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.*;
  27 import java.awt.event.*;
  28
  29 import javax.swing.*;
  30 import javax.swing.border.*;
  31 import javax.swing.event.*;
  32 import java.awt.Rectangle;
  33
  34 /**
  35  * DOCUMENT ME!
  36  *
  37  * @author $author$
  38  * @version $Revision$
  39  */
  40 public class GPreferences extends JPanel
  41 {
  42   JTabbedPane tabbedPane = new JTabbedPane();
  43
  44   JButton ok = new JButton();
  45
  46   JButton cancel = new JButton();
  47
  48   JPanel okCancelPanel = new JPanel();
  49
  50   BorderLayout borderLayout1 = new BorderLayout();
  51
  52   protected JCheckBox quality = new JCheckBox();
  53
  54   JPanel visualTab = new JPanel();
  55
  56   JPanel visual2Tab = new JPanel();
  57
  58   protected JCheckBox fullScreen = new JCheckBox();
  59
  60   protected JCheckBox conservation = new JCheckBox();
  61
  62   protected JCheckBox identity = new JCheckBox();
  63
  64   protected JCheckBox annotations = new JCheckBox();
  65
  66   protected JPanel minColour = new JPanel();
  67
  68   JLabel mincolourLabel = new JLabel();
  69
  70   protected JPanel maxColour = new JPanel();
  71
  72   JLabel maxcolourLabel = new JLabel();
  73
  74   JLabel gapLabel = new JLabel();
  75
  76   protected JComboBox colour = new JComboBox();
  77
  78   JLabel colourLabel = new JLabel();
  79
  80   JLabel fontLabel = new JLabel();
  81
  82   protected JComboBox fontSizeCB = new JComboBox();
  83
  84   protected JComboBox fontStyleCB = new JComboBox();
  85
  86   protected JComboBox fontNameCB = new JComboBox();
  87
  88   protected JComboBox gapSymbolCB = new JComboBox();
  89
  90   protected JCheckBox startupCheckbox = new JCheckBox();
  91
  92   protected JTextField startupFileTextfield = new JTextField();
  93
  94   JPanel connectTab = new JPanel();
  95
  96   JLabel serverLabel = new JLabel();
  97
  98   protected JList linkURLList = new JList();
  99
 100   protected JTextField proxyServerTB = new JTextField();
 101
 102   protected JTextField proxyPortTB = new JTextField();
 103
 104   JLabel portLabel = new JLabel();
 105
 106   JLabel browserLabel = new JLabel();
 107
 108   protected JTextField defaultBrowser = new JTextField();
 109
 110   JButton newLink = new JButton();
 111
 112   JButton editLink = new JButton();
 113
 114   JButton deleteLink = new JButton();
 115
 116   JScrollPane linkScrollPane = new JScrollPane();
 117
 118   JPanel linkPanel = new JPanel();
 119
 120   BorderLayout borderLayout2 = new BorderLayout();
 121
 122   JPanel editLinkButtons = new JPanel();
 123
 124   GridLayout gridLayout1 = new GridLayout();
 125
 126   protected JList linkNameList = new JList();
 127
 128   JPanel linkPanel2 = new JPanel();
 129
 130   BorderLayout borderLayout3 = new BorderLayout();
 131
 132   protected JCheckBox useProxy = new JCheckBox();
 133
 134   JPanel jPanel1 = new JPanel();
 135
 136   TitledBorder titledBorder1 = new TitledBorder(
 137           MessageManager.getString("label.proxy_server"));
 138
 139   TitledBorder titledBorder2 = new TitledBorder(
 140           MessageManager.getString("label.file_output"));
 141
 142   GridBagLayout gridBagLayout2 = new GridBagLayout();
 143
 144   GridBagLayout gridBagLayout1 = new GridBagLayout();
 145
 146   GridBagLayout gridBagLayout3 = new GridBagLayout();
 147
 148   protected JComboBox sortby = new JComboBox();
 149
 150   JLabel sortLabel = new JLabel();
 151
 152   JPanel jPanel2 = new JPanel();
 153
 154   JPanel visual2panel = new JPanel();
 155
 156   GridLayout gridLayout2 = new GridLayout();
 157
 158   GridLayout gridLayout4 = new GridLayout();
 159
 160   JPanel annsettingsPanel = new JPanel();
 161
 162   JPanel autoAnnotSettings1 = new JPanel();
 163
 164   JPanel autoAnnotSettings2 = new JPanel();
 165
 166   JPanel autoAnnotSettings3 = new JPanel();
 167
 168   JPanel exportTab = new JPanel();
 169
 170   JLabel epsLabel = new JLabel();
 171
 172   protected JComboBox epsRendering = new JComboBox();
 173
 174   protected JLabel userIdWidthlabel = new JLabel();
 175
 176   protected JCheckBox autoIdWidth = new JCheckBox();
 177
 178   protected JTextField userIdWidth = new JTextField();
 179
 180   JLabel jLabel1 = new JLabel();
 181
 182   protected JCheckBox blcjv = new JCheckBox();
 183
 184   protected JCheckBox pileupjv = new JCheckBox();
 185
 186   protected JCheckBox clustaljv = new JCheckBox();
 187
 188   protected JCheckBox msfjv = new JCheckBox();
 189
 190   protected JCheckBox fastajv = new JCheckBox();
 191
 192   protected JCheckBox pfamjv = new JCheckBox();
 193
 194   FlowLayout flowLayout1 = new FlowLayout();
 195
 196   protected JCheckBox pirjv = new JCheckBox();
 197
 198   JPanel jPanel11 = new JPanel();
 199
 200   Font verdana11 = JvSwingUtils.getLabelFont();
 201
 202   protected JCheckBox seqLimit = new JCheckBox();
 203
 204   GridLayout gridLayout3 = new GridLayout();
 205
 206   protected JCheckBox smoothFont = new JCheckBox();
 207
 208   JPanel calcTab = new JPanel();
 209
 210   protected JCheckBox autoCalculateConsCheck = new JCheckBox();
 211
 212   protected JCheckBox padGaps = new JCheckBox();
 213
 214   protected JCheckBox modellerOutput = new JCheckBox();
 215
 216   protected JPanel dasPanel = new JPanel();
 217
 218   BorderLayout borderLayout4 = new BorderLayout();
 219
 220   protected JPanel wsPanel = new JPanel();
 221
 222   BorderLayout borderLayout5 = new BorderLayout();
 223
 224   protected JCheckBox wrap = new JCheckBox();
 225
 226   protected JCheckBox rightAlign = new JCheckBox();
 227
 228   protected JCheckBox showUnconserved = new JCheckBox();
 229
 230   protected JCheckBox showDbRefTooltip = new JCheckBox();
 231
 232   protected JCheckBox showNpTooltip = new JCheckBox();
 233
 234   protected JCheckBox idItalics = new JCheckBox();
 235
 236   protected JCheckBox openoverv = new JCheckBox();
 237
 238   protected JCheckBox usagestats = new JCheckBox();
 239
 240   protected JCheckBox questionnaire = new JCheckBox();
 241
 242   protected JCheckBox versioncheck = new JCheckBox();
 243
 244   protected JLabel showGroupbits = new JLabel();
 245
 246   protected JLabel showConsensbits = new JLabel();
 247
 248   protected JCheckBox showConsensLogo = new JCheckBox();
 249
 250   protected JCheckBox showConsensHistogram = new JCheckBox();
 251
 252   protected JCheckBox showGroupConsensus = new JCheckBox();
 253
 254   protected JCheckBox showGroupConservation = new JCheckBox();
 255
 256   protected JCheckBox shareSelections = new JCheckBox();
 257
 258   protected JCheckBox followHighlight = new JCheckBox();
 259
 260   protected JCheckBox sortByTree = new JCheckBox();
 261
 262   /**
 263    * Creates a new GPreferences object.
 264    */
 265   public GPreferences()
 266   {
 267     try
 268     {
 269       jbInit();
 270     } catch (Exception ex)
 271     {
 272       ex.printStackTrace();
 273     }
 274   }
 275
 276   /**
 277    * DOCUMENT ME!
 278    *
 279    * @throws Exception
 280    *           DOCUMENT ME!
 281    */
 282   private void jbInit() throws Exception
 283   {
 284     this.setLayout(borderLayout1);
 285     ok.setText(MessageManager.getString("action.ok"));
 286     ok.addActionListener(new ActionListener()
 287     {
 288       public void actionPerformed(ActionEvent e)
 289       {
 290         ok_actionPerformed(e);
 291       }
 292     });
 293     cancel.setText(MessageManager.getString("action.cancel"));
 294     cancel.addActionListener(new ActionListener()
 295     {
 296       public void actionPerformed(ActionEvent e)
 297       {
 298         cancel_actionPerformed(e);
 299       }
 300     });
 301     quality.setEnabled(false);
 302     quality.setFont(verdana11);
 303     quality.setHorizontalAlignment(SwingConstants.RIGHT);
 304     quality.setHorizontalTextPosition(SwingConstants.LEFT);
 305     quality.setSelected(true);
 306     quality.setText(MessageManager.getString("label.quality"));
 307     visualTab.setBorder(new TitledBorder(MessageManager
 308             .getString("action.open_new_aligmnent")));
 309     visualTab.setLayout(null);
 310     visual2Tab.setBorder(new TitledBorder(MessageManager
 311             .getString("action.open_new_aligmnent")));
 312     visual2Tab.setLayout(new FlowLayout());
 313     fullScreen.setFont(verdana11);
 314     fullScreen.setHorizontalAlignment(SwingConstants.RIGHT);
 315     fullScreen.setHorizontalTextPosition(SwingConstants.LEFT);
 316     fullScreen.setText(MessageManager.getString("label.maximize_window"));
 317     conservation.setEnabled(false);
 318     conservation.setFont(verdana11);
 319     conservation.setHorizontalAlignment(SwingConstants.RIGHT);
 320     conservation.setHorizontalTextPosition(SwingConstants.LEFT);
 321     conservation.setSelected(true);
 322     conservation.setText(MessageManager.getString("label.conservation"));
 323     identity.setEnabled(false);
 324     identity.setFont(verdana11);
 325     identity.setHorizontalAlignment(SwingConstants.RIGHT);
 326     identity.setHorizontalTextPosition(SwingConstants.LEFT);
 327     identity.setSelected(true);
 328     identity.setText(MessageManager.getString("label.consensus"));
 329     showGroupbits.setFont(verdana11);
 330     showGroupbits.setHorizontalAlignment(SwingConstants.RIGHT);
 331     showGroupbits.setHorizontalTextPosition(SwingConstants.LEFT);
 332     showGroupbits.setText(MessageManager.getString("action.show_group")
 333             + ":");
 334     showConsensbits.setFont(verdana11);
 335     showConsensbits.setHorizontalAlignment(SwingConstants.RIGHT);
 336     showConsensbits.setHorizontalTextPosition(SwingConstants.LEFT);
 337     showConsensbits.setText(MessageManager.getString("label.consensus")
 338             + ":");
 339     showConsensHistogram.setEnabled(false);
 340     showConsensHistogram.setFont(verdana11);
 341     showConsensHistogram.setHorizontalAlignment(SwingConstants.RIGHT);
 342     showConsensHistogram.setHorizontalTextPosition(SwingConstants.LEFT);
 343     showConsensHistogram.setSelected(true);
 344     showConsensHistogram.setText(MessageManager
 345             .getString("label.histogram"));
 346     showConsensLogo.setEnabled(false);
 347     showConsensLogo.setFont(verdana11);
 348     showConsensLogo.setHorizontalAlignment(SwingConstants.RIGHT);
 349     showConsensLogo.setHorizontalTextPosition(SwingConstants.LEFT);
 350     showConsensLogo.setSelected(true);
 351     showConsensLogo.setText(MessageManager.getString("label.logo"));
 352     showGroupConsensus.setEnabled(false);
 353     showGroupConsensus.setFont(verdana11);
 354     showGroupConsensus.setHorizontalAlignment(SwingConstants.RIGHT);
 355     showGroupConsensus.setHorizontalTextPosition(SwingConstants.LEFT);
 356     showGroupConsensus.setSelected(true);
 357     showGroupConsensus.setText(MessageManager.getString("label.consensus"));
 358     showGroupConservation.setEnabled(false);
 359     showGroupConservation.setFont(verdana11);
 360     showGroupConservation.setHorizontalAlignment(SwingConstants.RIGHT);
 361     showGroupConservation.setHorizontalTextPosition(SwingConstants.LEFT);
 362     showGroupConservation.setSelected(true);
 363     showGroupConservation.setText(MessageManager
 364             .getString("label.conservation"));
 365     showNpTooltip.setEnabled(true);
 366     showNpTooltip.setFont(verdana11);
 367     showNpTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
 368     showNpTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
 369     showNpTooltip.setSelected(true);
 370     showNpTooltip.setText(MessageManager
 371             .getString("label.non_positional_features"));
 372     showDbRefTooltip.setEnabled(true);
 373     showDbRefTooltip.setFont(verdana11);
 374     showDbRefTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
 375     showDbRefTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
 376     showDbRefTooltip.setSelected(true);
 377     showDbRefTooltip.setText(MessageManager
 378             .getString("label.database_references"));
 379     annotations.setFont(verdana11);
 380     annotations.setHorizontalAlignment(SwingConstants.RIGHT);
 381     annotations.setHorizontalTextPosition(SwingConstants.LEADING);
 382     annotations.setSelected(true);
 383     annotations.setText(MessageManager.getString("label.show_annotations"));
 384     annotations.setBounds(new Rectangle(169, 12, 200, 23));
 385     annotations.addActionListener(new ActionListener()
 386     {
 387       public void actionPerformed(ActionEvent e)
 388       {
 389         annotations_actionPerformed(e);
 390       }
 391     });
 392     identity.addActionListener(new ActionListener()
 393     {
 394       public void actionPerformed(ActionEvent e)
 395       {
 396         annotations_actionPerformed(e);
 397       }
 398     });
 399     showGroupConsensus.addActionListener(new ActionListener()
 400     {
 401       public void actionPerformed(ActionEvent e)
 402       {
 403         annotations_actionPerformed(e);
 404       }
 405     });
 406     showUnconserved.setFont(verdana11);
 407     showUnconserved.setHorizontalAlignment(SwingConstants.RIGHT);
 408     showUnconserved.setHorizontalTextPosition(SwingConstants.LEFT);
 409     showUnconserved.setSelected(true);
 410     showUnconserved.setText(MessageManager
 411             .getString("action.show_unconserved"));
 412     showUnconserved.addActionListener(new ActionListener()
 413     {
 414       public void actionPerformed(ActionEvent e)
 415       {
 416         showunconserved_actionPerformed(e);
 417       }
 418     });
 419     // / TODO: fit these in to preferences panel!!!!!
 420     shareSelections.setFont(verdana11);
 421     shareSelections.setHorizontalAlignment(SwingConstants.RIGHT);
 422     shareSelections.setHorizontalTextPosition(SwingConstants.LEFT);
 423     shareSelections.setSelected(true);
 424     shareSelections.setText(MessageManager
 425             .getString("label.share_selection_across_views"));
 426     followHighlight.setFont(verdana11);
 427     followHighlight.setHorizontalAlignment(SwingConstants.RIGHT);
 428     followHighlight.setHorizontalTextPosition(SwingConstants.LEFT);
 429     // showUnconserved.setBounds(new Rectangle(169, 40, 200, 23));
 430     followHighlight.setSelected(true);
 431     followHighlight.setText(MessageManager
 432             .getString("label.scroll_highlighted_regions"));
 433
 434     gapLabel.setFont(verdana11);
 435     gapLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 436     gapLabel.setText(MessageManager.getString("label.gap_symbol") + " ");
 437     colour.setFont(verdana11);
 438     colour.setBounds(new Rectangle(172, 225, 155, 21));
 439     colourLabel.setFont(verdana11);
 440     colourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 441     colourLabel.setText(MessageManager.getString("label.alignment_colour")
 442             + " ");
 443     fontLabel.setFont(verdana11);
 444     fontLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 445     fontLabel.setText(MessageManager.getString("label.font"));
 446     fontSizeCB.setFont(verdana11);
 447     fontSizeCB.setBounds(new Rectangle(319, 104, 49, 23));
 448     fontStyleCB.setFont(verdana11);
 449     fontStyleCB.setBounds(new Rectangle(367, 104, 70, 23));
 450     fontNameCB.setFont(verdana11);
 451     fontNameCB.setBounds(new Rectangle(172, 104, 147, 23));
 452     gapSymbolCB.setFont(verdana11);
 453     gapSymbolCB.setBounds(new Rectangle(172, 204, 69, 23));
 454     mincolourLabel.setFont(verdana11);
 455     mincolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 456     mincolourLabel.setText(MessageManager.getString("label.min_colour"));
 457     minColour.setFont(verdana11);
 458     minColour.setBorder(BorderFactory.createEtchedBorder());
 459     minColour.setPreferredSize(new Dimension(40, 20));
 460     minColour.addMouseListener(new MouseAdapter()
 461     {
 462       public void mousePressed(MouseEvent e)
 463       {
 464         minColour_actionPerformed();
 465       }
 466     });
 467     maxcolourLabel.setFont(verdana11);
 468     maxcolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 469     maxcolourLabel.setText(MessageManager.getString("label.max_colour"));
 470     maxColour.setFont(verdana11);
 471     maxColour.setBorder(BorderFactory.createEtchedBorder());
 472     maxColour.setPreferredSize(new Dimension(40, 20));
 473     maxColour.addMouseListener(new MouseAdapter()
 474     {
 475       public void mousePressed(MouseEvent e)
 476       {
 477         maxColour_actionPerformed();
 478       }
 479     });
 480
 481     startupCheckbox.setText(MessageManager.getString("action.open_file"));
 482     startupCheckbox.setFont(verdana11);
 483     startupCheckbox.setHorizontalAlignment(SwingConstants.RIGHT);
 484     startupCheckbox.setHorizontalTextPosition(SwingConstants.LEFT);
 485     startupCheckbox.setSelected(true);
 486     startupFileTextfield.setFont(verdana11);
 487     startupFileTextfield.setBounds(new Rectangle(172, 273, 270, 20));
 488     startupFileTextfield.addMouseListener(new MouseAdapter()
 489     {
 490       public void mouseClicked(MouseEvent e)
 491       {
 492         if (e.getClickCount() > 1)
 493         {
 494           startupFileTextfield_mouseClicked();
 495         }
 496       }
 497     });
 498
 499     connectTab.setLayout(gridBagLayout3);
 500     serverLabel.setText(MessageManager.getString("label.address"));
 501     serverLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 502     serverLabel.setFont(verdana11);
 503     proxyServerTB.setFont(verdana11);
 504     proxyPortTB.setFont(verdana11);
 505     portLabel.setFont(verdana11);
 506     portLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 507     portLabel.setText(MessageManager.getString("label.port"));
 508     browserLabel.setFont(new java.awt.Font("SansSerif", 0, 11));
 509     browserLabel.setHorizontalAlignment(SwingConstants.TRAILING);
 510     browserLabel.setText(MessageManager
 511             .getString("label.default_browser_unix"));
 512     defaultBrowser.setFont(verdana11);
 513     defaultBrowser.setText("");
 514     usagestats.setText(MessageManager
 515             .getString("label.send_usage_statistics"));
 516     usagestats.setFont(verdana11);
 517     usagestats.setHorizontalAlignment(SwingConstants.RIGHT);
 518     usagestats.setHorizontalTextPosition(SwingConstants.LEADING);
 519     questionnaire.setText(MessageManager
 520             .getString("label.check_for_questionnaires"));
 521     questionnaire.setFont(verdana11);
 522     questionnaire.setHorizontalAlignment(SwingConstants.RIGHT);
 523     questionnaire.setHorizontalTextPosition(SwingConstants.LEADING);
 524     versioncheck.setText(MessageManager
 525             .getString("label.check_for_latest_version"));
 526     versioncheck.setFont(verdana11);
 527     versioncheck.setHorizontalAlignment(SwingConstants.RIGHT);
 528     versioncheck.setHorizontalTextPosition(SwingConstants.LEADING);
 529     newLink.setText(MessageManager.getString("action.new"));
 530     newLink.addActionListener(new java.awt.event.ActionListener()
 531     {
 532       public void actionPerformed(ActionEvent e)
 533       {
 534         newLink_actionPerformed(e);
 535       }
 536     });
 537     editLink.setText(MessageManager.getString("action.edit"));
 538     editLink.addActionListener(new java.awt.event.ActionListener()
 539     {
 540       public void actionPerformed(ActionEvent e)
 541       {
 542         editLink_actionPerformed(e);
 543       }
 544     });
 545     deleteLink.setText(MessageManager.getString("action.delete"));
 546     deleteLink.addActionListener(new java.awt.event.ActionListener()
 547     {
 548       public void actionPerformed(ActionEvent e)
 549       {
 550         deleteLink_actionPerformed(e);
 551       }
 552     });
 553
 554     linkURLList.addListSelectionListener(new ListSelectionListener()
 555     {
 556       public void valueChanged(ListSelectionEvent e)
 557       {
 558         int index = linkURLList.getSelectedIndex();
 559         linkNameList.setSelectedIndex(index);
 560       }
 561     });
 562
 563     linkNameList.addListSelectionListener(new ListSelectionListener()
 564     {
 565       public void valueChanged(ListSelectionEvent e)
 566       {
 567         int index = linkNameList.getSelectedIndex();
 568         linkURLList.setSelectedIndex(index);
 569       }
 570     });
 571
 572     linkScrollPane.setBorder(null);
 573     linkPanel.setBorder(new TitledBorder(MessageManager
 574             .getString("label.url_linkfrom_sequence_id")));
 575     linkPanel.setLayout(borderLayout2);
 576     editLinkButtons.setLayout(gridLayout1);
 577     gridLayout1.setRows(3);
 578     linkNameList.setFont(verdana11);
 579     linkNameList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
 580     linkPanel2.setLayout(borderLayout3);
 581     linkURLList.setFont(verdana11);
 582     linkURLList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
 583
 584     defaultBrowser.addMouseListener(new MouseAdapter()
 585     {
 586       public void mouseClicked(MouseEvent e)
 587       {
 588         if (e.getClickCount() > 1)
 589         {
 590           defaultBrowser_mouseClicked(e);
 591         }
 592       }
 593     });
 594     useProxy.setFont(verdana11);
 595     useProxy.setHorizontalAlignment(SwingConstants.RIGHT);
 596     useProxy.setHorizontalTextPosition(SwingConstants.LEADING);
 597     useProxy.setText(MessageManager.getString("label.use_proxy_server"));
 598     useProxy.addActionListener(new ActionListener()
 599     {
 600       public void actionPerformed(ActionEvent e)
 601       {
 602         useProxy_actionPerformed();
 603       }
 604     });
 605     jPanel1.setBorder(titledBorder1);
 606     jPanel1.setLayout(gridBagLayout1);
 607     sortby.setFont(verdana11);
 608     sortby.setBounds(new Rectangle(172, 249, 155, 21));
 609     sortLabel.setFont(verdana11);
 610     sortLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 611     sortLabel.setText(MessageManager.getString("label.sort_by"));
 612     jPanel2.setBounds(new Rectangle(7, 17, 158, 278));
 613     jPanel2.setLayout(gridLayout2);
 614     gridLayout2.setRows(12);
 615     exportTab.setLayout(null);
 616     epsLabel.setFont(verdana11);
 617     epsLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 618     epsLabel.setText(MessageManager.getString("label.eps_rendering_style"));
 619     epsLabel.setBounds(new Rectangle(9, 31, 140, 24));
 620     epsRendering.setFont(verdana11);
 621     epsRendering.setBounds(new Rectangle(154, 34, 187, 21));
 622     jLabel1.setFont(verdana11);
 623     jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
 624     jLabel1.setText(MessageManager.getString("label.append_start_end"));
 625     jLabel1.setFont(verdana11);
 626     fastajv.setFont(verdana11);
 627     fastajv.setHorizontalAlignment(SwingConstants.LEFT);
 628     clustaljv.setText(MessageManager.getString("label.clustal") + "     ");
 629     blcjv.setText(MessageManager.getString("label.blc") + "     ");
 630     fastajv.setText(MessageManager.getString("label.fasta") + "     ");
 631     msfjv.setText(MessageManager.getString("label.msf") + "     ");
 632     pfamjv.setText(MessageManager.getString("label.pfam") + "     ");
 633     pileupjv.setText(MessageManager.getString("label.pileup") + "     ");
 634     msfjv.setFont(verdana11);
 635     msfjv.setHorizontalAlignment(SwingConstants.LEFT);
 636     pirjv.setText(MessageManager.getString("label.pir") + "     ");
 637     jPanel11.setFont(verdana11);
 638     jPanel11.setBorder(titledBorder2);
 639     jPanel11.setBounds(new Rectangle(30, 72, 196, 182));
 640     jPanel11.setLayout(gridLayout3);
 641     blcjv.setFont(verdana11);
 642     blcjv.setHorizontalAlignment(SwingConstants.LEFT);
 643     clustaljv.setFont(verdana11);
 644     clustaljv.setHorizontalAlignment(SwingConstants.LEFT);
 645     pfamjv.setFont(verdana11);
 646     pfamjv.setHorizontalAlignment(SwingConstants.LEFT);
 647     pileupjv.setFont(verdana11);
 648     pileupjv.setHorizontalAlignment(SwingConstants.LEFT);
 649     pirjv.setFont(verdana11);
 650     pirjv.setHorizontalAlignment(SwingConstants.LEFT);
 651     seqLimit.setFont(verdana11);
 652     seqLimit.setHorizontalAlignment(SwingConstants.RIGHT);
 653     seqLimit.setHorizontalTextPosition(SwingConstants.LEFT);
 654     seqLimit.setText(MessageManager.getString("label.full_sequence_id"));
 655     gridLayout3.setRows(8);
 656     smoothFont.setFont(verdana11);
 657     smoothFont.setHorizontalAlignment(SwingConstants.RIGHT);
 658     smoothFont.setHorizontalTextPosition(SwingConstants.LEADING);
 659     smoothFont.setText(MessageManager.getString("label.smooth_font"));
 660     calcTab.setLayout(null);
 661     autoCalculateConsCheck.setFont(JvSwingUtils.getLabelFont());
 662     autoCalculateConsCheck.setText(MessageManager
 663             .getString("label.autocalculate_consensus"));
 664     autoCalculateConsCheck.setBounds(new Rectangle(21, 52, 209, 23));
 665     padGaps.setFont(JvSwingUtils.getLabelFont());
 666     padGaps.setText(MessageManager.getString("label.pad_gaps_when_editing"));
 667     padGaps.setBounds(new Rectangle(22, 94, 168, 23));
 668     sortByTree.setFont(JvSwingUtils.getLabelFont());
 669     sortByTree
 670             .setText(MessageManager.getString("label.sort_with_new_tree"));
 671     sortByTree
 672             .setToolTipText(MessageManager
 673                     .getString("label.any_trees_calculated_or_loaded_alignment_automatically_sort"));
 674     sortByTree.setBounds(new Rectangle(22, 136, 168, 23));
 675
 676     autoIdWidth.setFont(JvSwingUtils.getLabelFont());
 677     autoIdWidth.setText(MessageManager
 678             .getString("label.automatically_set_id_width"));
 679     autoIdWidth
 680             .setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.getString("label.adjusts_width_generated_eps_png")));
 681     autoIdWidth.setBounds(new Rectangle(228, 96, 188, 23));
 682     autoIdWidth.addActionListener(new ActionListener()
 683     {
 684
 685       @Override
 686       public void actionPerformed(ActionEvent e)
 687       {
 688         autoIdWidth_actionPerformed();
 689       }
 690     });
 691     userIdWidthlabel.setFont(JvSwingUtils.getLabelFont());
 692     userIdWidthlabel.setText(MessageManager
 693             .getString("label.figure_id_column_width"));
 694     userIdWidth
 695             .setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.getString("label.manually_specify_width_left_column")));
 696     userIdWidthlabel
 697             .setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.getString("label.manually_specify_width_left_column")));
 698     userIdWidthlabel.setBounds(new Rectangle(236, 120, 168, 23));
 699     userIdWidth.setFont(JvSwingUtils.getTextAreaFont());
 700     userIdWidth.setText("");
 701     userIdWidth.setBounds(new Rectangle(232, 144, 84, 23));
 702     userIdWidth.addActionListener(new ActionListener()
 703     {
 704
 705       @Override
 706       public void actionPerformed(ActionEvent e)
 707       {
 708         userIdWidth_actionPerformed();
 709       }
 710     });
 711     modellerOutput.setFont(JvSwingUtils.getLabelFont());
 712     modellerOutput.setText(MessageManager
 713             .getString("label.use_modeller_output"));
 714     modellerOutput.setBounds(new Rectangle(228, 226, 168, 23));
 715
 716     dasPanel.setLayout(borderLayout4);
 717     wsPanel.setLayout(borderLayout5);
 718     wrap.setFont(JvSwingUtils.getLabelFont());
 719     wrap.setHorizontalAlignment(SwingConstants.TRAILING);
 720     wrap.setHorizontalTextPosition(SwingConstants.LEADING);
 721     wrap.setText(MessageManager.getString("label.wrap_alignment"));
 722     rightAlign.setFont(JvSwingUtils.getLabelFont());
 723     rightAlign.setForeground(Color.black);
 724     rightAlign.setHorizontalAlignment(SwingConstants.RIGHT);
 725     rightAlign.setHorizontalTextPosition(SwingConstants.LEFT);
 726     rightAlign.setText(MessageManager.getString("label.right_align_ids"));
 727     idItalics.setFont(JvSwingUtils.getLabelFont());
 728     idItalics.setHorizontalAlignment(SwingConstants.RIGHT);
 729     idItalics.setHorizontalTextPosition(SwingConstants.LEADING);
 730     idItalics.setText(MessageManager
 731             .getString("label.sequence_name_italics"));
 732     openoverv.setFont(JvSwingUtils.getLabelFont());
 733     openoverv.setActionCommand(MessageManager
 734             .getString("label.open_overview"));
 735     openoverv.setHorizontalAlignment(SwingConstants.RIGHT);
 736     openoverv.setHorizontalTextPosition(SwingConstants.LEFT);
 737     openoverv.setText(MessageManager.getString(("label.open_overview")));
 738     jPanel2.add(fullScreen);
 739     jPanel2.add(openoverv);
 740     jPanel2.add(seqLimit);
 741     jPanel2.add(rightAlign);
 742     jPanel2.add(fontLabel);
 743     jPanel2.add(showUnconserved);
 744     jPanel2.add(idItalics);
 745     jPanel2.add(smoothFont);
 746     jPanel2.add(gapLabel);
 747     jPanel2.add(wrap);
 748     jPanel2.add(sortLabel);
 749     jPanel2.add(startupCheckbox);
 750     visualTab.add(annotations);
 751     visualTab.add(startupFileTextfield);
 752     visualTab.add(sortby);
 753     visualTab.add(gapSymbolCB);
 754     visualTab.add(fontNameCB);
 755     visualTab.add(fontSizeCB);
 756     visualTab.add(fontStyleCB);
 757     annsettingsPanel.setBounds(new Rectangle(173, 34, 300, 61));
 758     annsettingsPanel.setLayout(new FlowLayout(FlowLayout.LEFT, 0, 0));
 759     annsettingsPanel.add(autoAnnotSettings1);
 760     annsettingsPanel.add(autoAnnotSettings2);
 761     annsettingsPanel.add(autoAnnotSettings3);
 762     autoAnnotSettings1.setLayout(new GridLayout(3, 1, 0, 0));
 763     autoAnnotSettings2.setLayout(new GridLayout(3, 1, 0, 0));
 764     autoAnnotSettings3.setLayout(new GridLayout(3, 1, 0, 0));
 765     visualTab.add(annsettingsPanel);
 766     Border jb = new EmptyBorder(1, 1, 4, 5);
 767     quality.setBorder(jb);
 768     conservation.setBorder(jb);
 769     identity.setBorder(jb);
 770     showConsensbits.setBorder(jb);
 771     showGroupbits.setBorder(jb);
 772     showGroupConsensus.setBorder(jb);
 773     showGroupConservation.setBorder(jb);
 774     showConsensHistogram.setBorder(jb);
 775     showConsensLogo.setBorder(jb);
 776
 777     autoAnnotSettings2.add(conservation);
 778     autoAnnotSettings1.add(quality);
 779     autoAnnotSettings3.add(identity);
 780     autoAnnotSettings1.add(showGroupbits);
 781     autoAnnotSettings3.add(showGroupConsensus);
 782     autoAnnotSettings2.add(showGroupConservation);
 783     autoAnnotSettings1.add(showConsensbits);
 784     autoAnnotSettings2.add(showConsensHistogram);
 785     autoAnnotSettings3.add(showConsensLogo);
 786
 787     JPanel tooltipSettings = new JPanel();
 788     tooltipSettings.setBorder(new TitledBorder(MessageManager
 789             .getString("label.sequence_id_tooltip")));
 790     tooltipSettings.setBounds(173, 130, 200, 62);
 791     tooltipSettings.setLayout(new GridLayout(2, 1));
 792     tooltipSettings.add(showDbRefTooltip);
 793     tooltipSettings.add(showNpTooltip);
 794     visualTab.add(tooltipSettings);
 795     visualTab.add(jPanel2);
 796     JvSwingUtils.addtoLayout(visual2Tab, MessageManager
 797             .getString("label.default_colour_scheme_for_alignment"),
 798             colourLabel, colour);
 799     JPanel annotationShding = new JPanel();
 800     annotationShding.setBorder(new TitledBorder(MessageManager
 801             .getString("label.annotation_shading_default")));
 802     annotationShding.setLayout(new GridLayout(1, 2));
 803     JvSwingUtils.addtoLayout(annotationShding, MessageManager
 804             .getString("label.default_minimum_colour_annotation_shading"),
 805             mincolourLabel, minColour);
 806     JvSwingUtils.addtoLayout(annotationShding, MessageManager
 807             .getString("label.default_maximum_colour_annotation_shading"),
 808             maxcolourLabel, maxColour);
 809     visual2Tab.add(annotationShding); // , FlowLayout.LEFT);
 810
 811     // visual2panel.add(minColour);
 812     // visual2panel.add(maxColour);
 813     // visual2Tab.add(visual2panel);
 814
 815     linkPanel.add(editLinkButtons, BorderLayout.EAST);
 816     editLinkButtons.add(newLink, null);
 817     editLinkButtons.add(editLink, null);
 818     editLinkButtons.add(deleteLink, null);
 819     linkPanel.add(linkScrollPane, BorderLayout.CENTER);
 820     linkScrollPane.getViewport().add(linkPanel2, null);
 821     linkPanel2.add(linkURLList, BorderLayout.CENTER);
 822     linkPanel2.add(linkNameList, BorderLayout.WEST);
 823     okCancelPanel.add(ok);
 824     okCancelPanel.add(cancel);
 825     this.add(tabbedPane, java.awt.BorderLayout.CENTER);
 826
 827     this.add(okCancelPanel, java.awt.BorderLayout.SOUTH);
 828     jPanel1.add(serverLabel, new GridBagConstraints(0, 1, 1, 1, 0.0, 0.0,
 829             GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
 830                     2, 4, 0), 5, 0));
 831     jPanel1.add(portLabel, new GridBagConstraints(2, 1, 1, 1, 0.0, 0.0,
 832             GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
 833                     0, 4, 0), 11, 6));
 834     connectTab.add(linkPanel, new GridBagConstraints(0, 0, 2, 1, 1.0, 1.0,
 835             GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(
 836                     16, 0, 0, 12), 359, -17));
 837     connectTab.add(jPanel1, new GridBagConstraints(0, 2, 2, 1, 1.0, 1.0,
 838             GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(
 839                     21, 0, 35, 12), 4, 6));
 840     connectTab.add(browserLabel, new GridBagConstraints(0, 1, 1, 1, 0.0,
 841             0.0, GridBagConstraints.WEST, GridBagConstraints.NONE,
 842             new Insets(16, 0, 0, 0), 5, 1));
 843     jPanel1.add(proxyPortTB, new GridBagConstraints(3, 1, 1, 1, 1.0, 0.0,
 844             GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 845             new Insets(0, 2, 4, 2), 54, 1));
 846     jPanel1.add(proxyServerTB, new GridBagConstraints(1, 1, 1, 1, 1.0, 0.0,
 847             GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 848             new Insets(0, 2, 4, 0), 263, 1));
 849     connectTab.add(defaultBrowser, new GridBagConstraints(1, 1, 1, 1, 1.0,
 850             0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 851             new Insets(15, 0, 0, 15), 307, 1));
 852     connectTab.add(usagestats, new GridBagConstraints(0, 4, 1, 1, 1.0, 0.0,
 853             GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 854             new Insets(0, 2, 4, 2), 70, 1));
 855     connectTab.add(questionnaire, new GridBagConstraints(1, 4, 1, 1, 1.0,
 856             0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 857             new Insets(0, 2, 4, 2), 70, 1));
 858     connectTab.add(versioncheck, new GridBagConstraints(0, 5, 1, 1, 1.0,
 859             0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 860             new Insets(0, 2, 4, 2), 70, 1));
 861
 862     jPanel1.add(useProxy, new GridBagConstraints(0, 0, 2, 1, 0.0, 0.0,
 863             GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
 864                     2, 5, 185), 2, -4));
 865     DefaultListCellRenderer dlcr = new DefaultListCellRenderer();
 866     dlcr.setHorizontalAlignment(DefaultListCellRenderer.CENTER);
 867     gapSymbolCB.setRenderer(dlcr);
 868
 869     tabbedPane.add(visualTab, MessageManager.getString("label.visual"));
 870     tabbedPane.add(visual2Tab, MessageManager.getString("label.colours"));
 871     tabbedPane.add(connectTab,
 872             MessageManager.getString("label.connections"));
 873     tabbedPane.add(exportTab, MessageManager.getString("label.output"));
 874     jPanel11.add(jLabel1);
 875     jPanel11.add(blcjv);
 876     jPanel11.add(clustaljv);
 877     jPanel11.add(fastajv);
 878     jPanel11.add(msfjv);
 879     jPanel11.add(pfamjv);
 880     jPanel11.add(pileupjv);
 881     jPanel11.add(pirjv);
 882     exportTab.add(autoIdWidth);
 883     exportTab.add(userIdWidth);
 884     exportTab.add(userIdWidthlabel);
 885     exportTab.add(modellerOutput);
 886     tabbedPane.add(calcTab, MessageManager.getString("label.editing"));
 887     calcTab.add(autoCalculateConsCheck);
 888     calcTab.add(padGaps);
 889     calcTab.add(sortByTree);
 890
 891     tabbedPane
 892             .add(dasPanel, MessageManager.getString("label.das_settings"));
 893     tabbedPane.add(wsPanel, MessageManager.getString("label.web_services"));
 894
 895     exportTab.add(epsLabel);
 896     exportTab.add(epsRendering);
 897     exportTab.add(jPanel11);
 898   }
 899
 900   protected void autoIdWidth_actionPerformed()
 901   {
 902     // TODO Auto-generated method stub
 903
 904   }
 905
 906   protected void userIdWidth_actionPerformed()
 907   {
 908     // TODO Auto-generated method stub
 909
 910   }
 911
 912   protected void maxColour_actionPerformed()
 913   {
 914     // TODO Auto-generated method stub
 915
 916   }
 917
 918   protected void minColour_actionPerformed()
 919   {
 920     // TODO Auto-generated method stub
 921
 922   }
 923
 924   protected void showunconserved_actionPerformed(ActionEvent e)
 925   {
 926     // TODO Auto-generated method stub
 927
 928   }
 929
 930   /**
 931    * DOCUMENT ME!
 932    *
 933    * @param e
 934    *          DOCUMENT ME!
 935    */
 936   public void ok_actionPerformed(ActionEvent e)
 937   {
 938   }
 939
 940   /**
 941    * DOCUMENT ME!
 942    *
 943    * @param e
 944    *          DOCUMENT ME!
 945    */
 946   public void cancel_actionPerformed(ActionEvent e)
 947   {
 948   }
 949
 950   /**
 951    * DOCUMENT ME!
 952    *
 953    * @param e
 954    *          DOCUMENT ME!
 955    */
 956   public void annotations_actionPerformed(ActionEvent e)
 957   {
 958   }
 959
 960   /**
 961    * DOCUMENT ME!
 962    */
 963   public void startupFileTextfield_mouseClicked()
 964   {
 965   }
 966
 967   public void newLink_actionPerformed(ActionEvent e)
 968   {
 969
 970   }
 971
 972   public void editLink_actionPerformed(ActionEvent e)
 973   {
 974
 975   }
 976
 977   public void deleteLink_actionPerformed(ActionEvent e)
 978   {
 979
 980   }
 981
 982   public void defaultBrowser_mouseClicked(MouseEvent e)
 983   {
 984
 985   }
 986
 987   public void linkURLList_keyTyped(KeyEvent e)
 988   {
 989
 990   }
 991
 992   public void useProxy_actionPerformed()
 993   {
 994     proxyServerTB.setEnabled(useProxy.isSelected());
 995     proxyPortTB.setEnabled(useProxy.isSelected());
 996   }
 997
 998 }