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.util.MessageManager;
  25
  26 import java.awt.BorderLayout;
  27 import java.awt.Color;
  28 import java.awt.Dimension;
  29 import java.awt.FlowLayout;
  30 import java.awt.Font;
  31 import java.awt.GridBagConstraints;
  32 import java.awt.GridBagLayout;
  33 import java.awt.GridLayout;
  34 import java.awt.Insets;
  35 import java.awt.Rectangle;
  36 import java.awt.event.ActionEvent;
  37 import java.awt.event.ActionListener;
  38 import java.awt.event.KeyEvent;
  39 import java.awt.event.MouseAdapter;
  40 import java.awt.event.MouseEvent;
  41
  42 import javax.swing.BorderFactory;
  43 import javax.swing.DefaultListCellRenderer;
  44 import javax.swing.JButton;
  45 import javax.swing.JCheckBox;
  46 import javax.swing.JComboBox;
  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.TitledBorder;
  58 import javax.swing.event.ListSelectionEvent;
  59 import javax.swing.event.ListSelectionListener;
  60
  61 /**
  62  * DOCUMENT ME!
  63  *
  64  * @author $author$
  65  * @version $Revision$
  66  */
  67 public class GPreferences extends JPanel
  68 {
  69   JTabbedPane tabbedPane = new JTabbedPane();
  70
  71   JButton ok = new JButton();
  72
  73   JButton cancel = new JButton();
  74
  75   JPanel okCancelPanel = new JPanel();
  76
  77   BorderLayout borderLayout1 = new BorderLayout();
  78
  79   protected JCheckBox quality = new JCheckBox();
  80
  81   JPanel visualTab = new JPanel();
  82
  83   JPanel visual2Tab = new JPanel();
  84
  85   protected JCheckBox fullScreen = new JCheckBox();
  86
  87   protected JCheckBox conservation = new JCheckBox();
  88
  89   protected JCheckBox identity = new JCheckBox();
  90
  91   protected JCheckBox annotations = new JCheckBox();
  92
  93   protected JPanel minColour = new JPanel();
  94
  95   JLabel mincolourLabel = new JLabel();
  96
  97   protected JPanel maxColour = new JPanel();
  98
  99   JLabel maxcolourLabel = new JLabel();
 100
 101   JLabel gapLabel = new JLabel();
 102
 103   protected JComboBox<String> colour = new JComboBox<String>();
 104
 105   JLabel colourLabel = new JLabel();
 106
 107   JLabel fontLabel = new JLabel();
 108
 109   protected JComboBox<String> fontSizeCB = new JComboBox<String>();
 110
 111   protected JComboBox<String> fontStyleCB = new JComboBox<String>();
 112
 113   protected JComboBox<String> fontNameCB = new JComboBox<String>();
 114
 115   protected JComboBox<String> gapSymbolCB = new JComboBox<String>();
 116
 117   protected JCheckBox startupCheckbox = new JCheckBox();
 118
 119   protected JTextField startupFileTextfield = new JTextField();
 120
 121   JPanel connectTab = new JPanel();
 122
 123   JLabel serverLabel = new JLabel();
 124
 125   protected JList linkURLList = new JList();
 126
 127   protected JTextField proxyServerTB = new JTextField();
 128
 129   protected JTextField proxyPortTB = new JTextField();
 130
 131   JLabel portLabel = new JLabel();
 132
 133   JLabel browserLabel = new JLabel();
 134
 135   protected JTextField defaultBrowser = new JTextField();
 136
 137   JButton newLink = new JButton();
 138
 139   JButton editLink = new JButton();
 140
 141   JButton deleteLink = new JButton();
 142
 143   JScrollPane linkScrollPane = new JScrollPane();
 144
 145   JPanel linkPanel = new JPanel();
 146
 147   BorderLayout borderLayout2 = new BorderLayout();
 148
 149   JPanel editLinkButtons = new JPanel();
 150
 151   GridLayout gridLayout1 = new GridLayout();
 152
 153   protected JList linkNameList = new JList();
 154
 155   JPanel linkPanel2 = new JPanel();
 156
 157   BorderLayout borderLayout3 = new BorderLayout();
 158
 159   protected JCheckBox useProxy = new JCheckBox();
 160
 161   JPanel jPanel1 = new JPanel();
 162
 163   TitledBorder titledBorder1 = new TitledBorder(
 164           MessageManager.getString("label.proxy_server"));
 165
 166   TitledBorder titledBorder2 = new TitledBorder(
 167           MessageManager.getString("label.file_output"));
 168
 169   GridBagLayout gridBagLayout2 = new GridBagLayout();
 170
 171   GridBagLayout gridBagLayout1 = new GridBagLayout();
 172
 173   GridBagLayout gridBagLayout3 = new GridBagLayout();
 174
 175   protected JComboBox<String> sortby = new JComboBox<String>();
 176
 177   JLabel sortLabel = new JLabel();
 178
 179   protected JComboBox<String> sortAnnBy = new JComboBox<String>();
 180
 181   protected JComboBox<String> sortAutocalc = new JComboBox<String>();
 182
 183   JLabel sortAnnLabel = new JLabel();
 184
 185   JPanel jPanel2 = new JPanel();
 186
 187   JPanel visual2panel = new JPanel();
 188
 189   GridLayout gridLayout2 = new GridLayout();
 190
 191   GridLayout gridLayout4 = new GridLayout();
 192
 193   JPanel annsettingsPanel = new JPanel();
 194
 195   JPanel autoAnnotSettings1 = new JPanel();
 196
 197   JPanel autoAnnotSettings2 = new JPanel();
 198
 199   JPanel autoAnnotSettings3 = new JPanel();
 200
 201   JPanel exportTab = new JPanel();
 202
 203   JLabel epsLabel = new JLabel();
 204
 205   protected JComboBox<String> epsRendering = new JComboBox<String>();
 206
 207   protected JLabel userIdWidthlabel = new JLabel();
 208
 209   protected JCheckBox autoIdWidth = new JCheckBox();
 210
 211   protected JTextField userIdWidth = new JTextField();
 212
 213   JLabel jLabel1 = new JLabel();
 214
 215   protected JCheckBox blcjv = new JCheckBox();
 216
 217   protected JCheckBox pileupjv = new JCheckBox();
 218
 219   protected JCheckBox clustaljv = new JCheckBox();
 220
 221   protected JCheckBox msfjv = new JCheckBox();
 222
 223   protected JCheckBox fastajv = new JCheckBox();
 224
 225   protected JCheckBox pfamjv = new JCheckBox();
 226
 227   FlowLayout flowLayout1 = new FlowLayout();
 228
 229   protected JCheckBox pirjv = new JCheckBox();
 230
 231   JPanel jPanel11 = new JPanel();
 232
 233   Font verdana11 = JvSwingUtils.getLabelFont();
 234
 235   protected JCheckBox seqLimit = new JCheckBox();
 236
 237   GridLayout gridLayout3 = new GridLayout();
 238
 239   protected JCheckBox smoothFont = new JCheckBox();
 240
 241   JPanel calcTab = new JPanel();
 242
 243   protected JCheckBox autoCalculateConsCheck = new JCheckBox();
 244
 245   protected JCheckBox padGaps = new JCheckBox();
 246
 247   protected JCheckBox modellerOutput = new JCheckBox();
 248
 249   protected JPanel dasPanel = new JPanel();
 250
 251   BorderLayout borderLayout4 = new BorderLayout();
 252
 253   protected JPanel wsPanel = new JPanel();
 254
 255   BorderLayout borderLayout5 = new BorderLayout();
 256
 257   protected JCheckBox wrap = new JCheckBox();
 258
 259   protected JCheckBox rightAlign = new JCheckBox();
 260
 261   protected JCheckBox showUnconserved = new JCheckBox();
 262
 263   protected JCheckBox showDbRefTooltip = new JCheckBox();
 264
 265   protected JCheckBox showNpTooltip = new JCheckBox();
 266
 267   protected JCheckBox idItalics = new JCheckBox();
 268
 269   protected JCheckBox openoverv = new JCheckBox();
 270
 271   protected JCheckBox usagestats = new JCheckBox();
 272
 273   protected JCheckBox questionnaire = new JCheckBox();
 274
 275   protected JCheckBox versioncheck = new JCheckBox();
 276
 277   protected JLabel showGroupbits = new JLabel();
 278
 279   protected JLabel showConsensbits = new JLabel();
 280
 281   protected JCheckBox showConsensLogo = new JCheckBox();
 282
 283   protected JCheckBox showConsensHistogram = new JCheckBox();
 284
 285   protected JCheckBox showGroupConsensus = new JCheckBox();
 286
 287   protected JCheckBox showGroupConservation = new JCheckBox();
 288
 289   protected JCheckBox shareSelections = new JCheckBox();
 290
 291   protected JCheckBox followHighlight = new JCheckBox();
 292
 293   protected JCheckBox sortByTree = new JCheckBox();
 294
 295   /**
 296    * Creates a new GPreferences object.
 297    */
 298   public GPreferences()
 299   {
 300     try
 301     {
 302       jbInit();
 303     } catch (Exception ex)
 304     {
 305       ex.printStackTrace();
 306     }
 307   }
 308
 309   /**
 310    * DOCUMENT ME!
 311    *
 312    * @throws Exception
 313    *           DOCUMENT ME!
 314    */
 315   private void jbInit() throws Exception
 316   {
 317     this.setLayout(borderLayout1);
 318     ok.setText(MessageManager.getString("action.ok"));
 319     ok.addActionListener(new ActionListener()
 320     {
 321       public void actionPerformed(ActionEvent e)
 322       {
 323         ok_actionPerformed(e);
 324       }
 325     });
 326     cancel.setText(MessageManager.getString("action.cancel"));
 327     cancel.addActionListener(new ActionListener()
 328     {
 329       public void actionPerformed(ActionEvent e)
 330       {
 331         cancel_actionPerformed(e);
 332       }
 333     });
 334     quality.setEnabled(false);
 335     quality.setFont(verdana11);
 336     quality.setHorizontalAlignment(SwingConstants.RIGHT);
 337     quality.setHorizontalTextPosition(SwingConstants.LEFT);
 338     quality.setSelected(true);
 339     quality.setText(MessageManager.getString("label.quality"));
 340     visualTab.setBorder(new TitledBorder(MessageManager
 341             .getString("action.open_new_aligmnent")));
 342     visualTab.setLayout(null);
 343     visual2Tab.setBorder(new TitledBorder(MessageManager
 344             .getString("action.open_new_aligmnent")));
 345     visual2Tab.setLayout(new FlowLayout());
 346     fullScreen.setFont(verdana11);
 347     fullScreen.setHorizontalAlignment(SwingConstants.RIGHT);
 348     fullScreen.setHorizontalTextPosition(SwingConstants.LEFT);
 349     fullScreen.setText(MessageManager.getString("label.maximize_window"));
 350     conservation.setEnabled(false);
 351     conservation.setFont(verdana11);
 352     conservation.setHorizontalAlignment(SwingConstants.RIGHT);
 353     conservation.setHorizontalTextPosition(SwingConstants.LEFT);
 354     conservation.setSelected(true);
 355     conservation.setText(MessageManager.getString("label.conservation"));
 356     identity.setEnabled(false);
 357     identity.setFont(verdana11);
 358     identity.setHorizontalAlignment(SwingConstants.RIGHT);
 359     identity.setHorizontalTextPosition(SwingConstants.LEFT);
 360     identity.setSelected(true);
 361     identity.setText(MessageManager.getString("label.consensus"));
 362     showGroupbits.setFont(verdana11);
 363     showGroupbits.setHorizontalAlignment(SwingConstants.RIGHT);
 364     showGroupbits.setHorizontalTextPosition(SwingConstants.LEFT);
 365     showGroupbits.setText(MessageManager.getString("action.show_group")
 366             + ":");
 367     showConsensbits.setFont(verdana11);
 368     showConsensbits.setHorizontalAlignment(SwingConstants.RIGHT);
 369     showConsensbits.setHorizontalTextPosition(SwingConstants.LEFT);
 370     showConsensbits.setText(MessageManager.getString("label.consensus")
 371             + ":");
 372     showConsensHistogram.setEnabled(false);
 373     showConsensHistogram.setFont(verdana11);
 374     showConsensHistogram.setHorizontalAlignment(SwingConstants.RIGHT);
 375     showConsensHistogram.setHorizontalTextPosition(SwingConstants.LEFT);
 376     showConsensHistogram.setSelected(true);
 377     showConsensHistogram.setText(MessageManager
 378             .getString("label.histogram"));
 379     showConsensLogo.setEnabled(false);
 380     showConsensLogo.setFont(verdana11);
 381     showConsensLogo.setHorizontalAlignment(SwingConstants.RIGHT);
 382     showConsensLogo.setHorizontalTextPosition(SwingConstants.LEFT);
 383     showConsensLogo.setSelected(true);
 384     showConsensLogo.setText(MessageManager.getString("label.logo"));
 385     showGroupConsensus.setEnabled(false);
 386     showGroupConsensus.setFont(verdana11);
 387     showGroupConsensus.setHorizontalAlignment(SwingConstants.RIGHT);
 388     showGroupConsensus.setHorizontalTextPosition(SwingConstants.LEFT);
 389     showGroupConsensus.setSelected(true);
 390     showGroupConsensus.setText(MessageManager.getString("label.consensus"));
 391     showGroupConservation.setEnabled(false);
 392     showGroupConservation.setFont(verdana11);
 393     showGroupConservation.setHorizontalAlignment(SwingConstants.RIGHT);
 394     showGroupConservation.setHorizontalTextPosition(SwingConstants.LEFT);
 395     showGroupConservation.setSelected(true);
 396     showGroupConservation.setText(MessageManager
 397             .getString("label.conservation"));
 398     showNpTooltip.setEnabled(true);
 399     showNpTooltip.setFont(verdana11);
 400     showNpTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
 401     showNpTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
 402     showNpTooltip.setSelected(true);
 403     showNpTooltip.setText(MessageManager
 404             .getString("label.non_positional_features"));
 405     showDbRefTooltip.setEnabled(true);
 406     showDbRefTooltip.setFont(verdana11);
 407     showDbRefTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
 408     showDbRefTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
 409     showDbRefTooltip.setSelected(true);
 410     showDbRefTooltip.setText(MessageManager
 411             .getString("label.database_references"));
 412     annotations.setFont(verdana11);
 413     annotations.setHorizontalAlignment(SwingConstants.RIGHT);
 414     annotations.setHorizontalTextPosition(SwingConstants.LEADING);
 415     annotations.setSelected(true);
 416     annotations.setText(MessageManager.getString("label.show_annotations"));
 417     annotations.setBounds(new Rectangle(169, 12, 200, 23));
 418     annotations.addActionListener(new ActionListener()
 419     {
 420       public void actionPerformed(ActionEvent e)
 421       {
 422         annotations_actionPerformed(e);
 423       }
 424     });
 425     identity.addActionListener(new ActionListener()
 426     {
 427       public void actionPerformed(ActionEvent e)
 428       {
 429         annotations_actionPerformed(e);
 430       }
 431     });
 432     showGroupConsensus.addActionListener(new ActionListener()
 433     {
 434       public void actionPerformed(ActionEvent e)
 435       {
 436         annotations_actionPerformed(e);
 437       }
 438     });
 439     showUnconserved.setFont(verdana11);
 440     showUnconserved.setHorizontalAlignment(SwingConstants.RIGHT);
 441     showUnconserved.setHorizontalTextPosition(SwingConstants.LEFT);
 442     showUnconserved.setSelected(true);
 443     showUnconserved.setText(MessageManager
 444             .getString("action.show_unconserved"));
 445     showUnconserved.addActionListener(new ActionListener()
 446     {
 447       public void actionPerformed(ActionEvent e)
 448       {
 449         showunconserved_actionPerformed(e);
 450       }
 451     });
 452     // / TODO: fit these in to preferences panel!!!!!
 453     shareSelections.setFont(verdana11);
 454     shareSelections.setHorizontalAlignment(SwingConstants.RIGHT);
 455     shareSelections.setHorizontalTextPosition(SwingConstants.LEFT);
 456     shareSelections.setSelected(true);
 457     shareSelections.setText(MessageManager
 458             .getString("label.share_selection_across_views"));
 459     followHighlight.setFont(verdana11);
 460     followHighlight.setHorizontalAlignment(SwingConstants.RIGHT);
 461     followHighlight.setHorizontalTextPosition(SwingConstants.LEFT);
 462     // showUnconserved.setBounds(new Rectangle(169, 40, 200, 23));
 463     followHighlight.setSelected(true);
 464     followHighlight.setText(MessageManager
 465             .getString("label.scroll_highlighted_regions"));
 466
 467     gapLabel.setFont(verdana11);
 468     gapLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 469     gapLabel.setText(MessageManager.getString("label.gap_symbol") + " ");
 470     colour.setFont(verdana11);
 471     colour.setBounds(new Rectangle(172, 225, 155, 21));
 472     colourLabel.setFont(verdana11);
 473     colourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 474     colourLabel.setText(MessageManager.getString("label.alignment_colour")
 475             + " ");
 476     fontLabel.setFont(verdana11);
 477     fontLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 478     fontLabel.setText(MessageManager.getString("label.font"));
 479     fontSizeCB.setFont(verdana11);
 480     fontSizeCB.setBounds(new Rectangle(319, 104, 49, 23));
 481     fontStyleCB.setFont(verdana11);
 482     fontStyleCB.setBounds(new Rectangle(367, 104, 70, 23));
 483     fontNameCB.setFont(verdana11);
 484     fontNameCB.setBounds(new Rectangle(172, 104, 147, 23));
 485     gapSymbolCB.setFont(verdana11);
 486     gapSymbolCB.setBounds(new Rectangle(172, 196, 69, 23));
 487     mincolourLabel.setFont(verdana11);
 488     mincolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 489     mincolourLabel.setText(MessageManager.getString("label.min_colour"));
 490     minColour.setFont(verdana11);
 491     minColour.setBorder(BorderFactory.createEtchedBorder());
 492     minColour.setPreferredSize(new Dimension(40, 20));
 493     minColour.addMouseListener(new MouseAdapter()
 494     {
 495       public void mousePressed(MouseEvent e)
 496       {
 497         minColour_actionPerformed();
 498       }
 499     });
 500     maxcolourLabel.setFont(verdana11);
 501     maxcolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 502     maxcolourLabel.setText(MessageManager.getString("label.max_colour"));
 503     maxColour.setFont(verdana11);
 504     maxColour.setBorder(BorderFactory.createEtchedBorder());
 505     maxColour.setPreferredSize(new Dimension(40, 20));
 506     maxColour.addMouseListener(new MouseAdapter()
 507     {
 508       public void mousePressed(MouseEvent e)
 509       {
 510         maxColour_actionPerformed();
 511       }
 512     });
 513
 514     startupCheckbox.setText(MessageManager.getString("action.open_file"));
 515     startupCheckbox.setFont(verdana11);
 516     startupCheckbox.setHorizontalAlignment(SwingConstants.RIGHT);
 517     startupCheckbox.setHorizontalTextPosition(SwingConstants.LEFT);
 518     startupCheckbox.setSelected(true);
 519     startupFileTextfield.setFont(verdana11);
 520     startupFileTextfield.setBounds(new Rectangle(172, 287, 270, 20));
 521     startupFileTextfield.addMouseListener(new MouseAdapter()
 522     {
 523       public void mouseClicked(MouseEvent e)
 524       {
 525         if (e.getClickCount() > 1)
 526         {
 527           startupFileTextfield_mouseClicked();
 528         }
 529       }
 530     });
 531
 532     connectTab.setLayout(gridBagLayout3);
 533     serverLabel.setText(MessageManager.getString("label.address"));
 534     serverLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 535     serverLabel.setFont(verdana11);
 536     proxyServerTB.setFont(verdana11);
 537     proxyPortTB.setFont(verdana11);
 538     portLabel.setFont(verdana11);
 539     portLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 540     portLabel.setText(MessageManager.getString("label.port"));
 541     browserLabel.setFont(new java.awt.Font("SansSerif", 0, 11));
 542     browserLabel.setHorizontalAlignment(SwingConstants.TRAILING);
 543     browserLabel.setText(MessageManager
 544             .getString("label.default_browser_unix"));
 545     defaultBrowser.setFont(verdana11);
 546     defaultBrowser.setText("");
 547     usagestats.setText(MessageManager
 548             .getString("label.send_usage_statistics"));
 549     usagestats.setFont(verdana11);
 550     usagestats.setHorizontalAlignment(SwingConstants.RIGHT);
 551     usagestats.setHorizontalTextPosition(SwingConstants.LEADING);
 552     questionnaire.setText(MessageManager
 553             .getString("label.check_for_questionnaires"));
 554     questionnaire.setFont(verdana11);
 555     questionnaire.setHorizontalAlignment(SwingConstants.RIGHT);
 556     questionnaire.setHorizontalTextPosition(SwingConstants.LEADING);
 557     versioncheck.setText(MessageManager
 558             .getString("label.check_for_latest_version"));
 559     versioncheck.setFont(verdana11);
 560     versioncheck.setHorizontalAlignment(SwingConstants.RIGHT);
 561     versioncheck.setHorizontalTextPosition(SwingConstants.LEADING);
 562     newLink.setText(MessageManager.getString("action.new"));
 563     newLink.addActionListener(new java.awt.event.ActionListener()
 564     {
 565       public void actionPerformed(ActionEvent e)
 566       {
 567         newLink_actionPerformed(e);
 568       }
 569     });
 570     editLink.setText(MessageManager.getString("action.edit"));
 571     editLink.addActionListener(new java.awt.event.ActionListener()
 572     {
 573       public void actionPerformed(ActionEvent e)
 574       {
 575         editLink_actionPerformed(e);
 576       }
 577     });
 578     deleteLink.setText(MessageManager.getString("action.delete"));
 579     deleteLink.addActionListener(new java.awt.event.ActionListener()
 580     {
 581       public void actionPerformed(ActionEvent e)
 582       {
 583         deleteLink_actionPerformed(e);
 584       }
 585     });
 586
 587     linkURLList.addListSelectionListener(new ListSelectionListener()
 588     {
 589       public void valueChanged(ListSelectionEvent e)
 590       {
 591         int index = linkURLList.getSelectedIndex();
 592         linkNameList.setSelectedIndex(index);
 593       }
 594     });
 595
 596     linkNameList.addListSelectionListener(new ListSelectionListener()
 597     {
 598       public void valueChanged(ListSelectionEvent e)
 599       {
 600         int index = linkNameList.getSelectedIndex();
 601         linkURLList.setSelectedIndex(index);
 602       }
 603     });
 604
 605     linkScrollPane.setBorder(null);
 606     linkPanel.setBorder(new TitledBorder(MessageManager
 607             .getString("label.url_linkfrom_sequence_id")));
 608     linkPanel.setLayout(borderLayout2);
 609     editLinkButtons.setLayout(gridLayout1);
 610     gridLayout1.setRows(3);
 611     linkNameList.setFont(verdana11);
 612     linkNameList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
 613     linkPanel2.setLayout(borderLayout3);
 614     linkURLList.setFont(verdana11);
 615     linkURLList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
 616
 617     defaultBrowser.addMouseListener(new MouseAdapter()
 618     {
 619       public void mouseClicked(MouseEvent e)
 620       {
 621         if (e.getClickCount() > 1)
 622         {
 623           defaultBrowser_mouseClicked(e);
 624         }
 625       }
 626     });
 627     useProxy.setFont(verdana11);
 628     useProxy.setHorizontalAlignment(SwingConstants.RIGHT);
 629     useProxy.setHorizontalTextPosition(SwingConstants.LEADING);
 630     useProxy.setText(MessageManager.getString("label.use_proxy_server"));
 631     useProxy.addActionListener(new ActionListener()
 632     {
 633       public void actionPerformed(ActionEvent e)
 634       {
 635         useProxy_actionPerformed();
 636       }
 637     });
 638     jPanel1.setBorder(titledBorder1);
 639     jPanel1.setLayout(gridBagLayout1);
 640     sortby.setFont(verdana11);
 641     sortby.setBounds(new Rectangle(172, 240, 155, 21));
 642     sortLabel.setFont(verdana11);
 643     sortLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 644     sortLabel.setText(MessageManager.getString("label.sort_by"));
 645     sortAnnBy.setFont(verdana11);
 646     sortAnnBy.setBounds(new Rectangle(172, 264, 120, 21));
 647     sortAnnLabel.setFont(verdana11);
 648     sortAnnLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 649     sortAnnLabel.setText(MessageManager.getString("label.sort_ann_by"));
 650     sortAutocalc.setFont(verdana11);
 651     sortAutocalc.setBounds(new Rectangle(300, 264, 185, 21));
 652     jPanel2.setBounds(new Rectangle(7, 17, 158, 297));
 653     jPanel2.setLayout(gridLayout2);
 654     gridLayout2.setRows(13);
 655     exportTab.setLayout(null);
 656     epsLabel.setFont(verdana11);
 657     epsLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 658     epsLabel.setText(MessageManager.getString("label.eps_rendering_style"));
 659     epsLabel.setBounds(new Rectangle(9, 31, 140, 24));
 660     epsRendering.setFont(verdana11);
 661     epsRendering.setBounds(new Rectangle(154, 34, 187, 21));
 662     jLabel1.setFont(verdana11);
 663     jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
 664     jLabel1.setText(MessageManager.getString("label.append_start_end"));
 665     jLabel1.setFont(verdana11);
 666     fastajv.setFont(verdana11);
 667     fastajv.setHorizontalAlignment(SwingConstants.LEFT);
 668     clustaljv.setText(MessageManager.getString("label.clustal") + "     ");
 669     blcjv.setText(MessageManager.getString("label.blc") + "     ");
 670     fastajv.setText(MessageManager.getString("label.fasta") + "     ");
 671     msfjv.setText(MessageManager.getString("label.msf") + "     ");
 672     pfamjv.setText(MessageManager.getString("label.pfam") + "     ");
 673     pileupjv.setText(MessageManager.getString("label.pileup") + "     ");
 674     msfjv.setFont(verdana11);
 675     msfjv.setHorizontalAlignment(SwingConstants.LEFT);
 676     pirjv.setText(MessageManager.getString("label.pir") + "     ");
 677     jPanel11.setFont(verdana11);
 678     jPanel11.setBorder(titledBorder2);
 679     jPanel11.setBounds(new Rectangle(30, 72, 196, 182));
 680     jPanel11.setLayout(gridLayout3);
 681     blcjv.setFont(verdana11);
 682     blcjv.setHorizontalAlignment(SwingConstants.LEFT);
 683     clustaljv.setFont(verdana11);
 684     clustaljv.setHorizontalAlignment(SwingConstants.LEFT);
 685     pfamjv.setFont(verdana11);
 686     pfamjv.setHorizontalAlignment(SwingConstants.LEFT);
 687     pileupjv.setFont(verdana11);
 688     pileupjv.setHorizontalAlignment(SwingConstants.LEFT);
 689     pirjv.setFont(verdana11);
 690     pirjv.setHorizontalAlignment(SwingConstants.LEFT);
 691     seqLimit.setFont(verdana11);
 692     seqLimit.setHorizontalAlignment(SwingConstants.RIGHT);
 693     seqLimit.setHorizontalTextPosition(SwingConstants.LEFT);
 694     seqLimit.setText(MessageManager.getString("label.full_sequence_id"));
 695     gridLayout3.setRows(8);
 696     smoothFont.setFont(verdana11);
 697     smoothFont.setHorizontalAlignment(SwingConstants.RIGHT);
 698     smoothFont.setHorizontalTextPosition(SwingConstants.LEADING);
 699     smoothFont.setText(MessageManager.getString("label.smooth_font"));
 700     calcTab.setLayout(null);
 701     autoCalculateConsCheck.setFont(JvSwingUtils.getLabelFont());
 702     autoCalculateConsCheck.setText(MessageManager
 703             .getString("label.autocalculate_consensus"));
 704     autoCalculateConsCheck.setBounds(new Rectangle(21, 52, 209, 23));
 705     padGaps.setFont(JvSwingUtils.getLabelFont());
 706     padGaps.setText(MessageManager.getString("label.pad_gaps_when_editing"));
 707     padGaps.setBounds(new Rectangle(22, 94, 168, 23));
 708     sortByTree.setFont(JvSwingUtils.getLabelFont());
 709     sortByTree
 710             .setText(MessageManager.getString("label.sort_with_new_tree"));
 711     sortByTree
 712             .setToolTipText(MessageManager
 713                     .getString("label.any_trees_calculated_or_loaded_alignment_automatically_sort"));
 714     sortByTree.setBounds(new Rectangle(22, 136, 168, 23));
 715
 716     autoIdWidth.setFont(JvSwingUtils.getLabelFont());
 717     autoIdWidth.setText(MessageManager
 718             .getString("label.automatically_set_id_width"));
 719     autoIdWidth
 720             .setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.getString("label.adjusts_width_generated_eps_png")));
 721     autoIdWidth.setBounds(new Rectangle(228, 96, 188, 23));
 722     autoIdWidth.addActionListener(new ActionListener()
 723     {
 724
 725       @Override
 726       public void actionPerformed(ActionEvent e)
 727       {
 728         autoIdWidth_actionPerformed();
 729       }
 730     });
 731     userIdWidthlabel.setFont(JvSwingUtils.getLabelFont());
 732     userIdWidthlabel.setText(MessageManager
 733             .getString("label.figure_id_column_width"));
 734     userIdWidth
 735             .setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.getString("label.manually_specify_width_left_column")));
 736     userIdWidthlabel
 737             .setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.getString("label.manually_specify_width_left_column")));
 738     userIdWidthlabel.setBounds(new Rectangle(236, 120, 168, 23));
 739     userIdWidth.setFont(JvSwingUtils.getTextAreaFont());
 740     userIdWidth.setText("");
 741     userIdWidth.setBounds(new Rectangle(232, 144, 84, 23));
 742     userIdWidth.addActionListener(new ActionListener()
 743     {
 744
 745       @Override
 746       public void actionPerformed(ActionEvent e)
 747       {
 748         userIdWidth_actionPerformed();
 749       }
 750     });
 751     modellerOutput.setFont(JvSwingUtils.getLabelFont());
 752     modellerOutput.setText(MessageManager
 753             .getString("label.use_modeller_output"));
 754     modellerOutput.setBounds(new Rectangle(228, 226, 168, 23));
 755
 756     dasPanel.setLayout(borderLayout4);
 757     wsPanel.setLayout(borderLayout5);
 758     wrap.setFont(JvSwingUtils.getLabelFont());
 759     wrap.setHorizontalAlignment(SwingConstants.TRAILING);
 760     wrap.setHorizontalTextPosition(SwingConstants.LEADING);
 761     wrap.setText(MessageManager.getString("label.wrap_alignment"));
 762     rightAlign.setFont(JvSwingUtils.getLabelFont());
 763     rightAlign.setForeground(Color.black);
 764     rightAlign.setHorizontalAlignment(SwingConstants.RIGHT);
 765     rightAlign.setHorizontalTextPosition(SwingConstants.LEFT);
 766     rightAlign.setText(MessageManager.getString("label.right_align_ids"));
 767     idItalics.setFont(JvSwingUtils.getLabelFont());
 768     idItalics.setHorizontalAlignment(SwingConstants.RIGHT);
 769     idItalics.setHorizontalTextPosition(SwingConstants.LEADING);
 770     idItalics.setText(MessageManager
 771             .getString("label.sequence_name_italics"));
 772     openoverv.setFont(JvSwingUtils.getLabelFont());
 773     openoverv.setActionCommand(MessageManager
 774             .getString("label.open_overview"));
 775     openoverv.setHorizontalAlignment(SwingConstants.RIGHT);
 776     openoverv.setHorizontalTextPosition(SwingConstants.LEFT);
 777     openoverv.setText(MessageManager.getString(("label.open_overview")));
 778     jPanel2.add(fullScreen);
 779     jPanel2.add(openoverv);
 780     jPanel2.add(seqLimit);
 781     jPanel2.add(rightAlign);
 782     jPanel2.add(fontLabel);
 783     jPanel2.add(showUnconserved);
 784     jPanel2.add(idItalics);
 785     jPanel2.add(smoothFont);
 786     jPanel2.add(gapLabel);
 787     jPanel2.add(wrap);
 788     jPanel2.add(sortLabel);
 789     jPanel2.add(sortAnnLabel);
 790     jPanel2.add(startupCheckbox);
 791     visualTab.add(annotations);
 792     visualTab.add(startupFileTextfield);
 793     visualTab.add(sortby);
 794     visualTab.add(sortAnnBy);
 795     visualTab.add(sortAutocalc);
 796     visualTab.add(gapSymbolCB);
 797     visualTab.add(fontNameCB);
 798     visualTab.add(fontSizeCB);
 799     visualTab.add(fontStyleCB);
 800     annsettingsPanel.setBounds(new Rectangle(173, 34, 300, 61));
 801     annsettingsPanel.setLayout(new FlowLayout(FlowLayout.LEFT, 0, 0));
 802     annsettingsPanel.add(autoAnnotSettings1);
 803     annsettingsPanel.add(autoAnnotSettings2);
 804     annsettingsPanel.add(autoAnnotSettings3);
 805     autoAnnotSettings1.setLayout(new GridLayout(3, 1, 0, 0));
 806     autoAnnotSettings2.setLayout(new GridLayout(3, 1, 0, 0));
 807     autoAnnotSettings3.setLayout(new GridLayout(3, 1, 0, 0));
 808     visualTab.add(annsettingsPanel);
 809     Border jb = new EmptyBorder(1, 1, 4, 5);
 810     quality.setBorder(jb);
 811     conservation.setBorder(jb);
 812     identity.setBorder(jb);
 813     showConsensbits.setBorder(jb);
 814     showGroupbits.setBorder(jb);
 815     showGroupConsensus.setBorder(jb);
 816     showGroupConservation.setBorder(jb);
 817     showConsensHistogram.setBorder(jb);
 818     showConsensLogo.setBorder(jb);
 819
 820     autoAnnotSettings2.add(conservation);
 821     autoAnnotSettings1.add(quality);
 822     autoAnnotSettings3.add(identity);
 823     autoAnnotSettings1.add(showGroupbits);
 824     autoAnnotSettings3.add(showGroupConsensus);
 825     autoAnnotSettings2.add(showGroupConservation);
 826     autoAnnotSettings1.add(showConsensbits);
 827     autoAnnotSettings2.add(showConsensHistogram);
 828     autoAnnotSettings3.add(showConsensLogo);
 829
 830     JPanel tooltipSettings = new JPanel();
 831     tooltipSettings.setBorder(new TitledBorder(MessageManager
 832             .getString("label.sequence_id_tooltip")));
 833     tooltipSettings.setBounds(173, 130, 200, 62);
 834     tooltipSettings.setLayout(new GridLayout(2, 1));
 835     tooltipSettings.add(showDbRefTooltip);
 836     tooltipSettings.add(showNpTooltip);
 837     visualTab.add(tooltipSettings);
 838     visualTab.add(jPanel2);
 839     JvSwingUtils.addtoLayout(visual2Tab, MessageManager
 840             .getString("label.default_colour_scheme_for_alignment"),
 841             colourLabel, colour);
 842     JPanel annotationShding = new JPanel();
 843     annotationShding.setBorder(new TitledBorder(MessageManager
 844             .getString("label.annotation_shading_default")));
 845     annotationShding.setLayout(new GridLayout(1, 2));
 846     JvSwingUtils.addtoLayout(annotationShding, MessageManager
 847             .getString("label.default_minimum_colour_annotation_shading"),
 848             mincolourLabel, minColour);
 849     JvSwingUtils.addtoLayout(annotationShding, MessageManager
 850             .getString("label.default_maximum_colour_annotation_shading"),
 851             maxcolourLabel, maxColour);
 852     visual2Tab.add(annotationShding); // , FlowLayout.LEFT);
 853
 854     // visual2panel.add(minColour);
 855     // visual2panel.add(maxColour);
 856     // visual2Tab.add(visual2panel);
 857
 858     linkPanel.add(editLinkButtons, BorderLayout.EAST);
 859     editLinkButtons.add(newLink, null);
 860     editLinkButtons.add(editLink, null);
 861     editLinkButtons.add(deleteLink, null);
 862     linkPanel.add(linkScrollPane, BorderLayout.CENTER);
 863     linkScrollPane.getViewport().add(linkPanel2, null);
 864     linkPanel2.add(linkURLList, BorderLayout.CENTER);
 865     linkPanel2.add(linkNameList, BorderLayout.WEST);
 866     okCancelPanel.add(ok);
 867     okCancelPanel.add(cancel);
 868     this.add(tabbedPane, java.awt.BorderLayout.CENTER);
 869
 870     this.add(okCancelPanel, java.awt.BorderLayout.SOUTH);
 871     jPanel1.add(serverLabel, new GridBagConstraints(0, 1, 1, 1, 0.0, 0.0,
 872             GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
 873                     2, 4, 0), 5, 0));
 874     jPanel1.add(portLabel, new GridBagConstraints(2, 1, 1, 1, 0.0, 0.0,
 875             GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
 876                     0, 4, 0), 11, 6));
 877     connectTab.add(linkPanel, new GridBagConstraints(0, 0, 2, 1, 1.0, 1.0,
 878             GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(
 879                     16, 0, 0, 12), 359, -17));
 880     connectTab.add(jPanel1, new GridBagConstraints(0, 2, 2, 1, 1.0, 1.0,
 881             GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(
 882                     21, 0, 35, 12), 4, 6));
 883     connectTab.add(browserLabel, new GridBagConstraints(0, 1, 1, 1, 0.0,
 884             0.0, GridBagConstraints.WEST, GridBagConstraints.NONE,
 885             new Insets(16, 0, 0, 0), 5, 1));
 886     jPanel1.add(proxyPortTB, new GridBagConstraints(3, 1, 1, 1, 1.0, 0.0,
 887             GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 888             new Insets(0, 2, 4, 2), 54, 1));
 889     jPanel1.add(proxyServerTB, new GridBagConstraints(1, 1, 1, 1, 1.0, 0.0,
 890             GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 891             new Insets(0, 2, 4, 0), 263, 1));
 892     connectTab.add(defaultBrowser, new GridBagConstraints(1, 1, 1, 1, 1.0,
 893             0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 894             new Insets(15, 0, 0, 15), 307, 1));
 895     connectTab.add(usagestats, new GridBagConstraints(0, 4, 1, 1, 1.0, 0.0,
 896             GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 897             new Insets(0, 2, 4, 2), 70, 1));
 898     connectTab.add(questionnaire, new GridBagConstraints(1, 4, 1, 1, 1.0,
 899             0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 900             new Insets(0, 2, 4, 2), 70, 1));
 901     connectTab.add(versioncheck, new GridBagConstraints(0, 5, 1, 1, 1.0,
 902             0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 903             new Insets(0, 2, 4, 2), 70, 1));
 904
 905     jPanel1.add(useProxy, new GridBagConstraints(0, 0, 2, 1, 0.0, 0.0,
 906             GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
 907                     2, 5, 185), 2, -4));
 908     DefaultListCellRenderer dlcr = new DefaultListCellRenderer();
 909     dlcr.setHorizontalAlignment(DefaultListCellRenderer.CENTER);
 910     gapSymbolCB.setRenderer(dlcr);
 911
 912     tabbedPane.add(visualTab, MessageManager.getString("label.visual"));
 913     tabbedPane.add(visual2Tab, MessageManager.getString("label.colours"));
 914     tabbedPane.add(connectTab,
 915             MessageManager.getString("label.connections"));
 916     tabbedPane.add(exportTab, MessageManager.getString("label.output"));
 917     jPanel11.add(jLabel1);
 918     jPanel11.add(blcjv);
 919     jPanel11.add(clustaljv);
 920     jPanel11.add(fastajv);
 921     jPanel11.add(msfjv);
 922     jPanel11.add(pfamjv);
 923     jPanel11.add(pileupjv);
 924     jPanel11.add(pirjv);
 925     exportTab.add(autoIdWidth);
 926     exportTab.add(userIdWidth);
 927     exportTab.add(userIdWidthlabel);
 928     exportTab.add(modellerOutput);
 929     tabbedPane.add(calcTab, MessageManager.getString("label.editing"));
 930     calcTab.add(autoCalculateConsCheck);
 931     calcTab.add(padGaps);
 932     calcTab.add(sortByTree);
 933
 934     tabbedPane
 935             .add(dasPanel, MessageManager.getString("label.das_settings"));
 936     tabbedPane.add(wsPanel, MessageManager.getString("label.web_services"));
 937
 938     exportTab.add(epsLabel);
 939     exportTab.add(epsRendering);
 940     exportTab.add(jPanel11);
 941   }
 942
 943   protected void autoIdWidth_actionPerformed()
 944   {
 945     // TODO Auto-generated method stub
 946
 947   }
 948
 949   protected void userIdWidth_actionPerformed()
 950   {
 951     // TODO Auto-generated method stub
 952
 953   }
 954
 955   protected void maxColour_actionPerformed()
 956   {
 957     // TODO Auto-generated method stub
 958
 959   }
 960
 961   protected void minColour_actionPerformed()
 962   {
 963     // TODO Auto-generated method stub
 964
 965   }
 966
 967   protected void showunconserved_actionPerformed(ActionEvent e)
 968   {
 969     // TODO Auto-generated method stub
 970
 971   }
 972
 973   /**
 974    * DOCUMENT ME!
 975    *
 976    * @param e
 977    *          DOCUMENT ME!
 978    */
 979   public void ok_actionPerformed(ActionEvent e)
 980   {
 981   }
 982
 983   /**
 984    * DOCUMENT ME!
 985    *
 986    * @param e
 987    *          DOCUMENT ME!
 988    */
 989   public void cancel_actionPerformed(ActionEvent e)
 990   {
 991   }
 992
 993   /**
 994    * DOCUMENT ME!
 995    *
 996    * @param e
 997    *          DOCUMENT ME!
 998    */
 999   public void annotations_actionPerformed(ActionEvent e)
1000   {
1001   }
1002
1003   /**
1004    * DOCUMENT ME!
1005    */
1006   public void startupFileTextfield_mouseClicked()
1007   {
1008   }
1009
1010   public void newLink_actionPerformed(ActionEvent e)
1011   {
1012
1013   }
1014
1015   public void editLink_actionPerformed(ActionEvent e)
1016   {
1017
1018   }
1019
1020   public void deleteLink_actionPerformed(ActionEvent e)
1021   {
1022
1023   }
1024
1025   public void defaultBrowser_mouseClicked(MouseEvent e)
1026   {
1027
1028   }
1029
1030   public void linkURLList_keyTyped(KeyEvent e)
1031   {
1032
1033   }
1034
1035   public void useProxy_actionPerformed()
1036   {
1037     proxyServerTB.setEnabled(useProxy.isSelected());
1038     proxyPortTB.setEnabled(useProxy.isSelected());
1039   }
1040
1041 }