src/jalview/jbgui/GPreferences.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
   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 java.awt.*;
  21 import java.awt.event.*;
  22
  23 import javax.swing.*;
  24 import javax.swing.border.*;
  25 import javax.swing.event.*;
  26 import java.awt.Rectangle;
  27
  28 /**
  29  * DOCUMENT ME!
  30  *
  31  * @author $author$
  32  * @version $Revision$
  33  */
  34 public class GPreferences extends JPanel
  35 {
  36   JTabbedPane tabbedPane = new JTabbedPane();
  37
  38   JButton ok = new JButton();
  39
  40   JButton cancel = new JButton();
  41
  42   JPanel okCancelPanel = new JPanel();
  43
  44   BorderLayout borderLayout1 = new BorderLayout();
  45
  46   protected JCheckBox quality = new JCheckBox();
  47
  48   JPanel visualTab = new JPanel();
  49
  50   protected JCheckBox fullScreen = new JCheckBox();
  51
  52   protected JCheckBox conservation = new JCheckBox();
  53
  54   protected JCheckBox identity = new JCheckBox();
  55
  56   protected JCheckBox annotations = new JCheckBox();
  57
  58   JLabel gapLabel = new JLabel();
  59
  60   protected JComboBox colour = new JComboBox();
  61
  62   JLabel colourLabel = new JLabel();
  63
  64   JLabel fontLabel = new JLabel();
  65
  66   protected JComboBox fontSizeCB = new JComboBox();
  67
  68   protected JComboBox fontStyleCB = new JComboBox();
  69
  70   protected JComboBox fontNameCB = new JComboBox();
  71
  72   protected JComboBox gapSymbolCB = new JComboBox();
  73
  74   protected JCheckBox startupCheckbox = new JCheckBox();
  75
  76   protected JTextField startupFileTextfield = new JTextField();
  77
  78   JPanel connectTab = new JPanel();
  79
  80   JLabel serverLabel = new JLabel();
  81
  82   protected JList linkURLList = new JList();
  83
  84   protected JTextField proxyServerTB = new JTextField();
  85
  86   protected JTextField proxyPortTB = new JTextField();
  87
  88   JLabel portLabel = new JLabel();
  89
  90   JLabel browserLabel = new JLabel();
  91
  92   protected JTextField defaultBrowser = new JTextField();
  93
  94   JButton newLink = new JButton();
  95
  96   JButton editLink = new JButton();
  97
  98   JButton deleteLink = new JButton();
  99
 100   JScrollPane linkScrollPane = new JScrollPane();
 101
 102   JPanel linkPanel = new JPanel();
 103
 104   BorderLayout borderLayout2 = new BorderLayout();
 105
 106   JPanel editLinkButtons = new JPanel();
 107
 108   GridLayout gridLayout1 = new GridLayout();
 109
 110   protected JList linkNameList = new JList();
 111
 112   JPanel linkPanel2 = new JPanel();
 113
 114   BorderLayout borderLayout3 = new BorderLayout();
 115
 116   protected JCheckBox useProxy = new JCheckBox();
 117
 118   JPanel jPanel1 = new JPanel();
 119
 120   TitledBorder titledBorder1 = new TitledBorder("Proxy Server");
 121
 122   TitledBorder titledBorder2 = new TitledBorder("File Output");
 123
 124   GridBagLayout gridBagLayout2 = new GridBagLayout();
 125
 126   GridBagLayout gridBagLayout1 = new GridBagLayout();
 127
 128   GridBagLayout gridBagLayout3 = new GridBagLayout();
 129
 130   protected JComboBox sortby = new JComboBox();
 131
 132   JLabel sortLabel = new JLabel();
 133
 134   JPanel jPanel2 = new JPanel();
 135
 136   GridLayout gridLayout2 = new GridLayout();
 137
 138   JPanel annsettingsPanel = new JPanel();
 139
 140   JPanel autoAnnotSettings1 = new JPanel();
 141
 142   JPanel autoAnnotSettings2 = new JPanel();
 143
 144   JPanel autoAnnotSettings3 = new JPanel();
 145
 146   JPanel exportTab = new JPanel();
 147
 148   JLabel epsLabel = new JLabel();
 149
 150   protected JComboBox epsRendering = new JComboBox();
 151
 152   JLabel jLabel1 = new JLabel();
 153
 154   protected JCheckBox blcjv = new JCheckBox();
 155
 156   protected JCheckBox pileupjv = new JCheckBox();
 157
 158   protected JCheckBox clustaljv = new JCheckBox();
 159
 160   protected JCheckBox msfjv = new JCheckBox();
 161
 162   protected JCheckBox fastajv = new JCheckBox();
 163
 164   protected JCheckBox pfamjv = new JCheckBox();
 165
 166   FlowLayout flowLayout1 = new FlowLayout();
 167
 168   protected JCheckBox pirjv = new JCheckBox();
 169
 170   JPanel jPanel11 = new JPanel();
 171
 172   Font verdana11 = new java.awt.Font("Verdana", Font.PLAIN, 11);
 173
 174   protected JCheckBox seqLimit = new JCheckBox();
 175
 176   GridLayout gridLayout3 = new GridLayout();
 177
 178   protected JCheckBox smoothFont = new JCheckBox();
 179
 180   JPanel calcTab = new JPanel();
 181
 182   protected JCheckBox autoCalculateConsCheck = new JCheckBox();
 183
 184   protected JCheckBox padGaps = new JCheckBox();
 185
 186   protected JCheckBox modellerOutput = new JCheckBox();
 187
 188   protected JPanel dasPanel = new JPanel();
 189
 190   BorderLayout borderLayout4 = new BorderLayout();
 191
 192   protected JCheckBox wrap = new JCheckBox();
 193
 194   protected JCheckBox rightAlign = new JCheckBox();
 195
 196   protected JCheckBox showUnconserved = new JCheckBox();
 197
 198   protected JCheckBox showDbRefTooltip = new JCheckBox();
 199
 200   protected JCheckBox showNpTooltip = new JCheckBox();
 201
 202   protected JCheckBox idItalics = new JCheckBox();
 203
 204   protected JCheckBox openoverv = new JCheckBox();
 205
 206   protected JCheckBox usagestats = new JCheckBox();
 207
 208   protected JCheckBox questionnaire = new JCheckBox();
 209
 210   protected JCheckBox versioncheck = new JCheckBox();
 211
 212   protected JLabel showGroupbits = new JLabel();
 213
 214   protected JLabel showConsensbits = new JLabel();
 215
 216   protected JCheckBox showConsensLogo = new JCheckBox();
 217
 218   protected JCheckBox showConsensHistogram = new JCheckBox();
 219
 220   protected JCheckBox showGroupConsensus = new JCheckBox();
 221
 222   protected JCheckBox showGroupConservation = new JCheckBox();
 223
 224   protected JCheckBox shareSelections = new JCheckBox();
 225
 226   protected JCheckBox followHighlight = new JCheckBox();
 227
 228   /**
 229    * Creates a new GPreferences object.
 230    */
 231   public GPreferences()
 232   {
 233     try
 234     {
 235       jbInit();
 236     } catch (Exception ex)
 237     {
 238       ex.printStackTrace();
 239     }
 240   }
 241
 242   /**
 243    * DOCUMENT ME!
 244    *
 245    * @throws Exception
 246    *           DOCUMENT ME!
 247    */
 248   private void jbInit() throws Exception
 249   {
 250     this.setLayout(borderLayout1);
 251     ok.setText("OK");
 252     ok.addActionListener(new ActionListener()
 253     {
 254       public void actionPerformed(ActionEvent e)
 255       {
 256         ok_actionPerformed(e);
 257       }
 258     });
 259     cancel.setText("Cancel");
 260     cancel.addActionListener(new ActionListener()
 261     {
 262       public void actionPerformed(ActionEvent e)
 263       {
 264         cancel_actionPerformed(e);
 265       }
 266     });
 267     quality.setEnabled(false);
 268     quality.setFont(verdana11);
 269     quality.setHorizontalAlignment(SwingConstants.RIGHT);
 270     quality.setHorizontalTextPosition(SwingConstants.LEFT);
 271     quality.setSelected(true);
 272     quality.setText("Quality");
 273     visualTab.setBorder(new TitledBorder("Open new alignment"));
 274     visualTab.setLayout(null);
 275     fullScreen.setFont(verdana11);
 276     fullScreen.setHorizontalAlignment(SwingConstants.RIGHT);
 277     fullScreen.setHorizontalTextPosition(SwingConstants.LEFT);
 278     fullScreen.setText("Maximise Window");
 279     conservation.setEnabled(false);
 280     conservation.setFont(verdana11);
 281     conservation.setHorizontalAlignment(SwingConstants.RIGHT);
 282     conservation.setHorizontalTextPosition(SwingConstants.LEFT);
 283     conservation.setSelected(true);
 284     conservation.setText("Conservation");
 285     identity.setEnabled(false);
 286     identity.setFont(verdana11);
 287     identity.setHorizontalAlignment(SwingConstants.RIGHT);
 288     identity.setHorizontalTextPosition(SwingConstants.LEFT);
 289     identity.setSelected(true);
 290     identity.setText("Consensus");
 291     showGroupbits.setFont(verdana11);
 292     showGroupbits.setHorizontalAlignment(SwingConstants.RIGHT);
 293     showGroupbits.setHorizontalTextPosition(SwingConstants.LEFT);
 294     showGroupbits.setText("Show group:");
 295     showConsensbits.setFont(verdana11);
 296     showConsensbits.setHorizontalAlignment(SwingConstants.RIGHT);
 297     showConsensbits.setHorizontalTextPosition(SwingConstants.LEFT);
 298     showConsensbits.setText("Consensus:");
 299     showConsensHistogram.setEnabled(false);
 300     showConsensHistogram.setFont(verdana11);
 301     showConsensHistogram.setHorizontalAlignment(SwingConstants.RIGHT);
 302     showConsensHistogram.setHorizontalTextPosition(SwingConstants.LEFT);
 303     showConsensHistogram.setSelected(true);
 304     showConsensHistogram.setText("Histogram");
 305     showConsensLogo.setEnabled(false);
 306     showConsensLogo.setFont(verdana11);
 307     showConsensLogo.setHorizontalAlignment(SwingConstants.RIGHT);
 308     showConsensLogo.setHorizontalTextPosition(SwingConstants.LEFT);
 309     showConsensLogo.setSelected(true);
 310     showConsensLogo.setText("Logo");
 311     showGroupConsensus.setEnabled(false);
 312     showGroupConsensus.setFont(verdana11);
 313     showGroupConsensus.setHorizontalAlignment(SwingConstants.RIGHT);
 314     showGroupConsensus.setHorizontalTextPosition(SwingConstants.LEFT);
 315     showGroupConsensus.setSelected(true);
 316     showGroupConsensus.setText("Consensus");
 317     showGroupConservation.setEnabled(false);
 318     showGroupConservation.setFont(verdana11);
 319     showGroupConservation.setHorizontalAlignment(SwingConstants.RIGHT);
 320     showGroupConservation.setHorizontalTextPosition(SwingConstants.LEFT);
 321     showGroupConservation.setSelected(true);
 322     showGroupConservation.setText("Conservation");
 323     showNpTooltip.setEnabled(true);
 324     showNpTooltip.setFont(verdana11);
 325     showNpTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
 326     showNpTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
 327     showNpTooltip.setSelected(true);
 328     showNpTooltip.setText("Non-positional Features");
 329     showDbRefTooltip.setEnabled(true);
 330     showDbRefTooltip.setFont(verdana11);
 331     showDbRefTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
 332     showDbRefTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
 333     showDbRefTooltip.setSelected(true);
 334     showDbRefTooltip.setText("Database References");
 335     annotations.setFont(verdana11);
 336     annotations.setHorizontalAlignment(SwingConstants.RIGHT);
 337     annotations.setHorizontalTextPosition(SwingConstants.LEADING);
 338     annotations.setSelected(true);
 339     annotations.setText("Show Annotations");
 340     annotations.setBounds(new Rectangle(169, 12, 200, 23));
 341     annotations.addActionListener(new ActionListener()
 342     {
 343       public void actionPerformed(ActionEvent e)
 344       {
 345         annotations_actionPerformed(e);
 346       }
 347     });
 348     identity.addActionListener(new ActionListener()
 349     {
 350       public void actionPerformed(ActionEvent e)
 351       {
 352         annotations_actionPerformed(e);
 353       }
 354     });
 355     showGroupConsensus.addActionListener(new ActionListener()
 356     {
 357       public void actionPerformed(ActionEvent e)
 358       {
 359         annotations_actionPerformed(e);
 360       }
 361     });
 362     showUnconserved.setFont(verdana11);
 363     showUnconserved.setHorizontalAlignment(SwingConstants.RIGHT);
 364     showUnconserved.setHorizontalTextPosition(SwingConstants.LEFT);
 365     showUnconserved.setSelected(true);
 366     showUnconserved.setText("Show Unconserved");
 367     showUnconserved.addActionListener(new ActionListener()
 368     {
 369       public void actionPerformed(ActionEvent e)
 370       {
 371         showunconserved_actionPerformed(e);
 372       }
 373     });
 374     // / TODO: fit these in to preferences panel!!!!!
 375     shareSelections.setFont(verdana11);
 376     shareSelections.setHorizontalAlignment(SwingConstants.RIGHT);
 377     shareSelections.setHorizontalTextPosition(SwingConstants.LEFT);
 378     shareSelections.setSelected(true);
 379     shareSelections.setText("Share selection across views");
 380     followHighlight.setFont(verdana11);
 381     followHighlight.setHorizontalAlignment(SwingConstants.RIGHT);
 382     followHighlight.setHorizontalTextPosition(SwingConstants.LEFT);
 383     // showUnconserved.setBounds(new Rectangle(169, 40, 200, 23));
 384     followHighlight.setSelected(true);
 385     followHighlight.setText("Scroll to highlighted regions");
 386
 387     gapLabel.setFont(verdana11);
 388     gapLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 389     gapLabel.setText("Gap Symbol ");
 390     colour.setFont(verdana11);
 391     colour.setBounds(new Rectangle(172, 225, 155, 21));
 392     colourLabel.setFont(verdana11);
 393     colourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 394     colourLabel.setText("Colour ");
 395     fontLabel.setFont(verdana11);
 396     fontLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 397     fontLabel.setText("Font ");
 398     fontSizeCB.setFont(verdana11);
 399     fontSizeCB.setBounds(new Rectangle(319, 104, 49, 23));
 400     fontStyleCB.setFont(verdana11);
 401     fontStyleCB.setBounds(new Rectangle(367, 104, 70, 23));
 402     fontNameCB.setFont(verdana11);
 403     fontNameCB.setBounds(new Rectangle(172, 104, 147, 23));
 404     gapSymbolCB.setFont(verdana11);
 405     gapSymbolCB.setBounds(new Rectangle(172, 204, 69, 23));
 406     startupCheckbox.setText("Open file");
 407     startupCheckbox.setFont(verdana11);
 408     startupCheckbox.setHorizontalAlignment(SwingConstants.RIGHT);
 409     startupCheckbox.setHorizontalTextPosition(SwingConstants.LEFT);
 410     startupCheckbox.setSelected(true);
 411     startupFileTextfield.setFont(verdana11);
 412     startupFileTextfield.setBounds(new Rectangle(172, 273, 270, 20));
 413     startupFileTextfield.addMouseListener(new MouseAdapter()
 414     {
 415       public void mouseClicked(MouseEvent e)
 416       {
 417         if (e.getClickCount() > 1)
 418         {
 419           startupFileTextfield_mouseClicked();
 420         }
 421       }
 422     });
 423
 424     connectTab.setLayout(gridBagLayout3);
 425     serverLabel.setText("Address");
 426     serverLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 427     serverLabel.setFont(verdana11);
 428     proxyServerTB.setFont(verdana11);
 429     proxyPortTB.setFont(verdana11);
 430     portLabel.setFont(verdana11);
 431     portLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 432     portLabel.setText("Port");
 433     browserLabel.setFont(new java.awt.Font("SansSerif", 0, 11));
 434     browserLabel.setHorizontalAlignment(SwingConstants.TRAILING);
 435     browserLabel.setText("Default Browser (Unix)");
 436     defaultBrowser.setFont(verdana11);
 437     defaultBrowser.setText("");
 438     usagestats.setText("Send usage statistics");
 439     usagestats.setFont(verdana11);
 440     usagestats.setHorizontalAlignment(SwingConstants.RIGHT);
 441     usagestats.setHorizontalTextPosition(SwingConstants.LEADING);
 442     questionnaire.setText("Check for questionnaires");
 443     questionnaire.setFont(verdana11);
 444     questionnaire.setHorizontalAlignment(SwingConstants.RIGHT);
 445     questionnaire.setHorizontalTextPosition(SwingConstants.LEADING);
 446     versioncheck.setText("Check for latest version");
 447     versioncheck.setFont(verdana11);
 448     versioncheck.setHorizontalAlignment(SwingConstants.RIGHT);
 449     versioncheck.setHorizontalTextPosition(SwingConstants.LEADING);
 450     newLink.setText("New");
 451     newLink.addActionListener(new java.awt.event.ActionListener()
 452     {
 453       public void actionPerformed(ActionEvent e)
 454       {
 455         newLink_actionPerformed(e);
 456       }
 457     });
 458     editLink.setText("Edit");
 459     editLink.addActionListener(new java.awt.event.ActionListener()
 460     {
 461       public void actionPerformed(ActionEvent e)
 462       {
 463         editLink_actionPerformed(e);
 464       }
 465     });
 466     deleteLink.setText("Delete");
 467     deleteLink.addActionListener(new java.awt.event.ActionListener()
 468     {
 469       public void actionPerformed(ActionEvent e)
 470       {
 471         deleteLink_actionPerformed(e);
 472       }
 473     });
 474
 475     linkURLList.addListSelectionListener(new ListSelectionListener()
 476     {
 477       public void valueChanged(ListSelectionEvent e)
 478       {
 479         int index = linkURLList.getSelectedIndex();
 480         linkNameList.setSelectedIndex(index);
 481       }
 482     });
 483
 484     linkNameList.addListSelectionListener(new ListSelectionListener()
 485     {
 486       public void valueChanged(ListSelectionEvent e)
 487       {
 488         int index = linkNameList.getSelectedIndex();
 489         linkURLList.setSelectedIndex(index);
 490       }
 491     });
 492
 493     linkScrollPane.setBorder(null);
 494     linkPanel.setBorder(new TitledBorder("URL link from Sequence ID"));
 495     linkPanel.setLayout(borderLayout2);
 496     editLinkButtons.setLayout(gridLayout1);
 497     gridLayout1.setRows(3);
 498     linkNameList.setFont(verdana11);
 499     linkNameList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
 500     linkPanel2.setLayout(borderLayout3);
 501     linkURLList.setFont(verdana11);
 502     linkURLList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
 503
 504     defaultBrowser.addMouseListener(new MouseAdapter()
 505     {
 506       public void mouseClicked(MouseEvent e)
 507       {
 508         if (e.getClickCount() > 1)
 509         {
 510           defaultBrowser_mouseClicked(e);
 511         }
 512       }
 513     });
 514     useProxy.setFont(verdana11);
 515     useProxy.setHorizontalAlignment(SwingConstants.RIGHT);
 516     useProxy.setHorizontalTextPosition(SwingConstants.LEADING);
 517     useProxy.setText("Use a proxy server");
 518     useProxy.addActionListener(new ActionListener()
 519     {
 520       public void actionPerformed(ActionEvent e)
 521       {
 522         useProxy_actionPerformed();
 523       }
 524     });
 525     jPanel1.setBorder(titledBorder1);
 526     jPanel1.setLayout(gridBagLayout1);
 527     sortby.setFont(verdana11);
 528     sortby.setBounds(new Rectangle(172, 249, 155, 21));
 529     sortLabel.setFont(verdana11);
 530     sortLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 531     sortLabel.setText("Sort by ");
 532     jPanel2.setBounds(new Rectangle(7, 17, 158, 278));
 533     jPanel2.setLayout(gridLayout2);
 534     gridLayout2.setRows(13);
 535     exportTab.setLayout(null);
 536     epsLabel.setFont(verdana11);
 537     epsLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 538     epsLabel.setText("EPS Rendering Style");
 539     epsLabel.setBounds(new Rectangle(9, 31, 140, 24));
 540     epsRendering.setFont(verdana11);
 541     epsRendering.setBounds(new Rectangle(154, 34, 187, 21));
 542     jLabel1.setFont(verdana11);
 543     jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
 544     jLabel1.setText("Append /start-end (/15-380)");
 545     jLabel1.setFont(verdana11);
 546     fastajv.setFont(verdana11);
 547     fastajv.setHorizontalAlignment(SwingConstants.LEFT);
 548     clustaljv.setText("Clustal     ");
 549     blcjv.setText("BLC     ");
 550     fastajv.setText("Fasta     ");
 551     msfjv.setText("MSF     ");
 552     pfamjv.setText("PFAM     ");
 553     pileupjv.setText("Pileup     ");
 554     msfjv.setFont(verdana11);
 555     msfjv.setHorizontalAlignment(SwingConstants.LEFT);
 556     pirjv.setText("PIR     ");
 557     jPanel11.setFont(verdana11);
 558     jPanel11.setBorder(titledBorder2);
 559     jPanel11.setBounds(new Rectangle(30, 72, 196, 182));
 560     jPanel11.setLayout(gridLayout3);
 561     blcjv.setFont(verdana11);
 562     blcjv.setHorizontalAlignment(SwingConstants.LEFT);
 563     clustaljv.setFont(verdana11);
 564     clustaljv.setHorizontalAlignment(SwingConstants.LEFT);
 565     pfamjv.setFont(verdana11);
 566     pfamjv.setHorizontalAlignment(SwingConstants.LEFT);
 567     pileupjv.setFont(verdana11);
 568     pileupjv.setHorizontalAlignment(SwingConstants.LEFT);
 569     pirjv.setFont(verdana11);
 570     pirjv.setHorizontalAlignment(SwingConstants.LEFT);
 571     seqLimit.setFont(verdana11);
 572     seqLimit.setHorizontalAlignment(SwingConstants.RIGHT);
 573     seqLimit.setHorizontalTextPosition(SwingConstants.LEFT);
 574     seqLimit.setText("Full Sequence Id");
 575     gridLayout3.setRows(8);
 576     smoothFont.setFont(verdana11);
 577     smoothFont.setHorizontalAlignment(SwingConstants.RIGHT);
 578     smoothFont.setHorizontalTextPosition(SwingConstants.LEADING);
 579     smoothFont.setText("Smooth Font");
 580     calcTab.setLayout(null);
 581     autoCalculateConsCheck.setFont(new java.awt.Font("Verdana", Font.PLAIN,
 582             11));
 583     autoCalculateConsCheck.setText("AutoCalculate Consensus");
 584     autoCalculateConsCheck.setBounds(new Rectangle(21, 52, 209, 23));
 585     padGaps.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
 586     padGaps.setText("Pad gaps when editing");
 587     padGaps.setBounds(new Rectangle(22, 94, 168, 23));
 588     modellerOutput.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
 589     modellerOutput.setText("Use Modeller Output");
 590     modellerOutput.setBounds(new Rectangle(228, 226, 168, 23));
 591     dasPanel.setLayout(borderLayout4);
 592     wrap.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
 593     wrap.setHorizontalAlignment(SwingConstants.TRAILING);
 594     wrap.setHorizontalTextPosition(SwingConstants.LEADING);
 595     wrap.setText("Wrap Alignment");
 596     rightAlign.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
 597     rightAlign.setForeground(Color.black);
 598     rightAlign.setHorizontalAlignment(SwingConstants.RIGHT);
 599     rightAlign.setHorizontalTextPosition(SwingConstants.LEFT);
 600     rightAlign.setText("Right Align Ids");
 601     idItalics.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
 602     idItalics.setHorizontalAlignment(SwingConstants.RIGHT);
 603     idItalics.setHorizontalTextPosition(SwingConstants.LEADING);
 604     idItalics.setText("Sequence Name Italics");
 605     openoverv.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
 606     openoverv.setActionCommand("Open Overview");
 607     openoverv.setHorizontalAlignment(SwingConstants.RIGHT);
 608     openoverv.setHorizontalTextPosition(SwingConstants.LEFT);
 609     openoverv.setText("Open Overview");
 610     jPanel2.add(fullScreen);
 611     jPanel2.add(openoverv);
 612     jPanel2.add(seqLimit);
 613     jPanel2.add(rightAlign);
 614     jPanel2.add(fontLabel);
 615     jPanel2.add(showUnconserved);
 616     jPanel2.add(idItalics);
 617     jPanel2.add(smoothFont);
 618     jPanel2.add(wrap);
 619     jPanel2.add(gapLabel);
 620     jPanel2.add(colourLabel);
 621     jPanel2.add(sortLabel);
 622     jPanel2.add(startupCheckbox);
 623     visualTab.add(annotations);
 624     visualTab.add(startupFileTextfield);
 625     visualTab.add(sortby);
 626     visualTab.add(colour);
 627     visualTab.add(gapSymbolCB);
 628     visualTab.add(fontNameCB);
 629     visualTab.add(fontSizeCB);
 630     visualTab.add(fontStyleCB);
 631     annsettingsPanel.setBounds(new Rectangle(173, 34, 300, 61));
 632     annsettingsPanel.setLayout(new FlowLayout(FlowLayout.LEFT, 0, 0));
 633     annsettingsPanel.add(autoAnnotSettings1);
 634     annsettingsPanel.add(autoAnnotSettings2);
 635     annsettingsPanel.add(autoAnnotSettings3);
 636     autoAnnotSettings1.setLayout(new GridLayout(3, 1, 0, 0));
 637     autoAnnotSettings2.setLayout(new GridLayout(3, 1, 0, 0));
 638     autoAnnotSettings3.setLayout(new GridLayout(3, 1, 0, 0));
 639     visualTab.add(annsettingsPanel);
 640     Border jb = new EmptyBorder(1, 1, 4, 5);
 641     quality.setBorder(jb);
 642     conservation.setBorder(jb);
 643     identity.setBorder(jb);
 644     showConsensbits.setBorder(jb);
 645     showGroupbits.setBorder(jb);
 646     showGroupConsensus.setBorder(jb);
 647     showGroupConservation.setBorder(jb);
 648     showConsensHistogram.setBorder(jb);
 649     showConsensLogo.setBorder(jb);
 650
 651     autoAnnotSettings2.add(conservation);
 652     autoAnnotSettings1.add(quality);
 653     autoAnnotSettings3.add(identity);
 654     autoAnnotSettings1.add(showGroupbits);
 655     autoAnnotSettings3.add(showGroupConsensus);
 656     autoAnnotSettings2.add(showGroupConservation);
 657     autoAnnotSettings1.add(showConsensbits);
 658     autoAnnotSettings2.add(showConsensHistogram);
 659     autoAnnotSettings3.add(showConsensLogo);
 660
 661     JPanel tooltipSettings = new JPanel();
 662     tooltipSettings.setBorder(new TitledBorder("Sequence ID Tooltip"));
 663     tooltipSettings.setBounds(173, 130, 200, 62);
 664     tooltipSettings.setLayout(new GridLayout(2, 1));
 665     tooltipSettings.add(showDbRefTooltip);
 666     tooltipSettings.add(showNpTooltip);
 667     visualTab.add(tooltipSettings);
 668     visualTab.add(jPanel2);
 669
 670     linkPanel.add(editLinkButtons, BorderLayout.EAST);
 671     editLinkButtons.add(newLink, null);
 672     editLinkButtons.add(editLink, null);
 673     editLinkButtons.add(deleteLink, null);
 674     linkPanel.add(linkScrollPane, BorderLayout.CENTER);
 675     linkScrollPane.getViewport().add(linkPanel2, null);
 676     linkPanel2.add(linkURLList, BorderLayout.CENTER);
 677     linkPanel2.add(linkNameList, BorderLayout.WEST);
 678     okCancelPanel.add(ok);
 679     okCancelPanel.add(cancel);
 680     this.add(tabbedPane, java.awt.BorderLayout.CENTER);
 681
 682     this.add(okCancelPanel, java.awt.BorderLayout.SOUTH);
 683     jPanel1.add(serverLabel, new GridBagConstraints(0, 1, 1, 1, 0.0, 0.0,
 684             GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
 685                     2, 4, 0), 5, 0));
 686     jPanel1.add(portLabel, new GridBagConstraints(2, 1, 1, 1, 0.0, 0.0,
 687             GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
 688                     0, 4, 0), 11, 6));
 689     connectTab.add(linkPanel, new GridBagConstraints(0, 0, 2, 1, 1.0, 1.0,
 690             GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(
 691                     16, 0, 0, 12), 359, -17));
 692     connectTab.add(jPanel1, new GridBagConstraints(0, 2, 2, 1, 1.0, 1.0,
 693             GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(
 694                     21, 0, 35, 12), 4, 6));
 695     connectTab.add(browserLabel, new GridBagConstraints(0, 1, 1, 1, 0.0,
 696             0.0, GridBagConstraints.WEST, GridBagConstraints.NONE,
 697             new Insets(16, 0, 0, 0), 5, 1));
 698     jPanel1.add(proxyPortTB, new GridBagConstraints(3, 1, 1, 1, 1.0, 0.0,
 699             GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 700             new Insets(0, 2, 4, 2), 54, 1));
 701     jPanel1.add(proxyServerTB, new GridBagConstraints(1, 1, 1, 1, 1.0, 0.0,
 702             GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 703             new Insets(0, 2, 4, 0), 263, 1));
 704     connectTab.add(defaultBrowser, new GridBagConstraints(1, 1, 1, 1, 1.0,
 705             0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 706             new Insets(15, 0, 0, 15), 307, 1));
 707     connectTab.add(usagestats, new GridBagConstraints(0, 4, 1, 1, 1.0, 0.0,
 708             GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 709             new Insets(0, 2, 4, 2), 70, 1));
 710     connectTab.add(questionnaire, new GridBagConstraints(1, 4, 1, 1, 1.0,
 711             0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 712             new Insets(0, 2, 4, 2), 70, 1));
 713     connectTab.add(versioncheck, new GridBagConstraints(0, 5, 1, 1, 1.0,
 714             0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 715             new Insets(0, 2, 4, 2), 70, 1));
 716
 717     jPanel1.add(useProxy, new GridBagConstraints(0, 0, 2, 1, 0.0, 0.0,
 718             GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
 719                     2, 5, 185), 2, -4));
 720     DefaultListCellRenderer dlcr = new DefaultListCellRenderer();
 721     dlcr.setHorizontalAlignment(DefaultListCellRenderer.CENTER);
 722     gapSymbolCB.setRenderer(dlcr);
 723
 724     tabbedPane.add(visualTab, "Visual");
 725     tabbedPane.add(connectTab, "Connections");
 726     tabbedPane.add(exportTab, "Output");
 727     jPanel11.add(jLabel1);
 728     jPanel11.add(blcjv);
 729     jPanel11.add(clustaljv);
 730     jPanel11.add(fastajv);
 731     jPanel11.add(msfjv);
 732     jPanel11.add(pfamjv);
 733     jPanel11.add(pileupjv);
 734     jPanel11.add(pirjv);
 735     exportTab.add(modellerOutput);
 736     tabbedPane.add(calcTab, "Editing");
 737     calcTab.add(autoCalculateConsCheck);
 738     calcTab.add(padGaps);
 739     tabbedPane.add(dasPanel, "DAS Settings");
 740
 741     exportTab.add(epsLabel);
 742     exportTab.add(epsRendering);
 743     exportTab.add(jPanel11);
 744   }
 745
 746   protected void showunconserved_actionPerformed(ActionEvent e)
 747   {
 748     // TODO Auto-generated method stub
 749
 750   }
 751
 752   /**
 753    * DOCUMENT ME!
 754    *
 755    * @param e
 756    *          DOCUMENT ME!
 757    */
 758   public void ok_actionPerformed(ActionEvent e)
 759   {
 760   }
 761
 762   /**
 763    * DOCUMENT ME!
 764    *
 765    * @param e
 766    *          DOCUMENT ME!
 767    */
 768   public void cancel_actionPerformed(ActionEvent e)
 769   {
 770   }
 771
 772   /**
 773    * DOCUMENT ME!
 774    *
 775    * @param e
 776    *          DOCUMENT ME!
 777    */
 778   public void annotations_actionPerformed(ActionEvent e)
 779   {
 780   }
 781
 782   /**
 783    * DOCUMENT ME!
 784    */
 785   public void startupFileTextfield_mouseClicked()
 786   {
 787   }
 788
 789   public void newLink_actionPerformed(ActionEvent e)
 790   {
 791
 792   }
 793
 794   public void editLink_actionPerformed(ActionEvent e)
 795   {
 796
 797   }
 798
 799   public void deleteLink_actionPerformed(ActionEvent e)
 800   {
 801
 802   }
 803
 804   public void defaultBrowser_mouseClicked(MouseEvent e)
 805   {
 806
 807   }
 808
 809   public void linkURLList_keyTyped(KeyEvent e)
 810   {
 811
 812   }
 813
 814   public void useProxy_actionPerformed()
 815   {
 816     proxyServerTB.setEnabled(useProxy.isSelected());
 817     proxyPortTB.setEnabled(useProxy.isSelected());
 818   }
 819
 820 }