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.getWidth(),33);
 246     labPanel.setBounds(new Rectangle(7, 7, 158, 23));
 247     valPanel.setBounds(new Rectangle(172, 7, 270,23));
 248     labPanel.setLayout(new GridLayout());
 249     valPanel.setLayout(new GridLayout());
 250     labPanel.add(label);
 251     valPanel.add(valBox);
 252     laypanel.add(labPanel);
 253     laypanel.add(valPanel);
 254     panel.add(laypanel);
 255     valPanel.setToolTipText(tooltip);
 256     labPanel.setToolTipText(tooltip);
 257   }
 258   /**
 259    * Creates a new GPreferences object.
 260    */
 261   public GPreferences()
 262   {
 263     try
 264     {
 265       jbInit();
 266     } catch (Exception ex)
 267     {
 268       ex.printStackTrace();
 269     }
 270   }
 271
 272   /**
 273    * DOCUMENT ME!
 274    *
 275    * @throws Exception
 276    *           DOCUMENT ME!
 277    */
 278   private void jbInit() throws Exception
 279   {
 280     this.setLayout(borderLayout1);
 281     ok.setText("OK");
 282     ok.addActionListener(new ActionListener()
 283     {
 284       public void actionPerformed(ActionEvent e)
 285       {
 286         ok_actionPerformed(e);
 287       }
 288     });
 289     cancel.setText("Cancel");
 290     cancel.addActionListener(new ActionListener()
 291     {
 292       public void actionPerformed(ActionEvent e)
 293       {
 294         cancel_actionPerformed(e);
 295       }
 296     });
 297     quality.setEnabled(false);
 298     quality.setFont(verdana11);
 299     quality.setHorizontalAlignment(SwingConstants.RIGHT);
 300     quality.setHorizontalTextPosition(SwingConstants.LEFT);
 301     quality.setSelected(true);
 302     quality.setText("Quality");
 303     visualTab.setBorder(new TitledBorder("Open new alignment"));
 304     visualTab.setLayout(null);
 305     visual2Tab.setBorder(new TitledBorder("Open new alignment"));
 306     visual2Tab.setLayout(new FlowLayout());
 307     fullScreen.setFont(verdana11);
 308     fullScreen.setHorizontalAlignment(SwingConstants.RIGHT);
 309     fullScreen.setHorizontalTextPosition(SwingConstants.LEFT);
 310     fullScreen.setText("Maximise Window");
 311     conservation.setEnabled(false);
 312     conservation.setFont(verdana11);
 313     conservation.setHorizontalAlignment(SwingConstants.RIGHT);
 314     conservation.setHorizontalTextPosition(SwingConstants.LEFT);
 315     conservation.setSelected(true);
 316     conservation.setText("Conservation");
 317     identity.setEnabled(false);
 318     identity.setFont(verdana11);
 319     identity.setHorizontalAlignment(SwingConstants.RIGHT);
 320     identity.setHorizontalTextPosition(SwingConstants.LEFT);
 321     identity.setSelected(true);
 322     identity.setText("Consensus");
 323     showGroupbits.setFont(verdana11);
 324     showGroupbits.setHorizontalAlignment(SwingConstants.RIGHT);
 325     showGroupbits.setHorizontalTextPosition(SwingConstants.LEFT);
 326     showGroupbits.setText("Show group:");
 327     showConsensbits.setFont(verdana11);
 328     showConsensbits.setHorizontalAlignment(SwingConstants.RIGHT);
 329     showConsensbits.setHorizontalTextPosition(SwingConstants.LEFT);
 330     showConsensbits.setText("Consensus:");
 331     showConsensHistogram.setEnabled(false);
 332     showConsensHistogram.setFont(verdana11);
 333     showConsensHistogram.setHorizontalAlignment(SwingConstants.RIGHT);
 334     showConsensHistogram.setHorizontalTextPosition(SwingConstants.LEFT);
 335     showConsensHistogram.setSelected(true);
 336     showConsensHistogram.setText("Histogram");
 337     showConsensLogo.setEnabled(false);
 338     showConsensLogo.setFont(verdana11);
 339     showConsensLogo.setHorizontalAlignment(SwingConstants.RIGHT);
 340     showConsensLogo.setHorizontalTextPosition(SwingConstants.LEFT);
 341     showConsensLogo.setSelected(true);
 342     showConsensLogo.setText("Logo");
 343     showGroupConsensus.setEnabled(false);
 344     showGroupConsensus.setFont(verdana11);
 345     showGroupConsensus.setHorizontalAlignment(SwingConstants.RIGHT);
 346     showGroupConsensus.setHorizontalTextPosition(SwingConstants.LEFT);
 347     showGroupConsensus.setSelected(true);
 348     showGroupConsensus.setText("Consensus");
 349     showGroupConservation.setEnabled(false);
 350     showGroupConservation.setFont(verdana11);
 351     showGroupConservation.setHorizontalAlignment(SwingConstants.RIGHT);
 352     showGroupConservation.setHorizontalTextPosition(SwingConstants.LEFT);
 353     showGroupConservation.setSelected(true);
 354     showGroupConservation.setText("Conservation");
 355     showNpTooltip.setEnabled(true);
 356     showNpTooltip.setFont(verdana11);
 357     showNpTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
 358     showNpTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
 359     showNpTooltip.setSelected(true);
 360     showNpTooltip.setText("Non-positional Features");
 361     showDbRefTooltip.setEnabled(true);
 362     showDbRefTooltip.setFont(verdana11);
 363     showDbRefTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
 364     showDbRefTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
 365     showDbRefTooltip.setSelected(true);
 366     showDbRefTooltip.setText("Database References");
 367     annotations.setFont(verdana11);
 368     annotations.setHorizontalAlignment(SwingConstants.RIGHT);
 369     annotations.setHorizontalTextPosition(SwingConstants.LEADING);
 370     annotations.setSelected(true);
 371     annotations.setText("Show Annotations");
 372     annotations.setBounds(new Rectangle(169, 12, 200, 23));
 373     annotations.addActionListener(new ActionListener()
 374     {
 375       public void actionPerformed(ActionEvent e)
 376       {
 377         annotations_actionPerformed(e);
 378       }
 379     });
 380     identity.addActionListener(new ActionListener()
 381     {
 382       public void actionPerformed(ActionEvent e)
 383       {
 384         annotations_actionPerformed(e);
 385       }
 386     });
 387     showGroupConsensus.addActionListener(new ActionListener()
 388     {
 389       public void actionPerformed(ActionEvent e)
 390       {
 391         annotations_actionPerformed(e);
 392       }
 393     });
 394     showUnconserved.setFont(verdana11);
 395     showUnconserved.setHorizontalAlignment(SwingConstants.RIGHT);
 396     showUnconserved.setHorizontalTextPosition(SwingConstants.LEFT);
 397     showUnconserved.setSelected(true);
 398     showUnconserved.setText("Show Unconserved");
 399     showUnconserved.addActionListener(new ActionListener()
 400     {
 401       public void actionPerformed(ActionEvent e)
 402       {
 403         showunconserved_actionPerformed(e);
 404       }
 405     });
 406     // / TODO: fit these in to preferences panel!!!!!
 407     shareSelections.setFont(verdana11);
 408     shareSelections.setHorizontalAlignment(SwingConstants.RIGHT);
 409     shareSelections.setHorizontalTextPosition(SwingConstants.LEFT);
 410     shareSelections.setSelected(true);
 411     shareSelections.setText("Share selection across views");
 412     followHighlight.setFont(verdana11);
 413     followHighlight.setHorizontalAlignment(SwingConstants.RIGHT);
 414     followHighlight.setHorizontalTextPosition(SwingConstants.LEFT);
 415     // showUnconserved.setBounds(new Rectangle(169, 40, 200, 23));
 416     followHighlight.setSelected(true);
 417     followHighlight.setText("Scroll to highlighted regions");
 418
 419     gapLabel.setFont(verdana11);
 420     gapLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 421     gapLabel.setText("Gap Symbol ");
 422     colour.setFont(verdana11);
 423     colour.setBounds(new Rectangle(172, 225, 155, 21));
 424     colourLabel.setFont(verdana11);
 425     colourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 426     colourLabel.setText("Alignment Colour ");
 427     fontLabel.setFont(verdana11);
 428     fontLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 429     fontLabel.setText("Font ");
 430     fontSizeCB.setFont(verdana11);
 431     fontSizeCB.setBounds(new Rectangle(319, 104, 49, 23));
 432     fontStyleCB.setFont(verdana11);
 433     fontStyleCB.setBounds(new Rectangle(367, 104, 70, 23));
 434     fontNameCB.setFont(verdana11);
 435     fontNameCB.setBounds(new Rectangle(172, 104, 147, 23));
 436     gapSymbolCB.setFont(verdana11);
 437     gapSymbolCB.setBounds(new Rectangle(172, 204, 69, 23));
 438     mincolourLabel.setFont(verdana11);
 439     mincolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 440     mincolourLabel.setText("Minimum Colour");
 441     minColour.setFont(verdana11);
 442     minColour.setBorder(BorderFactory.createEtchedBorder());
 443     minColour.setPreferredSize(new Dimension(40, 20));
 444     minColour.addMouseListener(new MouseAdapter()
 445     {
 446       public void mousePressed(MouseEvent e)
 447       {
 448           minColour_actionPerformed();
 449       }
 450     });
 451     maxcolourLabel.setFont(verdana11);
 452     maxcolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 453     maxcolourLabel.setText("Maximumum Colour ");
 454     maxColour.setFont(verdana11);
 455     maxColour.setBorder(BorderFactory.createEtchedBorder());
 456     maxColour.setPreferredSize(new Dimension(40, 20));
 457     maxColour.addMouseListener(new MouseAdapter()
 458     {
 459       public void mousePressed(MouseEvent e)
 460       {
 461           maxColour_actionPerformed();
 462       }
 463     });
 464     startupCheckbox.setText("Open file");
 465     startupCheckbox.setFont(verdana11);
 466     startupCheckbox.setHorizontalAlignment(SwingConstants.RIGHT);
 467     startupCheckbox.setHorizontalTextPosition(SwingConstants.LEFT);
 468     startupCheckbox.setSelected(true);
 469     startupFileTextfield.setFont(verdana11);
 470     startupFileTextfield.setBounds(new Rectangle(172, 273, 270, 20));
 471     startupFileTextfield.addMouseListener(new MouseAdapter()
 472     {
 473       public void mouseClicked(MouseEvent e)
 474       {
 475         if (e.getClickCount() > 1)
 476         {
 477           startupFileTextfield_mouseClicked();
 478         }
 479       }
 480     });
 481
 482     connectTab.setLayout(gridBagLayout3);
 483     serverLabel.setText("Address");
 484     serverLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 485     serverLabel.setFont(verdana11);
 486     proxyServerTB.setFont(verdana11);
 487     proxyPortTB.setFont(verdana11);
 488     portLabel.setFont(verdana11);
 489     portLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 490     portLabel.setText("Port");
 491     browserLabel.setFont(new java.awt.Font("SansSerif", 0, 11));
 492     browserLabel.setHorizontalAlignment(SwingConstants.TRAILING);
 493     browserLabel.setText("Default Browser (Unix)");
 494     defaultBrowser.setFont(verdana11);
 495     defaultBrowser.setText("");
 496     usagestats.setText("Send usage statistics");
 497     usagestats.setFont(verdana11);
 498     usagestats.setHorizontalAlignment(SwingConstants.RIGHT);
 499     usagestats.setHorizontalTextPosition(SwingConstants.LEADING);
 500     questionnaire.setText("Check for questionnaires");
 501     questionnaire.setFont(verdana11);
 502     questionnaire.setHorizontalAlignment(SwingConstants.RIGHT);
 503     questionnaire.setHorizontalTextPosition(SwingConstants.LEADING);
 504     versioncheck.setText("Check for latest version");
 505     versioncheck.setFont(verdana11);
 506     versioncheck.setHorizontalAlignment(SwingConstants.RIGHT);
 507     versioncheck.setHorizontalTextPosition(SwingConstants.LEADING);
 508     newLink.setText("New");
 509     newLink.addActionListener(new java.awt.event.ActionListener()
 510     {
 511       public void actionPerformed(ActionEvent e)
 512       {
 513         newLink_actionPerformed(e);
 514       }
 515     });
 516     editLink.setText("Edit");
 517     editLink.addActionListener(new java.awt.event.ActionListener()
 518     {
 519       public void actionPerformed(ActionEvent e)
 520       {
 521         editLink_actionPerformed(e);
 522       }
 523     });
 524     deleteLink.setText("Delete");
 525     deleteLink.addActionListener(new java.awt.event.ActionListener()
 526     {
 527       public void actionPerformed(ActionEvent e)
 528       {
 529         deleteLink_actionPerformed(e);
 530       }
 531     });
 532
 533     linkURLList.addListSelectionListener(new ListSelectionListener()
 534     {
 535       public void valueChanged(ListSelectionEvent e)
 536       {
 537         int index = linkURLList.getSelectedIndex();
 538         linkNameList.setSelectedIndex(index);
 539       }
 540     });
 541
 542     linkNameList.addListSelectionListener(new ListSelectionListener()
 543     {
 544       public void valueChanged(ListSelectionEvent e)
 545       {
 546         int index = linkNameList.getSelectedIndex();
 547         linkURLList.setSelectedIndex(index);
 548       }
 549     });
 550
 551     linkScrollPane.setBorder(null);
 552     linkPanel.setBorder(new TitledBorder("URL link from Sequence ID"));
 553     linkPanel.setLayout(borderLayout2);
 554     editLinkButtons.setLayout(gridLayout1);
 555     gridLayout1.setRows(3);
 556     linkNameList.setFont(verdana11);
 557     linkNameList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
 558     linkPanel2.setLayout(borderLayout3);
 559     linkURLList.setFont(verdana11);
 560     linkURLList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
 561
 562     defaultBrowser.addMouseListener(new MouseAdapter()
 563     {
 564       public void mouseClicked(MouseEvent e)
 565       {
 566         if (e.getClickCount() > 1)
 567         {
 568           defaultBrowser_mouseClicked(e);
 569         }
 570       }
 571     });
 572     useProxy.setFont(verdana11);
 573     useProxy.setHorizontalAlignment(SwingConstants.RIGHT);
 574     useProxy.setHorizontalTextPosition(SwingConstants.LEADING);
 575     useProxy.setText("Use a proxy server");
 576     useProxy.addActionListener(new ActionListener()
 577     {
 578       public void actionPerformed(ActionEvent e)
 579       {
 580         useProxy_actionPerformed();
 581       }
 582     });
 583     jPanel1.setBorder(titledBorder1);
 584     jPanel1.setLayout(gridBagLayout1);
 585     sortby.setFont(verdana11);
 586     sortby.setBounds(new Rectangle(172, 249, 155, 21));
 587     sortLabel.setFont(verdana11);
 588     sortLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 589     sortLabel.setText("Sort by ");
 590     jPanel2.setBounds(new Rectangle(7, 17, 158, 278));
 591     jPanel2.setLayout(gridLayout2);
 592     gridLayout2.setRows(12);
 593     exportTab.setLayout(null);
 594     epsLabel.setFont(verdana11);
 595     epsLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 596     epsLabel.setText("EPS Rendering Style");
 597     epsLabel.setBounds(new Rectangle(9, 31, 140, 24));
 598     epsRendering.setFont(verdana11);
 599     epsRendering.setBounds(new Rectangle(154, 34, 187, 21));
 600     jLabel1.setFont(verdana11);
 601     jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
 602     jLabel1.setText("Append /start-end (/15-380)");
 603     jLabel1.setFont(verdana11);
 604     fastajv.setFont(verdana11);
 605     fastajv.setHorizontalAlignment(SwingConstants.LEFT);
 606     clustaljv.setText("Clustal     ");
 607     blcjv.setText("BLC     ");
 608     fastajv.setText("Fasta     ");
 609     msfjv.setText("MSF     ");
 610     pfamjv.setText("PFAM     ");
 611     pileupjv.setText("Pileup     ");
 612     msfjv.setFont(verdana11);
 613     msfjv.setHorizontalAlignment(SwingConstants.LEFT);
 614     pirjv.setText("PIR     ");
 615     jPanel11.setFont(verdana11);
 616     jPanel11.setBorder(titledBorder2);
 617     jPanel11.setBounds(new Rectangle(30, 72, 196, 182));
 618     jPanel11.setLayout(gridLayout3);
 619     blcjv.setFont(verdana11);
 620     blcjv.setHorizontalAlignment(SwingConstants.LEFT);
 621     clustaljv.setFont(verdana11);
 622     clustaljv.setHorizontalAlignment(SwingConstants.LEFT);
 623     pfamjv.setFont(verdana11);
 624     pfamjv.setHorizontalAlignment(SwingConstants.LEFT);
 625     pileupjv.setFont(verdana11);
 626     pileupjv.setHorizontalAlignment(SwingConstants.LEFT);
 627     pirjv.setFont(verdana11);
 628     pirjv.setHorizontalAlignment(SwingConstants.LEFT);
 629     seqLimit.setFont(verdana11);
 630     seqLimit.setHorizontalAlignment(SwingConstants.RIGHT);
 631     seqLimit.setHorizontalTextPosition(SwingConstants.LEFT);
 632     seqLimit.setText("Full Sequence Id");
 633     gridLayout3.setRows(8);
 634     smoothFont.setFont(verdana11);
 635     smoothFont.setHorizontalAlignment(SwingConstants.RIGHT);
 636     smoothFont.setHorizontalTextPosition(SwingConstants.LEADING);
 637     smoothFont.setText("Smooth Font");
 638     calcTab.setLayout(null);
 639     autoCalculateConsCheck.setFont(new java.awt.Font("Verdana", Font.PLAIN,
 640             11));
 641     autoCalculateConsCheck.setText("AutoCalculate Consensus");
 642     autoCalculateConsCheck.setBounds(new Rectangle(21, 52, 209, 23));
 643     padGaps.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
 644     padGaps.setText("Pad gaps when editing");
 645     padGaps.setBounds(new Rectangle(22, 94, 168, 23));
 646     modellerOutput.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
 647     modellerOutput.setText("Use Modeller Output");
 648     modellerOutput.setBounds(new Rectangle(228, 226, 168, 23));
 649     dasPanel.setLayout(borderLayout4);
 650     wsPanel.setLayout(borderLayout5);
 651     wrap.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
 652     wrap.setHorizontalAlignment(SwingConstants.TRAILING);
 653     wrap.setHorizontalTextPosition(SwingConstants.LEADING);
 654     wrap.setText("Wrap Alignment");
 655     rightAlign.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
 656     rightAlign.setForeground(Color.black);
 657     rightAlign.setHorizontalAlignment(SwingConstants.RIGHT);
 658     rightAlign.setHorizontalTextPosition(SwingConstants.LEFT);
 659     rightAlign.setText("Right Align Ids");
 660     idItalics.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
 661     idItalics.setHorizontalAlignment(SwingConstants.RIGHT);
 662     idItalics.setHorizontalTextPosition(SwingConstants.LEADING);
 663     idItalics.setText("Sequence Name Italics");
 664     openoverv.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
 665     openoverv.setActionCommand("Open Overview");
 666     openoverv.setHorizontalAlignment(SwingConstants.RIGHT);
 667     openoverv.setHorizontalTextPosition(SwingConstants.LEFT);
 668     openoverv.setText("Open Overview");
 669     jPanel2.add(fullScreen);
 670     jPanel2.add(openoverv);
 671     jPanel2.add(seqLimit);
 672     jPanel2.add(rightAlign);
 673     jPanel2.add(fontLabel);
 674     jPanel2.add(showUnconserved);
 675     jPanel2.add(idItalics);
 676     jPanel2.add(smoothFont);
 677     jPanel2.add(gapLabel);
 678     jPanel2.add(wrap);
 679     jPanel2.add(sortLabel);
 680     jPanel2.add(startupCheckbox);
 681     visualTab.add(annotations);
 682     visualTab.add(startupFileTextfield);
 683     visualTab.add(sortby);
 684     visualTab.add(gapSymbolCB);
 685     visualTab.add(fontNameCB);
 686     visualTab.add(fontSizeCB);
 687     visualTab.add(fontStyleCB);
 688     annsettingsPanel.setBounds(new Rectangle(173, 34, 300, 61));
 689     annsettingsPanel.setLayout(new FlowLayout(FlowLayout.LEFT, 0, 0));
 690     annsettingsPanel.add(autoAnnotSettings1);
 691     annsettingsPanel.add(autoAnnotSettings2);
 692     annsettingsPanel.add(autoAnnotSettings3);
 693     autoAnnotSettings1.setLayout(new GridLayout(3, 1, 0, 0));
 694     autoAnnotSettings2.setLayout(new GridLayout(3, 1, 0, 0));
 695     autoAnnotSettings3.setLayout(new GridLayout(3, 1, 0, 0));
 696     visualTab.add(annsettingsPanel);
 697     Border jb = new EmptyBorder(1, 1, 4, 5);
 698     quality.setBorder(jb);
 699     conservation.setBorder(jb);
 700     identity.setBorder(jb);
 701     showConsensbits.setBorder(jb);
 702     showGroupbits.setBorder(jb);
 703     showGroupConsensus.setBorder(jb);
 704     showGroupConservation.setBorder(jb);
 705     showConsensHistogram.setBorder(jb);
 706     showConsensLogo.setBorder(jb);
 707
 708     autoAnnotSettings2.add(conservation);
 709     autoAnnotSettings1.add(quality);
 710     autoAnnotSettings3.add(identity);
 711     autoAnnotSettings1.add(showGroupbits);
 712     autoAnnotSettings3.add(showGroupConsensus);
 713     autoAnnotSettings2.add(showGroupConservation);
 714     autoAnnotSettings1.add(showConsensbits);
 715     autoAnnotSettings2.add(showConsensHistogram);
 716     autoAnnotSettings3.add(showConsensLogo);
 717
 718     JPanel tooltipSettings = new JPanel();
 719     tooltipSettings.setBorder(new TitledBorder("Sequence ID Tooltip"));
 720     tooltipSettings.setBounds(173, 130, 200, 62);
 721     tooltipSettings.setLayout(new GridLayout(2, 1));
 722     tooltipSettings.add(showDbRefTooltip);
 723     tooltipSettings.add(showNpTooltip);
 724     visualTab.add(tooltipSettings);
 725     visualTab.add(jPanel2);
 726     addtoLayout(visual2Tab, "Default Colourscheme for alignment", colourLabel, colour);
 727     addtoLayout(visual2Tab, "Default Minimum Colour for annotation shading", mincolourLabel,minColour);
 728     addtoLayout(visual2Tab,"Default Maximum Colour for annotation shading", maxcolourLabel, maxColour);
 729
 730 //    visual2panel.add(minColour);
 731 //    visual2panel.add(maxColour);
 732 //    visual2Tab.add(visual2panel);
 733
 734     linkPanel.add(editLinkButtons, BorderLayout.EAST);
 735     editLinkButtons.add(newLink, null);
 736     editLinkButtons.add(editLink, null);
 737     editLinkButtons.add(deleteLink, null);
 738     linkPanel.add(linkScrollPane, BorderLayout.CENTER);
 739     linkScrollPane.getViewport().add(linkPanel2, null);
 740     linkPanel2.add(linkURLList, BorderLayout.CENTER);
 741     linkPanel2.add(linkNameList, BorderLayout.WEST);
 742     okCancelPanel.add(ok);
 743     okCancelPanel.add(cancel);
 744     this.add(tabbedPane, java.awt.BorderLayout.CENTER);
 745
 746     this.add(okCancelPanel, java.awt.BorderLayout.SOUTH);
 747     jPanel1.add(serverLabel, new GridBagConstraints(0, 1, 1, 1, 0.0, 0.0,
 748             GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
 749                     2, 4, 0), 5, 0));
 750     jPanel1.add(portLabel, new GridBagConstraints(2, 1, 1, 1, 0.0, 0.0,
 751             GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
 752                     0, 4, 0), 11, 6));
 753     connectTab.add(linkPanel, new GridBagConstraints(0, 0, 2, 1, 1.0, 1.0,
 754             GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(
 755                     16, 0, 0, 12), 359, -17));
 756     connectTab.add(jPanel1, new GridBagConstraints(0, 2, 2, 1, 1.0, 1.0,
 757             GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(
 758                     21, 0, 35, 12), 4, 6));
 759     connectTab.add(browserLabel, new GridBagConstraints(0, 1, 1, 1, 0.0,
 760             0.0, GridBagConstraints.WEST, GridBagConstraints.NONE,
 761             new Insets(16, 0, 0, 0), 5, 1));
 762     jPanel1.add(proxyPortTB, new GridBagConstraints(3, 1, 1, 1, 1.0, 0.0,
 763             GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 764             new Insets(0, 2, 4, 2), 54, 1));
 765     jPanel1.add(proxyServerTB, new GridBagConstraints(1, 1, 1, 1, 1.0, 0.0,
 766             GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 767             new Insets(0, 2, 4, 0), 263, 1));
 768     connectTab.add(defaultBrowser, new GridBagConstraints(1, 1, 1, 1, 1.0,
 769             0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 770             new Insets(15, 0, 0, 15), 307, 1));
 771     connectTab.add(usagestats, new GridBagConstraints(0, 4, 1, 1, 1.0, 0.0,
 772             GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 773             new Insets(0, 2, 4, 2), 70, 1));
 774     connectTab.add(questionnaire, new GridBagConstraints(1, 4, 1, 1, 1.0,
 775             0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 776             new Insets(0, 2, 4, 2), 70, 1));
 777     connectTab.add(versioncheck, new GridBagConstraints(0, 5, 1, 1, 1.0,
 778             0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 779             new Insets(0, 2, 4, 2), 70, 1));
 780
 781     jPanel1.add(useProxy, new GridBagConstraints(0, 0, 2, 1, 0.0, 0.0,
 782             GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
 783                     2, 5, 185), 2, -4));
 784     DefaultListCellRenderer dlcr = new DefaultListCellRenderer();
 785     dlcr.setHorizontalAlignment(DefaultListCellRenderer.CENTER);
 786     gapSymbolCB.setRenderer(dlcr);
 787
 788     tabbedPane.add(visualTab, "Visual");
 789     tabbedPane.add(visual2Tab,"Colours");
 790     tabbedPane.add(connectTab, "Connections");
 791     tabbedPane.add(exportTab, "Output");
 792     jPanel11.add(jLabel1);
 793     jPanel11.add(blcjv);
 794     jPanel11.add(clustaljv);
 795     jPanel11.add(fastajv);
 796     jPanel11.add(msfjv);
 797     jPanel11.add(pfamjv);
 798     jPanel11.add(pileupjv);
 799     jPanel11.add(pirjv);
 800     exportTab.add(modellerOutput);
 801     tabbedPane.add(calcTab, "Editing");
 802     calcTab.add(autoCalculateConsCheck);
 803     calcTab.add(padGaps);
 804     tabbedPane.add(dasPanel, "DAS Settings");
 805     tabbedPane.add(wsPanel, "Web Services");
 806
 807     exportTab.add(epsLabel);
 808     exportTab.add(epsRendering);
 809     exportTab.add(jPanel11);
 810   }
 811
 812   protected void maxColour_actionPerformed()
 813   {
 814     // TODO Auto-generated method stub
 815
 816   }
 817
 818   protected void minColour_actionPerformed()
 819   {
 820     // TODO Auto-generated method stub
 821
 822   }
 823
 824   protected void showunconserved_actionPerformed(ActionEvent e)
 825   {
 826     // TODO Auto-generated method stub
 827
 828   }
 829
 830   /**
 831    * DOCUMENT ME!
 832    *
 833    * @param e
 834    *          DOCUMENT ME!
 835    */
 836   public void ok_actionPerformed(ActionEvent e)
 837   {
 838   }
 839
 840   /**
 841    * DOCUMENT ME!
 842    *
 843    * @param e
 844    *          DOCUMENT ME!
 845    */
 846   public void cancel_actionPerformed(ActionEvent e)
 847   {
 848   }
 849
 850   /**
 851    * DOCUMENT ME!
 852    *
 853    * @param e
 854    *          DOCUMENT ME!
 855    */
 856   public void annotations_actionPerformed(ActionEvent e)
 857   {
 858   }
 859
 860   /**
 861    * DOCUMENT ME!
 862    */
 863   public void startupFileTextfield_mouseClicked()
 864   {
 865   }
 866
 867   public void newLink_actionPerformed(ActionEvent e)
 868   {
 869
 870   }
 871
 872   public void editLink_actionPerformed(ActionEvent e)
 873   {
 874
 875   }
 876
 877   public void deleteLink_actionPerformed(ActionEvent e)
 878   {
 879
 880   }
 881
 882   public void defaultBrowser_mouseClicked(MouseEvent e)
 883   {
 884
 885   }
 886
 887   public void linkURLList_keyTyped(KeyEvent e)
 888   {
 889
 890   }
 891
 892   public void useProxy_actionPerformed()
 893   {
 894     proxyServerTB.setEnabled(useProxy.isSelected());
 895     proxyPortTB.setEnabled(useProxy.isSelected());
 896   }
 897
 898 }