src/jalview/jbgui/GPreferences.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   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
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.jbgui;
  22
  23 import jalview.fts.core.FTSDataColumnPreferences;
  24 import jalview.fts.core.FTSDataColumnPreferences.PreferenceSource;
  25 import jalview.fts.service.pdb.PDBFTSRestClient;
  26 import jalview.gui.JvSwingUtils;
  27 import jalview.gui.StructureViewer.ViewerType;
  28 import jalview.util.MessageManager;
  29
  30 import java.awt.BorderLayout;
  31 import java.awt.Color;
  32 import java.awt.Component;
  33 import java.awt.Dimension;
  34 import java.awt.FlowLayout;
  35 import java.awt.Font;
  36 import java.awt.GridBagConstraints;
  37 import java.awt.GridBagLayout;
  38 import java.awt.GridLayout;
  39 import java.awt.Insets;
  40 import java.awt.Rectangle;
  41 import java.awt.event.ActionEvent;
  42 import java.awt.event.ActionListener;
  43 import java.awt.event.FocusEvent;
  44 import java.awt.event.KeyEvent;
  45 import java.awt.event.MouseAdapter;
  46 import java.awt.event.MouseEvent;
  47
  48 import javax.swing.AbstractCellEditor;
  49 import javax.swing.BorderFactory;
  50 import javax.swing.ButtonGroup;
  51 import javax.swing.DefaultListCellRenderer;
  52 import javax.swing.JButton;
  53 import javax.swing.JCheckBox;
  54 import javax.swing.JComboBox;
  55 import javax.swing.JFileChooser;
  56 import javax.swing.JLabel;
  57 import javax.swing.JPanel;
  58 import javax.swing.JRadioButton;
  59 import javax.swing.JScrollPane;
  60 import javax.swing.JTabbedPane;
  61 import javax.swing.JTable;
  62 import javax.swing.JTextField;
  63 import javax.swing.ListSelectionModel;
  64 import javax.swing.SwingConstants;
  65 import javax.swing.border.Border;
  66 import javax.swing.border.EmptyBorder;
  67 import javax.swing.border.EtchedBorder;
  68 import javax.swing.border.TitledBorder;
  69 import javax.swing.event.ChangeEvent;
  70 import javax.swing.event.ChangeListener;
  71 import javax.swing.table.TableCellEditor;
  72 import javax.swing.table.TableCellRenderer;
  73
  74 /**
  75  * Base class for the Preferences panel.
  76  *
  77  * @author $author$
  78  * @version $Revision$
  79  */
  80 public class GPreferences extends JPanel
  81 {
  82   private static final Font LABEL_FONT = JvSwingUtils.getLabelFont();
  83
  84   private static final Font LABEL_FONT_ITALIC = JvSwingUtils.getLabelFont(
  85           false, true);
  86
  87   /*
  88    * Visual tab components
  89    */
  90   protected JCheckBox fullScreen = new JCheckBox();
  91
  92   protected JCheckBox openoverv = new JCheckBox();
  93
  94   protected JCheckBox seqLimit = new JCheckBox();
  95
  96   protected JCheckBox rightAlign = new JCheckBox();
  97
  98   protected JComboBox<String> fontSizeCB = new JComboBox<String>();
  99
 100   protected JComboBox<String> fontStyleCB = new JComboBox<String>();
 101
 102   protected JComboBox<String> fontNameCB = new JComboBox<String>();
 103
 104   protected JCheckBox showUnconserved = new JCheckBox();
 105
 106   protected JCheckBox idItalics = new JCheckBox();
 107
 108   protected JCheckBox smoothFont = new JCheckBox();
 109
 110   protected JCheckBox scaleProteinToCdna = new JCheckBox();
 111
 112   protected JComboBox<String> gapSymbolCB = new JComboBox<String>();
 113
 114   protected JCheckBox wrap = new JCheckBox();
 115
 116   protected JComboBox<String> sortby = new JComboBox<String>();
 117
 118   protected JComboBox<String> sortAnnBy = new JComboBox<String>();
 119
 120   protected JComboBox<String> sortAutocalc = new JComboBox<String>();
 121
 122   protected JCheckBox startupCheckbox = new JCheckBox();
 123
 124   protected JTextField startupFileTextfield = new JTextField();
 125
 126   // below are in the 'second column'
 127   protected JCheckBox annotations = new JCheckBox();
 128
 129   protected JCheckBox quality = new JCheckBox();
 130
 131   protected JCheckBox conservation = new JCheckBox();
 132
 133   protected JCheckBox identity = new JCheckBox();
 134
 135   protected JCheckBox showGroupConsensus = new JCheckBox();
 136
 137   protected JCheckBox showGroupConservation = new JCheckBox();
 138
 139   protected JCheckBox showConsensHistogram = new JCheckBox();
 140
 141   protected JCheckBox showConsensLogo = new JCheckBox();
 142
 143   protected JCheckBox showDbRefTooltip = new JCheckBox();
 144
 145   protected JCheckBox showNpTooltip = new JCheckBox();
 146
 147   /*
 148    * Structure tab and components
 149    */
 150   protected JPanel structureTab;
 151
 152   protected JCheckBox structFromPdb = new JCheckBox();
 153
 154   protected JCheckBox useRnaView = new JCheckBox();
 155
 156   protected JCheckBox addSecondaryStructure = new JCheckBox();
 157
 158   protected JCheckBox addTempFactor = new JCheckBox();
 159
 160   protected JComboBox<String> structViewer = new JComboBox<String>();
 161
 162   protected JTextField chimeraPath = new JTextField();
 163
 164   protected ButtonGroup mappingMethod = new ButtonGroup();
 165
 166   protected JRadioButton siftsMapping = new JRadioButton();
 167
 168   protected JRadioButton nwMapping = new JRadioButton();
 169
 170   /*
 171    * Colours tab components
 172    */
 173   protected JPanel minColour = new JPanel();
 174
 175   protected JPanel maxColour = new JPanel();
 176
 177   protected JComboBox<String> protColour = new JComboBox<String>();
 178
 179   protected JComboBox<String> nucColour = new JComboBox<String>();
 180
 181   /*
 182    * Connections tab components
 183    */
 184   protected JTable linkUrlTable = new JTable();
 185
 186   protected JButton editLink = new JButton();
 187
 188   protected JButton deleteLink = new JButton();
 189
 190   protected JTextField filterTB = new JTextField();
 191
 192   protected JButton doReset = new JButton();
 193
 194   protected JButton userOnly = new JButton();
 195
 196   protected JLabel portLabel = new JLabel();
 197
 198   protected JLabel serverLabel = new JLabel();
 199
 200   protected JTextField proxyServerTB = new JTextField();
 201
 202   protected JTextField proxyPortTB = new JTextField();
 203
 204   protected JTextField defaultBrowser = new JTextField();
 205
 206   protected JCheckBox useProxy = new JCheckBox();
 207
 208   protected JCheckBox usagestats = new JCheckBox();
 209
 210   protected JCheckBox questionnaire = new JCheckBox();
 211
 212   protected JCheckBox versioncheck = new JCheckBox();
 213
 214   /*
 215    * Output tab components
 216    */
 217   protected JComboBox<Object> epsRendering = new JComboBox<Object>();
 218
 219   protected JLabel userIdWidthlabel = new JLabel();
 220
 221   protected JCheckBox autoIdWidth = new JCheckBox();
 222
 223   protected JTextField userIdWidth = new JTextField();
 224
 225   protected JCheckBox blcjv = new JCheckBox();
 226
 227   protected JCheckBox pileupjv = new JCheckBox();
 228
 229   protected JCheckBox clustaljv = new JCheckBox();
 230
 231   protected JCheckBox msfjv = new JCheckBox();
 232
 233   protected JCheckBox fastajv = new JCheckBox();
 234
 235   protected JCheckBox pfamjv = new JCheckBox();
 236
 237   protected JCheckBox pirjv = new JCheckBox();
 238
 239   protected JCheckBox modellerOutput = new JCheckBox();
 240
 241   protected JCheckBox embbedBioJSON = new JCheckBox();
 242
 243   /*
 244    * Editing tab components
 245    */
 246   protected JCheckBox autoCalculateConsCheck = new JCheckBox();
 247
 248   protected JCheckBox padGaps = new JCheckBox();
 249
 250   protected JCheckBox sortByTree = new JCheckBox();
 251
 252   /*
 253    * DAS Settings tab
 254    */
 255   protected JPanel dasTab = new JPanel();
 256
 257   /*
 258    * Web Services tab
 259    */
 260   protected JPanel wsTab = new JPanel();
 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    * Construct the panel and its tabbed sub-panels.
 278    *
 279    * @throws Exception
 280    */
 281   private void jbInit() throws Exception
 282   {
 283     final JTabbedPane tabbedPane = new JTabbedPane();
 284     this.setLayout(new BorderLayout());
 285     JPanel okCancelPanel = initOkCancelPanel();
 286     this.add(tabbedPane, BorderLayout.CENTER);
 287     this.add(okCancelPanel, BorderLayout.SOUTH);
 288
 289     tabbedPane.add(initVisualTab(),
 290             MessageManager.getString("label.visual"));
 291
 292     tabbedPane.add(initColoursTab(),
 293             MessageManager.getString("label.colours"));
 294
 295     tabbedPane.add(initStructureTab(),
 296             MessageManager.getString("label.structure"));
 297
 298     tabbedPane.add(initConnectionsTab(),
 299             MessageManager.getString("label.connections"));
 300
 301     tabbedPane.add(initLinksTab(),
 302             MessageManager.getString("label.urllinks"));
 303
 304     tabbedPane.add(initOutputTab(),
 305             MessageManager.getString("label.output"));
 306
 307     tabbedPane.add(initEditingTab(),
 308             MessageManager.getString("label.editing"));
 309
 310     /*
 311      * See DasSourceBrowser for the real work of configuring this tab.
 312      */
 313     dasTab.setLayout(new BorderLayout());
 314     tabbedPane.add(dasTab, MessageManager.getString("label.das_settings"));
 315
 316     /*
 317      * See WsPreferences for the real work of configuring this tab.
 318      */
 319     wsTab.setLayout(new BorderLayout());
 320     tabbedPane.add(wsTab, MessageManager.getString("label.web_services"));
 321
 322     /*
 323      * Handler to validate a tab before leaving it - currently only for
 324      * Structure.
 325      */
 326     tabbedPane.addChangeListener(new ChangeListener()
 327     {
 328       private Component lastTab;
 329
 330       @Override
 331       public void stateChanged(ChangeEvent e)
 332       {
 333         if (lastTab == structureTab
 334                 && tabbedPane.getSelectedComponent() != structureTab)
 335         {
 336           if (!validateStructure())
 337           {
 338             tabbedPane.setSelectedComponent(structureTab);
 339             return;
 340           }
 341         }
 342         lastTab = tabbedPane.getSelectedComponent();
 343       }
 344
 345     });
 346   }
 347
 348   /**
 349    * Initialises the Editing tabbed panel.
 350    *
 351    * @return
 352    */
 353   private JPanel initEditingTab()
 354   {
 355     JPanel editingTab = new JPanel();
 356     editingTab.setLayout(null);
 357     autoCalculateConsCheck.setFont(LABEL_FONT);
 358     autoCalculateConsCheck.setText(MessageManager
 359             .getString("label.autocalculate_consensus"));
 360     autoCalculateConsCheck.setBounds(new Rectangle(21, 52, 209, 23));
 361     padGaps.setFont(LABEL_FONT);
 362     padGaps.setText(MessageManager.getString("label.pad_gaps_when_editing"));
 363     padGaps.setBounds(new Rectangle(22, 94, 168, 23));
 364     sortByTree.setFont(LABEL_FONT);
 365     sortByTree
 366             .setText(MessageManager.getString("label.sort_with_new_tree"));
 367     sortByTree
 368             .setToolTipText(MessageManager
 369                     .getString("label.any_trees_calculated_or_loaded_alignment_automatically_sort"));
 370     sortByTree.setBounds(new Rectangle(22, 136, 168, 23));
 371     editingTab.add(autoCalculateConsCheck);
 372     editingTab.add(padGaps);
 373     editingTab.add(sortByTree);
 374     return editingTab;
 375   }
 376
 377   /**
 378    * Initialises the Output tabbed panel.
 379    *
 380    * @return
 381    */
 382   private JPanel initOutputTab()
 383   {
 384     JPanel outputTab = new JPanel();
 385     outputTab.setLayout(null);
 386     JLabel epsLabel = new JLabel();
 387     epsLabel.setFont(LABEL_FONT);
 388     epsLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 389     epsLabel.setText(MessageManager.getString("label.eps_rendering_style"));
 390     epsLabel.setBounds(new Rectangle(9, 31, 140, 24));
 391     epsRendering.setFont(LABEL_FONT);
 392     epsRendering.setBounds(new Rectangle(154, 34, 187, 21));
 393     JLabel jLabel1 = new JLabel();
 394     jLabel1.setFont(LABEL_FONT);
 395     jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
 396     jLabel1.setText(MessageManager.getString("label.append_start_end"));
 397     jLabel1.setFont(LABEL_FONT);
 398     fastajv.setFont(LABEL_FONT);
 399     fastajv.setHorizontalAlignment(SwingConstants.LEFT);
 400     clustaljv.setText(MessageManager.getString("label.clustal") + "     ");
 401     blcjv.setText(MessageManager.getString("label.blc") + "     ");
 402     fastajv.setText(MessageManager.getString("label.fasta") + "     ");
 403     msfjv.setText(MessageManager.getString("label.msf") + "     ");
 404     pfamjv.setText(MessageManager.getString("label.pfam") + "     ");
 405     pileupjv.setText(MessageManager.getString("label.pileup") + "     ");
 406     msfjv.setFont(LABEL_FONT);
 407     msfjv.setHorizontalAlignment(SwingConstants.LEFT);
 408     pirjv.setText(MessageManager.getString("label.pir") + "     ");
 409     JPanel jPanel11 = new JPanel();
 410     jPanel11.setFont(LABEL_FONT);
 411     TitledBorder titledBorder2 = new TitledBorder(
 412             MessageManager.getString("label.file_output"));
 413     jPanel11.setBorder(titledBorder2);
 414     jPanel11.setBounds(new Rectangle(30, 72, 196, 182));
 415     GridLayout gridLayout3 = new GridLayout();
 416     jPanel11.setLayout(gridLayout3);
 417     gridLayout3.setRows(8);
 418     blcjv.setFont(LABEL_FONT);
 419     blcjv.setHorizontalAlignment(SwingConstants.LEFT);
 420     clustaljv.setFont(LABEL_FONT);
 421     clustaljv.setHorizontalAlignment(SwingConstants.LEFT);
 422     pfamjv.setFont(LABEL_FONT);
 423     pfamjv.setHorizontalAlignment(SwingConstants.LEFT);
 424     pileupjv.setFont(LABEL_FONT);
 425     pileupjv.setHorizontalAlignment(SwingConstants.LEFT);
 426     pirjv.setFont(LABEL_FONT);
 427     pirjv.setHorizontalAlignment(SwingConstants.LEFT);
 428     autoIdWidth.setFont(LABEL_FONT);
 429     autoIdWidth.setText(MessageManager
 430             .getString("label.automatically_set_id_width"));
 431     autoIdWidth.setToolTipText(JvSwingUtils.wrapTooltip(true,
 432             MessageManager
 433                     .getString("label.adjusts_width_generated_eps_png")));
 434     autoIdWidth.setBounds(new Rectangle(228, 96, 188, 23));
 435     autoIdWidth.addActionListener(new ActionListener()
 436     {
 437
 438       @Override
 439       public void actionPerformed(ActionEvent e)
 440       {
 441         autoIdWidth_actionPerformed();
 442       }
 443     });
 444     userIdWidthlabel.setFont(LABEL_FONT);
 445     userIdWidthlabel.setText(MessageManager
 446             .getString("label.figure_id_column_width"));
 447     userIdWidth
 448             .setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager
 449                     .getString("label.manually_specify_width_left_column")));
 450     userIdWidthlabel
 451             .setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager
 452                     .getString("label.manually_specify_width_left_column")));
 453     userIdWidthlabel.setBounds(new Rectangle(236, 120, 168, 23));
 454     userIdWidth.setFont(JvSwingUtils.getTextAreaFont());
 455     userIdWidth.setText("");
 456     userIdWidth.setBounds(new Rectangle(232, 144, 84, 23));
 457     userIdWidth.addActionListener(new ActionListener()
 458     {
 459
 460       @Override
 461       public void actionPerformed(ActionEvent e)
 462       {
 463         userIdWidth_actionPerformed();
 464       }
 465     });
 466     modellerOutput.setFont(LABEL_FONT);
 467     modellerOutput.setText(MessageManager
 468             .getString("label.use_modeller_output"));
 469     modellerOutput.setBounds(new Rectangle(228, 226, 168, 23));
 470     embbedBioJSON.setFont(LABEL_FONT);
 471     embbedBioJSON.setText(MessageManager.getString("label.embbed_biojson"));
 472     embbedBioJSON.setBounds(new Rectangle(228, 200, 250, 23));
 473
 474     jPanel11.add(jLabel1);
 475     jPanel11.add(blcjv);
 476     jPanel11.add(clustaljv);
 477     jPanel11.add(fastajv);
 478     jPanel11.add(msfjv);
 479     jPanel11.add(pfamjv);
 480     jPanel11.add(pileupjv);
 481     jPanel11.add(pirjv);
 482     outputTab.add(autoIdWidth);
 483     outputTab.add(userIdWidth);
 484     outputTab.add(userIdWidthlabel);
 485     outputTab.add(modellerOutput);
 486     outputTab.add(embbedBioJSON);
 487     outputTab.add(epsLabel);
 488     outputTab.add(epsRendering);
 489     outputTab.add(jPanel11);
 490     return outputTab;
 491   }
 492
 493   /**
 494    * Initialises the Connections tabbed panel.
 495    *
 496    * @return
 497    */
 498   private JPanel initConnectionsTab()
 499   {
 500     JPanel connectTab = new JPanel();
 501     connectTab.setLayout(new GridBagLayout());
 502
 503     // Label for browser text box
 504     JLabel browserLabel = new JLabel();
 505     browserLabel.setFont(LABEL_FONT);
 506     browserLabel.setHorizontalAlignment(SwingConstants.TRAILING);
 507     browserLabel.setText(MessageManager
 508             .getString("label.default_browser_unix"));
 509     defaultBrowser.setFont(LABEL_FONT);
 510     defaultBrowser.setText("");
 511
 512     defaultBrowser.addMouseListener(new MouseAdapter()
 513     {
 514       @Override
 515       public void mouseClicked(MouseEvent e)
 516       {
 517         if (e.getClickCount() > 1)
 518         {
 519           defaultBrowser_mouseClicked(e);
 520         }
 521       }
 522     });
 523
 524     JPanel proxyPanel = initConnTabProxyPanel();
 525     initConnTabCheckboxes();
 526
 527     // Add default Browser text box
 528     connectTab.add(browserLabel, new GridBagConstraints(0, 0, 1, 1, 0.0,
 529             0.0, GridBagConstraints.WEST, GridBagConstraints.NONE,
 530             new Insets(10, 0, 5, 5), 5, 1));
 531     defaultBrowser.setFont(LABEL_FONT);
 532     defaultBrowser.setText("");
 533
 534     connectTab.add(defaultBrowser, new GridBagConstraints(1, 0, 1, 1, 1.0,
 535             0.0, GridBagConstraints.CENTER, GridBagConstraints.HORIZONTAL,
 536             new Insets(10, 0, 5, 10), 30, 1));
 537
 538     // Add proxy server panel
 539     connectTab.add(proxyPanel, new GridBagConstraints(0, 1, 2, 1, 1.0, 0.0,
 540             GridBagConstraints.CENTER, GridBagConstraints.HORIZONTAL,
 541             new Insets(10, 0, 5, 12), 4, 10));
 542
 543     // Add usage stats, version check and questionnaire checkboxes
 544     connectTab.add(usagestats, new GridBagConstraints(0, 2, 1, 1, 1.0, 0.0,
 545             GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 546             new Insets(0, 2, 5, 5), 70, 1));
 547     connectTab.add(questionnaire, new GridBagConstraints(1, 2, 1, 1, 1.0,
 548             0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 549             new Insets(0, 2, 5, 10), 70, 1));
 550     connectTab.add(versioncheck, new GridBagConstraints(0, 3, 1, 1, 1.0,
 551             0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 552             new Insets(0, 2, 5, 5), 70, 1));
 553
 554     // Add padding so the panel doesn't look ridiculous
 555     JPanel spacePanel = new JPanel();
 556     connectTab.add(spacePanel, new GridBagConstraints(0, 4, 1, 1, 1.0, 1.0,
 557             GridBagConstraints.WEST, GridBagConstraints.BOTH, new Insets(0,
 558                     0, 0, 5), 70, 1));
 559
 560     return connectTab;
 561   }
 562
 563   /**
 564    * Initialises the Links tabbed panel.
 565    *
 566    * @return
 567    */
 568   private JPanel initLinksTab()
 569   {
 570     JPanel linkTab = new JPanel();
 571     linkTab.setLayout(new GridBagLayout());
 572
 573     // Set up table for Url links
 574     linkUrlTable.setFillsViewportHeight(true);
 575     linkUrlTable.setAutoResizeMode(JTable.AUTO_RESIZE_ALL_COLUMNS);
 576     linkUrlTable.setAutoCreateRowSorter(true);
 577     linkUrlTable.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
 578
 579     // adjust row height so radio buttons actually fit
 580     // don't do this in the renderer, it causes the awt thread to activate
 581     // constantly
 582     JRadioButton temp = new JRadioButton();
 583     linkUrlTable.setRowHeight(temp.getMinimumSize().height);
 584
 585     // Table in scrollpane so that the table is given a scrollbar
 586     JScrollPane linkScrollPane = new JScrollPane(linkUrlTable);
 587     linkScrollPane.setBorder(null);
 588
 589     // Panel for links functionality
 590     JPanel linkPanel = new JPanel(new GridBagLayout());
 591     linkPanel.setBorder(new TitledBorder(MessageManager
 592             .getString("label.url_linkfrom_sequence_id")));
 593
 594     // Put the Url links panel together
 595
 596     // Buttons go at top right, resizing only resizes the blank space vertically
 597     JPanel buttonPanel = initLinkTabUrlButtons();
 598     GridBagConstraints linkConstraints1 = new GridBagConstraints();
 599     linkConstraints1.insets = new Insets(0, 0, 5, 0);
 600     linkConstraints1.gridx = 0;
 601     linkConstraints1.gridy = 0;
 602     linkConstraints1.weightx = 1.0;
 603     linkConstraints1.fill = GridBagConstraints.HORIZONTAL;
 604     linkTab.add(buttonPanel, linkConstraints1);
 605
 606     // Links table goes at top left, resizing resizes the table
 607     GridBagConstraints linkConstraints2 = new GridBagConstraints();
 608     linkConstraints2.insets = new Insets(0, 0, 5, 5);
 609     linkConstraints2.gridx = 0;
 610     linkConstraints2.gridy = 1;
 611     linkConstraints2.weightx = 1.0;
 612     linkConstraints2.weighty = 1.0;
 613     linkConstraints2.fill = GridBagConstraints.BOTH;
 614     linkTab.add(linkScrollPane, linkConstraints2);
 615
 616     // Filter box and buttons goes at bottom left, resizing resizes the text box
 617     JPanel filterPanel = initLinkTabFilterPanel();
 618     GridBagConstraints linkConstraints3 = new GridBagConstraints();
 619     linkConstraints3.insets = new Insets(0, 0, 0, 5);
 620     linkConstraints3.gridx = 0;
 621     linkConstraints3.gridy = 2;
 622     linkConstraints3.weightx = 1.0;
 623     linkConstraints3.fill = GridBagConstraints.HORIZONTAL;
 624     linkTab.add(filterPanel, linkConstraints3);
 625
 626     return linkTab;
 627   }
 628
 629   private JPanel initLinkTabFilterPanel()
 630   {
 631     // Filter textbox and reset button
 632     JLabel filterLabel = new JLabel(
 633             MessageManager.getString("label.filter"));
 634     filterLabel.setFont(LABEL_FONT);
 635     filterLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 636     filterLabel.setHorizontalTextPosition(SwingConstants.LEADING);
 637
 638     filterTB.setFont(LABEL_FONT);
 639     filterTB.setText("");
 640
 641     doReset.setText(MessageManager.getString("action.showall"));
 642     userOnly.setText(MessageManager.getString("action.customfilter"));
 643
 644     // Panel for filter functionality
 645     JPanel filterPanel = new JPanel(new GridBagLayout());
 646     filterPanel.setBorder(new TitledBorder("Filter"));
 647     GridBagConstraints gbc = new GridBagConstraints();
 648     gbc.gridx = 0;
 649     gbc.gridy = 0;
 650     gbc.fill = GridBagConstraints.NONE;
 651     gbc.anchor = GridBagConstraints.WEST;
 652
 653     filterPanel.add(filterLabel, gbc);
 654
 655     GridBagConstraints gbc1 = new GridBagConstraints();
 656     gbc1.gridx = 1;
 657     gbc1.gridwidth = 2;
 658     gbc1.fill = GridBagConstraints.HORIZONTAL;
 659     gbc1.anchor = GridBagConstraints.WEST;
 660     gbc1.weightx = 1.0;
 661     filterPanel.add(filterTB, gbc1);
 662
 663     GridBagConstraints gbc2 = new GridBagConstraints();
 664     gbc2.gridx = 3;
 665     gbc2.fill = GridBagConstraints.NONE;
 666     gbc2.anchor = GridBagConstraints.WEST;
 667     filterPanel.add(doReset, gbc2);
 668
 669     GridBagConstraints gbc3 = new GridBagConstraints();
 670     gbc3.gridx = 4;
 671     gbc3.fill = GridBagConstraints.NONE;
 672     gbc3.anchor = GridBagConstraints.WEST;
 673     filterPanel.add(userOnly, gbc3);
 674
 675     return filterPanel;
 676   }
 677
 678   private JPanel initLinkTabUrlButtons()
 679   {
 680     // Buttons for new / edit / delete Url links
 681     JButton newLink = new JButton();
 682     newLink.setText(MessageManager.getString("action.new"));
 683
 684     editLink.setText(MessageManager.getString("action.edit"));
 685
 686     deleteLink.setText(MessageManager.getString("action.delete"));
 687
 688     // no current selection, so initially disable delete/edit buttons
 689     editLink.setEnabled(false);
 690     deleteLink.setEnabled(false);
 691
 692     newLink.addActionListener(new java.awt.event.ActionListener()
 693     {
 694       @Override
 695       public void actionPerformed(ActionEvent e)
 696       {
 697         newLink_actionPerformed(e);
 698       }
 699     });
 700
 701     editLink.setText(MessageManager.getString("action.edit"));
 702     editLink.addActionListener(new java.awt.event.ActionListener()
 703     {
 704       @Override
 705       public void actionPerformed(ActionEvent e)
 706       {
 707         editLink_actionPerformed(e);
 708       }
 709     });
 710
 711     deleteLink.setText(MessageManager.getString("action.delete"));
 712     deleteLink.addActionListener(new java.awt.event.ActionListener()
 713     {
 714       @Override
 715       public void actionPerformed(ActionEvent e)
 716       {
 717         deleteLink_actionPerformed(e);
 718       }
 719     });
 720
 721     JPanel buttonPanel = new JPanel(new GridBagLayout());
 722     buttonPanel.setBorder(new TitledBorder("Edit links"));
 723     GridBagConstraints gbc = new GridBagConstraints();
 724     gbc.gridx = 0;
 725     gbc.gridy = 0;
 726     gbc.fill = GridBagConstraints.NONE;
 727     buttonPanel.add(newLink, gbc);
 728
 729     GridBagConstraints gbc1 = new GridBagConstraints();
 730     gbc1.gridx = 1;
 731     gbc1.gridy = 0;
 732     gbc1.fill = GridBagConstraints.NONE;
 733     buttonPanel.add(editLink, gbc1);
 734
 735     GridBagConstraints gbc2 = new GridBagConstraints();
 736     gbc2.gridx = 2;
 737     gbc2.gridy = 0;
 738     gbc2.fill = GridBagConstraints.NONE;
 739     buttonPanel.add(deleteLink, gbc2);
 740
 741     GridBagConstraints gbc3 = new GridBagConstraints();
 742     gbc3.gridx = 3;
 743     gbc3.gridy = 0;
 744     gbc3.fill = GridBagConstraints.HORIZONTAL;
 745     gbc3.weightx = 1.0;
 746     JPanel spacePanel = new JPanel();
 747     spacePanel.setBorder(null);
 748     buttonPanel.add(spacePanel, gbc3);
 749
 750     return buttonPanel;
 751   }
 752
 753   /**
 754    * Initialises the proxy server panel in the Connections tab
 755    *
 756    * @return the proxy server panel
 757    */
 758   private JPanel initConnTabProxyPanel()
 759   {
 760     // Label for server text box
 761     serverLabel.setText(MessageManager.getString("label.address"));
 762     serverLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 763     serverLabel.setFont(LABEL_FONT);
 764
 765     // Proxy server and port text boxes
 766     proxyServerTB.setFont(LABEL_FONT);
 767     proxyPortTB.setFont(LABEL_FONT);
 768
 769     // Label for Port text box
 770     portLabel.setFont(LABEL_FONT);
 771     portLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 772     portLabel.setText(MessageManager.getString("label.port"));
 773
 774     // Use proxy server checkbox
 775     useProxy.setFont(LABEL_FONT);
 776     useProxy.setHorizontalAlignment(SwingConstants.RIGHT);
 777     useProxy.setHorizontalTextPosition(SwingConstants.LEADING);
 778     useProxy.setText(MessageManager.getString("label.use_proxy_server"));
 779     useProxy.addActionListener(new ActionListener()
 780     {
 781       @Override
 782       public void actionPerformed(ActionEvent e)
 783       {
 784         useProxy_actionPerformed();
 785       }
 786     });
 787
 788     // Make proxy server panel
 789     JPanel proxyPanel = new JPanel();
 790     TitledBorder titledBorder1 = new TitledBorder(
 791             MessageManager.getString("label.proxy_server"));
 792     proxyPanel.setBorder(titledBorder1);
 793     proxyPanel.setLayout(new GridBagLayout());
 794     proxyPanel.add(serverLabel, new GridBagConstraints(0, 1, 1, 1, 0.0,
 795             0.0, GridBagConstraints.WEST, GridBagConstraints.NONE,
 796             new Insets(0, 2, 2, 0), 5, 0));
 797     proxyPanel.add(portLabel, new GridBagConstraints(2, 1, 1, 1, 0.0, 0.0,
 798             GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
 799                     0, 2, 0), 11, 0));
 800     proxyPanel.add(useProxy, new GridBagConstraints(0, 0, 2, 1, 0.0, 0.0,
 801             GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
 802                     2, 5, 185), 2, -4));
 803     proxyPanel.add(proxyPortTB, new GridBagConstraints(3, 1, 1, 1, 1.0,
 804             0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 805             new Insets(0, 2, 2, 2), 54, 1));
 806     proxyPanel.add(proxyServerTB, new GridBagConstraints(1, 1, 1, 1, 1.0,
 807             0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 808             new Insets(0, 2, 2, 0), 263, 1));
 809
 810     return proxyPanel;
 811   }
 812
 813   /**
 814    * Initialises the checkboxes in the Connections tab
 815    */
 816   private void initConnTabCheckboxes()
 817   {
 818     // Usage stats checkbox label
 819     usagestats.setText(MessageManager
 820             .getString("label.send_usage_statistics"));
 821     usagestats.setFont(LABEL_FONT);
 822     usagestats.setHorizontalAlignment(SwingConstants.RIGHT);
 823     usagestats.setHorizontalTextPosition(SwingConstants.LEADING);
 824
 825     // Questionnaire checkbox label
 826     questionnaire.setText(MessageManager
 827             .getString("label.check_for_questionnaires"));
 828     questionnaire.setFont(LABEL_FONT);
 829     questionnaire.setHorizontalAlignment(SwingConstants.RIGHT);
 830     questionnaire.setHorizontalTextPosition(SwingConstants.LEADING);
 831
 832     // Check for latest version checkbox label
 833     versioncheck.setText(MessageManager
 834             .getString("label.check_for_latest_version"));
 835     versioncheck.setFont(LABEL_FONT);
 836     versioncheck.setHorizontalAlignment(SwingConstants.RIGHT);
 837     versioncheck.setHorizontalTextPosition(SwingConstants.LEADING);
 838   }
 839
 840   /**
 841    * Initialises the parent panel which contains the tabbed sections.
 842    *
 843    * @return
 844    */
 845   private JPanel initOkCancelPanel()
 846   {
 847     JButton ok = new JButton();
 848     ok.setText(MessageManager.getString("action.ok"));
 849     ok.addActionListener(new ActionListener()
 850     {
 851       @Override
 852       public void actionPerformed(ActionEvent e)
 853       {
 854         ok_actionPerformed(e);
 855       }
 856     });
 857     JButton cancel = new JButton();
 858     cancel.setText(MessageManager.getString("action.cancel"));
 859     cancel.addActionListener(new ActionListener()
 860     {
 861       @Override
 862       public void actionPerformed(ActionEvent e)
 863       {
 864         cancel_actionPerformed(e);
 865       }
 866     });
 867     JPanel okCancelPanel = new JPanel();
 868     okCancelPanel.add(ok);
 869     okCancelPanel.add(cancel);
 870     return okCancelPanel;
 871   }
 872
 873   /**
 874    * Initialises the Colours tabbed panel.
 875    *
 876    * @return
 877    */
 878   private JPanel initColoursTab()
 879   {
 880     JPanel coloursTab = new JPanel();
 881     coloursTab.setBorder(new TitledBorder(MessageManager
 882             .getString("action.open_new_alignment")));
 883     coloursTab.setLayout(new FlowLayout());
 884     JLabel mincolourLabel = new JLabel();
 885     mincolourLabel.setFont(LABEL_FONT);
 886     mincolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 887     mincolourLabel.setText(MessageManager.getString("label.min_colour"));
 888     minColour.setFont(LABEL_FONT);
 889     minColour.setBorder(BorderFactory.createEtchedBorder());
 890     minColour.setPreferredSize(new Dimension(40, 20));
 891     minColour.addMouseListener(new MouseAdapter()
 892     {
 893       @Override
 894       public void mousePressed(MouseEvent e)
 895       {
 896         minColour_actionPerformed(minColour);
 897       }
 898     });
 899     JLabel maxcolourLabel = new JLabel();
 900     maxcolourLabel.setFont(LABEL_FONT);
 901     maxcolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 902     maxcolourLabel.setText(MessageManager.getString("label.max_colour"));
 903     maxColour.setFont(LABEL_FONT);
 904     maxColour.setBorder(BorderFactory.createEtchedBorder());
 905     maxColour.setPreferredSize(new Dimension(40, 20));
 906     maxColour.addMouseListener(new MouseAdapter()
 907     {
 908       @Override
 909       public void mousePressed(MouseEvent e)
 910       {
 911         maxColour_actionPerformed(maxColour);
 912       }
 913     });
 914
 915     protColour.setFont(LABEL_FONT);
 916     protColour.setBounds(new Rectangle(172, 225, 155, 21));
 917     JLabel protColourLabel = new JLabel();
 918     protColourLabel.setFont(LABEL_FONT);
 919     protColourLabel.setHorizontalAlignment(SwingConstants.LEFT);
 920     protColourLabel.setText(MessageManager
 921             .getString("label.prot_alignment_colour") + " ");
 922     JvSwingUtils.addtoLayout(coloursTab, MessageManager
 923             .getString("label.default_colour_scheme_for_alignment"),
 924             protColourLabel, protColour);
 925
 926     nucColour.setFont(LABEL_FONT);
 927     nucColour.setBounds(new Rectangle(172, 240, 155, 21));
 928     JLabel nucColourLabel = new JLabel();
 929     nucColourLabel.setFont(LABEL_FONT);
 930     nucColourLabel.setHorizontalAlignment(SwingConstants.LEFT);
 931     nucColourLabel.setText(MessageManager
 932             .getString("label.nuc_alignment_colour") + " ");
 933     JvSwingUtils.addtoLayout(coloursTab, MessageManager
 934             .getString("label.default_colour_scheme_for_alignment"),
 935             nucColourLabel, nucColour);
 936
 937     JPanel annotationShding = new JPanel();
 938     annotationShding.setBorder(new TitledBorder(MessageManager
 939             .getString("label.annotation_shading_default")));
 940     annotationShding.setLayout(new GridLayout(1, 2));
 941     JvSwingUtils.addtoLayout(annotationShding, MessageManager
 942             .getString("label.default_minimum_colour_annotation_shading"),
 943             mincolourLabel, minColour);
 944     JvSwingUtils.addtoLayout(annotationShding, MessageManager
 945             .getString("label.default_maximum_colour_annotation_shading"),
 946             maxcolourLabel, maxColour);
 947     coloursTab.add(annotationShding); // , FlowLayout.LEFT);
 948     return coloursTab;
 949   }
 950
 951   /**
 952    * Initialises the Structure tabbed panel.
 953    *
 954    * @return
 955    */
 956   private JPanel initStructureTab()
 957   {
 958     structureTab = new JPanel();
 959
 960     structureTab.setBorder(new TitledBorder(MessageManager
 961             .getString("label.structure_options")));
 962     structureTab.setLayout(null);
 963     final int width = 400;
 964     final int height = 22;
 965     final int lineSpacing = 25;
 966     int ypos = 15;
 967
 968     structFromPdb.setFont(LABEL_FONT);
 969     structFromPdb
 970             .setText(MessageManager.getString("label.struct_from_pdb"));
 971     structFromPdb.setBounds(new Rectangle(5, ypos, width, height));
 972     structFromPdb.addActionListener(new ActionListener()
 973     {
 974       @Override
 975       public void actionPerformed(ActionEvent e)
 976       {
 977         boolean selected = structFromPdb.isSelected();
 978         // enable other options only when the first is checked
 979         useRnaView.setEnabled(selected);
 980         addSecondaryStructure.setEnabled(selected);
 981         addTempFactor.setEnabled(selected);
 982       }
 983     });
 984     structureTab.add(structFromPdb);
 985
 986     // indent checkboxes that are conditional on the first one
 987     ypos += lineSpacing;
 988     useRnaView.setFont(LABEL_FONT);
 989     useRnaView.setText(MessageManager.getString("label.use_rnaview"));
 990     useRnaView.setBounds(new Rectangle(25, ypos, width, height));
 991     structureTab.add(useRnaView);
 992
 993     ypos += lineSpacing;
 994     addSecondaryStructure.setFont(LABEL_FONT);
 995     addSecondaryStructure.setText(MessageManager
 996             .getString("label.autoadd_secstr"));
 997     addSecondaryStructure.setBounds(new Rectangle(25, ypos, width, height));
 998     structureTab.add(addSecondaryStructure);
 999
1000     ypos += lineSpacing;
1001     addTempFactor.setFont(LABEL_FONT);
1002     addTempFactor.setText(MessageManager.getString("label.autoadd_temp"));
1003     addTempFactor.setBounds(new Rectangle(25, ypos, width, height));
1004     structureTab.add(addTempFactor);
1005
1006     ypos += lineSpacing;
1007     JLabel viewerLabel = new JLabel();
1008     viewerLabel.setFont(LABEL_FONT);
1009     viewerLabel.setHorizontalAlignment(SwingConstants.LEFT);
1010     viewerLabel.setText(MessageManager.getString("label.structure_viewer"));
1011     viewerLabel.setBounds(new Rectangle(10, ypos, 200, height));
1012     structureTab.add(viewerLabel);
1013
1014     structViewer.setFont(LABEL_FONT);
1015     structViewer.setBounds(new Rectangle(160, ypos, 120, height));
1016     structViewer.addItem(ViewerType.JMOL.name());
1017     structViewer.addItem(ViewerType.CHIMERA.name());
1018     structViewer.addActionListener(new ActionListener()
1019     {
1020       @Override
1021       public void actionPerformed(ActionEvent e)
1022       {
1023         structureViewer_actionPerformed((String) structViewer
1024                 .getSelectedItem());
1025       }
1026     });
1027     structureTab.add(structViewer);
1028
1029     ypos += lineSpacing;
1030     JLabel pathLabel = new JLabel();
1031     pathLabel.setFont(new java.awt.Font("SansSerif", 0, 11));
1032     pathLabel.setHorizontalAlignment(SwingConstants.LEFT);
1033     pathLabel.setText(MessageManager.getString("label.chimera_path"));
1034     final String tooltip = JvSwingUtils.wrapTooltip(true,
1035             MessageManager.getString("label.chimera_path_tip"));
1036     pathLabel.setToolTipText(tooltip);
1037     pathLabel.setBounds(new Rectangle(10, ypos, 140, height));
1038     structureTab.add(pathLabel);
1039
1040     chimeraPath.setFont(LABEL_FONT);
1041     chimeraPath.setText("");
1042     chimeraPath.setBounds(new Rectangle(160, ypos, 300, height));
1043     chimeraPath.addMouseListener(new MouseAdapter()
1044     {
1045       @Override
1046       public void mouseClicked(MouseEvent e)
1047       {
1048         if (e.getClickCount() == 2)
1049         {
1050           String chosen = openFileChooser();
1051           if (chosen != null)
1052           {
1053             chimeraPath.setText(chosen);
1054           }
1055         }
1056       }
1057     });
1058     structureTab.add(chimeraPath);
1059
1060     ypos += lineSpacing;
1061     nwMapping.setFont(LABEL_FONT);
1062     nwMapping.setText(MessageManager.getString("label.nw_mapping"));
1063     siftsMapping.setFont(LABEL_FONT);
1064     siftsMapping.setText(MessageManager.getString("label.sifts_mapping"));
1065     mappingMethod.add(nwMapping);
1066     mappingMethod.add(siftsMapping);
1067     JPanel mappingPanel = new JPanel();
1068     mappingPanel.setFont(LABEL_FONT);
1069     TitledBorder mmTitledBorder = new TitledBorder(
1070             MessageManager.getString("label.mapping_method"));
1071     mmTitledBorder.setTitleFont(LABEL_FONT);
1072     mappingPanel.setBorder(mmTitledBorder);
1073     mappingPanel.setBounds(new Rectangle(10, ypos, 452, 45));
1074     // GridLayout mappingLayout = new GridLayout();
1075     mappingPanel.setLayout(new GridLayout());
1076     mappingPanel.add(nwMapping);
1077     mappingPanel.add(siftsMapping);
1078     structureTab.add(mappingPanel);
1079
1080     ypos += lineSpacing;
1081     ypos += lineSpacing;
1082     FTSDataColumnPreferences docFieldPref = new FTSDataColumnPreferences(
1083             PreferenceSource.PREFERENCES, PDBFTSRestClient.getInstance());
1084     docFieldPref.setBounds(new Rectangle(10, ypos, 450, 120));
1085     structureTab.add(docFieldPref);
1086
1087     return structureTab;
1088   }
1089
1090   /**
1091    * Action on choosing a structure viewer from combobox options.
1092    *
1093    * @param selectedItem
1094    */
1095   protected void structureViewer_actionPerformed(String selectedItem)
1096   {
1097   }
1098
1099   /**
1100    * Show a dialog for the user to choose a file. Returns the chosen path, or
1101    * null on Cancel.
1102    *
1103    * @return
1104    */
1105   protected String openFileChooser()
1106   {
1107     String choice = null;
1108     JFileChooser chooser = new JFileChooser();
1109
1110     // chooser.setFileView(new JalviewFileView());
1111     chooser.setDialogTitle(MessageManager
1112             .getString("label.open_local_file"));
1113     chooser.setToolTipText(MessageManager.getString("action.open"));
1114
1115     int value = chooser.showOpenDialog(this);
1116
1117     if (value == JFileChooser.APPROVE_OPTION)
1118     {
1119       choice = chooser.getSelectedFile().getPath();
1120     }
1121     return choice;
1122   }
1123
1124   /**
1125    * Validate the structure tab preferences; if invalid, set focus on this tab.
1126    *
1127    * @param e
1128    */
1129   protected boolean validateStructure(FocusEvent e)
1130   {
1131     if (!validateStructure())
1132     {
1133       e.getComponent().requestFocusInWindow();
1134       return false;
1135     }
1136     return true;
1137   }
1138
1139   protected boolean validateStructure()
1140   {
1141     return false;
1142   }
1143
1144   /**
1145    * Initialises the Visual tabbed panel.
1146    *
1147    * @return
1148    */
1149   private JPanel initVisualTab()
1150   {
1151     JPanel visualTab = new JPanel();
1152     visualTab.setBorder(new TitledBorder(MessageManager
1153             .getString("action.open_new_alignment")));
1154     visualTab.setLayout(null);
1155     fullScreen.setFont(LABEL_FONT);
1156     fullScreen.setHorizontalAlignment(SwingConstants.RIGHT);
1157     fullScreen.setHorizontalTextPosition(SwingConstants.LEFT);
1158     fullScreen.setText(MessageManager.getString("label.maximize_window"));
1159     quality.setEnabled(false);
1160     quality.setFont(LABEL_FONT);
1161     quality.setHorizontalAlignment(SwingConstants.RIGHT);
1162     quality.setHorizontalTextPosition(SwingConstants.LEFT);
1163     quality.setSelected(true);
1164     quality.setText(MessageManager.getString("label.quality"));
1165     conservation.setEnabled(false);
1166     conservation.setFont(LABEL_FONT);
1167     conservation.setHorizontalAlignment(SwingConstants.RIGHT);
1168     conservation.setHorizontalTextPosition(SwingConstants.LEFT);
1169     conservation.setSelected(true);
1170     conservation.setText(MessageManager.getString("label.conservation"));
1171     identity.setEnabled(false);
1172     identity.setFont(LABEL_FONT);
1173     identity.setHorizontalAlignment(SwingConstants.RIGHT);
1174     identity.setHorizontalTextPosition(SwingConstants.LEFT);
1175     identity.setSelected(true);
1176     identity.setText(MessageManager.getString("label.consensus"));
1177     JLabel showGroupbits = new JLabel();
1178     showGroupbits.setFont(LABEL_FONT);
1179     showGroupbits.setHorizontalAlignment(SwingConstants.RIGHT);
1180     showGroupbits.setHorizontalTextPosition(SwingConstants.LEFT);
1181     showGroupbits.setText(MessageManager.getString("action.show_group")
1182             + ":");
1183     JLabel showConsensbits = new JLabel();
1184     showConsensbits.setFont(LABEL_FONT);
1185     showConsensbits.setHorizontalAlignment(SwingConstants.RIGHT);
1186     showConsensbits.setHorizontalTextPosition(SwingConstants.LEFT);
1187     showConsensbits.setText(MessageManager.getString("label.consensus")
1188             + ":");
1189     showConsensHistogram.setEnabled(false);
1190     showConsensHistogram.setFont(LABEL_FONT);
1191     showConsensHistogram.setHorizontalAlignment(SwingConstants.RIGHT);
1192     showConsensHistogram.setHorizontalTextPosition(SwingConstants.LEFT);
1193     showConsensHistogram.setSelected(true);
1194     showConsensHistogram.setText(MessageManager
1195             .getString("label.histogram"));
1196     showConsensLogo.setEnabled(false);
1197     showConsensLogo.setFont(LABEL_FONT);
1198     showConsensLogo.setHorizontalAlignment(SwingConstants.RIGHT);
1199     showConsensLogo.setHorizontalTextPosition(SwingConstants.LEFT);
1200     showConsensLogo.setSelected(true);
1201     showConsensLogo.setText(MessageManager.getString("label.logo"));
1202     showGroupConsensus.setEnabled(false);
1203     showGroupConsensus.setFont(LABEL_FONT);
1204     showGroupConsensus.setHorizontalAlignment(SwingConstants.RIGHT);
1205     showGroupConsensus.setHorizontalTextPosition(SwingConstants.LEFT);
1206     showGroupConsensus.setSelected(true);
1207     showGroupConsensus.setText(MessageManager.getString("label.consensus"));
1208     showGroupConservation.setEnabled(false);
1209     showGroupConservation.setFont(LABEL_FONT);
1210     showGroupConservation.setHorizontalAlignment(SwingConstants.RIGHT);
1211     showGroupConservation.setHorizontalTextPosition(SwingConstants.LEFT);
1212     showGroupConservation.setSelected(true);
1213     showGroupConservation.setText(MessageManager
1214             .getString("label.conservation"));
1215     showNpTooltip.setEnabled(true);
1216     showNpTooltip.setFont(LABEL_FONT);
1217     showNpTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
1218     showNpTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
1219     showNpTooltip.setSelected(true);
1220     showNpTooltip.setText(MessageManager
1221             .getString("label.non_positional_features"));
1222     showDbRefTooltip.setEnabled(true);
1223     showDbRefTooltip.setFont(LABEL_FONT);
1224     showDbRefTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
1225     showDbRefTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
1226     showDbRefTooltip.setSelected(true);
1227     showDbRefTooltip.setText(MessageManager
1228             .getString("label.database_references"));
1229     annotations.setFont(LABEL_FONT);
1230     annotations.setHorizontalAlignment(SwingConstants.RIGHT);
1231     annotations.setHorizontalTextPosition(SwingConstants.LEADING);
1232     annotations.setSelected(true);
1233     annotations.setText(MessageManager.getString("label.show_annotations"));
1234     annotations.setBounds(new Rectangle(169, 12, 200, 23));
1235     annotations.addActionListener(new ActionListener()
1236     {
1237       @Override
1238       public void actionPerformed(ActionEvent e)
1239       {
1240         annotations_actionPerformed(e);
1241       }
1242     });
1243     identity.addActionListener(new ActionListener()
1244     {
1245       @Override
1246       public void actionPerformed(ActionEvent e)
1247       {
1248         annotations_actionPerformed(e);
1249       }
1250     });
1251     showGroupConsensus.addActionListener(new ActionListener()
1252     {
1253       @Override
1254       public void actionPerformed(ActionEvent e)
1255       {
1256         annotations_actionPerformed(e);
1257       }
1258     });
1259     showUnconserved.setFont(LABEL_FONT);
1260     showUnconserved.setHorizontalAlignment(SwingConstants.RIGHT);
1261     showUnconserved.setHorizontalTextPosition(SwingConstants.LEFT);
1262     showUnconserved.setSelected(true);
1263     showUnconserved.setText(MessageManager
1264             .getString("action.show_unconserved"));
1265     showUnconserved.addActionListener(new ActionListener()
1266     {
1267       @Override
1268       public void actionPerformed(ActionEvent e)
1269       {
1270         showunconserved_actionPerformed(e);
1271       }
1272     });
1273
1274     // TODO these are not yet added to / action from Preferences
1275     // JCheckBox shareSelections = new JCheckBox();
1276     // shareSelections.setFont(verdana11);
1277     // shareSelections.setHorizontalAlignment(SwingConstants.RIGHT);
1278     // shareSelections.setHorizontalTextPosition(SwingConstants.LEFT);
1279     // shareSelections.setSelected(true);
1280     // shareSelections.setText(MessageManager
1281     // .getString("label.share_selection_across_views"));
1282     // JCheckBox followHighlight = new JCheckBox();
1283     // followHighlight.setFont(verdana11);
1284     // followHighlight.setHorizontalAlignment(SwingConstants.RIGHT);
1285     // followHighlight.setHorizontalTextPosition(SwingConstants.LEFT);
1286     // // showUnconserved.setBounds(new Rectangle(169, 40, 200, 23));
1287     // followHighlight.setSelected(true);
1288     // followHighlight.setText(MessageManager
1289     // .getString("label.scroll_highlighted_regions"));
1290
1291     seqLimit.setFont(LABEL_FONT);
1292     seqLimit.setHorizontalAlignment(SwingConstants.RIGHT);
1293     seqLimit.setHorizontalTextPosition(SwingConstants.LEFT);
1294     seqLimit.setText(MessageManager.getString("label.full_sequence_id"));
1295     smoothFont.setFont(LABEL_FONT);
1296     smoothFont.setHorizontalAlignment(SwingConstants.RIGHT);
1297     smoothFont.setHorizontalTextPosition(SwingConstants.LEADING);
1298     smoothFont.setText(MessageManager.getString("label.smooth_font"));
1299     scaleProteinToCdna.setFont(LABEL_FONT);
1300     scaleProteinToCdna.setHorizontalAlignment(SwingConstants.RIGHT);
1301     scaleProteinToCdna.setHorizontalTextPosition(SwingConstants.LEADING);
1302     scaleProteinToCdna.setText(MessageManager
1303             .getString("label.scale_protein_to_cdna"));
1304     scaleProteinToCdna.setToolTipText(MessageManager
1305             .getString("label.scale_protein_to_cdna_tip"));
1306     JLabel gapLabel = new JLabel();
1307     gapLabel.setFont(LABEL_FONT);
1308     gapLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1309     gapLabel.setText(MessageManager.getString("label.gap_symbol") + " ");
1310     JLabel fontLabel = new JLabel();
1311     fontLabel.setFont(LABEL_FONT);
1312     fontLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1313     fontLabel.setText(MessageManager.getString("label.font"));
1314     fontSizeCB.setFont(LABEL_FONT);
1315     fontSizeCB.setBounds(new Rectangle(320, 112, 65, 23));
1316     fontStyleCB.setFont(LABEL_FONT);
1317     fontStyleCB.setBounds(new Rectangle(382, 112, 80, 23));
1318     fontNameCB.setFont(LABEL_FONT);
1319     fontNameCB.setBounds(new Rectangle(172, 112, 147, 23));
1320     gapSymbolCB.setFont(LABEL_FONT);
1321     gapSymbolCB.setBounds(new Rectangle(172, 215, 69, 23));
1322     DefaultListCellRenderer dlcr = new DefaultListCellRenderer();
1323     dlcr.setHorizontalAlignment(DefaultListCellRenderer.CENTER);
1324     gapSymbolCB.setRenderer(dlcr);
1325
1326     startupCheckbox.setText(MessageManager.getString("action.open_file"));
1327     startupCheckbox.setFont(LABEL_FONT);
1328     startupCheckbox.setHorizontalAlignment(SwingConstants.RIGHT);
1329     startupCheckbox.setHorizontalTextPosition(SwingConstants.LEFT);
1330     startupCheckbox.setSelected(true);
1331     startupFileTextfield.setFont(LABEL_FONT);
1332     startupFileTextfield.setBounds(new Rectangle(172, 310, 330, 20));
1333     startupFileTextfield.addMouseListener(new MouseAdapter()
1334     {
1335       @Override
1336       public void mouseClicked(MouseEvent e)
1337       {
1338         if (e.getClickCount() > 1)
1339         {
1340           startupFileTextfield_mouseClicked();
1341         }
1342       }
1343     });
1344
1345     sortby.setFont(LABEL_FONT);
1346     sortby.setBounds(new Rectangle(172, 260, 155, 21));
1347     JLabel sortLabel = new JLabel();
1348     sortLabel.setFont(LABEL_FONT);
1349     sortLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1350     sortLabel.setText(MessageManager.getString("label.sort_by"));
1351     sortAnnBy.setFont(LABEL_FONT);
1352     sortAnnBy.setBounds(new Rectangle(172, 285, 110, 21));
1353     JLabel sortAnnLabel = new JLabel();
1354     sortAnnLabel.setFont(LABEL_FONT);
1355     sortAnnLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1356     sortAnnLabel.setText(MessageManager.getString("label.sort_ann_by"));
1357     sortAutocalc.setFont(LABEL_FONT);
1358     sortAutocalc.setBounds(new Rectangle(290, 285, 165, 21));
1359
1360     JPanel annsettingsPanel = new JPanel();
1361     annsettingsPanel.setBounds(new Rectangle(173, 34, 320, 75));
1362     annsettingsPanel.setLayout(new FlowLayout(FlowLayout.LEFT, 0, 0));
1363     annsettingsPanel.setBorder(new EtchedBorder());
1364     visualTab.add(annsettingsPanel);
1365     Border jb = new EmptyBorder(1, 1, 4, 5);
1366     quality.setBorder(jb);
1367     conservation.setBorder(jb);
1368     identity.setBorder(jb);
1369     showConsensbits.setBorder(jb);
1370     showGroupbits.setBorder(jb);
1371     showGroupConsensus.setBorder(jb);
1372     showGroupConservation.setBorder(jb);
1373     showConsensHistogram.setBorder(jb);
1374     showConsensLogo.setBorder(jb);
1375
1376     JPanel autoAnnotSettings = new JPanel();
1377     autoAnnotSettings.setLayout(new GridLayout(3, 3));
1378     annsettingsPanel.add(autoAnnotSettings);
1379     autoAnnotSettings.add(quality);
1380     autoAnnotSettings.add(conservation);
1381     autoAnnotSettings.add(identity);
1382     autoAnnotSettings.add(showGroupbits);
1383     autoAnnotSettings.add(showGroupConservation);
1384     autoAnnotSettings.add(showGroupConsensus);
1385     autoAnnotSettings.add(showConsensbits);
1386     autoAnnotSettings.add(showConsensHistogram);
1387     autoAnnotSettings.add(showConsensLogo);
1388
1389     JPanel tooltipSettings = new JPanel();
1390     tooltipSettings.setBorder(new TitledBorder(MessageManager
1391             .getString("label.sequence_id_tooltip")));
1392     tooltipSettings.setBounds(173, 140, 220, 62);
1393     tooltipSettings.setLayout(new GridLayout(2, 1));
1394     tooltipSettings.add(showDbRefTooltip);
1395     tooltipSettings.add(showNpTooltip);
1396     visualTab.add(tooltipSettings);
1397
1398     wrap.setFont(LABEL_FONT);
1399     wrap.setHorizontalAlignment(SwingConstants.TRAILING);
1400     wrap.setHorizontalTextPosition(SwingConstants.LEADING);
1401     wrap.setText(MessageManager.getString("label.wrap_alignment"));
1402     rightAlign.setFont(LABEL_FONT);
1403     rightAlign.setForeground(Color.black);
1404     rightAlign.setHorizontalAlignment(SwingConstants.RIGHT);
1405     rightAlign.setHorizontalTextPosition(SwingConstants.LEFT);
1406     rightAlign.setText(MessageManager.getString("label.right_align_ids"));
1407     idItalics.setFont(LABEL_FONT_ITALIC);
1408     idItalics.setHorizontalAlignment(SwingConstants.RIGHT);
1409     idItalics.setHorizontalTextPosition(SwingConstants.LEADING);
1410     idItalics.setText(MessageManager
1411             .getString("label.sequence_name_italics"));
1412     openoverv.setFont(LABEL_FONT);
1413     openoverv.setActionCommand(MessageManager
1414             .getString("label.open_overview"));
1415     openoverv.setHorizontalAlignment(SwingConstants.RIGHT);
1416     openoverv.setHorizontalTextPosition(SwingConstants.LEFT);
1417     openoverv.setText(MessageManager.getString("label.open_overview"));
1418     JPanel jPanel2 = new JPanel();
1419     jPanel2.setBounds(new Rectangle(7, 17, 158, 310));
1420     jPanel2.setLayout(new GridLayout(14, 1));
1421     jPanel2.add(fullScreen);
1422     jPanel2.add(openoverv);
1423     jPanel2.add(seqLimit);
1424     jPanel2.add(rightAlign);
1425     jPanel2.add(fontLabel);
1426     jPanel2.add(showUnconserved);
1427     jPanel2.add(idItalics);
1428     jPanel2.add(smoothFont);
1429     jPanel2.add(scaleProteinToCdna);
1430     jPanel2.add(gapLabel);
1431     jPanel2.add(wrap);
1432     jPanel2.add(sortLabel);
1433     jPanel2.add(sortAnnLabel);
1434     jPanel2.add(startupCheckbox);
1435     visualTab.add(jPanel2);
1436     visualTab.add(annotations);
1437     visualTab.add(startupFileTextfield);
1438     visualTab.add(sortby);
1439     visualTab.add(sortAnnBy);
1440     visualTab.add(sortAutocalc);
1441     visualTab.add(gapSymbolCB);
1442     visualTab.add(fontNameCB);
1443     visualTab.add(fontSizeCB);
1444     visualTab.add(fontStyleCB);
1445     return visualTab;
1446   }
1447
1448   protected void autoIdWidth_actionPerformed()
1449   {
1450     // TODO Auto-generated method stub
1451
1452   }
1453
1454   protected void userIdWidth_actionPerformed()
1455   {
1456     // TODO Auto-generated method stub
1457
1458   }
1459
1460   protected void maxColour_actionPerformed(JPanel panel)
1461   {
1462   }
1463
1464   protected void minColour_actionPerformed(JPanel panel)
1465   {
1466   }
1467
1468   protected void showunconserved_actionPerformed(ActionEvent e)
1469   {
1470     // TODO Auto-generated method stub
1471
1472   }
1473
1474   /**
1475    * DOCUMENT ME!
1476    *
1477    * @param e
1478    *          DOCUMENT ME!
1479    */
1480   public void ok_actionPerformed(ActionEvent e)
1481   {
1482   }
1483
1484   /**
1485    * DOCUMENT ME!
1486    *
1487    * @param e
1488    *          DOCUMENT ME!
1489    */
1490   public void cancel_actionPerformed(ActionEvent e)
1491   {
1492   }
1493
1494   /**
1495    * DOCUMENT ME!
1496    *
1497    * @param e
1498    *          DOCUMENT ME!
1499    */
1500   public void annotations_actionPerformed(ActionEvent e)
1501   {
1502   }
1503
1504   /**
1505    * DOCUMENT ME!
1506    */
1507   public void startupFileTextfield_mouseClicked()
1508   {
1509   }
1510
1511   public void newLink_actionPerformed(ActionEvent e)
1512   {
1513
1514   }
1515
1516   public void editLink_actionPerformed(ActionEvent e)
1517   {
1518
1519   }
1520
1521   public void deleteLink_actionPerformed(ActionEvent e)
1522   {
1523
1524   }
1525
1526   public void defaultBrowser_mouseClicked(MouseEvent e)
1527   {
1528
1529   }
1530
1531   public void linkURLList_keyTyped(KeyEvent e)
1532   {
1533
1534   }
1535
1536   public void useProxy_actionPerformed()
1537   {
1538     boolean enabled = useProxy.isSelected();
1539     portLabel.setEnabled(enabled);
1540     serverLabel.setEnabled(enabled);
1541     proxyServerTB.setEnabled(enabled);
1542     proxyPortTB.setEnabled(enabled);
1543   }
1544
1545   /**
1546    * Customer renderer for JTable: supports column of radio buttons
1547    */
1548   public class RadioButtonRenderer extends JRadioButton implements
1549           TableCellRenderer
1550   {
1551     public RadioButtonRenderer()
1552     {
1553       setHorizontalAlignment(CENTER);
1554       setToolTipText(MessageManager.getString("label.urltooltip"));
1555     }
1556
1557     @Override
1558     public Component getTableCellRendererComponent(JTable table,
1559             Object value, boolean isSelected, boolean hasFocus, int row,
1560             int column)
1561     {
1562       setSelected((boolean) value);
1563
1564       // set colours to match rest of table
1565       if (isSelected)
1566        {
1567          setBackground(table.getSelectionBackground());
1568          setForeground(table.getSelectionForeground());
1569        }
1570        else
1571        {
1572          setBackground(table.getBackground());
1573          setForeground(table.getForeground());
1574       }
1575       return this;
1576     }
1577   }
1578
1579   /**
1580    * Customer cell editor for JTable: supports column of radio buttons in
1581    * conjunction with renderer
1582    */
1583   public class RadioButtonEditor extends AbstractCellEditor implements
1584             TableCellEditor
1585     {
1586       private JRadioButton button = new JRadioButton();
1587
1588       public RadioButtonEditor()
1589       {
1590       button.setHorizontalAlignment(SwingConstants.CENTER);
1591       this.button.addActionListener(new ActionListener()
1592         {
1593           @Override
1594           public void actionPerformed(ActionEvent e)
1595           {
1596             fireEditingStopped();
1597           }
1598         });
1599       }
1600
1601       @Override
1602       public Component getTableCellEditorComponent(JTable table,
1603               Object value, boolean isSelected, int row, int column)
1604       {
1605       button.setSelected((boolean) value);
1606         return button;
1607       }
1608
1609       @Override
1610       public Object getCellEditorValue()
1611       {
1612       return button.isSelected();
1613       }
1614
1615   }
1616 }