src/jalview/jbgui/GPreferences.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
   3  * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
   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 of the License, or (at your option) any later version.
  10  *
  11  * Jalview is distributed in the hope that it will be useful, but
  12  * WITHOUT ANY WARRANTY; without even the implied warranty
  13  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  14  * PURPOSE.  See the GNU General Public License for more details.
  15  *
  16  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  17  */
  18 package jalview.jbgui;
  19
  20 import jalview.gui.JvSwingUtils;
  21
  22 import java.awt.*;
  23 import java.awt.event.*;
  24
  25 import javax.swing.*;
  26 import javax.swing.border.*;
  27 import javax.swing.event.*;
  28 import java.awt.Rectangle;
  29
  30 /**
  31  * DOCUMENT ME!
  32  *
  33  * @author $author$
  34  * @version $Revision$
  35  */
  36 public class GPreferences extends JPanel
  37 {
  38   JTabbedPane tabbedPane = new JTabbedPane();
  39
  40   JButton ok = new JButton();
  41
  42   JButton cancel = new JButton();
  43
  44   JPanel okCancelPanel = new JPanel();
  45
  46   BorderLayout borderLayout1 = new BorderLayout();
  47
  48   protected JCheckBox quality = new JCheckBox();
  49
  50   JPanel visualTab = new JPanel();
  51   JPanel visual2Tab = new JPanel();
  52
  53   protected JCheckBox fullScreen = new JCheckBox();
  54
  55   protected JCheckBox conservation = new JCheckBox();
  56
  57   protected JCheckBox identity = new JCheckBox();
  58
  59   protected JCheckBox annotations = new JCheckBox();
  60
  61   protected JPanel minColour = new JPanel();
  62   JLabel mincolourLabel = new JLabel();
  63
  64   protected JPanel maxColour = new JPanel();
  65   JLabel maxcolourLabel = new JLabel();
  66
  67   JLabel gapLabel = new JLabel();
  68
  69   protected JComboBox colour = new JComboBox();
  70
  71   JLabel colourLabel = new JLabel();
  72
  73   JLabel fontLabel = new JLabel();
  74
  75   protected JComboBox fontSizeCB = new JComboBox();
  76
  77   protected JComboBox fontStyleCB = new JComboBox();
  78
  79   protected JComboBox fontNameCB = new JComboBox();
  80
  81   protected JComboBox gapSymbolCB = new JComboBox();
  82
  83   protected JCheckBox startupCheckbox = new JCheckBox();
  84
  85   protected JTextField startupFileTextfield = new JTextField();
  86
  87   JPanel connectTab = new JPanel();
  88
  89   JLabel serverLabel = new JLabel();
  90
  91   protected JList linkURLList = new JList();
  92
  93   protected JTextField proxyServerTB = new JTextField();
  94
  95   protected JTextField proxyPortTB = new JTextField();
  96
  97   JLabel portLabel = new JLabel();
  98
  99   JLabel browserLabel = new JLabel();
 100
 101   protected JTextField defaultBrowser = new JTextField();
 102
 103   JButton newLink = new JButton();
 104
 105   JButton editLink = new JButton();
 106
 107   JButton deleteLink = new JButton();
 108
 109   JScrollPane linkScrollPane = new JScrollPane();
 110
 111   JPanel linkPanel = new JPanel();
 112
 113   BorderLayout borderLayout2 = new BorderLayout();
 114
 115   JPanel editLinkButtons = new JPanel();
 116
 117   GridLayout gridLayout1 = new GridLayout();
 118
 119   protected JList linkNameList = new JList();
 120
 121   JPanel linkPanel2 = new JPanel();
 122
 123   BorderLayout borderLayout3 = new BorderLayout();
 124
 125   protected JCheckBox useProxy = new JCheckBox();
 126
 127   JPanel jPanel1 = new JPanel();
 128
 129   TitledBorder titledBorder1 = new TitledBorder("Proxy Server");
 130
 131   TitledBorder titledBorder2 = new TitledBorder("File Output");
 132
 133   GridBagLayout gridBagLayout2 = new GridBagLayout();
 134
 135   GridBagLayout gridBagLayout1 = new GridBagLayout();
 136
 137   GridBagLayout gridBagLayout3 = new GridBagLayout();
 138
 139   protected JComboBox sortby = new JComboBox();
 140
 141   JLabel sortLabel = new JLabel();
 142
 143   JPanel jPanel2 = new JPanel();
 144   JPanel visual2panel = new JPanel();
 145
 146   GridLayout gridLayout2 = new GridLayout();
 147
 148   GridLayout gridLayout4 = new GridLayout();
 149
 150   JPanel annsettingsPanel = new JPanel();
 151
 152   JPanel autoAnnotSettings1 = new JPanel();
 153
 154   JPanel autoAnnotSettings2 = new JPanel();
 155
 156   JPanel autoAnnotSettings3 = new JPanel();
 157
 158   JPanel exportTab = new JPanel();
 159
 160   JLabel epsLabel = new JLabel();
 161
 162   protected JComboBox epsRendering = new JComboBox();
 163
 164   protected JLabel userIdWidthlabel = new JLabel();
 165   protected JCheckBox autoIdWidth = new JCheckBox();
 166   protected JTextField userIdWidth = new JTextField();
 167
 168
 169   JLabel jLabel1 = new JLabel();
 170
 171   protected JCheckBox blcjv = new JCheckBox();
 172
 173   protected JCheckBox pileupjv = new JCheckBox();
 174
 175   protected JCheckBox clustaljv = new JCheckBox();
 176
 177   protected JCheckBox msfjv = new JCheckBox();
 178
 179   protected JCheckBox fastajv = new JCheckBox();
 180
 181   protected JCheckBox pfamjv = new JCheckBox();
 182
 183   FlowLayout flowLayout1 = new FlowLayout();
 184
 185   protected JCheckBox pirjv = new JCheckBox();
 186
 187   JPanel jPanel11 = new JPanel();
 188
 189   Font verdana11 = JvSwingUtils.getLabelFont();
 190
 191   protected JCheckBox seqLimit = new JCheckBox();
 192
 193   GridLayout gridLayout3 = new GridLayout();
 194
 195   protected JCheckBox smoothFont = new JCheckBox();
 196
 197   JPanel calcTab = new JPanel();
 198
 199   protected JCheckBox autoCalculateConsCheck = new JCheckBox();
 200
 201   protected JCheckBox padGaps = new JCheckBox();
 202
 203   protected JCheckBox modellerOutput = new JCheckBox();
 204
 205   protected JPanel dasPanel = new JPanel();
 206
 207   BorderLayout borderLayout4 = new BorderLayout();
 208
 209   protected JPanel wsPanel = new JPanel();
 210
 211   BorderLayout borderLayout5 = new BorderLayout();
 212
 213   protected JCheckBox wrap = new JCheckBox();
 214
 215   protected JCheckBox rightAlign = new JCheckBox();
 216
 217   protected JCheckBox showUnconserved = new JCheckBox();
 218
 219   protected JCheckBox showDbRefTooltip = new JCheckBox();
 220
 221   protected JCheckBox showNpTooltip = new JCheckBox();
 222
 223   protected JCheckBox idItalics = new JCheckBox();
 224
 225   protected JCheckBox openoverv = new JCheckBox();
 226
 227   protected JCheckBox usagestats = new JCheckBox();
 228
 229   protected JCheckBox questionnaire = new JCheckBox();
 230
 231   protected JCheckBox versioncheck = new JCheckBox();
 232
 233   protected JLabel showGroupbits = new JLabel();
 234
 235   protected JLabel showConsensbits = new JLabel();
 236
 237   protected JCheckBox showConsensLogo = new JCheckBox();
 238
 239   protected JCheckBox showConsensHistogram = new JCheckBox();
 240
 241   protected JCheckBox showGroupConsensus = new JCheckBox();
 242
 243   protected JCheckBox showGroupConservation = new JCheckBox();
 244
 245   protected JCheckBox shareSelections = new JCheckBox();
 246
 247   protected JCheckBox followHighlight = new JCheckBox();
 248
 249   protected JCheckBox sortByTree= new JCheckBox();
 250
 251   /**
 252    * Creates a new GPreferences object.
 253    */
 254   public GPreferences()
 255   {
 256     try
 257     {
 258       jbInit();
 259     } catch (Exception ex)
 260     {
 261       ex.printStackTrace();
 262     }
 263   }
 264
 265   /**
 266    * DOCUMENT ME!
 267    *
 268    * @throws Exception
 269    *           DOCUMENT ME!
 270    */
 271   private void jbInit() throws Exception
 272   {
 273     this.setLayout(borderLayout1);
 274     ok.setText("OK");
 275     ok.addActionListener(new ActionListener()
 276     {
 277       public void actionPerformed(ActionEvent e)
 278       {
 279         ok_actionPerformed(e);
 280       }
 281     });
 282     cancel.setText("Cancel");
 283     cancel.addActionListener(new ActionListener()
 284     {
 285       public void actionPerformed(ActionEvent e)
 286       {
 287         cancel_actionPerformed(e);
 288       }
 289     });
 290     quality.setEnabled(false);
 291     quality.setFont(verdana11);
 292     quality.setHorizontalAlignment(SwingConstants.RIGHT);
 293     quality.setHorizontalTextPosition(SwingConstants.LEFT);
 294     quality.setSelected(true);
 295     quality.setText("Quality");
 296     visualTab.setBorder(new TitledBorder("Open new alignment"));
 297     visualTab.setLayout(null);
 298     visual2Tab.setBorder(new TitledBorder("Open new alignment"));
 299     visual2Tab.setLayout(new FlowLayout());
 300     fullScreen.setFont(verdana11);
 301     fullScreen.setHorizontalAlignment(SwingConstants.RIGHT);
 302     fullScreen.setHorizontalTextPosition(SwingConstants.LEFT);
 303     fullScreen.setText("Maximise Window");
 304     conservation.setEnabled(false);
 305     conservation.setFont(verdana11);
 306     conservation.setHorizontalAlignment(SwingConstants.RIGHT);
 307     conservation.setHorizontalTextPosition(SwingConstants.LEFT);
 308     conservation.setSelected(true);
 309     conservation.setText("Conservation");
 310     identity.setEnabled(false);
 311     identity.setFont(verdana11);
 312     identity.setHorizontalAlignment(SwingConstants.RIGHT);
 313     identity.setHorizontalTextPosition(SwingConstants.LEFT);
 314     identity.setSelected(true);
 315     identity.setText("Consensus");
 316     showGroupbits.setFont(verdana11);
 317     showGroupbits.setHorizontalAlignment(SwingConstants.RIGHT);
 318     showGroupbits.setHorizontalTextPosition(SwingConstants.LEFT);
 319     showGroupbits.setText("Show group:");
 320     showConsensbits.setFont(verdana11);
 321     showConsensbits.setHorizontalAlignment(SwingConstants.RIGHT);
 322     showConsensbits.setHorizontalTextPosition(SwingConstants.LEFT);
 323     showConsensbits.setText("Consensus:");
 324     showConsensHistogram.setEnabled(false);
 325     showConsensHistogram.setFont(verdana11);
 326     showConsensHistogram.setHorizontalAlignment(SwingConstants.RIGHT);
 327     showConsensHistogram.setHorizontalTextPosition(SwingConstants.LEFT);
 328     showConsensHistogram.setSelected(true);
 329     showConsensHistogram.setText("Histogram");
 330     showConsensLogo.setEnabled(false);
 331     showConsensLogo.setFont(verdana11);
 332     showConsensLogo.setHorizontalAlignment(SwingConstants.RIGHT);
 333     showConsensLogo.setHorizontalTextPosition(SwingConstants.LEFT);
 334     showConsensLogo.setSelected(true);
 335     showConsensLogo.setText("Logo");
 336     showGroupConsensus.setEnabled(false);
 337     showGroupConsensus.setFont(verdana11);
 338     showGroupConsensus.setHorizontalAlignment(SwingConstants.RIGHT);
 339     showGroupConsensus.setHorizontalTextPosition(SwingConstants.LEFT);
 340     showGroupConsensus.setSelected(true);
 341     showGroupConsensus.setText("Consensus");
 342     showGroupConservation.setEnabled(false);
 343     showGroupConservation.setFont(verdana11);
 344     showGroupConservation.setHorizontalAlignment(SwingConstants.RIGHT);
 345     showGroupConservation.setHorizontalTextPosition(SwingConstants.LEFT);
 346     showGroupConservation.setSelected(true);
 347     showGroupConservation.setText("Conservation");
 348     showNpTooltip.setEnabled(true);
 349     showNpTooltip.setFont(verdana11);
 350     showNpTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
 351     showNpTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
 352     showNpTooltip.setSelected(true);
 353     showNpTooltip.setText("Non-positional Features");
 354     showDbRefTooltip.setEnabled(true);
 355     showDbRefTooltip.setFont(verdana11);
 356     showDbRefTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
 357     showDbRefTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
 358     showDbRefTooltip.setSelected(true);
 359     showDbRefTooltip.setText("Database References");
 360     annotations.setFont(verdana11);
 361     annotations.setHorizontalAlignment(SwingConstants.RIGHT);
 362     annotations.setHorizontalTextPosition(SwingConstants.LEADING);
 363     annotations.setSelected(true);
 364     annotations.setText("Show Annotations");
 365     annotations.setBounds(new Rectangle(169, 12, 200, 23));
 366     annotations.addActionListener(new ActionListener()
 367     {
 368       public void actionPerformed(ActionEvent e)
 369       {
 370         annotations_actionPerformed(e);
 371       }
 372     });
 373     identity.addActionListener(new ActionListener()
 374     {
 375       public void actionPerformed(ActionEvent e)
 376       {
 377         annotations_actionPerformed(e);
 378       }
 379     });
 380     showGroupConsensus.addActionListener(new ActionListener()
 381     {
 382       public void actionPerformed(ActionEvent e)
 383       {
 384         annotations_actionPerformed(e);
 385       }
 386     });
 387     showUnconserved.setFont(verdana11);
 388     showUnconserved.setHorizontalAlignment(SwingConstants.RIGHT);
 389     showUnconserved.setHorizontalTextPosition(SwingConstants.LEFT);
 390     showUnconserved.setSelected(true);
 391     showUnconserved.setText("Show Unconserved");
 392     showUnconserved.addActionListener(new ActionListener()
 393     {
 394       public void actionPerformed(ActionEvent e)
 395       {
 396         showunconserved_actionPerformed(e);
 397       }
 398     });
 399     // / TODO: fit these in to preferences panel!!!!!
 400     shareSelections.setFont(verdana11);
 401     shareSelections.setHorizontalAlignment(SwingConstants.RIGHT);
 402     shareSelections.setHorizontalTextPosition(SwingConstants.LEFT);
 403     shareSelections.setSelected(true);
 404     shareSelections.setText("Share selection across views");
 405     followHighlight.setFont(verdana11);
 406     followHighlight.setHorizontalAlignment(SwingConstants.RIGHT);
 407     followHighlight.setHorizontalTextPosition(SwingConstants.LEFT);
 408     // showUnconserved.setBounds(new Rectangle(169, 40, 200, 23));
 409     followHighlight.setSelected(true);
 410     followHighlight.setText("Scroll to highlighted regions");
 411
 412     gapLabel.setFont(verdana11);
 413     gapLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 414     gapLabel.setText("Gap Symbol ");
 415     colour.setFont(verdana11);
 416     colour.setBounds(new Rectangle(172, 225, 155, 21));
 417     colourLabel.setFont(verdana11);
 418     colourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 419     colourLabel.setText("Alignment Colour ");
 420     fontLabel.setFont(verdana11);
 421     fontLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 422     fontLabel.setText("Font ");
 423     fontSizeCB.setFont(verdana11);
 424     fontSizeCB.setBounds(new Rectangle(319, 104, 49, 23));
 425     fontStyleCB.setFont(verdana11);
 426     fontStyleCB.setBounds(new Rectangle(367, 104, 70, 23));
 427     fontNameCB.setFont(verdana11);
 428     fontNameCB.setBounds(new Rectangle(172, 104, 147, 23));
 429     gapSymbolCB.setFont(verdana11);
 430     gapSymbolCB.setBounds(new Rectangle(172, 204, 69, 23));
 431     mincolourLabel.setFont(verdana11);
 432     mincolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 433     mincolourLabel.setText("Minimum Colour");
 434     minColour.setFont(verdana11);
 435     minColour.setBorder(BorderFactory.createEtchedBorder());
 436     minColour.setPreferredSize(new Dimension(40, 20));
 437     minColour.addMouseListener(new MouseAdapter()
 438     {
 439       public void mousePressed(MouseEvent e)
 440       {
 441           minColour_actionPerformed();
 442       }
 443     });
 444     maxcolourLabel.setFont(verdana11);
 445     maxcolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 446     maxcolourLabel.setText("Maximum Colour ");
 447     maxColour.setFont(verdana11);
 448     maxColour.setBorder(BorderFactory.createEtchedBorder());
 449     maxColour.setPreferredSize(new Dimension(40, 20));
 450     maxColour.addMouseListener(new MouseAdapter()
 451     {
 452       public void mousePressed(MouseEvent e)
 453       {
 454           maxColour_actionPerformed();
 455       }
 456     });
 457
 458     startupCheckbox.setText("Open file");
 459     startupCheckbox.setFont(verdana11);
 460     startupCheckbox.setHorizontalAlignment(SwingConstants.RIGHT);
 461     startupCheckbox.setHorizontalTextPosition(SwingConstants.LEFT);
 462     startupCheckbox.setSelected(true);
 463     startupFileTextfield.setFont(verdana11);
 464     startupFileTextfield.setBounds(new Rectangle(172, 273, 270, 20));
 465     startupFileTextfield.addMouseListener(new MouseAdapter()
 466     {
 467       public void mouseClicked(MouseEvent e)
 468       {
 469         if (e.getClickCount() > 1)
 470         {
 471           startupFileTextfield_mouseClicked();
 472         }
 473       }
 474     });
 475
 476     connectTab.setLayout(gridBagLayout3);
 477     serverLabel.setText("Address");
 478     serverLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 479     serverLabel.setFont(verdana11);
 480     proxyServerTB.setFont(verdana11);
 481     proxyPortTB.setFont(verdana11);
 482     portLabel.setFont(verdana11);
 483     portLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 484     portLabel.setText("Port");
 485     browserLabel.setFont(new java.awt.Font("SansSerif", 0, 11));
 486     browserLabel.setHorizontalAlignment(SwingConstants.TRAILING);
 487     browserLabel.setText("Default Browser (Unix)");
 488     defaultBrowser.setFont(verdana11);
 489     defaultBrowser.setText("");
 490     usagestats.setText("Send usage statistics");
 491     usagestats.setFont(verdana11);
 492     usagestats.setHorizontalAlignment(SwingConstants.RIGHT);
 493     usagestats.setHorizontalTextPosition(SwingConstants.LEADING);
 494     questionnaire.setText("Check for questionnaires");
 495     questionnaire.setFont(verdana11);
 496     questionnaire.setHorizontalAlignment(SwingConstants.RIGHT);
 497     questionnaire.setHorizontalTextPosition(SwingConstants.LEADING);
 498     versioncheck.setText("Check for latest version");
 499     versioncheck.setFont(verdana11);
 500     versioncheck.setHorizontalAlignment(SwingConstants.RIGHT);
 501     versioncheck.setHorizontalTextPosition(SwingConstants.LEADING);
 502     newLink.setText("New");
 503     newLink.addActionListener(new java.awt.event.ActionListener()
 504     {
 505       public void actionPerformed(ActionEvent e)
 506       {
 507         newLink_actionPerformed(e);
 508       }
 509     });
 510     editLink.setText("Edit");
 511     editLink.addActionListener(new java.awt.event.ActionListener()
 512     {
 513       public void actionPerformed(ActionEvent e)
 514       {
 515         editLink_actionPerformed(e);
 516       }
 517     });
 518     deleteLink.setText("Delete");
 519     deleteLink.addActionListener(new java.awt.event.ActionListener()
 520     {
 521       public void actionPerformed(ActionEvent e)
 522       {
 523         deleteLink_actionPerformed(e);
 524       }
 525     });
 526
 527     linkURLList.addListSelectionListener(new ListSelectionListener()
 528     {
 529       public void valueChanged(ListSelectionEvent e)
 530       {
 531         int index = linkURLList.getSelectedIndex();
 532         linkNameList.setSelectedIndex(index);
 533       }
 534     });
 535
 536     linkNameList.addListSelectionListener(new ListSelectionListener()
 537     {
 538       public void valueChanged(ListSelectionEvent e)
 539       {
 540         int index = linkNameList.getSelectedIndex();
 541         linkURLList.setSelectedIndex(index);
 542       }
 543     });
 544
 545     linkScrollPane.setBorder(null);
 546     linkPanel.setBorder(new TitledBorder("URL link from Sequence ID"));
 547     linkPanel.setLayout(borderLayout2);
 548     editLinkButtons.setLayout(gridLayout1);
 549     gridLayout1.setRows(3);
 550     linkNameList.setFont(verdana11);
 551     linkNameList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
 552     linkPanel2.setLayout(borderLayout3);
 553     linkURLList.setFont(verdana11);
 554     linkURLList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
 555
 556     defaultBrowser.addMouseListener(new MouseAdapter()
 557     {
 558       public void mouseClicked(MouseEvent e)
 559       {
 560         if (e.getClickCount() > 1)
 561         {
 562           defaultBrowser_mouseClicked(e);
 563         }
 564       }
 565     });
 566     useProxy.setFont(verdana11);
 567     useProxy.setHorizontalAlignment(SwingConstants.RIGHT);
 568     useProxy.setHorizontalTextPosition(SwingConstants.LEADING);
 569     useProxy.setText("Use a proxy server");
 570     useProxy.addActionListener(new ActionListener()
 571     {
 572       public void actionPerformed(ActionEvent e)
 573       {
 574         useProxy_actionPerformed();
 575       }
 576     });
 577     jPanel1.setBorder(titledBorder1);
 578     jPanel1.setLayout(gridBagLayout1);
 579     sortby.setFont(verdana11);
 580     sortby.setBounds(new Rectangle(172, 249, 155, 21));
 581     sortLabel.setFont(verdana11);
 582     sortLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 583     sortLabel.setText("Sort by ");
 584     jPanel2.setBounds(new Rectangle(7, 17, 158, 278));
 585     jPanel2.setLayout(gridLayout2);
 586     gridLayout2.setRows(12);
 587     exportTab.setLayout(null);
 588     epsLabel.setFont(verdana11);
 589     epsLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 590     epsLabel.setText("EPS Rendering Style");
 591     epsLabel.setBounds(new Rectangle(9, 31, 140, 24));
 592     epsRendering.setFont(verdana11);
 593     epsRendering.setBounds(new Rectangle(154, 34, 187, 21));
 594     jLabel1.setFont(verdana11);
 595     jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
 596     jLabel1.setText("Append /start-end (/15-380)");
 597     jLabel1.setFont(verdana11);
 598     fastajv.setFont(verdana11);
 599     fastajv.setHorizontalAlignment(SwingConstants.LEFT);
 600     clustaljv.setText("Clustal     ");
 601     blcjv.setText("BLC     ");
 602     fastajv.setText("Fasta     ");
 603     msfjv.setText("MSF     ");
 604     pfamjv.setText("PFAM     ");
 605     pileupjv.setText("Pileup     ");
 606     msfjv.setFont(verdana11);
 607     msfjv.setHorizontalAlignment(SwingConstants.LEFT);
 608     pirjv.setText("PIR     ");
 609     jPanel11.setFont(verdana11);
 610     jPanel11.setBorder(titledBorder2);
 611     jPanel11.setBounds(new Rectangle(30, 72, 196, 182));
 612     jPanel11.setLayout(gridLayout3);
 613     blcjv.setFont(verdana11);
 614     blcjv.setHorizontalAlignment(SwingConstants.LEFT);
 615     clustaljv.setFont(verdana11);
 616     clustaljv.setHorizontalAlignment(SwingConstants.LEFT);
 617     pfamjv.setFont(verdana11);
 618     pfamjv.setHorizontalAlignment(SwingConstants.LEFT);
 619     pileupjv.setFont(verdana11);
 620     pileupjv.setHorizontalAlignment(SwingConstants.LEFT);
 621     pirjv.setFont(verdana11);
 622     pirjv.setHorizontalAlignment(SwingConstants.LEFT);
 623     seqLimit.setFont(verdana11);
 624     seqLimit.setHorizontalAlignment(SwingConstants.RIGHT);
 625     seqLimit.setHorizontalTextPosition(SwingConstants.LEFT);
 626     seqLimit.setText("Full Sequence Id");
 627     gridLayout3.setRows(8);
 628     smoothFont.setFont(verdana11);
 629     smoothFont.setHorizontalAlignment(SwingConstants.RIGHT);
 630     smoothFont.setHorizontalTextPosition(SwingConstants.LEADING);
 631     smoothFont.setText("Smooth Font");
 632     calcTab.setLayout(null);
 633     autoCalculateConsCheck.setFont(JvSwingUtils.getLabelFont());
 634     autoCalculateConsCheck.setText("AutoCalculate Consensus");
 635     autoCalculateConsCheck.setBounds(new Rectangle(21, 52, 209, 23));
 636     padGaps.setFont(JvSwingUtils.getLabelFont());
 637     padGaps.setText("Pad Gaps When Editing");
 638     padGaps.setBounds(new Rectangle(22, 94, 168, 23));
 639     sortByTree.setFont(JvSwingUtils.getLabelFont());
 640     sortByTree.setText("Sort With New Tree");
 641     sortByTree.setToolTipText("When selected, any trees calculated or loaded onto the alignment will automatically sort the alignment.");
 642     sortByTree.setBounds(new Rectangle(22, 136, 168, 23));
 643
 644     autoIdWidth.setFont(JvSwingUtils.getLabelFont());
 645     autoIdWidth.setText("Autofit Figure ID width");
 646     autoIdWidth.setBounds(new Rectangle(228, 96,188,23));
 647     autoIdWidth.addActionListener(new ActionListener()
 648     {
 649
 650       @Override
 651       public void actionPerformed(ActionEvent e)
 652       {
 653         autoIdWidth_actionPerformed();
 654       }
 655     });
 656     userIdWidthlabel.setFont(JvSwingUtils.getLabelFont());
 657     userIdWidthlabel.setText("Figure ID column width");
 658     userIdWidthlabel.setBounds(new Rectangle(236, 120,168,23));
 659     userIdWidth.setFont(JvSwingUtils.getTextAreaFont());
 660     userIdWidth.setText("");
 661     userIdWidth.setBounds(new Rectangle(232,144,84,23));
 662     userIdWidth.addActionListener(new ActionListener()
 663     {
 664
 665       @Override
 666       public void actionPerformed(ActionEvent e)
 667       {
 668         userIdWidth_actionPerformed();
 669       }
 670     });
 671     modellerOutput.setFont(JvSwingUtils.getLabelFont());
 672     modellerOutput.setText("Use Modeller Output");
 673     modellerOutput.setBounds(new Rectangle(228, 226, 168, 23));
 674
 675     dasPanel.setLayout(borderLayout4);
 676     wsPanel.setLayout(borderLayout5);
 677     wrap.setFont(JvSwingUtils.getLabelFont());
 678     wrap.setHorizontalAlignment(SwingConstants.TRAILING);
 679     wrap.setHorizontalTextPosition(SwingConstants.LEADING);
 680     wrap.setText("Wrap Alignment");
 681     rightAlign.setFont(JvSwingUtils.getLabelFont());
 682     rightAlign.setForeground(Color.black);
 683     rightAlign.setHorizontalAlignment(SwingConstants.RIGHT);
 684     rightAlign.setHorizontalTextPosition(SwingConstants.LEFT);
 685     rightAlign.setText("Right Align Ids");
 686     idItalics.setFont(JvSwingUtils.getLabelFont());
 687     idItalics.setHorizontalAlignment(SwingConstants.RIGHT);
 688     idItalics.setHorizontalTextPosition(SwingConstants.LEADING);
 689     idItalics.setText("Sequence Name Italics");
 690     openoverv.setFont(JvSwingUtils.getLabelFont());
 691     openoverv.setActionCommand("Open Overview");
 692     openoverv.setHorizontalAlignment(SwingConstants.RIGHT);
 693     openoverv.setHorizontalTextPosition(SwingConstants.LEFT);
 694     openoverv.setText("Open Overview");
 695     jPanel2.add(fullScreen);
 696     jPanel2.add(openoverv);
 697     jPanel2.add(seqLimit);
 698     jPanel2.add(rightAlign);
 699     jPanel2.add(fontLabel);
 700     jPanel2.add(showUnconserved);
 701     jPanel2.add(idItalics);
 702     jPanel2.add(smoothFont);
 703     jPanel2.add(gapLabel);
 704     jPanel2.add(wrap);
 705     jPanel2.add(sortLabel);
 706     jPanel2.add(startupCheckbox);
 707     visualTab.add(annotations);
 708     visualTab.add(startupFileTextfield);
 709     visualTab.add(sortby);
 710     visualTab.add(gapSymbolCB);
 711     visualTab.add(fontNameCB);
 712     visualTab.add(fontSizeCB);
 713     visualTab.add(fontStyleCB);
 714     annsettingsPanel.setBounds(new Rectangle(173, 34, 300, 61));
 715     annsettingsPanel.setLayout(new FlowLayout(FlowLayout.LEFT, 0, 0));
 716     annsettingsPanel.add(autoAnnotSettings1);
 717     annsettingsPanel.add(autoAnnotSettings2);
 718     annsettingsPanel.add(autoAnnotSettings3);
 719     autoAnnotSettings1.setLayout(new GridLayout(3, 1, 0, 0));
 720     autoAnnotSettings2.setLayout(new GridLayout(3, 1, 0, 0));
 721     autoAnnotSettings3.setLayout(new GridLayout(3, 1, 0, 0));
 722     visualTab.add(annsettingsPanel);
 723     Border jb = new EmptyBorder(1, 1, 4, 5);
 724     quality.setBorder(jb);
 725     conservation.setBorder(jb);
 726     identity.setBorder(jb);
 727     showConsensbits.setBorder(jb);
 728     showGroupbits.setBorder(jb);
 729     showGroupConsensus.setBorder(jb);
 730     showGroupConservation.setBorder(jb);
 731     showConsensHistogram.setBorder(jb);
 732     showConsensLogo.setBorder(jb);
 733
 734     autoAnnotSettings2.add(conservation);
 735     autoAnnotSettings1.add(quality);
 736     autoAnnotSettings3.add(identity);
 737     autoAnnotSettings1.add(showGroupbits);
 738     autoAnnotSettings3.add(showGroupConsensus);
 739     autoAnnotSettings2.add(showGroupConservation);
 740     autoAnnotSettings1.add(showConsensbits);
 741     autoAnnotSettings2.add(showConsensHistogram);
 742     autoAnnotSettings3.add(showConsensLogo);
 743
 744     JPanel tooltipSettings = new JPanel();
 745     tooltipSettings.setBorder(new TitledBorder("Sequence ID Tooltip"));
 746     tooltipSettings.setBounds(173, 130, 200, 62);
 747     tooltipSettings.setLayout(new GridLayout(2, 1));
 748     tooltipSettings.add(showDbRefTooltip);
 749     tooltipSettings.add(showNpTooltip);
 750     visualTab.add(tooltipSettings);
 751     visualTab.add(jPanel2);
 752     JvSwingUtils.addtoLayout(visual2Tab, "Default Colourscheme for alignment", colourLabel, colour);
 753     JPanel annotationShding=new JPanel();
 754     annotationShding.setBorder(new TitledBorder("Annotation Shading Default"));
 755     annotationShding.setLayout(new GridLayout(1,2));
 756     JvSwingUtils.addtoLayout(annotationShding, "Default Minimum Colour for annotation shading", mincolourLabel,minColour);
 757     JvSwingUtils.addtoLayout(annotationShding,"Default Maximum Colour for annotation shading", maxcolourLabel, maxColour);
 758     visual2Tab.add(annotationShding); // , FlowLayout.LEFT);
 759
 760 //    visual2panel.add(minColour);
 761 //    visual2panel.add(maxColour);
 762 //    visual2Tab.add(visual2panel);
 763
 764     linkPanel.add(editLinkButtons, BorderLayout.EAST);
 765     editLinkButtons.add(newLink, null);
 766     editLinkButtons.add(editLink, null);
 767     editLinkButtons.add(deleteLink, null);
 768     linkPanel.add(linkScrollPane, BorderLayout.CENTER);
 769     linkScrollPane.getViewport().add(linkPanel2, null);
 770     linkPanel2.add(linkURLList, BorderLayout.CENTER);
 771     linkPanel2.add(linkNameList, BorderLayout.WEST);
 772     okCancelPanel.add(ok);
 773     okCancelPanel.add(cancel);
 774     this.add(tabbedPane, java.awt.BorderLayout.CENTER);
 775
 776     this.add(okCancelPanel, java.awt.BorderLayout.SOUTH);
 777     jPanel1.add(serverLabel, new GridBagConstraints(0, 1, 1, 1, 0.0, 0.0,
 778             GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
 779                     2, 4, 0), 5, 0));
 780     jPanel1.add(portLabel, new GridBagConstraints(2, 1, 1, 1, 0.0, 0.0,
 781             GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
 782                     0, 4, 0), 11, 6));
 783     connectTab.add(linkPanel, new GridBagConstraints(0, 0, 2, 1, 1.0, 1.0,
 784             GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(
 785                     16, 0, 0, 12), 359, -17));
 786     connectTab.add(jPanel1, new GridBagConstraints(0, 2, 2, 1, 1.0, 1.0,
 787             GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(
 788                     21, 0, 35, 12), 4, 6));
 789     connectTab.add(browserLabel, new GridBagConstraints(0, 1, 1, 1, 0.0,
 790             0.0, GridBagConstraints.WEST, GridBagConstraints.NONE,
 791             new Insets(16, 0, 0, 0), 5, 1));
 792     jPanel1.add(proxyPortTB, new GridBagConstraints(3, 1, 1, 1, 1.0, 0.0,
 793             GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 794             new Insets(0, 2, 4, 2), 54, 1));
 795     jPanel1.add(proxyServerTB, new GridBagConstraints(1, 1, 1, 1, 1.0, 0.0,
 796             GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 797             new Insets(0, 2, 4, 0), 263, 1));
 798     connectTab.add(defaultBrowser, new GridBagConstraints(1, 1, 1, 1, 1.0,
 799             0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 800             new Insets(15, 0, 0, 15), 307, 1));
 801     connectTab.add(usagestats, new GridBagConstraints(0, 4, 1, 1, 1.0, 0.0,
 802             GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 803             new Insets(0, 2, 4, 2), 70, 1));
 804     connectTab.add(questionnaire, new GridBagConstraints(1, 4, 1, 1, 1.0,
 805             0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 806             new Insets(0, 2, 4, 2), 70, 1));
 807     connectTab.add(versioncheck, new GridBagConstraints(0, 5, 1, 1, 1.0,
 808             0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 809             new Insets(0, 2, 4, 2), 70, 1));
 810
 811     jPanel1.add(useProxy, new GridBagConstraints(0, 0, 2, 1, 0.0, 0.0,
 812             GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
 813                     2, 5, 185), 2, -4));
 814     DefaultListCellRenderer dlcr = new DefaultListCellRenderer();
 815     dlcr.setHorizontalAlignment(DefaultListCellRenderer.CENTER);
 816     gapSymbolCB.setRenderer(dlcr);
 817
 818     tabbedPane.add(visualTab, "Visual");
 819     tabbedPane.add(visual2Tab,"Colours");
 820     tabbedPane.add(connectTab, "Connections");
 821     tabbedPane.add(exportTab, "Output");
 822     jPanel11.add(jLabel1);
 823     jPanel11.add(blcjv);
 824     jPanel11.add(clustaljv);
 825     jPanel11.add(fastajv);
 826     jPanel11.add(msfjv);
 827     jPanel11.add(pfamjv);
 828     jPanel11.add(pileupjv);
 829     jPanel11.add(pirjv);
 830     exportTab.add(autoIdWidth);
 831     exportTab.add(userIdWidth);
 832     exportTab.add(userIdWidthlabel);
 833     exportTab.add(modellerOutput);
 834     tabbedPane.add(calcTab, "Editing");
 835     calcTab.add(autoCalculateConsCheck);
 836     calcTab.add(padGaps);
 837     calcTab.add(sortByTree);
 838
 839     tabbedPane.add(dasPanel, "DAS Settings");
 840     tabbedPane.add(wsPanel, "Web Services");
 841
 842     exportTab.add(epsLabel);
 843     exportTab.add(epsRendering);
 844     exportTab.add(jPanel11);
 845   }
 846
 847   protected void autoIdWidth_actionPerformed()
 848   {
 849     // TODO Auto-generated method stub
 850
 851   }
 852
 853   protected void userIdWidth_actionPerformed()
 854   {
 855     // TODO Auto-generated method stub
 856
 857   }
 858
 859   protected void maxColour_actionPerformed()
 860   {
 861     // TODO Auto-generated method stub
 862
 863   }
 864
 865   protected void minColour_actionPerformed()
 866   {
 867     // TODO Auto-generated method stub
 868
 869   }
 870
 871   protected void showunconserved_actionPerformed(ActionEvent e)
 872   {
 873     // TODO Auto-generated method stub
 874
 875   }
 876
 877   /**
 878    * DOCUMENT ME!
 879    *
 880    * @param e
 881    *          DOCUMENT ME!
 882    */
 883   public void ok_actionPerformed(ActionEvent e)
 884   {
 885   }
 886
 887   /**
 888    * DOCUMENT ME!
 889    *
 890    * @param e
 891    *          DOCUMENT ME!
 892    */
 893   public void cancel_actionPerformed(ActionEvent e)
 894   {
 895   }
 896
 897   /**
 898    * DOCUMENT ME!
 899    *
 900    * @param e
 901    *          DOCUMENT ME!
 902    */
 903   public void annotations_actionPerformed(ActionEvent e)
 904   {
 905   }
 906
 907   /**
 908    * DOCUMENT ME!
 909    */
 910   public void startupFileTextfield_mouseClicked()
 911   {
 912   }
 913
 914   public void newLink_actionPerformed(ActionEvent e)
 915   {
 916
 917   }
 918
 919   public void editLink_actionPerformed(ActionEvent e)
 920   {
 921
 922   }
 923
 924   public void deleteLink_actionPerformed(ActionEvent e)
 925   {
 926
 927   }
 928
 929   public void defaultBrowser_mouseClicked(MouseEvent e)
 930   {
 931
 932   }
 933
 934   public void linkURLList_keyTyped(KeyEvent e)
 935   {
 936
 937   }
 938
 939   public void useProxy_actionPerformed()
 940   {
 941     proxyServerTB.setEnabled(useProxy.isSelected());
 942     proxyPortTB.setEnabled(useProxy.isSelected());
 943   }
 944
 945 }