src/jalview/jbgui/GPreferences.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.jbgui;
  22
  23 import java.awt.BorderLayout;
  24 import java.awt.Color;
  25 import java.awt.Component;
  26 import java.awt.Dimension;
  27 import java.awt.FlowLayout;
  28 import java.awt.Font;
  29 import java.awt.GridBagConstraints;
  30 import java.awt.GridBagLayout;
  31 import java.awt.GridLayout;
  32 import java.awt.Insets;
  33 import java.awt.Rectangle;
  34 import java.awt.event.ActionEvent;
  35 import java.awt.event.ActionListener;
  36 import java.awt.event.FocusEvent;
  37 import java.awt.event.KeyEvent;
  38 import java.awt.event.MouseAdapter;
  39 import java.awt.event.MouseEvent;
  40
  41 import javax.swing.BorderFactory;
  42 import javax.swing.DefaultListCellRenderer;
  43 import javax.swing.JButton;
  44 import javax.swing.JCheckBox;
  45 import javax.swing.JComboBox;
  46 import javax.swing.JFileChooser;
  47 import javax.swing.JLabel;
  48 import javax.swing.JList;
  49 import javax.swing.JPanel;
  50 import javax.swing.JScrollPane;
  51 import javax.swing.JTabbedPane;
  52 import javax.swing.JTextField;
  53 import javax.swing.ListSelectionModel;
  54 import javax.swing.SwingConstants;
  55 import javax.swing.border.Border;
  56 import javax.swing.border.EmptyBorder;
  57 import javax.swing.border.EtchedBorder;
  58 import javax.swing.border.TitledBorder;
  59 import javax.swing.event.ChangeEvent;
  60 import javax.swing.event.ChangeListener;
  61 import javax.swing.event.ListSelectionEvent;
  62 import javax.swing.event.ListSelectionListener;
  63
  64 import jalview.gui.JvSwingUtils;
  65 import jalview.gui.StructureViewer.ViewerType;
  66 import jalview.jbgui.PDBDocFieldPreferences.PreferenceSource;
  67 import jalview.util.MessageManager;
  68
  69 /**
  70  * Base class for the Preferences panel.
  71  *
  72  * @author $author$
  73  * @version $Revision$
  74  */
  75 public class GPreferences extends JPanel
  76 {
  77   private static final Font LABEL_FONT = JvSwingUtils.getLabelFont();
  78
  79   private static final Font LABEL_FONT_ITALIC = JvSwingUtils
  80           .getLabelFont(false, true);
  81
  82   /*
  83    * Visual tab components
  84    */
  85   protected JCheckBox fullScreen = new JCheckBox();
  86
  87   protected JCheckBox openoverv = new JCheckBox();
  88
  89   protected JCheckBox seqLimit = new JCheckBox();
  90
  91   protected JCheckBox rightAlign = new JCheckBox();
  92
  93   protected JComboBox<String> fontSizeCB = new JComboBox<String>();
  94
  95   protected JComboBox<String> fontStyleCB = new JComboBox<String>();
  96
  97   protected JComboBox<String> fontNameCB = new JComboBox<String>();
  98
  99   protected JCheckBox showUnconserved = new JCheckBox();
 100
 101   protected JCheckBox idItalics = new JCheckBox();
 102
 103   protected JCheckBox smoothFont = new JCheckBox();
 104
 105   protected JCheckBox scaleProteinToCdna = new JCheckBox();
 106
 107   protected JComboBox<String> gapSymbolCB = new JComboBox<String>();
 108
 109   protected JCheckBox wrap = new JCheckBox();
 110
 111   protected JComboBox<String> sortby = new JComboBox<String>();
 112
 113   protected JComboBox<String> sortAnnBy = new JComboBox<String>();
 114
 115   protected JComboBox<String> sortAutocalc = new JComboBox<String>();
 116
 117   protected JCheckBox startupCheckbox = new JCheckBox();
 118
 119   protected JTextField startupFileTextfield = new JTextField();
 120
 121   // below are in the 'second column'
 122   protected JCheckBox annotations = new JCheckBox();
 123
 124   protected JCheckBox quality = new JCheckBox();
 125
 126   protected JCheckBox conservation = new JCheckBox();
 127
 128   protected JCheckBox identity = new JCheckBox();
 129
 130   protected JCheckBox showGroupConsensus = new JCheckBox();
 131
 132   protected JCheckBox showGroupConservation = new JCheckBox();
 133
 134   protected JCheckBox showConsensHistogram = new JCheckBox();
 135
 136   protected JCheckBox showConsensLogo = new JCheckBox();
 137
 138   protected JCheckBox showDbRefTooltip = new JCheckBox();
 139
 140   protected JCheckBox showNpTooltip = new JCheckBox();
 141
 142   /*
 143    * Structure tab and components
 144    */
 145   protected JPanel structureTab;
 146
 147   protected JCheckBox structFromPdb = new JCheckBox();
 148
 149   protected JCheckBox useRnaView = new JCheckBox();
 150
 151   protected JCheckBox addSecondaryStructure = new JCheckBox();
 152
 153   protected JCheckBox addTempFactor = new JCheckBox();
 154
 155   protected JComboBox<String> structViewer = new JComboBox<String>();
 156
 157   protected JTextField chimeraPath = new JTextField();
 158
 159
 160   /*
 161    * Colours tab components
 162    */
 163   protected JPanel minColour = new JPanel();
 164
 165   protected JPanel maxColour = new JPanel();
 166
 167   protected JComboBox<String> protColour = new JComboBox<String>();
 168
 169   protected JComboBox<String> nucColour = new JComboBox<String>();
 170
 171   /*
 172    * Connections tab components
 173    */
 174   protected JList linkURLList = new JList();
 175
 176   protected JTextField proxyServerTB = new JTextField();
 177
 178   protected JTextField proxyPortTB = new JTextField();
 179
 180   protected JTextField defaultBrowser = new JTextField();
 181
 182   protected JList linkNameList = new JList();
 183
 184   protected JCheckBox useProxy = new JCheckBox();
 185
 186   protected JCheckBox usagestats = new JCheckBox();
 187
 188   protected JCheckBox questionnaire = new JCheckBox();
 189
 190   protected JCheckBox versioncheck = new JCheckBox();
 191
 192   /*
 193    * Output tab components
 194    */
 195   protected JComboBox<String> epsRendering = new JComboBox<String>();
 196
 197   protected JLabel userIdWidthlabel = new JLabel();
 198
 199   protected JCheckBox autoIdWidth = new JCheckBox();
 200
 201   protected JTextField userIdWidth = new JTextField();
 202
 203   protected JCheckBox blcjv = new JCheckBox();
 204
 205   protected JCheckBox pileupjv = new JCheckBox();
 206
 207   protected JCheckBox clustaljv = new JCheckBox();
 208
 209   protected JCheckBox msfjv = new JCheckBox();
 210
 211   protected JCheckBox fastajv = new JCheckBox();
 212
 213   protected JCheckBox pfamjv = new JCheckBox();
 214
 215   protected JCheckBox pirjv = new JCheckBox();
 216
 217   protected JCheckBox modellerOutput = new JCheckBox();
 218
 219   /*
 220    * Editing tab components
 221    */
 222   protected JCheckBox autoCalculateConsCheck = new JCheckBox();
 223
 224   protected JCheckBox padGaps = new JCheckBox();
 225
 226   protected JCheckBox sortByTree = new JCheckBox();
 227
 228   /*
 229    * DAS Settings tab
 230    */
 231   protected JPanel dasTab = new JPanel();
 232
 233   /*
 234    * Web Services tab
 235    */
 236   protected JPanel wsTab = new JPanel();
 237
 238   /**
 239    * Creates a new GPreferences object.
 240    */
 241   public GPreferences()
 242   {
 243     try
 244     {
 245       jbInit();
 246     } catch (Exception ex)
 247     {
 248       ex.printStackTrace();
 249     }
 250   }
 251
 252   /**
 253    * Construct the panel and its tabbed sub-panels.
 254    *
 255    * @throws Exception
 256    */
 257   private void jbInit() throws Exception
 258   {
 259     final JTabbedPane tabbedPane = new JTabbedPane();
 260     this.setLayout(new BorderLayout());
 261     JPanel okCancelPanel = initOkCancelPanel();
 262     this.add(tabbedPane, BorderLayout.CENTER);
 263     this.add(okCancelPanel, BorderLayout.SOUTH);
 264
 265     tabbedPane.add(initVisualTab(),
 266             MessageManager.getString("label.visual"));
 267
 268     tabbedPane.add(initColoursTab(),
 269             MessageManager.getString("label.colours"));
 270
 271     tabbedPane.add(initStructureTab(),
 272             MessageManager.getString("label.structure"));
 273
 274     tabbedPane.add(initConnectionsTab(),
 275             MessageManager.getString("label.connections"));
 276
 277     tabbedPane.add(initOutputTab(), MessageManager.getString("label.output"));
 278
 279     tabbedPane.add(initEditingTab(), MessageManager.getString("label.editing"));
 280
 281     /*
 282      * See DasSourceBrowser for the real work of configuring this tab.
 283      */
 284     dasTab.setLayout(new BorderLayout());
 285     tabbedPane
 286             .add(dasTab, MessageManager.getString("label.das_settings"));
 287
 288     /*
 289      * See WsPreferences for the real work of configuring this tab.
 290      */
 291     wsTab.setLayout(new BorderLayout());
 292     tabbedPane.add(wsTab, MessageManager.getString("label.web_services"));
 293
 294     /*
 295      * Handler to validate a tab before leaving it - currently only for
 296      * Structure.
 297      */
 298     tabbedPane.addChangeListener(new ChangeListener()
 299     {
 300       private Component lastTab;
 301
 302       @Override
 303       public void stateChanged(ChangeEvent e)
 304       {
 305         if (lastTab == structureTab
 306                 && tabbedPane.getSelectedComponent() != structureTab)
 307         {
 308           if (!validateStructure())
 309           {
 310             tabbedPane.setSelectedComponent(structureTab);
 311             return;
 312           }
 313         }
 314         lastTab = tabbedPane.getSelectedComponent();
 315       }
 316
 317     });
 318   }
 319
 320   /**
 321    * Initialises the Editing tabbed panel.
 322    *
 323    * @return
 324    */
 325   private JPanel initEditingTab()
 326   {
 327     JPanel editingTab = new JPanel();
 328     editingTab.setLayout(null);
 329     autoCalculateConsCheck.setFont(LABEL_FONT);
 330     autoCalculateConsCheck.setText(MessageManager
 331             .getString("label.autocalculate_consensus"));
 332     autoCalculateConsCheck.setBounds(new Rectangle(21, 52, 209, 23));
 333     padGaps.setFont(LABEL_FONT);
 334     padGaps.setText(MessageManager.getString("label.pad_gaps_when_editing"));
 335     padGaps.setBounds(new Rectangle(22, 94, 168, 23));
 336     sortByTree.setFont(LABEL_FONT);
 337     sortByTree
 338             .setText(MessageManager.getString("label.sort_with_new_tree"));
 339     sortByTree
 340             .setToolTipText(MessageManager
 341                     .getString("label.any_trees_calculated_or_loaded_alignment_automatically_sort"));
 342     sortByTree.setBounds(new Rectangle(22, 136, 168, 23));
 343     editingTab.add(autoCalculateConsCheck);
 344     editingTab.add(padGaps);
 345     editingTab.add(sortByTree);
 346     return editingTab;
 347   }
 348
 349   /**
 350    * Initialises the Output tabbed panel.
 351    *
 352    * @return
 353    */
 354   private JPanel initOutputTab()
 355   {
 356     JPanel outputTab = new JPanel();
 357     outputTab.setLayout(null);
 358     JLabel epsLabel = new JLabel();
 359     epsLabel.setFont(LABEL_FONT);
 360     epsLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 361     epsLabel.setText(MessageManager.getString("label.eps_rendering_style"));
 362     epsLabel.setBounds(new Rectangle(9, 31, 140, 24));
 363     epsRendering.setFont(LABEL_FONT);
 364     epsRendering.setBounds(new Rectangle(154, 34, 187, 21));
 365     JLabel jLabel1 = new JLabel();
 366     jLabel1.setFont(LABEL_FONT);
 367     jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
 368     jLabel1.setText(MessageManager.getString("label.append_start_end"));
 369     jLabel1.setFont(LABEL_FONT);
 370     fastajv.setFont(LABEL_FONT);
 371     fastajv.setHorizontalAlignment(SwingConstants.LEFT);
 372     clustaljv.setText(MessageManager.getString("label.clustal") + "     ");
 373     blcjv.setText(MessageManager.getString("label.blc") + "     ");
 374     fastajv.setText(MessageManager.getString("label.fasta") + "     ");
 375     msfjv.setText(MessageManager.getString("label.msf") + "     ");
 376     pfamjv.setText(MessageManager.getString("label.pfam") + "     ");
 377     pileupjv.setText(MessageManager.getString("label.pileup") + "     ");
 378     msfjv.setFont(LABEL_FONT);
 379     msfjv.setHorizontalAlignment(SwingConstants.LEFT);
 380     pirjv.setText(MessageManager.getString("label.pir") + "     ");
 381     JPanel jPanel11 = new JPanel();
 382     jPanel11.setFont(LABEL_FONT);
 383     TitledBorder titledBorder2 = new TitledBorder(
 384             MessageManager.getString("label.file_output"));
 385     jPanel11.setBorder(titledBorder2);
 386     jPanel11.setBounds(new Rectangle(30, 72, 196, 182));
 387     GridLayout gridLayout3 = new GridLayout();
 388     jPanel11.setLayout(gridLayout3);
 389     gridLayout3.setRows(8);
 390     blcjv.setFont(LABEL_FONT);
 391     blcjv.setHorizontalAlignment(SwingConstants.LEFT);
 392     clustaljv.setFont(LABEL_FONT);
 393     clustaljv.setHorizontalAlignment(SwingConstants.LEFT);
 394     pfamjv.setFont(LABEL_FONT);
 395     pfamjv.setHorizontalAlignment(SwingConstants.LEFT);
 396     pileupjv.setFont(LABEL_FONT);
 397     pileupjv.setHorizontalAlignment(SwingConstants.LEFT);
 398     pirjv.setFont(LABEL_FONT);
 399     pirjv.setHorizontalAlignment(SwingConstants.LEFT);
 400     autoIdWidth.setFont(LABEL_FONT);
 401     autoIdWidth.setText(MessageManager
 402             .getString("label.automatically_set_id_width"));
 403     autoIdWidth
 404             .setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.getString("label.adjusts_width_generated_eps_png")));
 405     autoIdWidth.setBounds(new Rectangle(228, 96, 188, 23));
 406     autoIdWidth.addActionListener(new ActionListener()
 407     {
 408
 409       @Override
 410       public void actionPerformed(ActionEvent e)
 411       {
 412         autoIdWidth_actionPerformed();
 413       }
 414     });
 415     userIdWidthlabel.setFont(LABEL_FONT);
 416     userIdWidthlabel.setText(MessageManager
 417             .getString("label.figure_id_column_width"));
 418     userIdWidth
 419             .setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.getString("label.manually_specify_width_left_column")));
 420     userIdWidthlabel
 421             .setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.getString("label.manually_specify_width_left_column")));
 422     userIdWidthlabel.setBounds(new Rectangle(236, 120, 168, 23));
 423     userIdWidth.setFont(JvSwingUtils.getTextAreaFont());
 424     userIdWidth.setText("");
 425     userIdWidth.setBounds(new Rectangle(232, 144, 84, 23));
 426     userIdWidth.addActionListener(new ActionListener()
 427     {
 428
 429       @Override
 430       public void actionPerformed(ActionEvent e)
 431       {
 432         userIdWidth_actionPerformed();
 433       }
 434     });
 435     jPanel11.add(jLabel1);
 436     jPanel11.add(blcjv);
 437     jPanel11.add(clustaljv);
 438     jPanel11.add(fastajv);
 439     jPanel11.add(msfjv);
 440     jPanel11.add(pfamjv);
 441     jPanel11.add(pileupjv);
 442     jPanel11.add(pirjv);
 443     outputTab.add(autoIdWidth);
 444     outputTab.add(userIdWidth);
 445     outputTab.add(userIdWidthlabel);
 446     outputTab.add(modellerOutput);
 447     outputTab.add(epsLabel);
 448     outputTab.add(epsRendering);
 449     outputTab.add(jPanel11);
 450     modellerOutput.setFont(LABEL_FONT);
 451     modellerOutput.setText(MessageManager
 452             .getString("label.use_modeller_output"));
 453     modellerOutput.setBounds(new Rectangle(228, 226, 168, 23));
 454     return outputTab;
 455   }
 456
 457   /**
 458    * Initialises the Connections tabbed panel.
 459    *
 460    * @return
 461    */
 462   private JPanel initConnectionsTab()
 463   {
 464     JPanel connectTab = new JPanel();
 465     connectTab.setLayout(new GridBagLayout());
 466     JLabel serverLabel = new JLabel();
 467     serverLabel.setText(MessageManager.getString("label.address"));
 468     serverLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 469     serverLabel.setFont(LABEL_FONT);
 470     proxyServerTB.setFont(LABEL_FONT);
 471     proxyPortTB.setFont(LABEL_FONT);
 472     JLabel portLabel = new JLabel();
 473     portLabel.setFont(LABEL_FONT);
 474     portLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 475     portLabel.setText(MessageManager.getString("label.port"));
 476     JLabel browserLabel = new JLabel();
 477     browserLabel.setFont(new java.awt.Font("SansSerif", 0, 11));
 478     browserLabel.setHorizontalAlignment(SwingConstants.TRAILING);
 479     browserLabel.setText(MessageManager
 480             .getString("label.default_browser_unix"));
 481     defaultBrowser.setFont(LABEL_FONT);
 482     defaultBrowser.setText("");
 483     usagestats.setText(MessageManager
 484             .getString("label.send_usage_statistics"));
 485     usagestats.setFont(LABEL_FONT);
 486     usagestats.setHorizontalAlignment(SwingConstants.RIGHT);
 487     usagestats.setHorizontalTextPosition(SwingConstants.LEADING);
 488     questionnaire.setText(MessageManager
 489             .getString("label.check_for_questionnaires"));
 490     questionnaire.setFont(LABEL_FONT);
 491     questionnaire.setHorizontalAlignment(SwingConstants.RIGHT);
 492     questionnaire.setHorizontalTextPosition(SwingConstants.LEADING);
 493     versioncheck.setText(MessageManager
 494             .getString("label.check_for_latest_version"));
 495     versioncheck.setFont(LABEL_FONT);
 496     versioncheck.setHorizontalAlignment(SwingConstants.RIGHT);
 497     versioncheck.setHorizontalTextPosition(SwingConstants.LEADING);
 498     JButton newLink = new JButton();
 499     newLink.setText(MessageManager.getString("action.new"));
 500     newLink.addActionListener(new java.awt.event.ActionListener()
 501     {
 502       public void actionPerformed(ActionEvent e)
 503       {
 504         newLink_actionPerformed(e);
 505       }
 506     });
 507     JButton editLink = new JButton();
 508     editLink.setText(MessageManager.getString("action.edit"));
 509     editLink.addActionListener(new java.awt.event.ActionListener()
 510     {
 511       public void actionPerformed(ActionEvent e)
 512       {
 513         editLink_actionPerformed(e);
 514       }
 515     });
 516     JButton deleteLink = new JButton();
 517     deleteLink.setText(MessageManager.getString("action.delete"));
 518     deleteLink.addActionListener(new java.awt.event.ActionListener()
 519     {
 520       public void actionPerformed(ActionEvent e)
 521       {
 522         deleteLink_actionPerformed(e);
 523       }
 524     });
 525
 526     linkURLList.addListSelectionListener(new ListSelectionListener()
 527     {
 528       public void valueChanged(ListSelectionEvent e)
 529       {
 530         int index = linkURLList.getSelectedIndex();
 531         linkNameList.setSelectedIndex(index);
 532       }
 533     });
 534
 535     linkNameList.addListSelectionListener(new ListSelectionListener()
 536     {
 537       public void valueChanged(ListSelectionEvent e)
 538       {
 539         int index = linkNameList.getSelectedIndex();
 540         linkURLList.setSelectedIndex(index);
 541       }
 542     });
 543
 544     JScrollPane linkScrollPane = new JScrollPane();
 545     linkScrollPane.setBorder(null);
 546     JPanel linkPanel = new JPanel();
 547     linkPanel.setBorder(new TitledBorder(MessageManager
 548             .getString("label.url_linkfrom_sequence_id")));
 549     linkPanel.setLayout(new BorderLayout());
 550     GridLayout gridLayout1 = new GridLayout();
 551     JPanel editLinkButtons = new JPanel();
 552     editLinkButtons.setLayout(gridLayout1);
 553     gridLayout1.setRows(3);
 554     linkNameList.setFont(LABEL_FONT);
 555     linkNameList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
 556     BorderLayout borderLayout3 = new BorderLayout();
 557     JPanel linkPanel2 = new JPanel();
 558     linkPanel2.setLayout(borderLayout3);
 559     linkURLList.setFont(LABEL_FONT);
 560     linkURLList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
 561
 562     defaultBrowser.addMouseListener(new MouseAdapter()
 563     {
 564       public void mouseClicked(MouseEvent e)
 565       {
 566         if (e.getClickCount() > 1)
 567         {
 568           defaultBrowser_mouseClicked(e);
 569         }
 570       }
 571     });
 572     useProxy.setFont(LABEL_FONT);
 573     useProxy.setHorizontalAlignment(SwingConstants.RIGHT);
 574     useProxy.setHorizontalTextPosition(SwingConstants.LEADING);
 575     useProxy.setText(MessageManager.getString("label.use_proxy_server"));
 576     useProxy.addActionListener(new ActionListener()
 577     {
 578       public void actionPerformed(ActionEvent e)
 579       {
 580         useProxy_actionPerformed();
 581       }
 582     });
 583     linkPanel.add(editLinkButtons, BorderLayout.EAST);
 584     editLinkButtons.add(newLink, null);
 585     editLinkButtons.add(editLink, null);
 586     editLinkButtons.add(deleteLink, null);
 587     linkPanel.add(linkScrollPane, BorderLayout.CENTER);
 588     linkScrollPane.getViewport().add(linkPanel2, null);
 589     linkPanel2.add(linkURLList, BorderLayout.CENTER);
 590     linkPanel2.add(linkNameList, BorderLayout.WEST);
 591     JPanel jPanel1 = new JPanel();
 592     TitledBorder titledBorder1 = new TitledBorder(
 593             MessageManager.getString("label.proxy_server"));
 594     jPanel1.setBorder(titledBorder1);
 595     jPanel1.setLayout(new GridBagLayout());
 596     jPanel1.add(serverLabel, new GridBagConstraints(0, 1, 1, 1, 0.0, 0.0,
 597             GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
 598                     2, 4, 0), 5, 0));
 599     jPanel1.add(portLabel, new GridBagConstraints(2, 1, 1, 1, 0.0, 0.0,
 600             GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
 601                     0, 4, 0), 11, 6));
 602     connectTab.add(linkPanel, new GridBagConstraints(0, 0, 2, 1, 1.0, 1.0,
 603             GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(
 604                     16, 0, 0, 12), 359, -17));
 605     connectTab.add(jPanel1, new GridBagConstraints(0, 2, 2, 1, 1.0, 1.0,
 606             GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(
 607                     21, 0, 35, 12), 4, 6));
 608     connectTab.add(browserLabel, new GridBagConstraints(0, 1, 1, 1, 0.0,
 609             0.0, GridBagConstraints.WEST, GridBagConstraints.NONE,
 610             new Insets(16, 0, 0, 0), 5, 1));
 611     jPanel1.add(useProxy, new GridBagConstraints(0, 0, 2, 1, 0.0, 0.0,
 612             GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
 613                     2, 5, 185), 2, -4));
 614     jPanel1.add(proxyPortTB, new GridBagConstraints(3, 1, 1, 1, 1.0, 0.0,
 615             GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 616             new Insets(0, 2, 4, 2), 54, 1));
 617     jPanel1.add(proxyServerTB, new GridBagConstraints(1, 1, 1, 1, 1.0, 0.0,
 618             GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 619             new Insets(0, 2, 4, 0), 263, 1));
 620     connectTab.add(defaultBrowser, new GridBagConstraints(1, 1, 1, 1, 1.0,
 621             0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 622             new Insets(15, 0, 0, 15), 307, 1));
 623     connectTab.add(usagestats, new GridBagConstraints(0, 4, 1, 1, 1.0, 0.0,
 624             GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 625             new Insets(0, 2, 4, 2), 70, 1));
 626     connectTab.add(questionnaire, new GridBagConstraints(1, 4, 1, 1, 1.0,
 627             0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 628             new Insets(0, 2, 4, 2), 70, 1));
 629     connectTab.add(versioncheck, new GridBagConstraints(0, 5, 1, 1, 1.0,
 630             0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 631             new Insets(0, 2, 4, 2), 70, 1));
 632     return connectTab;
 633   }
 634
 635   /**
 636    * Initialises the parent panel which contains the tabbed sections.
 637    *
 638    * @return
 639    */
 640   private JPanel initOkCancelPanel()
 641   {
 642     JButton ok = new JButton();
 643     ok.setText(MessageManager.getString("action.ok"));
 644     ok.addActionListener(new ActionListener()
 645     {
 646       public void actionPerformed(ActionEvent e)
 647       {
 648         ok_actionPerformed(e);
 649       }
 650     });
 651     JButton cancel = new JButton();
 652     cancel.setText(MessageManager.getString("action.cancel"));
 653     cancel.addActionListener(new ActionListener()
 654     {
 655       public void actionPerformed(ActionEvent e)
 656       {
 657         cancel_actionPerformed(e);
 658       }
 659     });
 660     JPanel okCancelPanel = new JPanel();
 661     okCancelPanel.add(ok);
 662     okCancelPanel.add(cancel);
 663     return okCancelPanel;
 664   }
 665
 666   /**
 667    * Initialises the Colours tabbed panel.
 668    *
 669    * @return
 670    */
 671   private JPanel initColoursTab()
 672   {
 673     JPanel coloursTab = new JPanel();
 674     coloursTab.setBorder(new TitledBorder(MessageManager
 675             .getString("action.open_new_alignment")));
 676     coloursTab.setLayout(new FlowLayout());
 677     JLabel mincolourLabel = new JLabel();
 678     mincolourLabel.setFont(LABEL_FONT);
 679     mincolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 680     mincolourLabel.setText(MessageManager.getString("label.min_colour"));
 681     minColour.setFont(LABEL_FONT);
 682     minColour.setBorder(BorderFactory.createEtchedBorder());
 683     minColour.setPreferredSize(new Dimension(40, 20));
 684     minColour.addMouseListener(new MouseAdapter()
 685     {
 686       public void mousePressed(MouseEvent e)
 687       {
 688         minColour_actionPerformed(minColour);
 689       }
 690     });
 691     JLabel maxcolourLabel = new JLabel();
 692     maxcolourLabel.setFont(LABEL_FONT);
 693     maxcolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 694     maxcolourLabel.setText(MessageManager.getString("label.max_colour"));
 695     maxColour.setFont(LABEL_FONT);
 696     maxColour.setBorder(BorderFactory.createEtchedBorder());
 697     maxColour.setPreferredSize(new Dimension(40, 20));
 698     maxColour.addMouseListener(new MouseAdapter()
 699     {
 700       public void mousePressed(MouseEvent e)
 701       {
 702         maxColour_actionPerformed(maxColour);
 703       }
 704     });
 705
 706     protColour.setFont(LABEL_FONT);
 707     protColour.setBounds(new Rectangle(172, 225, 155, 21));
 708     JLabel protColourLabel = new JLabel();
 709     protColourLabel.setFont(LABEL_FONT);
 710     protColourLabel.setHorizontalAlignment(SwingConstants.LEFT);
 711     protColourLabel.setText(MessageManager
 712             .getString("label.prot_alignment_colour") + " ");
 713     JvSwingUtils.addtoLayout(coloursTab, MessageManager
 714             .getString("label.default_colour_scheme_for_alignment"),
 715             protColourLabel, protColour);
 716
 717     nucColour.setFont(LABEL_FONT);
 718     nucColour.setBounds(new Rectangle(172, 240, 155, 21));
 719     JLabel nucColourLabel = new JLabel();
 720     nucColourLabel.setFont(LABEL_FONT);
 721     nucColourLabel.setHorizontalAlignment(SwingConstants.LEFT);
 722     nucColourLabel.setText(MessageManager
 723             .getString("label.nuc_alignment_colour")
 724             + " ");
 725     JvSwingUtils.addtoLayout(coloursTab, MessageManager
 726             .getString("label.default_colour_scheme_for_alignment"),
 727             nucColourLabel, nucColour);
 728
 729     JPanel annotationShding = new JPanel();
 730     annotationShding.setBorder(new TitledBorder(MessageManager
 731             .getString("label.annotation_shading_default")));
 732     annotationShding.setLayout(new GridLayout(1, 2));
 733     JvSwingUtils.addtoLayout(annotationShding, MessageManager
 734             .getString("label.default_minimum_colour_annotation_shading"),
 735             mincolourLabel, minColour);
 736     JvSwingUtils.addtoLayout(annotationShding, MessageManager
 737             .getString("label.default_maximum_colour_annotation_shading"),
 738             maxcolourLabel, maxColour);
 739     coloursTab.add(annotationShding); // , FlowLayout.LEFT);
 740     return coloursTab;
 741   }
 742
 743   /**
 744    * Initialises the Structure tabbed panel.
 745    *
 746    * @return
 747    */
 748   private JPanel initStructureTab()
 749   {
 750     structureTab = new JPanel();
 751
 752     structureTab.setBorder(new TitledBorder(MessageManager
 753             .getString("label.structure_options")));
 754     structureTab.setLayout(null);
 755     final int width = 400;
 756     final int height = 22;
 757     final int lineSpacing = 25;
 758     int ypos = 30;
 759
 760     structFromPdb.setFont(LABEL_FONT);
 761     structFromPdb.setText(MessageManager.getString("label.struct_from_pdb"));
 762     structFromPdb.setBounds(new Rectangle(5, ypos, width, height));
 763     structFromPdb.addActionListener(new ActionListener()
 764     {
 765       @Override
 766       public void actionPerformed(ActionEvent e)
 767       {
 768         boolean selected = structFromPdb.isSelected();
 769         // enable other options only when the first is checked
 770         useRnaView.setEnabled(selected);
 771         addSecondaryStructure.setEnabled(selected);
 772         addTempFactor.setEnabled(selected);
 773       }
 774     });
 775     structureTab.add(structFromPdb);
 776
 777     // indent checkboxes that are conditional on the first one
 778     ypos += lineSpacing;
 779     useRnaView.setFont(LABEL_FONT);
 780     useRnaView.setText(MessageManager.getString("label.use_rnaview"));
 781     useRnaView.setBounds(new Rectangle(25, ypos, width, height));
 782     structureTab.add(useRnaView);
 783
 784     ypos += lineSpacing;
 785     addSecondaryStructure.setFont(LABEL_FONT);
 786     addSecondaryStructure.setText(MessageManager
 787             .getString("label.autoadd_secstr"));
 788     addSecondaryStructure.setBounds(new Rectangle(25, ypos, width, height));
 789     structureTab.add(addSecondaryStructure);
 790
 791     ypos += lineSpacing;
 792     addTempFactor.setFont(LABEL_FONT);
 793     addTempFactor.setText(MessageManager.getString("label.autoadd_temp"));
 794     addTempFactor.setBounds(new Rectangle(25, ypos, width, height));
 795     structureTab.add(addTempFactor);
 796
 797     ypos += lineSpacing;
 798     JLabel viewerLabel = new JLabel();
 799     viewerLabel.setFont(LABEL_FONT);
 800     viewerLabel.setHorizontalAlignment(SwingConstants.LEFT);
 801     viewerLabel.setText(MessageManager.getString("label.structure_viewer"));
 802     viewerLabel.setBounds(new Rectangle(10, ypos, 200, height));
 803     structureTab.add(viewerLabel);
 804
 805     structViewer.setFont(LABEL_FONT);
 806     structViewer.setBounds(new Rectangle(160, ypos, 120, height));
 807     structViewer.addItem(ViewerType.JMOL.name());
 808     structViewer.addItem(ViewerType.CHIMERA.name());
 809     structViewer.addActionListener(new ActionListener()
 810     {
 811       @Override
 812       public void actionPerformed(ActionEvent e)
 813       {
 814         structureViewer_actionPerformed((String) structViewer
 815                 .getSelectedItem());
 816       }
 817     });
 818     structureTab.add(structViewer);
 819
 820     ypos += lineSpacing;
 821     JLabel pathLabel = new JLabel();
 822     pathLabel.setFont(new java.awt.Font("SansSerif", 0, 11));
 823     pathLabel.setHorizontalAlignment(SwingConstants.LEFT);
 824     pathLabel.setText(MessageManager.getString("label.chimera_path"));
 825     final String tooltip = JvSwingUtils.wrapTooltip(true,
 826             MessageManager.getString("label.chimera_path_tip"));
 827     pathLabel.setToolTipText(tooltip);
 828     pathLabel.setBounds(new Rectangle(10, ypos, 140, height));
 829     structureTab.add(pathLabel);
 830
 831     chimeraPath.setFont(LABEL_FONT);
 832     chimeraPath.setText("");
 833     chimeraPath.setBounds(new Rectangle(160, ypos, 300, height));
 834     chimeraPath.addMouseListener(new MouseAdapter()
 835     {
 836       @Override
 837       public void mouseClicked(MouseEvent e)
 838       {
 839         if (e.getClickCount() == 2)
 840         {
 841           String chosen = openFileChooser();
 842           if (chosen != null)
 843           {
 844             chimeraPath.setText(chosen);
 845           }
 846         }
 847       }
 848     });
 849     structureTab.add(chimeraPath);
 850
 851     ypos += lineSpacing;
 852     // scrl_pdbDocFieldConfig.setPreferredSize(new Dimension(450, 100));
 853     // scrl_pdbDocFieldConfig
 854     // .setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_NEVER);
 855     // scrl_pdbDocFieldConfig.setBounds();
 856     PDBDocFieldPreferences docFieldPref = new PDBDocFieldPreferences(
 857             PreferenceSource.PREFERENCES);
 858     docFieldPref.setBounds(new Rectangle(10, ypos + 5, 450, 120));
 859     structureTab.add(docFieldPref);
 860
 861
 862
 863
 864     return structureTab;
 865   }
 866
 867
 868   /**
 869    * Action on choosing a structure viewer from combobox options.
 870    *
 871    * @param selectedItem
 872    */
 873   protected void structureViewer_actionPerformed(String selectedItem)
 874   {
 875   }
 876
 877   /**
 878    * Show a dialog for the user to choose a file. Returns the chosen path, or
 879    * null on Cancel.
 880    *
 881    * @return
 882    */
 883   protected String openFileChooser()
 884   {
 885     String choice = null;
 886     JFileChooser chooser = new JFileChooser();
 887
 888     // chooser.setFileView(new JalviewFileView());
 889     chooser.setDialogTitle(MessageManager
 890             .getString("label.open_local_file"));
 891     chooser.setToolTipText(MessageManager.getString("action.open"));
 892
 893     int value = chooser.showOpenDialog(this);
 894
 895     if (value == JFileChooser.APPROVE_OPTION)
 896     {
 897       choice = chooser.getSelectedFile().getPath();
 898     }
 899     return choice;
 900   }
 901
 902   /**
 903    * Validate the structure tab preferences; if invalid, set focus on this tab.
 904    *
 905    * @param e
 906    */
 907   protected boolean validateStructure(FocusEvent e)
 908   {
 909     if (!validateStructure())
 910     {
 911       e.getComponent().requestFocusInWindow();
 912       return false;
 913     }
 914     return true;
 915   }
 916
 917   protected boolean validateStructure()
 918   {
 919     return false;
 920   }
 921
 922   /**
 923    * Initialises the Visual tabbed panel.
 924    *
 925    * @return
 926    */
 927   private JPanel initVisualTab()
 928   {
 929     JPanel visualTab = new JPanel();
 930     visualTab.setBorder(new TitledBorder(MessageManager
 931             .getString("action.open_new_alignment")));
 932     visualTab.setLayout(null);
 933     fullScreen.setFont(LABEL_FONT);
 934     fullScreen.setHorizontalAlignment(SwingConstants.RIGHT);
 935     fullScreen.setHorizontalTextPosition(SwingConstants.LEFT);
 936     fullScreen.setText(MessageManager.getString("label.maximize_window"));
 937     quality.setEnabled(false);
 938     quality.setFont(LABEL_FONT);
 939     quality.setHorizontalAlignment(SwingConstants.RIGHT);
 940     quality.setHorizontalTextPosition(SwingConstants.LEFT);
 941     quality.setSelected(true);
 942     quality.setText(MessageManager.getString("label.quality"));
 943     conservation.setEnabled(false);
 944     conservation.setFont(LABEL_FONT);
 945     conservation.setHorizontalAlignment(SwingConstants.RIGHT);
 946     conservation.setHorizontalTextPosition(SwingConstants.LEFT);
 947     conservation.setSelected(true);
 948     conservation.setText(MessageManager.getString("label.conservation"));
 949     identity.setEnabled(false);
 950     identity.setFont(LABEL_FONT);
 951     identity.setHorizontalAlignment(SwingConstants.RIGHT);
 952     identity.setHorizontalTextPosition(SwingConstants.LEFT);
 953     identity.setSelected(true);
 954     identity.setText(MessageManager.getString("label.consensus"));
 955     JLabel showGroupbits = new JLabel();
 956     showGroupbits.setFont(LABEL_FONT);
 957     showGroupbits.setHorizontalAlignment(SwingConstants.RIGHT);
 958     showGroupbits.setHorizontalTextPosition(SwingConstants.LEFT);
 959     showGroupbits.setText(MessageManager.getString("action.show_group")
 960             + ":");
 961     JLabel showConsensbits = new JLabel();
 962     showConsensbits.setFont(LABEL_FONT);
 963     showConsensbits.setHorizontalAlignment(SwingConstants.RIGHT);
 964     showConsensbits.setHorizontalTextPosition(SwingConstants.LEFT);
 965     showConsensbits.setText(MessageManager.getString("label.consensus")
 966             + ":");
 967     showConsensHistogram.setEnabled(false);
 968     showConsensHistogram.setFont(LABEL_FONT);
 969     showConsensHistogram.setHorizontalAlignment(SwingConstants.RIGHT);
 970     showConsensHistogram.setHorizontalTextPosition(SwingConstants.LEFT);
 971     showConsensHistogram.setSelected(true);
 972     showConsensHistogram.setText(MessageManager
 973             .getString("label.histogram"));
 974     showConsensLogo.setEnabled(false);
 975     showConsensLogo.setFont(LABEL_FONT);
 976     showConsensLogo.setHorizontalAlignment(SwingConstants.RIGHT);
 977     showConsensLogo.setHorizontalTextPosition(SwingConstants.LEFT);
 978     showConsensLogo.setSelected(true);
 979     showConsensLogo.setText(MessageManager.getString("label.logo"));
 980     showGroupConsensus.setEnabled(false);
 981     showGroupConsensus.setFont(LABEL_FONT);
 982     showGroupConsensus.setHorizontalAlignment(SwingConstants.RIGHT);
 983     showGroupConsensus.setHorizontalTextPosition(SwingConstants.LEFT);
 984     showGroupConsensus.setSelected(true);
 985     showGroupConsensus.setText(MessageManager.getString("label.consensus"));
 986     showGroupConservation.setEnabled(false);
 987     showGroupConservation.setFont(LABEL_FONT);
 988     showGroupConservation.setHorizontalAlignment(SwingConstants.RIGHT);
 989     showGroupConservation.setHorizontalTextPosition(SwingConstants.LEFT);
 990     showGroupConservation.setSelected(true);
 991     showGroupConservation.setText(MessageManager
 992             .getString("label.conservation"));
 993     showNpTooltip.setEnabled(true);
 994     showNpTooltip.setFont(LABEL_FONT);
 995     showNpTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
 996     showNpTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
 997     showNpTooltip.setSelected(true);
 998     showNpTooltip.setText(MessageManager
 999             .getString("label.non_positional_features"));
1000     showDbRefTooltip.setEnabled(true);
1001     showDbRefTooltip.setFont(LABEL_FONT);
1002     showDbRefTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
1003     showDbRefTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
1004     showDbRefTooltip.setSelected(true);
1005     showDbRefTooltip.setText(MessageManager
1006             .getString("label.database_references"));
1007     annotations.setFont(LABEL_FONT);
1008     annotations.setHorizontalAlignment(SwingConstants.RIGHT);
1009     annotations.setHorizontalTextPosition(SwingConstants.LEADING);
1010     annotations.setSelected(true);
1011     annotations.setText(MessageManager.getString("label.show_annotations"));
1012     annotations.setBounds(new Rectangle(169, 12, 200, 23));
1013     annotations.addActionListener(new ActionListener()
1014     {
1015       public void actionPerformed(ActionEvent e)
1016       {
1017         annotations_actionPerformed(e);
1018       }
1019     });
1020     identity.addActionListener(new ActionListener()
1021     {
1022       public void actionPerformed(ActionEvent e)
1023       {
1024         annotations_actionPerformed(e);
1025       }
1026     });
1027     showGroupConsensus.addActionListener(new ActionListener()
1028     {
1029       public void actionPerformed(ActionEvent e)
1030       {
1031         annotations_actionPerformed(e);
1032       }
1033     });
1034     showUnconserved.setFont(LABEL_FONT);
1035     showUnconserved.setHorizontalAlignment(SwingConstants.RIGHT);
1036     showUnconserved.setHorizontalTextPosition(SwingConstants.LEFT);
1037     showUnconserved.setSelected(true);
1038     showUnconserved.setText(MessageManager
1039             .getString("action.show_unconserved"));
1040     showUnconserved.addActionListener(new ActionListener()
1041     {
1042       public void actionPerformed(ActionEvent e)
1043       {
1044         showunconserved_actionPerformed(e);
1045       }
1046     });
1047
1048     // TODO these are not yet added to / action from Preferences
1049     // JCheckBox shareSelections = new JCheckBox();
1050     // shareSelections.setFont(verdana11);
1051     // shareSelections.setHorizontalAlignment(SwingConstants.RIGHT);
1052     // shareSelections.setHorizontalTextPosition(SwingConstants.LEFT);
1053     // shareSelections.setSelected(true);
1054     // shareSelections.setText(MessageManager
1055     // .getString("label.share_selection_across_views"));
1056     // JCheckBox followHighlight = new JCheckBox();
1057     // followHighlight.setFont(verdana11);
1058     // followHighlight.setHorizontalAlignment(SwingConstants.RIGHT);
1059     // followHighlight.setHorizontalTextPosition(SwingConstants.LEFT);
1060     // // showUnconserved.setBounds(new Rectangle(169, 40, 200, 23));
1061     // followHighlight.setSelected(true);
1062     // followHighlight.setText(MessageManager
1063     // .getString("label.scroll_highlighted_regions"));
1064
1065     seqLimit.setFont(LABEL_FONT);
1066     seqLimit.setHorizontalAlignment(SwingConstants.RIGHT);
1067     seqLimit.setHorizontalTextPosition(SwingConstants.LEFT);
1068     seqLimit.setText(MessageManager.getString("label.full_sequence_id"));
1069     smoothFont.setFont(LABEL_FONT);
1070     smoothFont.setHorizontalAlignment(SwingConstants.RIGHT);
1071     smoothFont.setHorizontalTextPosition(SwingConstants.LEADING);
1072     smoothFont.setText(MessageManager.getString("label.smooth_font"));
1073     scaleProteinToCdna.setFont(LABEL_FONT);
1074     scaleProteinToCdna.setHorizontalAlignment(SwingConstants.RIGHT);
1075     scaleProteinToCdna.setHorizontalTextPosition(SwingConstants.LEADING);
1076     scaleProteinToCdna.setText(MessageManager
1077             .getString("label.scale_protein_to_cdna"));
1078     scaleProteinToCdna.setToolTipText(MessageManager
1079             .getString("label.scale_protein_to_cdna_tip"));
1080     JLabel gapLabel = new JLabel();
1081     gapLabel.setFont(LABEL_FONT);
1082     gapLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1083     gapLabel.setText(MessageManager.getString("label.gap_symbol") + " ");
1084     JLabel fontLabel = new JLabel();
1085     fontLabel.setFont(LABEL_FONT);
1086     fontLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1087     fontLabel.setText(MessageManager.getString("label.font"));
1088     fontSizeCB.setFont(LABEL_FONT);
1089     fontSizeCB.setBounds(new Rectangle(320, 112, 65, 23));
1090     fontStyleCB.setFont(LABEL_FONT);
1091     fontStyleCB.setBounds(new Rectangle(382, 112, 80, 23));
1092     fontNameCB.setFont(LABEL_FONT);
1093     fontNameCB.setBounds(new Rectangle(172, 112, 147, 23));
1094     gapSymbolCB.setFont(LABEL_FONT);
1095     gapSymbolCB.setBounds(new Rectangle(172, 215, 69, 23));
1096     DefaultListCellRenderer dlcr = new DefaultListCellRenderer();
1097     dlcr.setHorizontalAlignment(DefaultListCellRenderer.CENTER);
1098     gapSymbolCB.setRenderer(dlcr);
1099
1100     startupCheckbox.setText(MessageManager.getString("action.open_file"));
1101     startupCheckbox.setFont(LABEL_FONT);
1102     startupCheckbox.setHorizontalAlignment(SwingConstants.RIGHT);
1103     startupCheckbox.setHorizontalTextPosition(SwingConstants.LEFT);
1104     startupCheckbox.setSelected(true);
1105     startupFileTextfield.setFont(LABEL_FONT);
1106     startupFileTextfield.setBounds(new Rectangle(172, 310, 330, 20));
1107     startupFileTextfield.addMouseListener(new MouseAdapter()
1108     {
1109       public void mouseClicked(MouseEvent e)
1110       {
1111         if (e.getClickCount() > 1)
1112         {
1113           startupFileTextfield_mouseClicked();
1114         }
1115       }
1116     });
1117
1118     sortby.setFont(LABEL_FONT);
1119     sortby.setBounds(new Rectangle(172, 260, 155, 21));
1120     JLabel sortLabel = new JLabel();
1121     sortLabel.setFont(LABEL_FONT);
1122     sortLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1123     sortLabel.setText(MessageManager.getString("label.sort_by"));
1124     sortAnnBy.setFont(LABEL_FONT);
1125     sortAnnBy.setBounds(new Rectangle(172, 285, 110, 21));
1126     JLabel sortAnnLabel = new JLabel();
1127     sortAnnLabel.setFont(LABEL_FONT);
1128     sortAnnLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1129     sortAnnLabel.setText(MessageManager.getString("label.sort_ann_by"));
1130     sortAutocalc.setFont(LABEL_FONT);
1131     sortAutocalc.setBounds(new Rectangle(290, 285, 165, 21));
1132
1133     JPanel annsettingsPanel = new JPanel();
1134     annsettingsPanel.setBounds(new Rectangle(173, 34, 320, 75));
1135     annsettingsPanel.setLayout(new FlowLayout(FlowLayout.LEFT, 0, 0));
1136     annsettingsPanel.setBorder(new EtchedBorder());
1137     visualTab.add(annsettingsPanel);
1138     Border jb = new EmptyBorder(1, 1, 4, 5);
1139     quality.setBorder(jb);
1140     conservation.setBorder(jb);
1141     identity.setBorder(jb);
1142     showConsensbits.setBorder(jb);
1143     showGroupbits.setBorder(jb);
1144     showGroupConsensus.setBorder(jb);
1145     showGroupConservation.setBorder(jb);
1146     showConsensHistogram.setBorder(jb);
1147     showConsensLogo.setBorder(jb);
1148
1149     JPanel autoAnnotSettings = new JPanel();
1150     autoAnnotSettings.setLayout(new GridLayout(3, 3));
1151     annsettingsPanel.add(autoAnnotSettings);
1152     autoAnnotSettings.add(quality);
1153     autoAnnotSettings.add(conservation);
1154     autoAnnotSettings.add(identity);
1155     autoAnnotSettings.add(showGroupbits);
1156     autoAnnotSettings.add(showGroupConservation);
1157     autoAnnotSettings.add(showGroupConsensus);
1158     autoAnnotSettings.add(showConsensbits);
1159     autoAnnotSettings.add(showConsensHistogram);
1160     autoAnnotSettings.add(showConsensLogo);
1161
1162     JPanel tooltipSettings = new JPanel();
1163     tooltipSettings.setBorder(new TitledBorder(MessageManager
1164             .getString("label.sequence_id_tooltip")));
1165     tooltipSettings.setBounds(173, 140, 220, 62);
1166     tooltipSettings.setLayout(new GridLayout(2, 1));
1167     tooltipSettings.add(showDbRefTooltip);
1168     tooltipSettings.add(showNpTooltip);
1169     visualTab.add(tooltipSettings);
1170
1171     wrap.setFont(LABEL_FONT);
1172     wrap.setHorizontalAlignment(SwingConstants.TRAILING);
1173     wrap.setHorizontalTextPosition(SwingConstants.LEADING);
1174     wrap.setText(MessageManager.getString("label.wrap_alignment"));
1175     rightAlign.setFont(LABEL_FONT);
1176     rightAlign.setForeground(Color.black);
1177     rightAlign.setHorizontalAlignment(SwingConstants.RIGHT);
1178     rightAlign.setHorizontalTextPosition(SwingConstants.LEFT);
1179     rightAlign.setText(MessageManager.getString("label.right_align_ids"));
1180     idItalics.setFont(LABEL_FONT_ITALIC);
1181     idItalics.setHorizontalAlignment(SwingConstants.RIGHT);
1182     idItalics.setHorizontalTextPosition(SwingConstants.LEADING);
1183     idItalics.setText(MessageManager
1184             .getString("label.sequence_name_italics"));
1185     openoverv.setFont(LABEL_FONT);
1186     openoverv.setActionCommand(MessageManager
1187             .getString("label.open_overview"));
1188     openoverv.setHorizontalAlignment(SwingConstants.RIGHT);
1189     openoverv.setHorizontalTextPosition(SwingConstants.LEFT);
1190     openoverv.setText(MessageManager.getString(("label.open_overview")));
1191     JPanel jPanel2 = new JPanel();
1192     jPanel2.setBounds(new Rectangle(7, 17, 158, 310));
1193     jPanel2.setLayout(new GridLayout(14, 1));
1194     jPanel2.add(fullScreen);
1195     jPanel2.add(openoverv);
1196     jPanel2.add(seqLimit);
1197     jPanel2.add(rightAlign);
1198     jPanel2.add(fontLabel);
1199     jPanel2.add(showUnconserved);
1200     jPanel2.add(idItalics);
1201     jPanel2.add(smoothFont);
1202     jPanel2.add(scaleProteinToCdna);
1203     jPanel2.add(gapLabel);
1204     jPanel2.add(wrap);
1205     jPanel2.add(sortLabel);
1206     jPanel2.add(sortAnnLabel);
1207     jPanel2.add(startupCheckbox);
1208     visualTab.add(jPanel2);
1209     visualTab.add(annotations);
1210     visualTab.add(startupFileTextfield);
1211     visualTab.add(sortby);
1212     visualTab.add(sortAnnBy);
1213     visualTab.add(sortAutocalc);
1214     visualTab.add(gapSymbolCB);
1215     visualTab.add(fontNameCB);
1216     visualTab.add(fontSizeCB);
1217     visualTab.add(fontStyleCB);
1218     return visualTab;
1219   }
1220
1221   protected void autoIdWidth_actionPerformed()
1222   {
1223     // TODO Auto-generated method stub
1224
1225   }
1226
1227   protected void userIdWidth_actionPerformed()
1228   {
1229     // TODO Auto-generated method stub
1230
1231   }
1232
1233   protected void maxColour_actionPerformed(JPanel panel)
1234   {
1235   }
1236
1237   protected void minColour_actionPerformed(JPanel panel)
1238   {
1239   }
1240
1241   protected void showunconserved_actionPerformed(ActionEvent e)
1242   {
1243     // TODO Auto-generated method stub
1244
1245   }
1246
1247   /**
1248    * DOCUMENT ME!
1249    *
1250    * @param e
1251    *          DOCUMENT ME!
1252    */
1253   public void ok_actionPerformed(ActionEvent e)
1254   {
1255   }
1256
1257   /**
1258    * DOCUMENT ME!
1259    *
1260    * @param e
1261    *          DOCUMENT ME!
1262    */
1263   public void cancel_actionPerformed(ActionEvent e)
1264   {
1265   }
1266
1267   /**
1268    * DOCUMENT ME!
1269    *
1270    * @param e
1271    *          DOCUMENT ME!
1272    */
1273   public void annotations_actionPerformed(ActionEvent e)
1274   {
1275   }
1276
1277   /**
1278    * DOCUMENT ME!
1279    */
1280   public void startupFileTextfield_mouseClicked()
1281   {
1282   }
1283
1284   public void newLink_actionPerformed(ActionEvent e)
1285   {
1286
1287   }
1288
1289   public void editLink_actionPerformed(ActionEvent e)
1290   {
1291
1292   }
1293
1294   public void deleteLink_actionPerformed(ActionEvent e)
1295   {
1296
1297   }
1298
1299   public void defaultBrowser_mouseClicked(MouseEvent e)
1300   {
1301
1302   }
1303
1304   public void linkURLList_keyTyped(KeyEvent e)
1305   {
1306
1307   }
1308
1309   public void useProxy_actionPerformed()
1310   {
1311     proxyServerTB.setEnabled(useProxy.isSelected());
1312     proxyPortTB.setEnabled(useProxy.isSelected());
1313   }
1314
1315 }