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, J Engelhardt, LM Lui, 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   protected JCheckBox sortByTree= new JCheckBox();
 245
 246   /**
 247    * Creates a new GPreferences object.
 248    */
 249   public GPreferences()
 250   {
 251     try
 252     {
 253       jbInit();
 254     } catch (Exception ex)
 255     {
 256       ex.printStackTrace();
 257     }
 258   }
 259
 260   /**
 261    * DOCUMENT ME!
 262    *
 263    * @throws Exception
 264    *           DOCUMENT ME!
 265    */
 266   private void jbInit() throws Exception
 267   {
 268     this.setLayout(borderLayout1);
 269     ok.setText("OK");
 270     ok.addActionListener(new ActionListener()
 271     {
 272       public void actionPerformed(ActionEvent e)
 273       {
 274         ok_actionPerformed(e);
 275       }
 276     });
 277     cancel.setText("Cancel");
 278     cancel.addActionListener(new ActionListener()
 279     {
 280       public void actionPerformed(ActionEvent e)
 281       {
 282         cancel_actionPerformed(e);
 283       }
 284     });
 285     quality.setEnabled(false);
 286     quality.setFont(verdana11);
 287     quality.setHorizontalAlignment(SwingConstants.RIGHT);
 288     quality.setHorizontalTextPosition(SwingConstants.LEFT);
 289     quality.setSelected(true);
 290     quality.setText("Quality");
 291     visualTab.setBorder(new TitledBorder("Open new alignment"));
 292     visualTab.setLayout(null);
 293     visual2Tab.setBorder(new TitledBorder("Open new alignment"));
 294     visual2Tab.setLayout(new FlowLayout());
 295     fullScreen.setFont(verdana11);
 296     fullScreen.setHorizontalAlignment(SwingConstants.RIGHT);
 297     fullScreen.setHorizontalTextPosition(SwingConstants.LEFT);
 298     fullScreen.setText("Maximise Window");
 299     conservation.setEnabled(false);
 300     conservation.setFont(verdana11);
 301     conservation.setHorizontalAlignment(SwingConstants.RIGHT);
 302     conservation.setHorizontalTextPosition(SwingConstants.LEFT);
 303     conservation.setSelected(true);
 304     conservation.setText("Conservation");
 305     identity.setEnabled(false);
 306     identity.setFont(verdana11);
 307     identity.setHorizontalAlignment(SwingConstants.RIGHT);
 308     identity.setHorizontalTextPosition(SwingConstants.LEFT);
 309     identity.setSelected(true);
 310     identity.setText("Consensus");
 311     showGroupbits.setFont(verdana11);
 312     showGroupbits.setHorizontalAlignment(SwingConstants.RIGHT);
 313     showGroupbits.setHorizontalTextPosition(SwingConstants.LEFT);
 314     showGroupbits.setText("Show group:");
 315     showConsensbits.setFont(verdana11);
 316     showConsensbits.setHorizontalAlignment(SwingConstants.RIGHT);
 317     showConsensbits.setHorizontalTextPosition(SwingConstants.LEFT);
 318     showConsensbits.setText("Consensus:");
 319     showConsensHistogram.setEnabled(false);
 320     showConsensHistogram.setFont(verdana11);
 321     showConsensHistogram.setHorizontalAlignment(SwingConstants.RIGHT);
 322     showConsensHistogram.setHorizontalTextPosition(SwingConstants.LEFT);
 323     showConsensHistogram.setSelected(true);
 324     showConsensHistogram.setText("Histogram");
 325     showConsensLogo.setEnabled(false);
 326     showConsensLogo.setFont(verdana11);
 327     showConsensLogo.setHorizontalAlignment(SwingConstants.RIGHT);
 328     showConsensLogo.setHorizontalTextPosition(SwingConstants.LEFT);
 329     showConsensLogo.setSelected(true);
 330     showConsensLogo.setText("Logo");
 331     showGroupConsensus.setEnabled(false);
 332     showGroupConsensus.setFont(verdana11);
 333     showGroupConsensus.setHorizontalAlignment(SwingConstants.RIGHT);
 334     showGroupConsensus.setHorizontalTextPosition(SwingConstants.LEFT);
 335     showGroupConsensus.setSelected(true);
 336     showGroupConsensus.setText("Consensus");
 337     showGroupConservation.setEnabled(false);
 338     showGroupConservation.setFont(verdana11);
 339     showGroupConservation.setHorizontalAlignment(SwingConstants.RIGHT);
 340     showGroupConservation.setHorizontalTextPosition(SwingConstants.LEFT);
 341     showGroupConservation.setSelected(true);
 342     showGroupConservation.setText("Conservation");
 343     showNpTooltip.setEnabled(true);
 344     showNpTooltip.setFont(verdana11);
 345     showNpTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
 346     showNpTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
 347     showNpTooltip.setSelected(true);
 348     showNpTooltip.setText("Non-positional Features");
 349     showDbRefTooltip.setEnabled(true);
 350     showDbRefTooltip.setFont(verdana11);
 351     showDbRefTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
 352     showDbRefTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
 353     showDbRefTooltip.setSelected(true);
 354     showDbRefTooltip.setText("Database References");
 355     annotations.setFont(verdana11);
 356     annotations.setHorizontalAlignment(SwingConstants.RIGHT);
 357     annotations.setHorizontalTextPosition(SwingConstants.LEADING);
 358     annotations.setSelected(true);
 359     annotations.setText("Show Annotations");
 360     annotations.setBounds(new Rectangle(169, 12, 200, 23));
 361     annotations.addActionListener(new ActionListener()
 362     {
 363       public void actionPerformed(ActionEvent e)
 364       {
 365         annotations_actionPerformed(e);
 366       }
 367     });
 368     identity.addActionListener(new ActionListener()
 369     {
 370       public void actionPerformed(ActionEvent e)
 371       {
 372         annotations_actionPerformed(e);
 373       }
 374     });
 375     showGroupConsensus.addActionListener(new ActionListener()
 376     {
 377       public void actionPerformed(ActionEvent e)
 378       {
 379         annotations_actionPerformed(e);
 380       }
 381     });
 382     showUnconserved.setFont(verdana11);
 383     showUnconserved.setHorizontalAlignment(SwingConstants.RIGHT);
 384     showUnconserved.setHorizontalTextPosition(SwingConstants.LEFT);
 385     showUnconserved.setSelected(true);
 386     showUnconserved.setText("Show Unconserved");
 387     showUnconserved.addActionListener(new ActionListener()
 388     {
 389       public void actionPerformed(ActionEvent e)
 390       {
 391         showunconserved_actionPerformed(e);
 392       }
 393     });
 394     // / TODO: fit these in to preferences panel!!!!!
 395     shareSelections.setFont(verdana11);
 396     shareSelections.setHorizontalAlignment(SwingConstants.RIGHT);
 397     shareSelections.setHorizontalTextPosition(SwingConstants.LEFT);
 398     shareSelections.setSelected(true);
 399     shareSelections.setText("Share selection across views");
 400     followHighlight.setFont(verdana11);
 401     followHighlight.setHorizontalAlignment(SwingConstants.RIGHT);
 402     followHighlight.setHorizontalTextPosition(SwingConstants.LEFT);
 403     // showUnconserved.setBounds(new Rectangle(169, 40, 200, 23));
 404     followHighlight.setSelected(true);
 405     followHighlight.setText("Scroll to highlighted regions");
 406
 407     gapLabel.setFont(verdana11);
 408     gapLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 409     gapLabel.setText("Gap Symbol ");
 410     colour.setFont(verdana11);
 411     colour.setBounds(new Rectangle(172, 225, 155, 21));
 412     colourLabel.setFont(verdana11);
 413     colourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 414     colourLabel.setText("Alignment Colour ");
 415     fontLabel.setFont(verdana11);
 416     fontLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 417     fontLabel.setText("Font ");
 418     fontSizeCB.setFont(verdana11);
 419     fontSizeCB.setBounds(new Rectangle(319, 104, 49, 23));
 420     fontStyleCB.setFont(verdana11);
 421     fontStyleCB.setBounds(new Rectangle(367, 104, 70, 23));
 422     fontNameCB.setFont(verdana11);
 423     fontNameCB.setBounds(new Rectangle(172, 104, 147, 23));
 424     gapSymbolCB.setFont(verdana11);
 425     gapSymbolCB.setBounds(new Rectangle(172, 204, 69, 23));
 426     mincolourLabel.setFont(verdana11);
 427     mincolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 428     mincolourLabel.setText("Minimum Colour");
 429     minColour.setFont(verdana11);
 430     minColour.setBorder(BorderFactory.createEtchedBorder());
 431     minColour.setPreferredSize(new Dimension(40, 20));
 432     minColour.addMouseListener(new MouseAdapter()
 433     {
 434       public void mousePressed(MouseEvent e)
 435       {
 436           minColour_actionPerformed();
 437       }
 438     });
 439     maxcolourLabel.setFont(verdana11);
 440     maxcolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 441     maxcolourLabel.setText("Maximum Colour ");
 442     maxColour.setFont(verdana11);
 443     maxColour.setBorder(BorderFactory.createEtchedBorder());
 444     maxColour.setPreferredSize(new Dimension(40, 20));
 445     maxColour.addMouseListener(new MouseAdapter()
 446     {
 447       public void mousePressed(MouseEvent e)
 448       {
 449           maxColour_actionPerformed();
 450       }
 451     });
 452
 453     startupCheckbox.setText("Open file");
 454     startupCheckbox.setFont(verdana11);
 455     startupCheckbox.setHorizontalAlignment(SwingConstants.RIGHT);
 456     startupCheckbox.setHorizontalTextPosition(SwingConstants.LEFT);
 457     startupCheckbox.setSelected(true);
 458     startupFileTextfield.setFont(verdana11);
 459     startupFileTextfield.setBounds(new Rectangle(172, 273, 270, 20));
 460     startupFileTextfield.addMouseListener(new MouseAdapter()
 461     {
 462       public void mouseClicked(MouseEvent e)
 463       {
 464         if (e.getClickCount() > 1)
 465         {
 466           startupFileTextfield_mouseClicked();
 467         }
 468       }
 469     });
 470
 471     connectTab.setLayout(gridBagLayout3);
 472     serverLabel.setText("Address");
 473     serverLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 474     serverLabel.setFont(verdana11);
 475     proxyServerTB.setFont(verdana11);
 476     proxyPortTB.setFont(verdana11);
 477     portLabel.setFont(verdana11);
 478     portLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 479     portLabel.setText("Port");
 480     browserLabel.setFont(new java.awt.Font("SansSerif", 0, 11));
 481     browserLabel.setHorizontalAlignment(SwingConstants.TRAILING);
 482     browserLabel.setText("Default Browser (Unix)");
 483     defaultBrowser.setFont(verdana11);
 484     defaultBrowser.setText("");
 485     usagestats.setText("Send usage statistics");
 486     usagestats.setFont(verdana11);
 487     usagestats.setHorizontalAlignment(SwingConstants.RIGHT);
 488     usagestats.setHorizontalTextPosition(SwingConstants.LEADING);
 489     questionnaire.setText("Check for questionnaires");
 490     questionnaire.setFont(verdana11);
 491     questionnaire.setHorizontalAlignment(SwingConstants.RIGHT);
 492     questionnaire.setHorizontalTextPosition(SwingConstants.LEADING);
 493     versioncheck.setText("Check for latest version");
 494     versioncheck.setFont(verdana11);
 495     versioncheck.setHorizontalAlignment(SwingConstants.RIGHT);
 496     versioncheck.setHorizontalTextPosition(SwingConstants.LEADING);
 497     newLink.setText("New");
 498     newLink.addActionListener(new java.awt.event.ActionListener()
 499     {
 500       public void actionPerformed(ActionEvent e)
 501       {
 502         newLink_actionPerformed(e);
 503       }
 504     });
 505     editLink.setText("Edit");
 506     editLink.addActionListener(new java.awt.event.ActionListener()
 507     {
 508       public void actionPerformed(ActionEvent e)
 509       {
 510         editLink_actionPerformed(e);
 511       }
 512     });
 513     deleteLink.setText("Delete");
 514     deleteLink.addActionListener(new java.awt.event.ActionListener()
 515     {
 516       public void actionPerformed(ActionEvent e)
 517       {
 518         deleteLink_actionPerformed(e);
 519       }
 520     });
 521
 522     linkURLList.addListSelectionListener(new ListSelectionListener()
 523     {
 524       public void valueChanged(ListSelectionEvent e)
 525       {
 526         int index = linkURLList.getSelectedIndex();
 527         linkNameList.setSelectedIndex(index);
 528       }
 529     });
 530
 531     linkNameList.addListSelectionListener(new ListSelectionListener()
 532     {
 533       public void valueChanged(ListSelectionEvent e)
 534       {
 535         int index = linkNameList.getSelectedIndex();
 536         linkURLList.setSelectedIndex(index);
 537       }
 538     });
 539
 540     linkScrollPane.setBorder(null);
 541     linkPanel.setBorder(new TitledBorder("URL link from Sequence ID"));
 542     linkPanel.setLayout(borderLayout2);
 543     editLinkButtons.setLayout(gridLayout1);
 544     gridLayout1.setRows(3);
 545     linkNameList.setFont(verdana11);
 546     linkNameList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
 547     linkPanel2.setLayout(borderLayout3);
 548     linkURLList.setFont(verdana11);
 549     linkURLList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
 550
 551     defaultBrowser.addMouseListener(new MouseAdapter()
 552     {
 553       public void mouseClicked(MouseEvent e)
 554       {
 555         if (e.getClickCount() > 1)
 556         {
 557           defaultBrowser_mouseClicked(e);
 558         }
 559       }
 560     });
 561     useProxy.setFont(verdana11);
 562     useProxy.setHorizontalAlignment(SwingConstants.RIGHT);
 563     useProxy.setHorizontalTextPosition(SwingConstants.LEADING);
 564     useProxy.setText("Use a proxy server");
 565     useProxy.addActionListener(new ActionListener()
 566     {
 567       public void actionPerformed(ActionEvent e)
 568       {
 569         useProxy_actionPerformed();
 570       }
 571     });
 572     jPanel1.setBorder(titledBorder1);
 573     jPanel1.setLayout(gridBagLayout1);
 574     sortby.setFont(verdana11);
 575     sortby.setBounds(new Rectangle(172, 249, 155, 21));
 576     sortLabel.setFont(verdana11);
 577     sortLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 578     sortLabel.setText("Sort by ");
 579     jPanel2.setBounds(new Rectangle(7, 17, 158, 278));
 580     jPanel2.setLayout(gridLayout2);
 581     gridLayout2.setRows(12);
 582     exportTab.setLayout(null);
 583     epsLabel.setFont(verdana11);
 584     epsLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 585     epsLabel.setText("EPS Rendering Style");
 586     epsLabel.setBounds(new Rectangle(9, 31, 140, 24));
 587     epsRendering.setFont(verdana11);
 588     epsRendering.setBounds(new Rectangle(154, 34, 187, 21));
 589     jLabel1.setFont(verdana11);
 590     jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
 591     jLabel1.setText("Append /start-end (/15-380)");
 592     jLabel1.setFont(verdana11);
 593     fastajv.setFont(verdana11);
 594     fastajv.setHorizontalAlignment(SwingConstants.LEFT);
 595     clustaljv.setText("Clustal     ");
 596     blcjv.setText("BLC     ");
 597     fastajv.setText("Fasta     ");
 598     msfjv.setText("MSF     ");
 599     pfamjv.setText("PFAM     ");
 600     pileupjv.setText("Pileup     ");
 601     msfjv.setFont(verdana11);
 602     msfjv.setHorizontalAlignment(SwingConstants.LEFT);
 603     pirjv.setText("PIR     ");
 604     jPanel11.setFont(verdana11);
 605     jPanel11.setBorder(titledBorder2);
 606     jPanel11.setBounds(new Rectangle(30, 72, 196, 182));
 607     jPanel11.setLayout(gridLayout3);
 608     blcjv.setFont(verdana11);
 609     blcjv.setHorizontalAlignment(SwingConstants.LEFT);
 610     clustaljv.setFont(verdana11);
 611     clustaljv.setHorizontalAlignment(SwingConstants.LEFT);
 612     pfamjv.setFont(verdana11);
 613     pfamjv.setHorizontalAlignment(SwingConstants.LEFT);
 614     pileupjv.setFont(verdana11);
 615     pileupjv.setHorizontalAlignment(SwingConstants.LEFT);
 616     pirjv.setFont(verdana11);
 617     pirjv.setHorizontalAlignment(SwingConstants.LEFT);
 618     seqLimit.setFont(verdana11);
 619     seqLimit.setHorizontalAlignment(SwingConstants.RIGHT);
 620     seqLimit.setHorizontalTextPosition(SwingConstants.LEFT);
 621     seqLimit.setText("Full Sequence Id");
 622     gridLayout3.setRows(8);
 623     smoothFont.setFont(verdana11);
 624     smoothFont.setHorizontalAlignment(SwingConstants.RIGHT);
 625     smoothFont.setHorizontalTextPosition(SwingConstants.LEADING);
 626     smoothFont.setText("Smooth Font");
 627     calcTab.setLayout(null);
 628     autoCalculateConsCheck.setFont(JvSwingUtils.getLabelFont());
 629     autoCalculateConsCheck.setText("AutoCalculate Consensus");
 630     autoCalculateConsCheck.setBounds(new Rectangle(21, 52, 209, 23));
 631     padGaps.setFont(JvSwingUtils.getLabelFont());
 632     padGaps.setText("Pad Gaps When Editing");
 633     padGaps.setBounds(new Rectangle(22, 94, 168, 23));
 634     sortByTree.setFont(JvSwingUtils.getLabelFont());
 635     sortByTree.setText("Sort With New Tree");
 636     sortByTree.setToolTipText("When selected, any trees calculated or loaded onto the alignment will automatically sort the alignment.");
 637     sortByTree.setBounds(new Rectangle(22, 136, 168, 23));
 638     modellerOutput.setFont(JvSwingUtils.getLabelFont());
 639     modellerOutput.setText("Use Modeller Output");
 640     modellerOutput.setBounds(new Rectangle(228, 226, 168, 23));
 641     dasPanel.setLayout(borderLayout4);
 642     wsPanel.setLayout(borderLayout5);
 643     wrap.setFont(JvSwingUtils.getLabelFont());
 644     wrap.setHorizontalAlignment(SwingConstants.TRAILING);
 645     wrap.setHorizontalTextPosition(SwingConstants.LEADING);
 646     wrap.setText("Wrap Alignment");
 647     rightAlign.setFont(JvSwingUtils.getLabelFont());
 648     rightAlign.setForeground(Color.black);
 649     rightAlign.setHorizontalAlignment(SwingConstants.RIGHT);
 650     rightAlign.setHorizontalTextPosition(SwingConstants.LEFT);
 651     rightAlign.setText("Right Align Ids");
 652     idItalics.setFont(JvSwingUtils.getLabelFont());
 653     idItalics.setHorizontalAlignment(SwingConstants.RIGHT);
 654     idItalics.setHorizontalTextPosition(SwingConstants.LEADING);
 655     idItalics.setText("Sequence Name Italics");
 656     openoverv.setFont(JvSwingUtils.getLabelFont());
 657     openoverv.setActionCommand("Open Overview");
 658     openoverv.setHorizontalAlignment(SwingConstants.RIGHT);
 659     openoverv.setHorizontalTextPosition(SwingConstants.LEFT);
 660     openoverv.setText("Open Overview");
 661     jPanel2.add(fullScreen);
 662     jPanel2.add(openoverv);
 663     jPanel2.add(seqLimit);
 664     jPanel2.add(rightAlign);
 665     jPanel2.add(fontLabel);
 666     jPanel2.add(showUnconserved);
 667     jPanel2.add(idItalics);
 668     jPanel2.add(smoothFont);
 669     jPanel2.add(gapLabel);
 670     jPanel2.add(wrap);
 671     jPanel2.add(sortLabel);
 672     jPanel2.add(startupCheckbox);
 673     visualTab.add(annotations);
 674     visualTab.add(startupFileTextfield);
 675     visualTab.add(sortby);
 676     visualTab.add(gapSymbolCB);
 677     visualTab.add(fontNameCB);
 678     visualTab.add(fontSizeCB);
 679     visualTab.add(fontStyleCB);
 680     annsettingsPanel.setBounds(new Rectangle(173, 34, 300, 61));
 681     annsettingsPanel.setLayout(new FlowLayout(FlowLayout.LEFT, 0, 0));
 682     annsettingsPanel.add(autoAnnotSettings1);
 683     annsettingsPanel.add(autoAnnotSettings2);
 684     annsettingsPanel.add(autoAnnotSettings3);
 685     autoAnnotSettings1.setLayout(new GridLayout(3, 1, 0, 0));
 686     autoAnnotSettings2.setLayout(new GridLayout(3, 1, 0, 0));
 687     autoAnnotSettings3.setLayout(new GridLayout(3, 1, 0, 0));
 688     visualTab.add(annsettingsPanel);
 689     Border jb = new EmptyBorder(1, 1, 4, 5);
 690     quality.setBorder(jb);
 691     conservation.setBorder(jb);
 692     identity.setBorder(jb);
 693     showConsensbits.setBorder(jb);
 694     showGroupbits.setBorder(jb);
 695     showGroupConsensus.setBorder(jb);
 696     showGroupConservation.setBorder(jb);
 697     showConsensHistogram.setBorder(jb);
 698     showConsensLogo.setBorder(jb);
 699
 700     autoAnnotSettings2.add(conservation);
 701     autoAnnotSettings1.add(quality);
 702     autoAnnotSettings3.add(identity);
 703     autoAnnotSettings1.add(showGroupbits);
 704     autoAnnotSettings3.add(showGroupConsensus);
 705     autoAnnotSettings2.add(showGroupConservation);
 706     autoAnnotSettings1.add(showConsensbits);
 707     autoAnnotSettings2.add(showConsensHistogram);
 708     autoAnnotSettings3.add(showConsensLogo);
 709
 710     JPanel tooltipSettings = new JPanel();
 711     tooltipSettings.setBorder(new TitledBorder("Sequence ID Tooltip"));
 712     tooltipSettings.setBounds(173, 130, 200, 62);
 713     tooltipSettings.setLayout(new GridLayout(2, 1));
 714     tooltipSettings.add(showDbRefTooltip);
 715     tooltipSettings.add(showNpTooltip);
 716     visualTab.add(tooltipSettings);
 717     visualTab.add(jPanel2);
 718     JvSwingUtils.addtoLayout(visual2Tab, "Default Colourscheme for alignment", colourLabel, colour);
 719     JPanel annotationShding=new JPanel();
 720     annotationShding.setBorder(new TitledBorder("Annotation Shading Default"));
 721     annotationShding.setLayout(new GridLayout(1,2));
 722     JvSwingUtils.addtoLayout(annotationShding, "Default Minimum Colour for annotation shading", mincolourLabel,minColour);
 723     JvSwingUtils.addtoLayout(annotationShding,"Default Maximum Colour for annotation shading", maxcolourLabel, maxColour);
 724     visual2Tab.add(annotationShding); // , FlowLayout.LEFT);
 725
 726 //    visual2panel.add(minColour);
 727 //    visual2panel.add(maxColour);
 728 //    visual2Tab.add(visual2panel);
 729
 730     linkPanel.add(editLinkButtons, BorderLayout.EAST);
 731     editLinkButtons.add(newLink, null);
 732     editLinkButtons.add(editLink, null);
 733     editLinkButtons.add(deleteLink, null);
 734     linkPanel.add(linkScrollPane, BorderLayout.CENTER);
 735     linkScrollPane.getViewport().add(linkPanel2, null);
 736     linkPanel2.add(linkURLList, BorderLayout.CENTER);
 737     linkPanel2.add(linkNameList, BorderLayout.WEST);
 738     okCancelPanel.add(ok);
 739     okCancelPanel.add(cancel);
 740     this.add(tabbedPane, java.awt.BorderLayout.CENTER);
 741
 742     this.add(okCancelPanel, java.awt.BorderLayout.SOUTH);
 743     jPanel1.add(serverLabel, new GridBagConstraints(0, 1, 1, 1, 0.0, 0.0,
 744             GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
 745                     2, 4, 0), 5, 0));
 746     jPanel1.add(portLabel, new GridBagConstraints(2, 1, 1, 1, 0.0, 0.0,
 747             GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
 748                     0, 4, 0), 11, 6));
 749     connectTab.add(linkPanel, new GridBagConstraints(0, 0, 2, 1, 1.0, 1.0,
 750             GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(
 751                     16, 0, 0, 12), 359, -17));
 752     connectTab.add(jPanel1, new GridBagConstraints(0, 2, 2, 1, 1.0, 1.0,
 753             GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(
 754                     21, 0, 35, 12), 4, 6));
 755     connectTab.add(browserLabel, new GridBagConstraints(0, 1, 1, 1, 0.0,
 756             0.0, GridBagConstraints.WEST, GridBagConstraints.NONE,
 757             new Insets(16, 0, 0, 0), 5, 1));
 758     jPanel1.add(proxyPortTB, new GridBagConstraints(3, 1, 1, 1, 1.0, 0.0,
 759             GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 760             new Insets(0, 2, 4, 2), 54, 1));
 761     jPanel1.add(proxyServerTB, new GridBagConstraints(1, 1, 1, 1, 1.0, 0.0,
 762             GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 763             new Insets(0, 2, 4, 0), 263, 1));
 764     connectTab.add(defaultBrowser, new GridBagConstraints(1, 1, 1, 1, 1.0,
 765             0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 766             new Insets(15, 0, 0, 15), 307, 1));
 767     connectTab.add(usagestats, new GridBagConstraints(0, 4, 1, 1, 1.0, 0.0,
 768             GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 769             new Insets(0, 2, 4, 2), 70, 1));
 770     connectTab.add(questionnaire, new GridBagConstraints(1, 4, 1, 1, 1.0,
 771             0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 772             new Insets(0, 2, 4, 2), 70, 1));
 773     connectTab.add(versioncheck, new GridBagConstraints(0, 5, 1, 1, 1.0,
 774             0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 775             new Insets(0, 2, 4, 2), 70, 1));
 776
 777     jPanel1.add(useProxy, new GridBagConstraints(0, 0, 2, 1, 0.0, 0.0,
 778             GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
 779                     2, 5, 185), 2, -4));
 780     DefaultListCellRenderer dlcr = new DefaultListCellRenderer();
 781     dlcr.setHorizontalAlignment(DefaultListCellRenderer.CENTER);
 782     gapSymbolCB.setRenderer(dlcr);
 783
 784     tabbedPane.add(visualTab, "Visual");
 785     tabbedPane.add(visual2Tab,"Colours");
 786     tabbedPane.add(connectTab, "Connections");
 787     tabbedPane.add(exportTab, "Output");
 788     jPanel11.add(jLabel1);
 789     jPanel11.add(blcjv);
 790     jPanel11.add(clustaljv);
 791     jPanel11.add(fastajv);
 792     jPanel11.add(msfjv);
 793     jPanel11.add(pfamjv);
 794     jPanel11.add(pileupjv);
 795     jPanel11.add(pirjv);
 796     exportTab.add(modellerOutput);
 797     tabbedPane.add(calcTab, "Editing");
 798     calcTab.add(autoCalculateConsCheck);
 799     calcTab.add(padGaps);
 800     calcTab.add(sortByTree);
 801
 802     tabbedPane.add(dasPanel, "DAS Settings");
 803     tabbedPane.add(wsPanel, "Web Services");
 804
 805     exportTab.add(epsLabel);
 806     exportTab.add(epsRendering);
 807     exportTab.add(jPanel11);
 808   }
 809
 810   protected void maxColour_actionPerformed()
 811   {
 812     // TODO Auto-generated method stub
 813
 814   }
 815
 816   protected void minColour_actionPerformed()
 817   {
 818     // TODO Auto-generated method stub
 819
 820   }
 821
 822   protected void showunconserved_actionPerformed(ActionEvent e)
 823   {
 824     // TODO Auto-generated method stub
 825
 826   }
 827
 828   /**
 829    * DOCUMENT ME!
 830    *
 831    * @param e
 832    *          DOCUMENT ME!
 833    */
 834   public void ok_actionPerformed(ActionEvent e)
 835   {
 836   }
 837
 838   /**
 839    * DOCUMENT ME!
 840    *
 841    * @param e
 842    *          DOCUMENT ME!
 843    */
 844   public void cancel_actionPerformed(ActionEvent e)
 845   {
 846   }
 847
 848   /**
 849    * DOCUMENT ME!
 850    *
 851    * @param e
 852    *          DOCUMENT ME!
 853    */
 854   public void annotations_actionPerformed(ActionEvent e)
 855   {
 856   }
 857
 858   /**
 859    * DOCUMENT ME!
 860    */
 861   public void startupFileTextfield_mouseClicked()
 862   {
 863   }
 864
 865   public void newLink_actionPerformed(ActionEvent e)
 866   {
 867
 868   }
 869
 870   public void editLink_actionPerformed(ActionEvent e)
 871   {
 872
 873   }
 874
 875   public void deleteLink_actionPerformed(ActionEvent e)
 876   {
 877
 878   }
 879
 880   public void defaultBrowser_mouseClicked(MouseEvent e)
 881   {
 882
 883   }
 884
 885   public void linkURLList_keyTyped(KeyEvent e)
 886   {
 887
 888   }
 889
 890   public void useProxy_actionPerformed()
 891   {
 892     proxyServerTB.setEnabled(useProxy.isSelected());
 893     proxyPortTB.setEnabled(useProxy.isSelected());
 894   }
 895
 896 }