src/jalview/jbgui/GPreferences.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
   3  * Copyright (C) 2010 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   JLabel jLabel1 = new JLabel();
 165
 166   protected JCheckBox blcjv = new JCheckBox();
 167
 168   protected JCheckBox pileupjv = new JCheckBox();
 169
 170   protected JCheckBox clustaljv = new JCheckBox();
 171
 172   protected JCheckBox msfjv = new JCheckBox();
 173
 174   protected JCheckBox fastajv = new JCheckBox();
 175
 176   protected JCheckBox pfamjv = new JCheckBox();
 177
 178   FlowLayout flowLayout1 = new FlowLayout();
 179
 180   protected JCheckBox pirjv = new JCheckBox();
 181
 182   JPanel jPanel11 = new JPanel();
 183
 184   Font verdana11 = JvSwingUtils.getLabelFont();
 185
 186   protected JCheckBox seqLimit = new JCheckBox();
 187
 188   GridLayout gridLayout3 = new GridLayout();
 189
 190   protected JCheckBox smoothFont = new JCheckBox();
 191
 192   JPanel calcTab = new JPanel();
 193
 194   protected JCheckBox autoCalculateConsCheck = new JCheckBox();
 195
 196   protected JCheckBox padGaps = new JCheckBox();
 197
 198   protected JCheckBox modellerOutput = new JCheckBox();
 199
 200   protected JPanel dasPanel = new JPanel();
 201
 202   BorderLayout borderLayout4 = new BorderLayout();
 203
 204   protected JPanel wsPanel = new JPanel();
 205
 206   BorderLayout borderLayout5 = new BorderLayout();
 207
 208   protected JCheckBox wrap = new JCheckBox();
 209
 210   protected JCheckBox rightAlign = new JCheckBox();
 211
 212   protected JCheckBox showUnconserved = new JCheckBox();
 213
 214   protected JCheckBox showDbRefTooltip = new JCheckBox();
 215
 216   protected JCheckBox showNpTooltip = new JCheckBox();
 217
 218   protected JCheckBox idItalics = new JCheckBox();
 219
 220   protected JCheckBox openoverv = new JCheckBox();
 221
 222   protected JCheckBox usagestats = new JCheckBox();
 223
 224   protected JCheckBox questionnaire = new JCheckBox();
 225
 226   protected JCheckBox versioncheck = new JCheckBox();
 227
 228   protected JLabel showGroupbits = new JLabel();
 229
 230   protected JLabel showConsensbits = new JLabel();
 231
 232   protected JCheckBox showConsensLogo = new JCheckBox();
 233
 234   protected JCheckBox showConsensHistogram = new JCheckBox();
 235
 236   protected JCheckBox showGroupConsensus = new JCheckBox();
 237
 238   protected JCheckBox showGroupConservation = new JCheckBox();
 239
 240   protected JCheckBox shareSelections = new JCheckBox();
 241
 242   protected JCheckBox followHighlight = new JCheckBox();
 243
 244   /**
 245    * Creates a new GPreferences object.
 246    */
 247   public GPreferences()
 248   {
 249     try
 250     {
 251       jbInit();
 252     } catch (Exception ex)
 253     {
 254       ex.printStackTrace();
 255     }
 256   }
 257
 258   /**
 259    * DOCUMENT ME!
 260    *
 261    * @throws Exception
 262    *           DOCUMENT ME!
 263    */
 264   private void jbInit() throws Exception
 265   {
 266     this.setLayout(borderLayout1);
 267     ok.setText("OK");
 268     ok.addActionListener(new ActionListener()
 269     {
 270       public void actionPerformed(ActionEvent e)
 271       {
 272         ok_actionPerformed(e);
 273       }
 274     });
 275     cancel.setText("Cancel");
 276     cancel.addActionListener(new ActionListener()
 277     {
 278       public void actionPerformed(ActionEvent e)
 279       {
 280         cancel_actionPerformed(e);
 281       }
 282     });
 283     quality.setEnabled(false);
 284     quality.setFont(verdana11);
 285     quality.setHorizontalAlignment(SwingConstants.RIGHT);
 286     quality.setHorizontalTextPosition(SwingConstants.LEFT);
 287     quality.setSelected(true);
 288     quality.setText("Quality");
 289     visualTab.setBorder(new TitledBorder("Open new alignment"));
 290     visualTab.setLayout(null);
 291     visual2Tab.setBorder(new TitledBorder("Open new alignment"));
 292     visual2Tab.setLayout(new FlowLayout());
 293     fullScreen.setFont(verdana11);
 294     fullScreen.setHorizontalAlignment(SwingConstants.RIGHT);
 295     fullScreen.setHorizontalTextPosition(SwingConstants.LEFT);
 296     fullScreen.setText("Maximise Window");
 297     conservation.setEnabled(false);
 298     conservation.setFont(verdana11);
 299     conservation.setHorizontalAlignment(SwingConstants.RIGHT);
 300     conservation.setHorizontalTextPosition(SwingConstants.LEFT);
 301     conservation.setSelected(true);
 302     conservation.setText("Conservation");
 303     identity.setEnabled(false);
 304     identity.setFont(verdana11);
 305     identity.setHorizontalAlignment(SwingConstants.RIGHT);
 306     identity.setHorizontalTextPosition(SwingConstants.LEFT);
 307     identity.setSelected(true);
 308     identity.setText("Consensus");
 309     showGroupbits.setFont(verdana11);
 310     showGroupbits.setHorizontalAlignment(SwingConstants.RIGHT);
 311     showGroupbits.setHorizontalTextPosition(SwingConstants.LEFT);
 312     showGroupbits.setText("Show group:");
 313     showConsensbits.setFont(verdana11);
 314     showConsensbits.setHorizontalAlignment(SwingConstants.RIGHT);
 315     showConsensbits.setHorizontalTextPosition(SwingConstants.LEFT);
 316     showConsensbits.setText("Consensus:");
 317     showConsensHistogram.setEnabled(false);
 318     showConsensHistogram.setFont(verdana11);
 319     showConsensHistogram.setHorizontalAlignment(SwingConstants.RIGHT);
 320     showConsensHistogram.setHorizontalTextPosition(SwingConstants.LEFT);
 321     showConsensHistogram.setSelected(true);
 322     showConsensHistogram.setText("Histogram");
 323     showConsensLogo.setEnabled(false);
 324     showConsensLogo.setFont(verdana11);
 325     showConsensLogo.setHorizontalAlignment(SwingConstants.RIGHT);
 326     showConsensLogo.setHorizontalTextPosition(SwingConstants.LEFT);
 327     showConsensLogo.setSelected(true);
 328     showConsensLogo.setText("Logo");
 329     showGroupConsensus.setEnabled(false);
 330     showGroupConsensus.setFont(verdana11);
 331     showGroupConsensus.setHorizontalAlignment(SwingConstants.RIGHT);
 332     showGroupConsensus.setHorizontalTextPosition(SwingConstants.LEFT);
 333     showGroupConsensus.setSelected(true);
 334     showGroupConsensus.setText("Consensus");
 335     showGroupConservation.setEnabled(false);
 336     showGroupConservation.setFont(verdana11);
 337     showGroupConservation.setHorizontalAlignment(SwingConstants.RIGHT);
 338     showGroupConservation.setHorizontalTextPosition(SwingConstants.LEFT);
 339     showGroupConservation.setSelected(true);
 340     showGroupConservation.setText("Conservation");
 341     showNpTooltip.setEnabled(true);
 342     showNpTooltip.setFont(verdana11);
 343     showNpTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
 344     showNpTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
 345     showNpTooltip.setSelected(true);
 346     showNpTooltip.setText("Non-positional Features");
 347     showDbRefTooltip.setEnabled(true);
 348     showDbRefTooltip.setFont(verdana11);
 349     showDbRefTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
 350     showDbRefTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
 351     showDbRefTooltip.setSelected(true);
 352     showDbRefTooltip.setText("Database References");
 353     annotations.setFont(verdana11);
 354     annotations.setHorizontalAlignment(SwingConstants.RIGHT);
 355     annotations.setHorizontalTextPosition(SwingConstants.LEADING);
 356     annotations.setSelected(true);
 357     annotations.setText("Show Annotations");
 358     annotations.setBounds(new Rectangle(169, 12, 200, 23));
 359     annotations.addActionListener(new ActionListener()
 360     {
 361       public void actionPerformed(ActionEvent e)
 362       {
 363         annotations_actionPerformed(e);
 364       }
 365     });
 366     identity.addActionListener(new ActionListener()
 367     {
 368       public void actionPerformed(ActionEvent e)
 369       {
 370         annotations_actionPerformed(e);
 371       }
 372     });
 373     showGroupConsensus.addActionListener(new ActionListener()
 374     {
 375       public void actionPerformed(ActionEvent e)
 376       {
 377         annotations_actionPerformed(e);
 378       }
 379     });
 380     showUnconserved.setFont(verdana11);
 381     showUnconserved.setHorizontalAlignment(SwingConstants.RIGHT);
 382     showUnconserved.setHorizontalTextPosition(SwingConstants.LEFT);
 383     showUnconserved.setSelected(true);
 384     showUnconserved.setText("Show Unconserved");
 385     showUnconserved.addActionListener(new ActionListener()
 386     {
 387       public void actionPerformed(ActionEvent e)
 388       {
 389         showunconserved_actionPerformed(e);
 390       }
 391     });
 392     // / TODO: fit these in to preferences panel!!!!!
 393     shareSelections.setFont(verdana11);
 394     shareSelections.setHorizontalAlignment(SwingConstants.RIGHT);
 395     shareSelections.setHorizontalTextPosition(SwingConstants.LEFT);
 396     shareSelections.setSelected(true);
 397     shareSelections.setText("Share selection across views");
 398     followHighlight.setFont(verdana11);
 399     followHighlight.setHorizontalAlignment(SwingConstants.RIGHT);
 400     followHighlight.setHorizontalTextPosition(SwingConstants.LEFT);
 401     // showUnconserved.setBounds(new Rectangle(169, 40, 200, 23));
 402     followHighlight.setSelected(true);
 403     followHighlight.setText("Scroll to highlighted regions");
 404
 405     gapLabel.setFont(verdana11);
 406     gapLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 407     gapLabel.setText("Gap Symbol ");
 408     colour.setFont(verdana11);
 409     colour.setBounds(new Rectangle(172, 225, 155, 21));
 410     colourLabel.setFont(verdana11);
 411     colourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 412     colourLabel.setText("Alignment Colour ");
 413     fontLabel.setFont(verdana11);
 414     fontLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 415     fontLabel.setText("Font ");
 416     fontSizeCB.setFont(verdana11);
 417     fontSizeCB.setBounds(new Rectangle(319, 104, 49, 23));
 418     fontStyleCB.setFont(verdana11);
 419     fontStyleCB.setBounds(new Rectangle(367, 104, 70, 23));
 420     fontNameCB.setFont(verdana11);
 421     fontNameCB.setBounds(new Rectangle(172, 104, 147, 23));
 422     gapSymbolCB.setFont(verdana11);
 423     gapSymbolCB.setBounds(new Rectangle(172, 204, 69, 23));
 424     mincolourLabel.setFont(verdana11);
 425     mincolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 426     mincolourLabel.setText("Minimum Colour");
 427     minColour.setFont(verdana11);
 428     minColour.setBorder(BorderFactory.createEtchedBorder());
 429     minColour.setPreferredSize(new Dimension(40, 20));
 430     minColour.addMouseListener(new MouseAdapter()
 431     {
 432       public void mousePressed(MouseEvent e)
 433       {
 434           minColour_actionPerformed();
 435       }
 436     });
 437     maxcolourLabel.setFont(verdana11);
 438     maxcolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 439     maxcolourLabel.setText("Maximum Colour ");
 440     maxColour.setFont(verdana11);
 441     maxColour.setBorder(BorderFactory.createEtchedBorder());
 442     maxColour.setPreferredSize(new Dimension(40, 20));
 443     maxColour.addMouseListener(new MouseAdapter()
 444     {
 445       public void mousePressed(MouseEvent e)
 446       {
 447           maxColour_actionPerformed();
 448       }
 449     });
 450     startupCheckbox.setText("Open file");
 451     startupCheckbox.setFont(verdana11);
 452     startupCheckbox.setHorizontalAlignment(SwingConstants.RIGHT);
 453     startupCheckbox.setHorizontalTextPosition(SwingConstants.LEFT);
 454     startupCheckbox.setSelected(true);
 455     startupFileTextfield.setFont(verdana11);
 456     startupFileTextfield.setBounds(new Rectangle(172, 273, 270, 20));
 457     startupFileTextfield.addMouseListener(new MouseAdapter()
 458     {
 459       public void mouseClicked(MouseEvent e)
 460       {
 461         if (e.getClickCount() > 1)
 462         {
 463           startupFileTextfield_mouseClicked();
 464         }
 465       }
 466     });
 467
 468     connectTab.setLayout(gridBagLayout3);
 469     serverLabel.setText("Address");
 470     serverLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 471     serverLabel.setFont(verdana11);
 472     proxyServerTB.setFont(verdana11);
 473     proxyPortTB.setFont(verdana11);
 474     portLabel.setFont(verdana11);
 475     portLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 476     portLabel.setText("Port");
 477     browserLabel.setFont(new java.awt.Font("SansSerif", 0, 11));
 478     browserLabel.setHorizontalAlignment(SwingConstants.TRAILING);
 479     browserLabel.setText("Default Browser (Unix)");
 480     defaultBrowser.setFont(verdana11);
 481     defaultBrowser.setText("");
 482     usagestats.setText("Send usage statistics");
 483     usagestats.setFont(verdana11);
 484     usagestats.setHorizontalAlignment(SwingConstants.RIGHT);
 485     usagestats.setHorizontalTextPosition(SwingConstants.LEADING);
 486     questionnaire.setText("Check for questionnaires");
 487     questionnaire.setFont(verdana11);
 488     questionnaire.setHorizontalAlignment(SwingConstants.RIGHT);
 489     questionnaire.setHorizontalTextPosition(SwingConstants.LEADING);
 490     versioncheck.setText("Check for latest version");
 491     versioncheck.setFont(verdana11);
 492     versioncheck.setHorizontalAlignment(SwingConstants.RIGHT);
 493     versioncheck.setHorizontalTextPosition(SwingConstants.LEADING);
 494     newLink.setText("New");
 495     newLink.addActionListener(new java.awt.event.ActionListener()
 496     {
 497       public void actionPerformed(ActionEvent e)
 498       {
 499         newLink_actionPerformed(e);
 500       }
 501     });
 502     editLink.setText("Edit");
 503     editLink.addActionListener(new java.awt.event.ActionListener()
 504     {
 505       public void actionPerformed(ActionEvent e)
 506       {
 507         editLink_actionPerformed(e);
 508       }
 509     });
 510     deleteLink.setText("Delete");
 511     deleteLink.addActionListener(new java.awt.event.ActionListener()
 512     {
 513       public void actionPerformed(ActionEvent e)
 514       {
 515         deleteLink_actionPerformed(e);
 516       }
 517     });
 518
 519     linkURLList.addListSelectionListener(new ListSelectionListener()
 520     {
 521       public void valueChanged(ListSelectionEvent e)
 522       {
 523         int index = linkURLList.getSelectedIndex();
 524         linkNameList.setSelectedIndex(index);
 525       }
 526     });
 527
 528     linkNameList.addListSelectionListener(new ListSelectionListener()
 529     {
 530       public void valueChanged(ListSelectionEvent e)
 531       {
 532         int index = linkNameList.getSelectedIndex();
 533         linkURLList.setSelectedIndex(index);
 534       }
 535     });
 536
 537     linkScrollPane.setBorder(null);
 538     linkPanel.setBorder(new TitledBorder("URL link from Sequence ID"));
 539     linkPanel.setLayout(borderLayout2);
 540     editLinkButtons.setLayout(gridLayout1);
 541     gridLayout1.setRows(3);
 542     linkNameList.setFont(verdana11);
 543     linkNameList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
 544     linkPanel2.setLayout(borderLayout3);
 545     linkURLList.setFont(verdana11);
 546     linkURLList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
 547
 548     defaultBrowser.addMouseListener(new MouseAdapter()
 549     {
 550       public void mouseClicked(MouseEvent e)
 551       {
 552         if (e.getClickCount() > 1)
 553         {
 554           defaultBrowser_mouseClicked(e);
 555         }
 556       }
 557     });
 558     useProxy.setFont(verdana11);
 559     useProxy.setHorizontalAlignment(SwingConstants.RIGHT);
 560     useProxy.setHorizontalTextPosition(SwingConstants.LEADING);
 561     useProxy.setText("Use a proxy server");
 562     useProxy.addActionListener(new ActionListener()
 563     {
 564       public void actionPerformed(ActionEvent e)
 565       {
 566         useProxy_actionPerformed();
 567       }
 568     });
 569     jPanel1.setBorder(titledBorder1);
 570     jPanel1.setLayout(gridBagLayout1);
 571     sortby.setFont(verdana11);
 572     sortby.setBounds(new Rectangle(172, 249, 155, 21));
 573     sortLabel.setFont(verdana11);
 574     sortLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 575     sortLabel.setText("Sort by ");
 576     jPanel2.setBounds(new Rectangle(7, 17, 158, 278));
 577     jPanel2.setLayout(gridLayout2);
 578     gridLayout2.setRows(12);
 579     exportTab.setLayout(null);
 580     epsLabel.setFont(verdana11);
 581     epsLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 582     epsLabel.setText("EPS Rendering Style");
 583     epsLabel.setBounds(new Rectangle(9, 31, 140, 24));
 584     epsRendering.setFont(verdana11);
 585     epsRendering.setBounds(new Rectangle(154, 34, 187, 21));
 586     jLabel1.setFont(verdana11);
 587     jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
 588     jLabel1.setText("Append /start-end (/15-380)");
 589     jLabel1.setFont(verdana11);
 590     fastajv.setFont(verdana11);
 591     fastajv.setHorizontalAlignment(SwingConstants.LEFT);
 592     clustaljv.setText("Clustal     ");
 593     blcjv.setText("BLC     ");
 594     fastajv.setText("Fasta     ");
 595     msfjv.setText("MSF     ");
 596     pfamjv.setText("PFAM     ");
 597     pileupjv.setText("Pileup     ");
 598     msfjv.setFont(verdana11);
 599     msfjv.setHorizontalAlignment(SwingConstants.LEFT);
 600     pirjv.setText("PIR     ");
 601     jPanel11.setFont(verdana11);
 602     jPanel11.setBorder(titledBorder2);
 603     jPanel11.setBounds(new Rectangle(30, 72, 196, 182));
 604     jPanel11.setLayout(gridLayout3);
 605     blcjv.setFont(verdana11);
 606     blcjv.setHorizontalAlignment(SwingConstants.LEFT);
 607     clustaljv.setFont(verdana11);
 608     clustaljv.setHorizontalAlignment(SwingConstants.LEFT);
 609     pfamjv.setFont(verdana11);
 610     pfamjv.setHorizontalAlignment(SwingConstants.LEFT);
 611     pileupjv.setFont(verdana11);
 612     pileupjv.setHorizontalAlignment(SwingConstants.LEFT);
 613     pirjv.setFont(verdana11);
 614     pirjv.setHorizontalAlignment(SwingConstants.LEFT);
 615     seqLimit.setFont(verdana11);
 616     seqLimit.setHorizontalAlignment(SwingConstants.RIGHT);
 617     seqLimit.setHorizontalTextPosition(SwingConstants.LEFT);
 618     seqLimit.setText("Full Sequence Id");
 619     gridLayout3.setRows(8);
 620     smoothFont.setFont(verdana11);
 621     smoothFont.setHorizontalAlignment(SwingConstants.RIGHT);
 622     smoothFont.setHorizontalTextPosition(SwingConstants.LEADING);
 623     smoothFont.setText("Smooth Font");
 624     calcTab.setLayout(null);
 625     autoCalculateConsCheck.setFont(JvSwingUtils.getLabelFont());
 626     autoCalculateConsCheck.setText("AutoCalculate Consensus");
 627     autoCalculateConsCheck.setBounds(new Rectangle(21, 52, 209, 23));
 628     padGaps.setFont(JvSwingUtils.getLabelFont());
 629     padGaps.setText("Pad gaps when editing");
 630     padGaps.setBounds(new Rectangle(22, 94, 168, 23));
 631     modellerOutput.setFont(JvSwingUtils.getLabelFont());
 632     modellerOutput.setText("Use Modeller Output");
 633     modellerOutput.setBounds(new Rectangle(228, 226, 168, 23));
 634     dasPanel.setLayout(borderLayout4);
 635     wsPanel.setLayout(borderLayout5);
 636     wrap.setFont(JvSwingUtils.getLabelFont());
 637     wrap.setHorizontalAlignment(SwingConstants.TRAILING);
 638     wrap.setHorizontalTextPosition(SwingConstants.LEADING);
 639     wrap.setText("Wrap Alignment");
 640     rightAlign.setFont(JvSwingUtils.getLabelFont());
 641     rightAlign.setForeground(Color.black);
 642     rightAlign.setHorizontalAlignment(SwingConstants.RIGHT);
 643     rightAlign.setHorizontalTextPosition(SwingConstants.LEFT);
 644     rightAlign.setText("Right Align Ids");
 645     idItalics.setFont(JvSwingUtils.getLabelFont());
 646     idItalics.setHorizontalAlignment(SwingConstants.RIGHT);
 647     idItalics.setHorizontalTextPosition(SwingConstants.LEADING);
 648     idItalics.setText("Sequence Name Italics");
 649     openoverv.setFont(JvSwingUtils.getLabelFont());
 650     openoverv.setActionCommand("Open Overview");
 651     openoverv.setHorizontalAlignment(SwingConstants.RIGHT);
 652     openoverv.setHorizontalTextPosition(SwingConstants.LEFT);
 653     openoverv.setText("Open Overview");
 654     jPanel2.add(fullScreen);
 655     jPanel2.add(openoverv);
 656     jPanel2.add(seqLimit);
 657     jPanel2.add(rightAlign);
 658     jPanel2.add(fontLabel);
 659     jPanel2.add(showUnconserved);
 660     jPanel2.add(idItalics);
 661     jPanel2.add(smoothFont);
 662     jPanel2.add(gapLabel);
 663     jPanel2.add(wrap);
 664     jPanel2.add(sortLabel);
 665     jPanel2.add(startupCheckbox);
 666     visualTab.add(annotations);
 667     visualTab.add(startupFileTextfield);
 668     visualTab.add(sortby);
 669     visualTab.add(gapSymbolCB);
 670     visualTab.add(fontNameCB);
 671     visualTab.add(fontSizeCB);
 672     visualTab.add(fontStyleCB);
 673     annsettingsPanel.setBounds(new Rectangle(173, 34, 300, 61));
 674     annsettingsPanel.setLayout(new FlowLayout(FlowLayout.LEFT, 0, 0));
 675     annsettingsPanel.add(autoAnnotSettings1);
 676     annsettingsPanel.add(autoAnnotSettings2);
 677     annsettingsPanel.add(autoAnnotSettings3);
 678     autoAnnotSettings1.setLayout(new GridLayout(3, 1, 0, 0));
 679     autoAnnotSettings2.setLayout(new GridLayout(3, 1, 0, 0));
 680     autoAnnotSettings3.setLayout(new GridLayout(3, 1, 0, 0));
 681     visualTab.add(annsettingsPanel);
 682     Border jb = new EmptyBorder(1, 1, 4, 5);
 683     quality.setBorder(jb);
 684     conservation.setBorder(jb);
 685     identity.setBorder(jb);
 686     showConsensbits.setBorder(jb);
 687     showGroupbits.setBorder(jb);
 688     showGroupConsensus.setBorder(jb);
 689     showGroupConservation.setBorder(jb);
 690     showConsensHistogram.setBorder(jb);
 691     showConsensLogo.setBorder(jb);
 692
 693     autoAnnotSettings2.add(conservation);
 694     autoAnnotSettings1.add(quality);
 695     autoAnnotSettings3.add(identity);
 696     autoAnnotSettings1.add(showGroupbits);
 697     autoAnnotSettings3.add(showGroupConsensus);
 698     autoAnnotSettings2.add(showGroupConservation);
 699     autoAnnotSettings1.add(showConsensbits);
 700     autoAnnotSettings2.add(showConsensHistogram);
 701     autoAnnotSettings3.add(showConsensLogo);
 702
 703     JPanel tooltipSettings = new JPanel();
 704     tooltipSettings.setBorder(new TitledBorder("Sequence ID Tooltip"));
 705     tooltipSettings.setBounds(173, 130, 200, 62);
 706     tooltipSettings.setLayout(new GridLayout(2, 1));
 707     tooltipSettings.add(showDbRefTooltip);
 708     tooltipSettings.add(showNpTooltip);
 709     visualTab.add(tooltipSettings);
 710     visualTab.add(jPanel2);
 711     JvSwingUtils.addtoLayout(visual2Tab, "Default Colourscheme for alignment", colourLabel, colour);
 712     JPanel annotationShding=new JPanel();
 713     annotationShding.setBorder(new TitledBorder("Annotation Shading Default"));
 714     annotationShding.setLayout(new GridLayout(1,2));
 715     JvSwingUtils.addtoLayout(annotationShding, "Default Minimum Colour for annotation shading", mincolourLabel,minColour);
 716     JvSwingUtils.addtoLayout(annotationShding,"Default Maximum Colour for annotation shading", maxcolourLabel, maxColour);
 717     visual2Tab.add(annotationShding); // , FlowLayout.LEFT);
 718
 719 //    visual2panel.add(minColour);
 720 //    visual2panel.add(maxColour);
 721 //    visual2Tab.add(visual2panel);
 722
 723     linkPanel.add(editLinkButtons, BorderLayout.EAST);
 724     editLinkButtons.add(newLink, null);
 725     editLinkButtons.add(editLink, null);
 726     editLinkButtons.add(deleteLink, null);
 727     linkPanel.add(linkScrollPane, BorderLayout.CENTER);
 728     linkScrollPane.getViewport().add(linkPanel2, null);
 729     linkPanel2.add(linkURLList, BorderLayout.CENTER);
 730     linkPanel2.add(linkNameList, BorderLayout.WEST);
 731     okCancelPanel.add(ok);
 732     okCancelPanel.add(cancel);
 733     this.add(tabbedPane, java.awt.BorderLayout.CENTER);
 734
 735     this.add(okCancelPanel, java.awt.BorderLayout.SOUTH);
 736     jPanel1.add(serverLabel, new GridBagConstraints(0, 1, 1, 1, 0.0, 0.0,
 737             GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
 738                     2, 4, 0), 5, 0));
 739     jPanel1.add(portLabel, new GridBagConstraints(2, 1, 1, 1, 0.0, 0.0,
 740             GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
 741                     0, 4, 0), 11, 6));
 742     connectTab.add(linkPanel, new GridBagConstraints(0, 0, 2, 1, 1.0, 1.0,
 743             GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(
 744                     16, 0, 0, 12), 359, -17));
 745     connectTab.add(jPanel1, new GridBagConstraints(0, 2, 2, 1, 1.0, 1.0,
 746             GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(
 747                     21, 0, 35, 12), 4, 6));
 748     connectTab.add(browserLabel, new GridBagConstraints(0, 1, 1, 1, 0.0,
 749             0.0, GridBagConstraints.WEST, GridBagConstraints.NONE,
 750             new Insets(16, 0, 0, 0), 5, 1));
 751     jPanel1.add(proxyPortTB, new GridBagConstraints(3, 1, 1, 1, 1.0, 0.0,
 752             GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 753             new Insets(0, 2, 4, 2), 54, 1));
 754     jPanel1.add(proxyServerTB, new GridBagConstraints(1, 1, 1, 1, 1.0, 0.0,
 755             GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 756             new Insets(0, 2, 4, 0), 263, 1));
 757     connectTab.add(defaultBrowser, new GridBagConstraints(1, 1, 1, 1, 1.0,
 758             0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 759             new Insets(15, 0, 0, 15), 307, 1));
 760     connectTab.add(usagestats, new GridBagConstraints(0, 4, 1, 1, 1.0, 0.0,
 761             GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 762             new Insets(0, 2, 4, 2), 70, 1));
 763     connectTab.add(questionnaire, new GridBagConstraints(1, 4, 1, 1, 1.0,
 764             0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 765             new Insets(0, 2, 4, 2), 70, 1));
 766     connectTab.add(versioncheck, new GridBagConstraints(0, 5, 1, 1, 1.0,
 767             0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 768             new Insets(0, 2, 4, 2), 70, 1));
 769
 770     jPanel1.add(useProxy, new GridBagConstraints(0, 0, 2, 1, 0.0, 0.0,
 771             GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
 772                     2, 5, 185), 2, -4));
 773     DefaultListCellRenderer dlcr = new DefaultListCellRenderer();
 774     dlcr.setHorizontalAlignment(DefaultListCellRenderer.CENTER);
 775     gapSymbolCB.setRenderer(dlcr);
 776
 777     tabbedPane.add(visualTab, "Visual");
 778     tabbedPane.add(visual2Tab,"Colours");
 779     tabbedPane.add(connectTab, "Connections");
 780     tabbedPane.add(exportTab, "Output");
 781     jPanel11.add(jLabel1);
 782     jPanel11.add(blcjv);
 783     jPanel11.add(clustaljv);
 784     jPanel11.add(fastajv);
 785     jPanel11.add(msfjv);
 786     jPanel11.add(pfamjv);
 787     jPanel11.add(pileupjv);
 788     jPanel11.add(pirjv);
 789     exportTab.add(modellerOutput);
 790     tabbedPane.add(calcTab, "Editing");
 791     calcTab.add(autoCalculateConsCheck);
 792     calcTab.add(padGaps);
 793     tabbedPane.add(dasPanel, "DAS Settings");
 794     tabbedPane.add(wsPanel, "Web Services");
 795
 796     exportTab.add(epsLabel);
 797     exportTab.add(epsRendering);
 798     exportTab.add(jPanel11);
 799   }
 800
 801   protected void maxColour_actionPerformed()
 802   {
 803     // TODO Auto-generated method stub
 804
 805   }
 806
 807   protected void minColour_actionPerformed()
 808   {
 809     // TODO Auto-generated method stub
 810
 811   }
 812
 813   protected void showunconserved_actionPerformed(ActionEvent e)
 814   {
 815     // TODO Auto-generated method stub
 816
 817   }
 818
 819   /**
 820    * DOCUMENT ME!
 821    *
 822    * @param e
 823    *          DOCUMENT ME!
 824    */
 825   public void ok_actionPerformed(ActionEvent e)
 826   {
 827   }
 828
 829   /**
 830    * DOCUMENT ME!
 831    *
 832    * @param e
 833    *          DOCUMENT ME!
 834    */
 835   public void cancel_actionPerformed(ActionEvent e)
 836   {
 837   }
 838
 839   /**
 840    * DOCUMENT ME!
 841    *
 842    * @param e
 843    *          DOCUMENT ME!
 844    */
 845   public void annotations_actionPerformed(ActionEvent e)
 846   {
 847   }
 848
 849   /**
 850    * DOCUMENT ME!
 851    */
 852   public void startupFileTextfield_mouseClicked()
 853   {
 854   }
 855
 856   public void newLink_actionPerformed(ActionEvent e)
 857   {
 858
 859   }
 860
 861   public void editLink_actionPerformed(ActionEvent e)
 862   {
 863
 864   }
 865
 866   public void deleteLink_actionPerformed(ActionEvent e)
 867   {
 868
 869   }
 870
 871   public void defaultBrowser_mouseClicked(MouseEvent e)
 872   {
 873
 874   }
 875
 876   public void linkURLList_keyTyped(KeyEvent e)
 877   {
 878
 879   }
 880
 881   public void useProxy_actionPerformed()
 882   {
 883     proxyServerTB.setEnabled(useProxy.isSelected());
 884     proxyPortTB.setEnabled(useProxy.isSelected());
 885   }
 886
 887 }