnotSettings1);
1084     JPanel autoAnnotSettings2 = new JPanel();
1085     autoAnnotSettings2.setLayout(new GridLayout(3, 1, 0, 0));
1086     annsettingsPanel.add(autoAnnotSettings2);
1087     JPanel autoAnnotSettings3 = new JPanel();
1088     autoAnnotSettings3.setLayout(new GridLayout(3, 1, 0, 0));
1089     annsettingsPanel.add(autoAnnotSettings3);
1090     visualTab.add(annsettingsPanel);
1091     Border jb = new EmptyBorder(1, 1, 4, 5);
1092     quality.setBorder(jb);
1093     conservation.setBorder(jb);
1094     identity.setBorder(jb);
1095     showConsensbits.setBorder(jb);
1096     showGroupbits.setBorder(jb);
1097     showGroupConsensus.setBorder(jb);
1098     showGroupConservation.setBorder(jb);
1099     showConsensHistogram.setBorder(jb);
1100     showConsensLogo.setBorder(jb);
1101
1102     autoAnnotSettings2.add(conservation);
1103     autoAnnotSettings1.add(quality);
1104     autoAnnotSettings3.add(identity);
1105     autoAnnotSettings1.add(showGroupbits);
1106     autoAnnotSettings3.add(showGroupConsensus);
1107     autoAnnotSettings2.add(showGroupConservation);
1108     autoAnnotSettings1.add(showConsensbits);
1109     autoAnnotSettings2.add(showConsensHistogram);
1110     autoAnnotSettings3.add(showConsensLogo);
1111
1112     JPanel tooltipSettings = new JPanel();
1113     tooltipSettings.setBorder(new TitledBorder(MessageManager
1114             .getString("label.sequence_id_tooltip")));
1115     tooltipSettings.setBounds(173, 130, 200, 62);
1116     tooltipSettings.setLayout(new GridLayout(2, 1));
1117     tooltipSettings.add(showDbRefTooltip);
1118     tooltipSettings.add(showNpTooltip);
1119     visualTab.add(tooltipSettings);
1120
1121     wrap.setFont(verdana11);
1122     wrap.setHorizontalAlignment(SwingConstants.TRAILING);
1123     wrap.setHorizontalTextPosition(SwingConstants.LEADING);
1124     wrap.setText(MessageManager.getString("label.wrap_alignment"));
1125     rightAlign.setFont(verdana11);
1126     rightAlign.setForeground(Color.black);
1127     rightAlign.setHorizontalAlignment(SwingConstants.RIGHT);
1128     rightAlign.setHorizontalTextPosition(SwingConstants.LEFT);
1129     rightAlign.setText(MessageManager.getString("label.right_align_ids"));
1130     idItalics.setFont(verdana11);
1131     idItalics.setHorizontalAlignment(SwingConstants.RIGHT);
1132     idItalics.setHorizontalTextPosition(SwingConstants.LEADING);
1133     idItalics.setText(MessageManager
1134             .getString("label.sequence_name_italics"));
1135     openoverv.setFont(verdana11);
1136     openoverv.setActionCommand(MessageManager
1137             .getString("label.open_overview"));
1138     openoverv.setHorizontalAlignment(SwingConstants.RIGHT);
1139     openoverv.setHorizontalTextPosition(SwingConstants.LEFT);
1140     openoverv.setText(MessageManager.getString(("label.open_overview")));
1141     JPanel jPanel2 = new JPanel();
1142     jPanel2.setBounds(new Rectangle(7, 17, 158, 297));
1143     GridLayout gridLayout2 = new GridLayout();
1144     jPanel2.setLayout(gridLayout2);
1145     gridLayout2.setRows(13);
1146     jPanel2.add(fullScreen);
1147     jPanel2.add(openoverv);
1148     jPanel2.add(seqLimit);
1149     jPanel2.add(rightAlign);
1150     jPanel2.add(fontLabel);
1151     jPanel2.add(showUnconserved);
1152     jPanel2.add(idItalics);
1153     jPanel2.add(smoothFont);
1154     jPanel2.add(gapLabel);
1155     jPanel2.add(wrap);
1156     jPanel2.add(sortLabel);
1157     jPanel2.add(sortAnnLabel);
1158     jPanel2.add(startupCheckbox);
1159     visualTab.add(jPanel2);
1160     visualTab.add(annotations);
1161     visualTab.add(startupFileTextfield);
1162     visualTab.add(sortby);
1163     visualTab.add(sortAnnBy);
1164     visualTab.add(sortAutocalc);
1165     visualTab.add(gapSymbolCB);
1166     visualTab.add(fontNameCB);
1167     visualTab.add(fontSizeCB);
1168     visualTab.add(fontStyleCB);
1169     return visualTab;
1170   }
1171
1172   protected void autoIdWidth_actionPerformed()
1173   {
1174     // TODO Auto-generated method stub
1175
1176   }
1177
1178   protected void userIdWidth_actionPerformed()
1179   {
1180     // TODO Auto-generated method stub
1181
1182   }
1183
1184   protected void maxColour_actionPerformed(JPanel panel)
1185   {
1186   }
1187
1188   protected void minColour_actionPerformed(JPanel panel)
1189   {
1190   }
1191
1192   protected void showunconserved_actionPerformed(ActionEvent e)
1193   {
1194     // TODO Auto-generated method stub
1195
1196   }
1197
1198   /**
1199    * DOCUMENT ME!
1200    *
1201    * @param e
1202    *          DOCUMENT ME!
1203    */
1204   public void ok_actionPerformed(ActionEvent e)
1205   {
1206   }
1207
1208   /**
1209    * DOCUMENT ME!
1210    *
1211    * @param e
1212    *          DOCUMENT ME!
1213    */
1214   public void cancel_actionPerformed(ActionEvent e)
1215   {
1216   }
1217
1218   /**
1219    * DOCUMENT ME!
1220    *
1221    * @param e
1222    *          DOCUMENT ME!
1223    */
1224   public void annotations_actionPerformed(ActionEvent e)
1225   {
1226   }
1227
1228   /**
1229    * DOCUMENT ME!
1230    */
1231   public void startupFileTextfield_mouseClicked()
1232   {
1233   }
1234
1235   public void newLink_actionPerformed(ActionEvent e)
1236   {
1237
1238   }
1239
1240   public void editLink_actionPerformed(ActionEvent e)
1241   {
1242
1243   }
1244
1245   public void deleteLink_actionPerformed(ActionEvent e)
1246   {
1247
1248   }
1249
1250   public void defaultBrowser_mouseClicked(MouseEvent e)
1251   {
1252
1253   }
1254
1255   public void linkURLList_keyTyped(KeyEvent e)
1256   {
1257
1258   }
1259
1260   public void useProxy_actionPerformed()
1261   {
1262     proxyServerTB.setEnabled(useProxy.isSelected());
1263     proxyPortTB.setEnabled(useProxy.isSelected());
1264   }
1265
1266 }