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 colour = new JComboBox();
 104
 105   JLabel colourLabel = new JLabel();
 106
 107   JLabel fontLabel = new JLabel();
 108
 109   protected JComboBox fontSizeCB = new JComboBox();
 110
 111   protected JComboBox fontStyleCB = new JComboBox();
 112
 113   protected JComboBox fontNameCB = new JComboBox();
 114
 115   protected JComboBox gapSymbolCB = new JComboBox();
 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 sortby = new JComboBox();
 176
 177   JLabel sortLabel = new JLabel();
 178
 179   JPanel jPanel2 = new JPanel();
 180
 181   JPanel visual2panel = new JPanel();
 182
 183   GridLayout gridLayout2 = new GridLayout();
 184
 185   GridLayout gridLayout4 = new GridLayout();
 186
 187   JPanel annsettingsPanel = new JPanel();
 188
 189   JPanel autoAnnotSettings1 = new JPanel();
 190
 191   JPanel autoAnnotSettings2 = new JPanel();
 192
 193   JPanel autoAnnotSettings3 = new JPanel();
 194
 195   JPanel exportTab = new JPanel();
 196
 197   JLabel epsLabel = new JLabel();
 198
 199   protected JComboBox epsRendering = new JComboBox();
 200
 201   protected JLabel userIdWidthlabel = new JLabel();
 202
 203   protected JCheckBox autoIdWidth = new JCheckBox();
 204
 205   protected JTextField userIdWidth = new JTextField();
 206
 207   JLabel jLabel1 = new JLabel();
 208
 209   protected JCheckBox blcjv = new JCheckBox();
 210
 211   protected JCheckBox pileupjv = new JCheckBox();
 212
 213   protected JCheckBox clustaljv = new JCheckBox();
 214
 215   protected JCheckBox megajv = new JCheckBox();
 216
 217   protected JCheckBox msfjv = new JCheckBox();
 218
 219   protected JCheckBox fastajv = new JCheckBox();
 220
 221   protected JCheckBox pfamjv = new JCheckBox();
 222
 223   FlowLayout flowLayout1 = new FlowLayout();
 224
 225   protected JCheckBox pirjv = new JCheckBox();
 226
 227   JPanel jPanel11 = new JPanel();
 228
 229   Font verdana11 = JvSwingUtils.getLabelFont();
 230
 231   protected JCheckBox seqLimit = new JCheckBox();
 232
 233   GridLayout gridLayout3 = new GridLayout();
 234
 235   protected JCheckBox smoothFont = new JCheckBox();
 236
 237   JPanel calcTab = new JPanel();
 238
 239   protected JCheckBox autoCalculateConsCheck = new JCheckBox();
 240
 241   protected JCheckBox padGaps = new JCheckBox();
 242
 243   protected JCheckBox modellerOutput = new JCheckBox();
 244
 245   protected JPanel dasPanel = new JPanel();
 246
 247   BorderLayout borderLayout4 = new BorderLayout();
 248
 249   protected JPanel wsPanel = new JPanel();
 250
 251   BorderLayout borderLayout5 = new BorderLayout();
 252
 253   protected JCheckBox wrap = new JCheckBox();
 254
 255   protected JCheckBox rightAlign = new JCheckBox();
 256
 257   protected JCheckBox showUnconserved = new JCheckBox();
 258
 259   protected JCheckBox showDbRefTooltip = new JCheckBox();
 260
 261   protected JCheckBox showNpTooltip = new JCheckBox();
 262
 263   protected JCheckBox idItalics = new JCheckBox();
 264
 265   protected JCheckBox openoverv = new JCheckBox();
 266
 267   protected JCheckBox usagestats = new JCheckBox();
 268
 269   protected JCheckBox questionnaire = new JCheckBox();
 270
 271   protected JCheckBox versioncheck = new JCheckBox();
 272
 273   protected JLabel showGroupbits = new JLabel();
 274
 275   protected JLabel showConsensbits = new JLabel();
 276
 277   protected JCheckBox showConsensLogo = new JCheckBox();
 278
 279   protected JCheckBox showConsensHistogram = new JCheckBox();
 280
 281   protected JCheckBox showGroupConsensus = new JCheckBox();
 282
 283   protected JCheckBox showGroupConservation = new JCheckBox();
 284
 285   protected JCheckBox shareSelections = new JCheckBox();
 286
 287   protected JCheckBox followHighlight = new JCheckBox();
 288
 289   protected JCheckBox sortByTree = new JCheckBox();
 290
 291   /**
 292    * Creates a new GPreferences object.
 293    */
 294   public GPreferences()
 295   {
 296     try
 297     {
 298       jbInit();
 299     } catch (Exception ex)
 300     {
 301       ex.printStackTrace();
 302     }
 303   }
 304
 305   /**
 306    * DOCUMENT ME!
 307    *
 308    * @throws Exception
 309    *           DOCUMENT ME!
 310    */
 311   private void jbInit() throws Exception
 312   {
 313     this.setLayout(borderLayout1);
 314     ok.setText(MessageManager.getString("action.ok"));
 315     ok.addActionListener(new ActionListener()
 316     {
 317       @Override
 318       public void actionPerformed(ActionEvent e)
 319       {
 320         ok_actionPerformed(e);
 321       }
 322     });
 323     cancel.setText(MessageManager.getString("action.cancel"));
 324     cancel.addActionListener(new ActionListener()
 325     {
 326       @Override
 327       public void actionPerformed(ActionEvent e)
 328       {
 329         cancel_actionPerformed(e);
 330       }
 331     });
 332     quality.setEnabled(false);
 333     quality.setFont(verdana11);
 334     quality.setHorizontalAlignment(SwingConstants.RIGHT);
 335     quality.setHorizontalTextPosition(SwingConstants.LEFT);
 336     quality.setSelected(true);
 337     quality.setText(MessageManager.getString("label.quality"));
 338     visualTab.setBorder(new TitledBorder(MessageManager
 339             .getString("action.open_new_aligmnent")));
 340     visualTab.setLayout(null);
 341     visual2Tab.setBorder(new TitledBorder(MessageManager
 342             .getString("action.open_new_aligmnent")));
 343     visual2Tab.setLayout(new FlowLayout());
 344     fullScreen.setFont(verdana11);
 345     fullScreen.setHorizontalAlignment(SwingConstants.RIGHT);
 346     fullScreen.setHorizontalTextPosition(SwingConstants.LEFT);
 347     fullScreen.setText(MessageManager.getString("label.maximize_window"));
 348     conservation.setEnabled(false);
 349     conservation.setFont(verdana11);
 350     conservation.setHorizontalAlignment(SwingConstants.RIGHT);
 351     conservation.setHorizontalTextPosition(SwingConstants.LEFT);
 352     conservation.setSelected(true);
 353     conservation.setText(MessageManager.getString("label.conservation"));
 354     identity.setEnabled(false);
 355     identity.setFont(verdana11);
 356     identity.setHorizontalAlignment(SwingConstants.RIGHT);
 357     identity.setHorizontalTextPosition(SwingConstants.LEFT);
 358     identity.setSelected(true);
 359     identity.setText(MessageManager.getString("label.consensus"));
 360     showGroupbits.setFont(verdana11);
 361     showGroupbits.setHorizontalAlignment(SwingConstants.RIGHT);
 362     showGroupbits.setHorizontalTextPosition(SwingConstants.LEFT);
 363     showGroupbits.setText(MessageManager.getString("action.show_group")
 364             + ":");
 365     showConsensbits.setFont(verdana11);
 366     showConsensbits.setHorizontalAlignment(SwingConstants.RIGHT);
 367     showConsensbits.setHorizontalTextPosition(SwingConstants.LEFT);
 368     showConsensbits.setText(MessageManager.getString("label.consensus")
 369             + ":");
 370     showConsensHistogram.setEnabled(false);
 371     showConsensHistogram.setFont(verdana11);
 372     showConsensHistogram.setHorizontalAlignment(SwingConstants.RIGHT);
 373     showConsensHistogram.setHorizontalTextPosition(SwingConstants.LEFT);
 374     showConsensHistogram.setSelected(true);
 375     showConsensHistogram.setText(MessageManager
 376             .getString("label.histogram"));
 377     showConsensLogo.setEnabled(false);
 378     showConsensLogo.setFont(verdana11);
 379     showConsensLogo.setHorizontalAlignment(SwingConstants.RIGHT);
 380     showConsensLogo.setHorizontalTextPosition(SwingConstants.LEFT);
 381     showConsensLogo.setSelected(true);
 382     showConsensLogo.setText(MessageManager.getString("label.logo"));
 383     showGroupConsensus.setEnabled(false);
 384     showGroupConsensus.setFont(verdana11);
 385     showGroupConsensus.setHorizontalAlignment(SwingConstants.RIGHT);
 386     showGroupConsensus.setHorizontalTextPosition(SwingConstants.LEFT);
 387     showGroupConsensus.setSelected(true);
 388     showGroupConsensus.setText(MessageManager.getString("label.consensus"));
 389     showGroupConservation.setEnabled(false);
 390     showGroupConservation.setFont(verdana11);
 391     showGroupConservation.setHorizontalAlignment(SwingConstants.RIGHT);
 392     showGroupConservation.setHorizontalTextPosition(SwingConstants.LEFT);
 393     showGroupConservation.setSelected(true);
 394     showGroupConservation.setText(MessageManager
 395             .getString("label.conservation"));
 396     showNpTooltip.setEnabled(true);
 397     showNpTooltip.setFont(verdana11);
 398     showNpTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
 399     showNpTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
 400     showNpTooltip.setSelected(true);
 401     showNpTooltip.setText(MessageManager
 402             .getString("label.non_positional_features"));
 403     showDbRefTooltip.setEnabled(true);
 404     showDbRefTooltip.setFont(verdana11);
 405     showDbRefTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
 406     showDbRefTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
 407     showDbRefTooltip.setSelected(true);
 408     showDbRefTooltip.setText(MessageManager
 409             .getString("label.database_references"));
 410     annotations.setFont(verdana11);
 411     annotations.setHorizontalAlignment(SwingConstants.RIGHT);
 412     annotations.setHorizontalTextPosition(SwingConstants.LEADING);
 413     annotations.setSelected(true);
 414     annotations.setText(MessageManager.getString("label.show_annotations"));
 415     annotations.setBounds(new Rectangle(169, 12, 200, 23));
 416     annotations.addActionListener(new ActionListener()
 417     {
 418       @Override
 419       public void actionPerformed(ActionEvent e)
 420       {
 421         annotations_actionPerformed(e);
 422       }
 423     });
 424     identity.addActionListener(new ActionListener()
 425     {
 426       @Override
 427       public void actionPerformed(ActionEvent e)
 428       {
 429         annotations_actionPerformed(e);
 430       }
 431     });
 432     showGroupConsensus.addActionListener(new ActionListener()
 433     {
 434       @Override
 435       public void actionPerformed(ActionEvent e)
 436       {
 437         annotations_actionPerformed(e);
 438       }
 439     });
 440     showUnconserved.setFont(verdana11);
 441     showUnconserved.setHorizontalAlignment(SwingConstants.RIGHT);
 442     showUnconserved.setHorizontalTextPosition(SwingConstants.LEFT);
 443     showUnconserved.setSelected(true);
 444     showUnconserved.setText(MessageManager
 445             .getString("action.show_unconserved"));
 446     showUnconserved.addActionListener(new ActionListener()
 447     {
 448       @Override
 449       public void actionPerformed(ActionEvent e)
 450       {
 451         showunconserved_actionPerformed(e);
 452       }
 453     });
 454     // / TODO: fit these in to preferences panel!!!!!
 455     shareSelections.setFont(verdana11);
 456     shareSelections.setHorizontalAlignment(SwingConstants.RIGHT);
 457     shareSelections.setHorizontalTextPosition(SwingConstants.LEFT);
 458     shareSelections.setSelected(true);
 459     shareSelections.setText(MessageManager
 460             .getString("label.share_selection_across_views"));
 461     followHighlight.setFont(verdana11);
 462     followHighlight.setHorizontalAlignment(SwingConstants.RIGHT);
 463     followHighlight.setHorizontalTextPosition(SwingConstants.LEFT);
 464     // showUnconserved.setBounds(new Rectangle(169, 40, 200, 23));
 465     followHighlight.setSelected(true);
 466     followHighlight.setText(MessageManager
 467             .getString("label.scroll_highlighted_regions"));
 468
 469     gapLabel.setFont(verdana11);
 470     gapLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 471     gapLabel.setText(MessageManager.getString("label.gap_symbol") + " ");
 472     colour.setFont(verdana11);
 473     colour.setBounds(new Rectangle(172, 225, 155, 21));
 474     colourLabel.setFont(verdana11);
 475     colourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 476     colourLabel.setText(MessageManager.getString("label.alignment_colour")
 477             + " ");
 478     fontLabel.setFont(verdana11);
 479     fontLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 480     fontLabel.setText(MessageManager.getString("label.font"));
 481     fontSizeCB.setFont(verdana11);
 482     fontSizeCB.setBounds(new Rectangle(319, 104, 49, 23));
 483     fontStyleCB.setFont(verdana11);
 484     fontStyleCB.setBounds(new Rectangle(367, 104, 70, 23));
 485     fontNameCB.setFont(verdana11);
 486     fontNameCB.setBounds(new Rectangle(172, 104, 147, 23));
 487     gapSymbolCB.setFont(verdana11);
 488     gapSymbolCB.setBounds(new Rectangle(172, 204, 69, 23));
 489     mincolourLabel.setFont(verdana11);
 490     mincolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 491     mincolourLabel.setText(MessageManager.getString("label.min_colour"));
 492     minColour.setFont(verdana11);
 493     minColour.setBorder(BorderFactory.createEtchedBorder());
 494     minColour.setPreferredSize(new Dimension(40, 20));
 495     minColour.addMouseListener(new MouseAdapter()
 496     {
 497       @Override
 498       public void mousePressed(MouseEvent e)
 499       {
 500         minColour_actionPerformed();
 501       }
 502     });
 503     maxcolourLabel.setFont(verdana11);
 504     maxcolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 505     maxcolourLabel.setText(MessageManager.getString("label.max_colour"));
 506     maxColour.setFont(verdana11);
 507     maxColour.setBorder(BorderFactory.createEtchedBorder());
 508     maxColour.setPreferredSize(new Dimension(40, 20));
 509     maxColour.addMouseListener(new MouseAdapter()
 510     {
 511       @Override
 512       public void mousePressed(MouseEvent e)
 513       {
 514         maxColour_actionPerformed();
 515       }
 516     });
 517
 518     startupCheckbox.setText(MessageManager.getString("action.open_file"));
 519     startupCheckbox.setFont(verdana11);
 520     startupCheckbox.setHorizontalAlignment(SwingConstants.RIGHT);
 521     startupCheckbox.setHorizontalTextPosition(SwingConstants.LEFT);
 522     startupCheckbox.setSelected(true);
 523     startupFileTextfield.setFont(verdana11);
 524     startupFileTextfield.setBounds(new Rectangle(172, 273, 270, 20));
 525     startupFileTextfield.addMouseListener(new MouseAdapter()
 526     {
 527       @Override
 528       public void mouseClicked(MouseEvent e)
 529       {
 530         if (e.getClickCount() > 1)
 531         {
 532           startupFileTextfield_mouseClicked();
 533         }
 534       }
 535     });
 536
 537     connectTab.setLayout(gridBagLayout3);
 538     serverLabel.setText(MessageManager.getString("label.address"));
 539     serverLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 540     serverLabel.setFont(verdana11);
 541     proxyServerTB.setFont(verdana11);
 542     proxyPortTB.setFont(verdana11);
 543     portLabel.setFont(verdana11);
 544     portLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 545     portLabel.setText(MessageManager.getString("label.port"));
 546     browserLabel.setFont(new java.awt.Font("SansSerif", 0, 11));
 547     browserLabel.setHorizontalAlignment(SwingConstants.TRAILING);
 548     browserLabel.setText(MessageManager
 549             .getString("label.default_browser_unix"));
 550     defaultBrowser.setFont(verdana11);
 551     defaultBrowser.setText("");
 552     usagestats.setText(MessageManager
 553             .getString("label.send_usage_statistics"));
 554     usagestats.setFont(verdana11);
 555     usagestats.setHorizontalAlignment(SwingConstants.RIGHT);
 556     usagestats.setHorizontalTextPosition(SwingConstants.LEADING);
 557     questionnaire.setText(MessageManager
 558             .getString("label.check_for_questionnaires"));
 559     questionnaire.setFont(verdana11);
 560     questionnaire.setHorizontalAlignment(SwingConstants.RIGHT);
 561     questionnaire.setHorizontalTextPosition(SwingConstants.LEADING);
 562     versioncheck.setText(MessageManager
 563             .getString("label.check_for_latest_version"));
 564     versioncheck.setFont(verdana11);
 565     versioncheck.setHorizontalAlignment(SwingConstants.RIGHT);
 566     versioncheck.setHorizontalTextPosition(SwingConstants.LEADING);
 567     newLink.setText(MessageManager.getString("action.new"));
 568     newLink.addActionListener(new java.awt.event.ActionListener()
 569     {
 570       @Override
 571       public void actionPerformed(ActionEvent e)
 572       {
 573         newLink_actionPerformed(e);
 574       }
 575     });
 576     editLink.setText(MessageManager.getString("action.edit"));
 577     editLink.addActionListener(new java.awt.event.ActionListener()
 578     {
 579       @Override
 580       public void actionPerformed(ActionEvent e)
 581       {
 582         editLink_actionPerformed(e);
 583       }
 584     });
 585     deleteLink.setText(MessageManager.getString("action.delete"));
 586     deleteLink.addActionListener(new java.awt.event.ActionListener()
 587     {
 588       @Override
 589       public void actionPerformed(ActionEvent e)
 590       {
 591         deleteLink_actionPerformed(e);
 592       }
 593     });
 594
 595     linkURLList.addListSelectionListener(new ListSelectionListener()
 596     {
 597       @Override
 598       public void valueChanged(ListSelectionEvent e)
 599       {
 600         int index = linkURLList.getSelectedIndex();
 601         linkNameList.setSelectedIndex(index);
 602       }
 603     });
 604
 605     linkNameList.addListSelectionListener(new ListSelectionListener()
 606     {
 607       @Override
 608       public void valueChanged(ListSelectionEvent e)
 609       {
 610         int index = linkNameList.getSelectedIndex();
 611         linkURLList.setSelectedIndex(index);
 612       }
 613     });
 614
 615     linkScrollPane.setBorder(null);
 616     linkPanel.setBorder(new TitledBorder(MessageManager
 617             .getString("label.url_linkfrom_sequence_id")));
 618     linkPanel.setLayout(borderLayout2);
 619     editLinkButtons.setLayout(gridLayout1);
 620     gridLayout1.setRows(3);
 621     linkNameList.setFont(verdana11);
 622     linkNameList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
 623     linkPanel2.setLayout(borderLayout3);
 624     linkURLList.setFont(verdana11);
 625     linkURLList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
 626
 627     defaultBrowser.addMouseListener(new MouseAdapter()
 628     {
 629       @Override
 630       public void mouseClicked(MouseEvent e)
 631       {
 632         if (e.getClickCount() > 1)
 633         {
 634           defaultBrowser_mouseClicked(e);
 635         }
 636       }
 637     });
 638     useProxy.setFont(verdana11);
 639     useProxy.setHorizontalAlignment(SwingConstants.RIGHT);
 640     useProxy.setHorizontalTextPosition(SwingConstants.LEADING);
 641     useProxy.setText(MessageManager.getString("label.use_proxy_server"));
 642     useProxy.addActionListener(new ActionListener()
 643     {
 644       @Override
 645       public void actionPerformed(ActionEvent e)
 646       {
 647         useProxy_actionPerformed();
 648       }
 649     });
 650     jPanel1.setBorder(titledBorder1);
 651     jPanel1.setLayout(gridBagLayout1);
 652     sortby.setFont(verdana11);
 653     sortby.setBounds(new Rectangle(172, 249, 155, 21));
 654     sortLabel.setFont(verdana11);
 655     sortLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 656     sortLabel.setText(MessageManager.getString("label.sort_by"));
 657     jPanel2.setBounds(new Rectangle(7, 17, 158, 278));
 658     jPanel2.setLayout(gridLayout2);
 659     gridLayout2.setRows(12);
 660     exportTab.setLayout(null);
 661     epsLabel.setFont(verdana11);
 662     epsLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 663     epsLabel.setText(MessageManager.getString("label.eps_rendering_style"));
 664     epsLabel.setBounds(new Rectangle(9, 31, 140, 24));
 665     epsRendering.setFont(verdana11);
 666     epsRendering.setBounds(new Rectangle(154, 34, 187, 21));
 667     jLabel1.setFont(verdana11);
 668     jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
 669     jLabel1.setText(MessageManager.getString("label.append_start_end"));
 670     jLabel1.setFont(verdana11);
 671     fastajv.setFont(verdana11);
 672     fastajv.setHorizontalAlignment(SwingConstants.LEFT);
 673     clustaljv.setText(MessageManager.getString("label.clustal") + "     ");
 674     blcjv.setText(MessageManager.getString("label.blc") + "     ");
 675     fastajv.setText(MessageManager.getString("label.fasta") + "     ");
 676     msfjv.setText(MessageManager.getString("label.msf") + "     ");
 677     pfamjv.setText(MessageManager.getString("label.pfam") + "     ");
 678     pileupjv.setText(MessageManager.getString("label.pileup") + "     ");
 679     msfjv.setFont(verdana11);
 680     msfjv.setHorizontalAlignment(SwingConstants.LEFT);
 681     pirjv.setText(MessageManager.getString("label.pir") + "     ");
 682     jPanel11.setFont(verdana11);
 683     jPanel11.setBorder(titledBorder2);
 684     jPanel11.setBounds(new Rectangle(30, 72, 196, 182));
 685     jPanel11.setLayout(gridLayout3);
 686     blcjv.setFont(verdana11);
 687     blcjv.setHorizontalAlignment(SwingConstants.LEFT);
 688     clustaljv.setFont(verdana11);
 689     clustaljv.setHorizontalAlignment(SwingConstants.LEFT);
 690     pfamjv.setFont(verdana11);
 691     pfamjv.setHorizontalAlignment(SwingConstants.LEFT);
 692     pileupjv.setFont(verdana11);
 693     pileupjv.setHorizontalAlignment(SwingConstants.LEFT);
 694     pirjv.setFont(verdana11);
 695     pirjv.setHorizontalAlignment(SwingConstants.LEFT);
 696     seqLimit.setFont(verdana11);
 697     seqLimit.setHorizontalAlignment(SwingConstants.RIGHT);
 698     seqLimit.setHorizontalTextPosition(SwingConstants.LEFT);
 699     seqLimit.setText(MessageManager.getString("label.full_sequence_id"));
 700     gridLayout3.setRows(8);
 701     smoothFont.setFont(verdana11);
 702     smoothFont.setHorizontalAlignment(SwingConstants.RIGHT);
 703     smoothFont.setHorizontalTextPosition(SwingConstants.LEADING);
 704     smoothFont.setText(MessageManager.getString("label.smooth_font"));
 705     calcTab.setLayout(null);
 706     autoCalculateConsCheck.setFont(JvSwingUtils.getLabelFont());
 707     autoCalculateConsCheck.setText(MessageManager
 708             .getString("label.autocalculate_consensus"));
 709     autoCalculateConsCheck.setBounds(new Rectangle(21, 52, 209, 23));
 710     padGaps.setFont(JvSwingUtils.getLabelFont());
 711     padGaps.setText(MessageManager.getString("label.pad_gaps_when_editing"));
 712     padGaps.setBounds(new Rectangle(22, 94, 168, 23));
 713     sortByTree.setFont(JvSwingUtils.getLabelFont());
 714     sortByTree
 715             .setText(MessageManager.getString("label.sort_with_new_tree"));
 716     sortByTree
 717             .setToolTipText(MessageManager
 718                     .getString("label.any_trees_calculated_or_loaded_alignment_automatically_sort"));
 719     sortByTree.setBounds(new Rectangle(22, 136, 168, 23));
 720
 721     autoIdWidth.setFont(JvSwingUtils.getLabelFont());
 722     autoIdWidth.setText(MessageManager
 723             .getString("label.automatically_set_id_width"));
 724     autoIdWidth
 725             .setToolTipText("<html>"
 726                     + JvSwingUtils
 727                             .wrapTooltip("Adjusts the width of the generated EPS or PNG file to ensure even the longest sequence ID or annotation label is displayed")
 728                     + "</html>");
 729     autoIdWidth.setBounds(new Rectangle(228, 96, 188, 23));
 730     autoIdWidth.addActionListener(new ActionListener()
 731     {
 732
 733       @Override
 734       public void actionPerformed(ActionEvent e)
 735       {
 736         autoIdWidth_actionPerformed();
 737       }
 738     });
 739     userIdWidthlabel.setFont(JvSwingUtils.getLabelFont());
 740     userIdWidthlabel.setText(MessageManager
 741             .getString("label.figure_id_column_width"));
 742     userIdWidth
 743             .setToolTipText("<html>"
 744                     + JvSwingUtils
 745                             .wrapTooltip("Manually specify the width of the left hand column where sequence IDs and annotation labels will be rendered in exported alignment figures. This setting will be ignored if 'Automatically set ID width' is set")
 746                     + "</html>");
 747     userIdWidthlabel
 748             .setToolTipText("<html>"
 749                     + JvSwingUtils
 750                             .wrapTooltip("Manually specify the width of the left hand column where sequence IDs and annotation labels will be rendered in exported alignment figures. This setting will be ignored if 'Automatically set ID width' is set")
 751                     + "</html>");
 752     userIdWidthlabel.setBounds(new Rectangle(236, 120, 168, 23));
 753     userIdWidth.setFont(JvSwingUtils.getTextAreaFont());
 754     userIdWidth.setText("");
 755     userIdWidth.setBounds(new Rectangle(232, 144, 84, 23));
 756     userIdWidth.addActionListener(new ActionListener()
 757     {
 758
 759       @Override
 760       public void actionPerformed(ActionEvent e)
 761       {
 762         userIdWidth_actionPerformed();
 763       }
 764     });
 765     modellerOutput.setFont(JvSwingUtils.getLabelFont());
 766     modellerOutput.setText(MessageManager
 767             .getString("label.use_modeller_output"));
 768     modellerOutput.setBounds(new Rectangle(228, 226, 168, 23));
 769
 770     dasPanel.setLayout(borderLayout4);
 771     wsPanel.setLayout(borderLayout5);
 772     wrap.setFont(JvSwingUtils.getLabelFont());
 773     wrap.setHorizontalAlignment(SwingConstants.TRAILING);
 774     wrap.setHorizontalTextPosition(SwingConstants.LEADING);
 775     wrap.setText(MessageManager.getString("label.wrap_alignment"));
 776     rightAlign.setFont(JvSwingUtils.getLabelFont());
 777     rightAlign.setForeground(Color.black);
 778     rightAlign.setHorizontalAlignment(SwingConstants.RIGHT);
 779     rightAlign.setHorizontalTextPosition(SwingConstants.LEFT);
 780     rightAlign.setText(MessageManager.getString("label.right_align_ids"));
 781     idItalics.setFont(JvSwingUtils.getLabelFont());
 782     idItalics.setHorizontalAlignment(SwingConstants.RIGHT);
 783     idItalics.setHorizontalTextPosition(SwingConstants.LEADING);
 784     idItalics.setText(MessageManager
 785             .getString("label.sequence_name_italics"));
 786     openoverv.setFont(JvSwingUtils.getLabelFont());
 787     openoverv.setActionCommand(MessageManager
 788             .getString("label.open_overview"));
 789     openoverv.setHorizontalAlignment(SwingConstants.RIGHT);
 790     openoverv.setHorizontalTextPosition(SwingConstants.LEFT);
 791     openoverv.setText(MessageManager.getString(("label.open_overview")));
 792     jPanel2.add(fullScreen);
 793     jPanel2.add(openoverv);
 794     jPanel2.add(seqLimit);
 795     jPanel2.add(rightAlign);
 796     jPanel2.add(fontLabel);
 797     jPanel2.add(showUnconserved);
 798     jPanel2.add(idItalics);
 799     jPanel2.add(smoothFont);
 800     jPanel2.add(gapLabel);
 801     jPanel2.add(wrap);
 802     jPanel2.add(sortLabel);
 803     jPanel2.add(startupCheckbox);
 804     visualTab.add(annotations);
 805     visualTab.add(startupFileTextfield);
 806     visualTab.add(sortby);
 807     visualTab.add(gapSymbolCB);
 808     visualTab.add(fontNameCB);
 809     visualTab.add(fontSizeCB);
 810     visualTab.add(fontStyleCB);
 811     annsettingsPanel.setBounds(new Rectangle(173, 34, 300, 61));
 812     annsettingsPanel.setLayout(new FlowLayout(FlowLayout.LEFT, 0, 0));
 813     annsettingsPanel.add(autoAnnotSettings1);
 814     annsettingsPanel.add(autoAnnotSettings2);
 815     annsettingsPanel.add(autoAnnotSettings3);
 816     autoAnnotSettings1.setLayout(new GridLayout(3, 1, 0, 0));
 817     autoAnnotSettings2.setLayout(new GridLayout(3, 1, 0, 0));
 818     autoAnnotSettings3.setLayout(new GridLayout(3, 1, 0, 0));
 819     visualTab.add(annsettingsPanel);
 820     Border jb = new EmptyBorder(1, 1, 4, 5);
 821     quality.setBorder(jb);
 822     conservation.setBorder(jb);
 823     identity.setBorder(jb);
 824     showConsensbits.setBorder(jb);
 825     showGroupbits.setBorder(jb);
 826     showGroupConsensus.setBorder(jb);
 827     showGroupConservation.setBorder(jb);
 828     showConsensHistogram.setBorder(jb);
 829     showConsensLogo.setBorder(jb);
 830
 831     autoAnnotSettings2.add(conservation);
 832     autoAnnotSettings1.add(quality);
 833     autoAnnotSettings3.add(identity);
 834     autoAnnotSettings1.add(showGroupbits);
 835     autoAnnotSettings3.add(showGroupConsensus);
 836     autoAnnotSettings2.add(showGroupConservation);
 837     autoAnnotSettings1.add(showConsensbits);
 838     autoAnnotSettings2.add(showConsensHistogram);
 839     autoAnnotSettings3.add(showConsensLogo);
 840
 841     JPanel tooltipSettings = new JPanel();
 842     tooltipSettings.setBorder(new TitledBorder(MessageManager
 843             .getString("label.sequence_id_tooltip")));
 844     tooltipSettings.setBounds(173, 130, 200, 62);
 845     tooltipSettings.setLayout(new GridLayout(2, 1));
 846     tooltipSettings.add(showDbRefTooltip);
 847     tooltipSettings.add(showNpTooltip);
 848     visualTab.add(tooltipSettings);
 849     visualTab.add(jPanel2);
 850     JvSwingUtils.addtoLayout(visual2Tab, MessageManager
 851             .getString("label.default_colour_scheme_for_alignment"),
 852             colourLabel, colour);
 853     JPanel annotationShding = new JPanel();
 854     annotationShding.setBorder(new TitledBorder(MessageManager
 855             .getString("label.annotation_shading_default")));
 856     annotationShding.setLayout(new GridLayout(1, 2));
 857     JvSwingUtils.addtoLayout(annotationShding, MessageManager
 858             .getString("label.default_minimum_colour_annotation_shading"),
 859             mincolourLabel, minColour);
 860     JvSwingUtils.addtoLayout(annotationShding, MessageManager
 861             .getString("label.default_maximum_colour_annotation_shading"),
 862             maxcolourLabel, maxColour);
 863     visual2Tab.add(annotationShding); // , FlowLayout.LEFT);
 864
 865     // visual2panel.add(minColour);
 866     // visual2panel.add(maxColour);
 867     // visual2Tab.add(visual2panel);
 868
 869     linkPanel.add(editLinkButtons, BorderLayout.EAST);
 870     editLinkButtons.add(newLink, null);
 871     editLinkButtons.add(editLink, null);
 872     editLinkButtons.add(deleteLink, null);
 873     linkPanel.add(linkScrollPane, BorderLayout.CENTER);
 874     linkScrollPane.getViewport().add(linkPanel2, null);
 875     linkPanel2.add(linkURLList, BorderLayout.CENTER);
 876     linkPanel2.add(linkNameList, BorderLayout.WEST);
 877     okCancelPanel.add(ok);
 878     okCancelPanel.add(cancel);
 879     this.add(tabbedPane, java.awt.BorderLayout.CENTER);
 880
 881     this.add(okCancelPanel, java.awt.BorderLayout.SOUTH);
 882     jPanel1.add(serverLabel, new GridBagConstraints(0, 1, 1, 1, 0.0, 0.0,
 883             GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
 884                     2, 4, 0), 5, 0));
 885     jPanel1.add(portLabel, new GridBagConstraints(2, 1, 1, 1, 0.0, 0.0,
 886             GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
 887                     0, 4, 0), 11, 6));
 888     connectTab.add(linkPanel, new GridBagConstraints(0, 0, 2, 1, 1.0, 1.0,
 889             GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(
 890                     16, 0, 0, 12), 359, -17));
 891     connectTab.add(jPanel1, new GridBagConstraints(0, 2, 2, 1, 1.0, 1.0,
 892             GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(
 893                     21, 0, 35, 12), 4, 6));
 894     connectTab.add(browserLabel, new GridBagConstraints(0, 1, 1, 1, 0.0,
 895             0.0, GridBagConstraints.WEST, GridBagConstraints.NONE,
 896             new Insets(16, 0, 0, 0), 5, 1));
 897     jPanel1.add(proxyPortTB, new GridBagConstraints(3, 1, 1, 1, 1.0, 0.0,
 898             GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 899             new Insets(0, 2, 4, 2), 54, 1));
 900     jPanel1.add(proxyServerTB, new GridBagConstraints(1, 1, 1, 1, 1.0, 0.0,
 901             GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 902             new Insets(0, 2, 4, 0), 263, 1));
 903     connectTab.add(defaultBrowser, new GridBagConstraints(1, 1, 1, 1, 1.0,
 904             0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 905             new Insets(15, 0, 0, 15), 307, 1));
 906     connectTab.add(usagestats, new GridBagConstraints(0, 4, 1, 1, 1.0, 0.0,
 907             GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 908             new Insets(0, 2, 4, 2), 70, 1));
 909     connectTab.add(questionnaire, new GridBagConstraints(1, 4, 1, 1, 1.0,
 910             0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 911             new Insets(0, 2, 4, 2), 70, 1));
 912     connectTab.add(versioncheck, new GridBagConstraints(0, 5, 1, 1, 1.0,
 913             0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 914             new Insets(0, 2, 4, 2), 70, 1));
 915
 916     jPanel1.add(useProxy, new GridBagConstraints(0, 0, 2, 1, 0.0, 0.0,
 917             GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
 918                     2, 5, 185), 2, -4));
 919     DefaultListCellRenderer dlcr = new DefaultListCellRenderer();
 920     dlcr.setHorizontalAlignment(DefaultListCellRenderer.CENTER);
 921     gapSymbolCB.setRenderer(dlcr);
 922
 923     tabbedPane.add(visualTab, MessageManager.getString("label.visual"));
 924     tabbedPane.add(visual2Tab, MessageManager.getString("label.colours"));
 925     tabbedPane.add(connectTab,
 926             MessageManager.getString("label.connections"));
 927     tabbedPane.add(exportTab, MessageManager.getString("label.output"));
 928     jPanel11.add(jLabel1);
 929     jPanel11.add(blcjv);
 930     jPanel11.add(clustaljv);
 931     jPanel11.add(fastajv);
 932     jPanel11.add(msfjv);
 933     jPanel11.add(pfamjv);
 934     jPanel11.add(pileupjv);
 935     jPanel11.add(pirjv);
 936     exportTab.add(autoIdWidth);
 937     exportTab.add(userIdWidth);
 938     exportTab.add(userIdWidthlabel);
 939     exportTab.add(modellerOutput);
 940     tabbedPane.add(calcTab, MessageManager.getString("label.editing"));
 941     calcTab.add(autoCalculateConsCheck);
 942     calcTab.add(padGaps);
 943     calcTab.add(sortByTree);
 944
 945     tabbedPane
 946             .add(dasPanel, MessageManager.getString("label.das_settings"));
 947     tabbedPane.add(wsPanel, MessageManager.getString("label.web_services"));
 948
 949     exportTab.add(epsLabel);
 950     exportTab.add(epsRendering);
 951     exportTab.add(jPanel11);
 952   }
 953
 954   protected void autoIdWidth_actionPerformed()
 955   {
 956     // TODO Auto-generated method stub
 957
 958   }
 959
 960   protected void userIdWidth_actionPerformed()
 961   {
 962     // TODO Auto-generated method stub
 963
 964   }
 965
 966   protected void maxColour_actionPerformed()
 967   {
 968     // TODO Auto-generated method stub
 969
 970   }
 971
 972   protected void minColour_actionPerformed()
 973   {
 974     // TODO Auto-generated method stub
 975
 976   }
 977
 978   protected void showunconserved_actionPerformed(ActionEvent e)
 979   {
 980     // TODO Auto-generated method stub
 981
 982   }
 983
 984   /**
 985    * DOCUMENT ME!
 986    *
 987    * @param e
 988    *          DOCUMENT ME!
 989    */
 990   public void ok_actionPerformed(ActionEvent e)
 991   {
 992   }
 993
 994   /**
 995    * DOCUMENT ME!
 996    *
 997    * @param e
 998    *          DOCUMENT ME!
 999    */
1000   public void cancel_actionPerformed(ActionEvent e)
1001   {
1002   }
1003
1004   /**
1005    * DOCUMENT ME!
1006    *
1007    * @param e
1008    *          DOCUMENT ME!
1009    */
1010   public void annotations_actionPerformed(ActionEvent e)
1011   {
1012   }
1013
1014   /**
1015    * DOCUMENT ME!
1016    */
1017   public void startupFileTextfield_mouseClicked()
1018   {
1019   }
1020
1021   public void newLink_actionPerformed(ActionEvent e)
1022   {
1023
1024   }
1025
1026   public void editLink_actionPerformed(ActionEvent e)
1027   {
1028
1029   }
1030
1031   public void deleteLink_actionPerformed(ActionEvent e)
1032   {
1033
1034   }
1035
1036   public void defaultBrowser_mouseClicked(MouseEvent e)
1037   {
1038
1039   }
1040
1041   public void linkURLList_keyTyped(KeyEvent e)
1042   {
1043
1044   }
1045
1046   public void useProxy_actionPerformed()
1047   {
1048     proxyServerTB.setEnabled(useProxy.isSelected());
1049     proxyPortTB.setEnabled(useProxy.isSelected());
1050   }
1051
1052 }