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