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