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
  85           .getLabelFont(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<>();
  99
 100   protected JComboBox<String> fontStyleCB = new JComboBox<>();
 101
 102   protected JComboBox<String> fontNameCB = new JComboBox<>();
 103
 104   protected JCheckBox showOccupancy = new JCheckBox();
 105
 106   protected JCheckBox showUnconserved = new JCheckBox();
 107
 108   protected JCheckBox idItalics = new JCheckBox();
 109
 110   protected JCheckBox smoothFont = new JCheckBox();
 111
 112   protected JCheckBox scaleProteinToCdna = new JCheckBox();
 113
 114   protected JComboBox<String> gapSymbolCB = new JComboBox<>();
 115
 116   protected JCheckBox wrap = new JCheckBox();
 117
 118   protected JComboBox<String> sortby = new JComboBox<>();
 119
 120   protected JComboBox<String> sortAnnBy = new JComboBox<>();
 121
 122   protected JComboBox<String> sortAutocalc = new JComboBox<>();
 123
 124   protected JCheckBox startupCheckbox = new JCheckBox();
 125
 126   protected JTextField startupFileTextfield = new JTextField();
 127
 128   // below are in the 'second column'
 129   protected JCheckBox annotations = new JCheckBox();
 130
 131   protected JCheckBox quality = new JCheckBox();
 132
 133   protected JCheckBox conservation = new JCheckBox();
 134
 135   protected JCheckBox identity = new JCheckBox();
 136
 137   protected JCheckBox showGroupConsensus = new JCheckBox();
 138
 139   protected JCheckBox showGroupConservation = new JCheckBox();
 140
 141   protected JCheckBox showConsensHistogram = new JCheckBox();
 142
 143   protected JCheckBox showConsensLogo = new JCheckBox();
 144
 145   protected JCheckBox showDbRefTooltip = new JCheckBox();
 146
 147   protected JCheckBox showNpTooltip = new JCheckBox();
 148
 149   /*
 150    * Structure tab and components
 151    */
 152   protected JPanel structureTab;
 153
 154   protected JCheckBox structFromPdb = new JCheckBox();
 155
 156   protected JCheckBox useRnaView = new JCheckBox();
 157
 158   protected JCheckBox addSecondaryStructure = new JCheckBox();
 159
 160   protected JCheckBox addTempFactor = new JCheckBox();
 161
 162   protected JComboBox<String> structViewer = new JComboBox<>();
 163
 164   protected JTextField chimeraPath = new JTextField();
 165
 166   protected ButtonGroup mappingMethod = new ButtonGroup();
 167
 168   protected JRadioButton siftsMapping = new JRadioButton();
 169
 170   protected JRadioButton nwMapping = new JRadioButton();
 171
 172   /*
 173    * Colours tab components
 174    */
 175   protected JPanel minColour = new JPanel();
 176
 177   protected JPanel maxColour = new JPanel();
 178
 179   protected JComboBox<String> protColour = new JComboBox<>();
 180
 181   protected JComboBox<String> nucColour = new JComboBox<>();
 182
 183   protected JButton gapColour = new JButton();
 184
 185   protected JButton hiddenColour = new JButton();
 186
 187   /*
 188    * Connections tab components
 189    */
 190   protected JTable linkUrlTable = new JTable();
 191
 192   protected JButton editLink = new JButton();
 193
 194   protected JButton deleteLink = new JButton();
 195
 196   protected JTextField filterTB = new JTextField();
 197
 198   protected JButton doReset = new JButton();
 199
 200   protected JButton userOnly = new JButton();
 201
 202   protected JLabel portLabel = new JLabel();
 203
 204   protected JLabel serverLabel = new JLabel();
 205
 206   protected JTextField proxyServerTB = new JTextField();
 207
 208   protected JTextField proxyPortTB = new JTextField();
 209
 210   protected JTextField defaultBrowser = new JTextField();
 211
 212   protected JCheckBox useProxy = new JCheckBox();
 213
 214   protected JCheckBox usagestats = new JCheckBox();
 215
 216   protected JCheckBox questionnaire = new JCheckBox();
 217
 218   protected JCheckBox versioncheck = new JCheckBox();
 219
 220   /*
 221    * Output tab components
 222    */
 223   protected JComboBox<Object> epsRendering = new JComboBox<>();
 224
 225   protected JLabel userIdWidthlabel = new JLabel();
 226
 227   protected JCheckBox autoIdWidth = new JCheckBox();
 228
 229   protected JTextField userIdWidth = new JTextField();
 230
 231   protected JCheckBox blcjv = new JCheckBox();
 232
 233   protected JCheckBox pileupjv = new JCheckBox();
 234
 235   protected JCheckBox clustaljv = new JCheckBox();
 236
 237   protected JCheckBox msfjv = new JCheckBox();
 238
 239   protected JCheckBox fastajv = new JCheckBox();
 240
 241   protected JCheckBox pfamjv = new JCheckBox();
 242
 243   protected JCheckBox pirjv = new JCheckBox();
 244
 245   protected JCheckBox modellerOutput = new JCheckBox();
 246
 247   protected JCheckBox embbedBioJSON = new JCheckBox();
 248
 249   /*
 250    * Editing tab components
 251    */
 252   protected JCheckBox autoCalculateConsCheck = new JCheckBox();
 253
 254   protected JCheckBox padGaps = new JCheckBox();
 255
 256   protected JCheckBox sortByTree = new JCheckBox();
 257
 258   /*
 259    * DAS Settings tab
 260    */
 261   protected JPanel dasTab = new JPanel();
 262
 263   /*
 264    * Web Services tab
 265    */
 266   protected JPanel wsTab = new JPanel();
 267
 268   /**
 269    * Creates a new GPreferences object.
 270    */
 271   public GPreferences()
 272   {
 273     try
 274     {
 275       jbInit();
 276     } catch (Exception ex)
 277     {
 278       ex.printStackTrace();
 279     }
 280   }
 281
 282   /**
 283    * Construct the panel and its tabbed sub-panels.
 284    *
 285    * @throws Exception
 286    */
 287   private void jbInit() throws Exception
 288   {
 289     final JTabbedPane tabbedPane = new JTabbedPane();
 290     this.setLayout(new BorderLayout());
 291     JPanel okCancelPanel = initOkCancelPanel();
 292     this.add(tabbedPane, BorderLayout.CENTER);
 293     this.add(okCancelPanel, BorderLayout.SOUTH);
 294
 295     tabbedPane.add(initVisualTab(),
 296             MessageManager.getString("label.visual"));
 297
 298     tabbedPane.add(initColoursTab(),
 299             MessageManager.getString("label.colours"));
 300
 301     tabbedPane.add(initStructureTab(),
 302             MessageManager.getString("label.structure"));
 303
 304     tabbedPane.add(initConnectionsTab(),
 305             MessageManager.getString("label.connections"));
 306
 307     tabbedPane.add(initLinksTab(),
 308             MessageManager.getString("label.urllinks"));
 309
 310     tabbedPane.add(initOutputTab(),
 311             MessageManager.getString("label.output"));
 312
 313     tabbedPane.add(initEditingTab(),
 314             MessageManager.getString("label.editing"));
 315
 316     /*
 317      * See DasSourceBrowser for the real work of configuring this tab.
 318      */
 319     dasTab.setLayout(new BorderLayout());
 320     tabbedPane.add(dasTab, MessageManager.getString("label.das_settings"));
 321
 322     /*
 323      * See WsPreferences for the real work of configuring this tab.
 324      */
 325     wsTab.setLayout(new BorderLayout());
 326     tabbedPane.add(wsTab, MessageManager.getString("label.web_services"));
 327
 328     /*
 329      * Handler to validate a tab before leaving it - currently only for
 330      * Structure.
 331      */
 332     tabbedPane.addChangeListener(new ChangeListener()
 333     {
 334       private Component lastTab;
 335
 336       @Override
 337       public void stateChanged(ChangeEvent e)
 338       {
 339         if (lastTab == structureTab
 340                 && tabbedPane.getSelectedComponent() != structureTab)
 341         {
 342           if (!validateStructure())
 343           {
 344             tabbedPane.setSelectedComponent(structureTab);
 345             return;
 346           }
 347         }
 348         lastTab = tabbedPane.getSelectedComponent();
 349       }
 350
 351     });
 352   }
 353
 354   /**
 355    * Initialises the Editing tabbed panel.
 356    *
 357    * @return
 358    */
 359   private JPanel initEditingTab()
 360   {
 361     JPanel editingTab = new JPanel();
 362     editingTab.setLayout(null);
 363     autoCalculateConsCheck.setFont(LABEL_FONT);
 364     autoCalculateConsCheck.setText(
 365             MessageManager.getString("label.autocalculate_consensus"));
 366     autoCalculateConsCheck.setBounds(new Rectangle(21, 52, 209, 23));
 367     padGaps.setFont(LABEL_FONT);
 368     padGaps.setText(
 369             MessageManager.getString("label.pad_gaps_when_editing"));
 370     padGaps.setBounds(new Rectangle(22, 94, 168, 23));
 371     sortByTree.setFont(LABEL_FONT);
 372     sortByTree
 373             .setText(MessageManager.getString("label.sort_with_new_tree"));
 374     sortByTree.setToolTipText(MessageManager.getString(
 375             "label.any_trees_calculated_or_loaded_alignment_automatically_sort"));
 376     sortByTree.setBounds(new Rectangle(22, 136, 168, 23));
 377     editingTab.add(autoCalculateConsCheck);
 378     editingTab.add(padGaps);
 379     editingTab.add(sortByTree);
 380     return editingTab;
 381   }
 382
 383   /**
 384    * Initialises the Output tabbed panel.
 385    *
 386    * @return
 387    */
 388   private JPanel initOutputTab()
 389   {
 390     JPanel outputTab = new JPanel();
 391     outputTab.setLayout(null);
 392     JLabel epsLabel = new JLabel();
 393     epsLabel.setFont(LABEL_FONT);
 394     epsLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 395     epsLabel.setText(MessageManager.getString("label.eps_rendering_style"));
 396     epsLabel.setBounds(new Rectangle(9, 31, 140, 24));
 397     epsRendering.setFont(LABEL_FONT);
 398     epsRendering.setBounds(new Rectangle(154, 34, 187, 21));
 399     JLabel jLabel1 = new JLabel();
 400     jLabel1.setFont(LABEL_FONT);
 401     jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
 402     jLabel1.setText(MessageManager.getString("label.append_start_end"));
 403     jLabel1.setFont(LABEL_FONT);
 404     fastajv.setFont(LABEL_FONT);
 405     fastajv.setHorizontalAlignment(SwingConstants.LEFT);
 406     clustaljv.setText(MessageManager.getString("label.clustal") + "     ");
 407     blcjv.setText(MessageManager.getString("label.blc") + "     ");
 408     fastajv.setText(MessageManager.getString("label.fasta") + "     ");
 409     msfjv.setText(MessageManager.getString("label.msf") + "     ");
 410     pfamjv.setText(MessageManager.getString("label.pfam") + "     ");
 411     pileupjv.setText(MessageManager.getString("label.pileup") + "     ");
 412     msfjv.setFont(LABEL_FONT);
 413     msfjv.setHorizontalAlignment(SwingConstants.LEFT);
 414     pirjv.setText(MessageManager.getString("label.pir") + "     ");
 415     JPanel jPanel11 = new JPanel();
 416     jPanel11.setFont(LABEL_FONT);
 417     TitledBorder titledBorder2 = new TitledBorder(
 418             MessageManager.getString("label.file_output"));
 419     jPanel11.setBorder(titledBorder2);
 420     jPanel11.setBounds(new Rectangle(30, 72, 196, 182));
 421     GridLayout gridLayout3 = new GridLayout();
 422     jPanel11.setLayout(gridLayout3);
 423     gridLayout3.setRows(8);
 424     blcjv.setFont(LABEL_FONT);
 425     blcjv.setHorizontalAlignment(SwingConstants.LEFT);
 426     clustaljv.setFont(LABEL_FONT);
 427     clustaljv.setHorizontalAlignment(SwingConstants.LEFT);
 428     pfamjv.setFont(LABEL_FONT);
 429     pfamjv.setHorizontalAlignment(SwingConstants.LEFT);
 430     pileupjv.setFont(LABEL_FONT);
 431     pileupjv.setHorizontalAlignment(SwingConstants.LEFT);
 432     pirjv.setFont(LABEL_FONT);
 433     pirjv.setHorizontalAlignment(SwingConstants.LEFT);
 434     autoIdWidth.setFont(LABEL_FONT);
 435     autoIdWidth.setText(
 436             MessageManager.getString("label.automatically_set_id_width"));
 437     autoIdWidth.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager
 438             .getString("label.adjusts_width_generated_eps_png")));
 439     autoIdWidth.setBounds(new Rectangle(228, 96, 188, 23));
 440     autoIdWidth.addActionListener(new ActionListener()
 441     {
 442
 443       @Override
 444       public void actionPerformed(ActionEvent e)
 445       {
 446         autoIdWidth_actionPerformed();
 447       }
 448     });
 449     userIdWidthlabel.setFont(LABEL_FONT);
 450     userIdWidthlabel.setText(
 451             MessageManager.getString("label.figure_id_column_width"));
 452     userIdWidth.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager
 453             .getString("label.manually_specify_width_left_column")));
 454     userIdWidthlabel.setToolTipText(
 455             JvSwingUtils.wrapTooltip(true, MessageManager.getString(
 456                     "label.manually_specify_width_left_column")));
 457     userIdWidthlabel.setBounds(new Rectangle(236, 120, 168, 23));
 458     userIdWidth.setFont(JvSwingUtils.getTextAreaFont());
 459     userIdWidth.setText("");
 460     userIdWidth.setBounds(new Rectangle(232, 144, 84, 23));
 461     userIdWidth.addActionListener(new ActionListener()
 462     {
 463
 464       @Override
 465       public void actionPerformed(ActionEvent e)
 466       {
 467         userIdWidth_actionPerformed();
 468       }
 469     });
 470     modellerOutput.setFont(LABEL_FONT);
 471     modellerOutput
 472             .setText(MessageManager.getString("label.use_modeller_output"));
 473     modellerOutput.setBounds(new Rectangle(228, 226, 168, 23));
 474     embbedBioJSON.setFont(LABEL_FONT);
 475     embbedBioJSON.setText(MessageManager.getString("label.embbed_biojson"));
 476     embbedBioJSON.setBounds(new Rectangle(228, 200, 250, 23));
 477
 478     jPanel11.add(jLabel1);
 479     jPanel11.add(blcjv);
 480     jPanel11.add(clustaljv);
 481     jPanel11.add(fastajv);
 482     jPanel11.add(msfjv);
 483     jPanel11.add(pfamjv);
 484     jPanel11.add(pileupjv);
 485     jPanel11.add(pirjv);
 486     outputTab.add(autoIdWidth);
 487     outputTab.add(userIdWidth);
 488     outputTab.add(userIdWidthlabel);
 489     outputTab.add(modellerOutput);
 490     outputTab.add(embbedBioJSON);
 491     outputTab.add(epsLabel);
 492     outputTab.add(epsRendering);
 493     outputTab.add(jPanel11);
 494     return outputTab;
 495   }
 496
 497   /**
 498    * Initialises the Connections tabbed panel.
 499    *
 500    * @return
 501    */
 502   private JPanel initConnectionsTab()
 503   {
 504     JPanel connectTab = new JPanel();
 505     connectTab.setLayout(new GridBagLayout());
 506
 507     // Label for browser text box
 508     JLabel browserLabel = new JLabel();
 509     browserLabel.setFont(LABEL_FONT);
 510     browserLabel.setHorizontalAlignment(SwingConstants.TRAILING);
 511     browserLabel.setText(
 512             MessageManager.getString("label.default_browser_unix"));
 513     defaultBrowser.setFont(LABEL_FONT);
 514     defaultBrowser.setText("");
 515
 516     defaultBrowser.addMouseListener(new MouseAdapter()
 517     {
 518       @Override
 519       public void mouseClicked(MouseEvent e)
 520       {
 521         if (e.getClickCount() > 1)
 522         {
 523           defaultBrowser_mouseClicked(e);
 524         }
 525       }
 526     });
 527
 528     JPanel proxyPanel = initConnTabProxyPanel();
 529     initConnTabCheckboxes();
 530
 531     // Add default Browser text box
 532     connectTab.add(browserLabel,
 533             new GridBagConstraints(0, 0, 1, 1, 0.0, 0.0,
 534                     GridBagConstraints.WEST, GridBagConstraints.NONE,
 535                     new Insets(10, 0, 5, 5), 5, 1));
 536     defaultBrowser.setFont(LABEL_FONT);
 537     defaultBrowser.setText("");
 538
 539     connectTab.add(defaultBrowser, new GridBagConstraints(1, 0, 1, 1, 1.0,
 540             0.0, GridBagConstraints.CENTER, GridBagConstraints.HORIZONTAL,
 541             new Insets(10, 0, 5, 10), 30, 1));
 542
 543     // Add proxy server panel
 544     connectTab.add(proxyPanel, new GridBagConstraints(0, 1, 2, 1, 1.0, 0.0,
 545             GridBagConstraints.CENTER, GridBagConstraints.HORIZONTAL,
 546             new Insets(10, 0, 5, 12), 4, 10));
 547
 548     // Add usage stats, version check and questionnaire checkboxes
 549     connectTab.add(usagestats,
 550             new GridBagConstraints(0, 2, 1, 1, 1.0, 0.0,
 551                     GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 552                     new Insets(0, 2, 5, 5), 70, 1));
 553     connectTab.add(questionnaire,
 554             new GridBagConstraints(1, 2, 1, 1, 1.0, 0.0,
 555                     GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 556                     new Insets(0, 2, 5, 10), 70, 1));
 557     connectTab.add(versioncheck,
 558             new GridBagConstraints(0, 3, 1, 1, 1.0, 0.0,
 559                     GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 560                     new Insets(0, 2, 5, 5), 70, 1));
 561
 562     // Add padding so the panel doesn't look ridiculous
 563     JPanel spacePanel = new JPanel();
 564     connectTab.add(spacePanel,
 565             new GridBagConstraints(0, 4, 1, 1, 1.0, 1.0,
 566                     GridBagConstraints.WEST, GridBagConstraints.BOTH,
 567                     new Insets(0, 0, 0, 5), 70, 1));
 568
 569     return connectTab;
 570   }
 571
 572   /**
 573    * Initialises the Links tabbed panel.
 574    *
 575    * @return
 576    */
 577   private JPanel initLinksTab()
 578   {
 579     JPanel linkTab = new JPanel();
 580     linkTab.setLayout(new GridBagLayout());
 581
 582     // Set up table for Url links
 583     linkUrlTable.setFillsViewportHeight(true);
 584     linkUrlTable.setAutoResizeMode(JTable.AUTO_RESIZE_ALL_COLUMNS);
 585     linkUrlTable.setAutoCreateRowSorter(true);
 586     linkUrlTable.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
 587
 588     // adjust row height so radio buttons actually fit
 589     // don't do this in the renderer, it causes the awt thread to activate
 590     // constantly
 591     JRadioButton temp = new JRadioButton();
 592     linkUrlTable.setRowHeight(temp.getMinimumSize().height);
 593
 594     // Table in scrollpane so that the table is given a scrollbar
 595     JScrollPane linkScrollPane = new JScrollPane(linkUrlTable);
 596     linkScrollPane.setBorder(null);
 597
 598     // Panel for links functionality
 599     JPanel linkPanel = new JPanel(new GridBagLayout());
 600     linkPanel.setBorder(new TitledBorder(
 601             MessageManager.getString("label.url_linkfrom_sequence_id")));
 602
 603     // Put the Url links panel together
 604
 605     // Buttons go at top right, resizing only resizes the blank space vertically
 606     JPanel buttonPanel = initLinkTabUrlButtons();
 607     GridBagConstraints linkConstraints1 = new GridBagConstraints();
 608     linkConstraints1.insets = new Insets(0, 0, 5, 0);
 609     linkConstraints1.gridx = 0;
 610     linkConstraints1.gridy = 0;
 611     linkConstraints1.weightx = 1.0;
 612     linkConstraints1.fill = GridBagConstraints.HORIZONTAL;
 613     linkTab.add(buttonPanel, linkConstraints1);
 614
 615     // Links table goes at top left, resizing resizes the table
 616     GridBagConstraints linkConstraints2 = new GridBagConstraints();
 617     linkConstraints2.insets = new Insets(0, 0, 5, 5);
 618     linkConstraints2.gridx = 0;
 619     linkConstraints2.gridy = 1;
 620     linkConstraints2.weightx = 1.0;
 621     linkConstraints2.weighty = 1.0;
 622     linkConstraints2.fill = GridBagConstraints.BOTH;
 623     linkTab.add(linkScrollPane, linkConstraints2);
 624
 625     // Filter box and buttons goes at bottom left, resizing resizes the text box
 626     JPanel filterPanel = initLinkTabFilterPanel();
 627     GridBagConstraints linkConstraints3 = new GridBagConstraints();
 628     linkConstraints3.insets = new Insets(0, 0, 0, 5);
 629     linkConstraints3.gridx = 0;
 630     linkConstraints3.gridy = 2;
 631     linkConstraints3.weightx = 1.0;
 632     linkConstraints3.fill = GridBagConstraints.HORIZONTAL;
 633     linkTab.add(filterPanel, linkConstraints3);
 634
 635     return linkTab;
 636   }
 637
 638   private JPanel initLinkTabFilterPanel()
 639   {
 640     // Filter textbox and reset button
 641     JLabel filterLabel = new JLabel(
 642             MessageManager.getString("label.filter"));
 643     filterLabel.setFont(LABEL_FONT);
 644     filterLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 645     filterLabel.setHorizontalTextPosition(SwingConstants.LEADING);
 646
 647     filterTB.setFont(LABEL_FONT);
 648     filterTB.setText("");
 649
 650     doReset.setText(MessageManager.getString("action.showall"));
 651     userOnly.setText(MessageManager.getString("action.customfilter"));
 652
 653     // Panel for filter functionality
 654     JPanel filterPanel = new JPanel(new GridBagLayout());
 655     filterPanel.setBorder(new TitledBorder("Filter"));
 656     GridBagConstraints gbc = new GridBagConstraints();
 657     gbc.gridx = 0;
 658     gbc.gridy = 0;
 659     gbc.fill = GridBagConstraints.NONE;
 660     gbc.anchor = GridBagConstraints.WEST;
 661
 662     filterPanel.add(filterLabel, gbc);
 663
 664     GridBagConstraints gbc1 = new GridBagConstraints();
 665     gbc1.gridx = 1;
 666     gbc1.gridwidth = 2;
 667     gbc1.fill = GridBagConstraints.HORIZONTAL;
 668     gbc1.anchor = GridBagConstraints.WEST;
 669     gbc1.weightx = 1.0;
 670     filterPanel.add(filterTB, gbc1);
 671
 672     GridBagConstraints gbc2 = new GridBagConstraints();
 673     gbc2.gridx = 3;
 674     gbc2.fill = GridBagConstraints.NONE;
 675     gbc2.anchor = GridBagConstraints.WEST;
 676     filterPanel.add(doReset, gbc2);
 677
 678     GridBagConstraints gbc3 = new GridBagConstraints();
 679     gbc3.gridx = 4;
 680     gbc3.fill = GridBagConstraints.NONE;
 681     gbc3.anchor = GridBagConstraints.WEST;
 682     filterPanel.add(userOnly, gbc3);
 683
 684     return filterPanel;
 685   }
 686
 687   private JPanel initLinkTabUrlButtons()
 688   {
 689     // Buttons for new / edit / delete Url links
 690     JButton newLink = new JButton();
 691     newLink.setText(MessageManager.getString("action.new"));
 692
 693     editLink.setText(MessageManager.getString("action.edit"));
 694
 695     deleteLink.setText(MessageManager.getString("action.delete"));
 696
 697     // no current selection, so initially disable delete/edit buttons
 698     editLink.setEnabled(false);
 699     deleteLink.setEnabled(false);
 700
 701     newLink.addActionListener(new java.awt.event.ActionListener()
 702     {
 703       @Override
 704       public void actionPerformed(ActionEvent e)
 705       {
 706         newLink_actionPerformed(e);
 707       }
 708     });
 709
 710     editLink.setText(MessageManager.getString("action.edit"));
 711     editLink.addActionListener(new java.awt.event.ActionListener()
 712     {
 713       @Override
 714       public void actionPerformed(ActionEvent e)
 715       {
 716         editLink_actionPerformed(e);
 717       }
 718     });
 719
 720     deleteLink.setText(MessageManager.getString("action.delete"));
 721     deleteLink.addActionListener(new java.awt.event.ActionListener()
 722     {
 723       @Override
 724       public void actionPerformed(ActionEvent e)
 725       {
 726         deleteLink_actionPerformed(e);
 727       }
 728     });
 729
 730     JPanel buttonPanel = new JPanel(new GridBagLayout());
 731     buttonPanel.setBorder(new TitledBorder("Edit links"));
 732     GridBagConstraints gbc = new GridBagConstraints();
 733     gbc.gridx = 0;
 734     gbc.gridy = 0;
 735     gbc.fill = GridBagConstraints.NONE;
 736     buttonPanel.add(newLink, gbc);
 737
 738     GridBagConstraints gbc1 = new GridBagConstraints();
 739     gbc1.gridx = 1;
 740     gbc1.gridy = 0;
 741     gbc1.fill = GridBagConstraints.NONE;
 742     buttonPanel.add(editLink, gbc1);
 743
 744     GridBagConstraints gbc2 = new GridBagConstraints();
 745     gbc2.gridx = 2;
 746     gbc2.gridy = 0;
 747     gbc2.fill = GridBagConstraints.NONE;
 748     buttonPanel.add(deleteLink, gbc2);
 749
 750     GridBagConstraints gbc3 = new GridBagConstraints();
 751     gbc3.gridx = 3;
 752     gbc3.gridy = 0;
 753     gbc3.fill = GridBagConstraints.HORIZONTAL;
 754     gbc3.weightx = 1.0;
 755     JPanel spacePanel = new JPanel();
 756     spacePanel.setBorder(null);
 757     buttonPanel.add(spacePanel, gbc3);
 758
 759     return buttonPanel;
 760   }
 761
 762   /**
 763    * Initialises the proxy server panel in the Connections tab
 764    *
 765    * @return the proxy server panel
 766    */
 767   private JPanel initConnTabProxyPanel()
 768   {
 769     // Label for server text box
 770     serverLabel.setText(MessageManager.getString("label.address"));
 771     serverLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 772     serverLabel.setFont(LABEL_FONT);
 773
 774     // Proxy server and port text boxes
 775     proxyServerTB.setFont(LABEL_FONT);
 776     proxyPortTB.setFont(LABEL_FONT);
 777
 778     // Label for Port text box
 779     portLabel.setFont(LABEL_FONT);
 780     portLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 781     portLabel.setText(MessageManager.getString("label.port"));
 782
 783     // Use proxy server checkbox
 784     useProxy.setFont(LABEL_FONT);
 785     useProxy.setHorizontalAlignment(SwingConstants.RIGHT);
 786     useProxy.setHorizontalTextPosition(SwingConstants.LEADING);
 787     useProxy.setText(MessageManager.getString("label.use_proxy_server"));
 788     useProxy.addActionListener(new ActionListener()
 789     {
 790       @Override
 791       public void actionPerformed(ActionEvent e)
 792       {
 793         useProxy_actionPerformed();
 794       }
 795     });
 796
 797     // Make proxy server panel
 798     JPanel proxyPanel = new JPanel();
 799     TitledBorder titledBorder1 = new TitledBorder(
 800             MessageManager.getString("label.proxy_server"));
 801     proxyPanel.setBorder(titledBorder1);
 802     proxyPanel.setLayout(new GridBagLayout());
 803     proxyPanel.add(serverLabel,
 804             new GridBagConstraints(0, 1, 1, 1, 0.0, 0.0,
 805                     GridBagConstraints.WEST, GridBagConstraints.NONE,
 806                     new Insets(0, 2, 2, 0), 5, 0));
 807     proxyPanel.add(portLabel,
 808             new GridBagConstraints(2, 1, 1, 1, 0.0, 0.0,
 809                     GridBagConstraints.WEST, GridBagConstraints.NONE,
 810                     new Insets(0, 0, 2, 0), 11, 0));
 811     proxyPanel.add(useProxy,
 812             new GridBagConstraints(0, 0, 2, 1, 0.0, 0.0,
 813                     GridBagConstraints.WEST, GridBagConstraints.NONE,
 814                     new Insets(0, 2, 5, 185), 2, -4));
 815     proxyPanel.add(proxyPortTB,
 816             new GridBagConstraints(3, 1, 1, 1, 1.0, 0.0,
 817                     GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 818                     new Insets(0, 2, 2, 2), 54, 1));
 819     proxyPanel.add(proxyServerTB,
 820             new GridBagConstraints(1, 1, 1, 1, 1.0, 0.0,
 821                     GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 822                     new Insets(0, 2, 2, 0), 263, 1));
 823
 824     return proxyPanel;
 825   }
 826
 827   /**
 828    * Initialises the checkboxes in the Connections tab
 829    */
 830   private void initConnTabCheckboxes()
 831   {
 832     // Usage stats checkbox label
 833     usagestats.setText(
 834             MessageManager.getString("label.send_usage_statistics"));
 835     usagestats.setFont(LABEL_FONT);
 836     usagestats.setHorizontalAlignment(SwingConstants.RIGHT);
 837     usagestats.setHorizontalTextPosition(SwingConstants.LEADING);
 838
 839     // Questionnaire checkbox label
 840     questionnaire.setText(
 841             MessageManager.getString("label.check_for_questionnaires"));
 842     questionnaire.setFont(LABEL_FONT);
 843     questionnaire.setHorizontalAlignment(SwingConstants.RIGHT);
 844     questionnaire.setHorizontalTextPosition(SwingConstants.LEADING);
 845
 846     // Check for latest version checkbox label
 847     versioncheck.setText(
 848             MessageManager.getString("label.check_for_latest_version"));
 849     versioncheck.setFont(LABEL_FONT);
 850     versioncheck.setHorizontalAlignment(SwingConstants.RIGHT);
 851     versioncheck.setHorizontalTextPosition(SwingConstants.LEADING);
 852   }
 853
 854   /**
 855    * Initialises the parent panel which contains the tabbed sections.
 856    *
 857    * @return
 858    */
 859   private JPanel initOkCancelPanel()
 860   {
 861     JButton ok = new JButton();
 862     ok.setText(MessageManager.getString("action.ok"));
 863     ok.addActionListener(new ActionListener()
 864     {
 865       @Override
 866       public void actionPerformed(ActionEvent e)
 867       {
 868         ok_actionPerformed(e);
 869       }
 870     });
 871     JButton cancel = new JButton();
 872     cancel.setText(MessageManager.getString("action.cancel"));
 873     cancel.addActionListener(new ActionListener()
 874     {
 875       @Override
 876       public void actionPerformed(ActionEvent e)
 877       {
 878         cancel_actionPerformed(e);
 879       }
 880     });
 881     JPanel okCancelPanel = new JPanel();
 882     okCancelPanel.add(ok);
 883     okCancelPanel.add(cancel);
 884     return okCancelPanel;
 885   }
 886
 887   /**
 888    * Initialises the Colours tabbed panel.
 889    *
 890    * @return
 891    */
 892   private JPanel initColoursTab()
 893   {
 894     JPanel coloursTab = new JPanel();
 895     JPanel alignmentPanel = new JPanel();
 896     alignmentPanel.setBorder(new TitledBorder(
 897             MessageManager.getString("action.open_new_alignment")));
 898     alignmentPanel.setLayout(new FlowLayout());
 899     JLabel mincolourLabel = new JLabel();
 900     mincolourLabel.setFont(LABEL_FONT);
 901     mincolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 902     mincolourLabel.setText(MessageManager.getString("label.min_colour"));
 903     minColour.setFont(LABEL_FONT);
 904     minColour.setBorder(BorderFactory.createEtchedBorder());
 905     minColour.setPreferredSize(new Dimension(40, 20));
 906     minColour.addMouseListener(new MouseAdapter()
 907     {
 908       @Override
 909       public void mousePressed(MouseEvent e)
 910       {
 911         minColour_actionPerformed(minColour);
 912       }
 913     });
 914     JLabel maxcolourLabel = new JLabel();
 915     maxcolourLabel.setFont(LABEL_FONT);
 916     maxcolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 917     maxcolourLabel.setText(MessageManager.getString("label.max_colour"));
 918     maxColour.setFont(LABEL_FONT);
 919     maxColour.setBorder(BorderFactory.createEtchedBorder());
 920     maxColour.setPreferredSize(new Dimension(40, 20));
 921     maxColour.addMouseListener(new MouseAdapter()
 922     {
 923       @Override
 924       public void mousePressed(MouseEvent e)
 925       {
 926         maxColour_actionPerformed(maxColour);
 927       }
 928     });
 929
 930     protColour.setFont(LABEL_FONT);
 931     protColour.setBounds(new Rectangle(172, 225, 155, 21));
 932     JLabel protColourLabel = new JLabel();
 933     protColourLabel.setFont(LABEL_FONT);
 934     protColourLabel.setHorizontalAlignment(SwingConstants.LEFT);
 935     protColourLabel.setText(
 936             MessageManager.getString("label.prot_alignment_colour") + " ");
 937     JvSwingUtils.addtoLayout(alignmentPanel,
 938             MessageManager
 939                     .getString("label.default_colour_scheme_for_alignment"),
 940             protColourLabel, protColour);
 941
 942     nucColour.setFont(LABEL_FONT);
 943     nucColour.setBounds(new Rectangle(172, 240, 155, 21));
 944     JLabel nucColourLabel = new JLabel();
 945     nucColourLabel.setFont(LABEL_FONT);
 946     nucColourLabel.setHorizontalAlignment(SwingConstants.LEFT);
 947     nucColourLabel.setText(
 948             MessageManager.getString("label.nuc_alignment_colour") + " ");
 949     JvSwingUtils.addtoLayout(alignmentPanel,
 950             MessageManager
 951                     .getString("label.default_colour_scheme_for_alignment"),
 952             nucColourLabel, nucColour);
 953
 954     JPanel annotationShding = new JPanel();
 955     annotationShding.setBorder(new TitledBorder(
 956             MessageManager.getString("label.annotation_shading_default")));
 957     annotationShding.setLayout(new GridLayout(1, 2));
 958     JvSwingUtils.addtoLayout(annotationShding,
 959             MessageManager.getString(
 960                     "label.default_minimum_colour_annotation_shading"),
 961             mincolourLabel, minColour);
 962     JvSwingUtils.addtoLayout(annotationShding,
 963             MessageManager.getString(
 964                     "label.default_maximum_colour_annotation_shading"),
 965             maxcolourLabel, maxColour);
 966     alignmentPanel.add(annotationShding); // , FlowLayout.LEFT);
 967
 968     JPanel overviewPanel = new JPanel();
 969     overviewPanel.setBorder(new TitledBorder(
 970             MessageManager.getString("label.overview_settings")));
 971     overviewPanel.setLayout(new FlowLayout());
 972
 973     gapColour.setFont(LABEL_FONT);
 974     gapColour.setBorder(BorderFactory.createEtchedBorder());
 975     gapColour.setPreferredSize(new Dimension(40, 20));
 976     gapColour.addMouseListener(new MouseAdapter()
 977     {
 978       @Override
 979       public void mousePressed(MouseEvent e)
 980       {
 981         gapColour_actionPerformed(gapColour);
 982       }
 983     });
 984
 985     hiddenColour.setFont(LABEL_FONT);
 986     hiddenColour.setBorder(BorderFactory.createEtchedBorder());
 987     hiddenColour.setPreferredSize(new Dimension(40, 20));
 988     hiddenColour.addMouseListener(new MouseAdapter()
 989     {
 990       @Override
 991       public void mousePressed(MouseEvent e)
 992       {
 993         hiddenColour_actionPerformed(hiddenColour);
 994       }
 995     });
 996
 997     JCheckBox gapSetting = new JCheckBox(
 998             MessageManager.getString("label.ov_legacy_gap"));
 999     gapSetting.setFont(LABEL_FONT);
1000     gapSetting.setHorizontalAlignment(SwingConstants.LEFT);
1001     JLabel gapLabel = new JLabel(
1002             MessageManager.getString("label.gap_colour"));
1003     gapLabel.setFont(LABEL_FONT);
1004     gapLabel.setHorizontalAlignment(SwingConstants.LEFT);
1005     JCheckBox hiddenSetting = new JCheckBox(
1006             MessageManager.getString("label.ov_show_hide_default"));
1007     hiddenSetting.setFont(LABEL_FONT);
1008     hiddenSetting.setHorizontalAlignment(SwingConstants.LEFT);
1009     JLabel hiddenLabel = new JLabel(
1010             MessageManager.getString("label.hidden_colour"));
1011     hiddenLabel.setFont(LABEL_FONT);
1012     hiddenLabel.setHorizontalAlignment(SwingConstants.LEFT);
1013
1014     overviewPanel.setLayout(new GridBagLayout());
1015     GridBagConstraints c1 = new GridBagConstraints();
1016
1017     c1.fill = GridBagConstraints.HORIZONTAL;
1018     c1.gridx = 0;
1019     c1.gridy = 0;
1020     c1.weightx = 1;
1021     c1.anchor = GridBagConstraints.FIRST_LINE_START;
1022     overviewPanel.add(gapSetting, c1);
1023
1024     GridBagConstraints c2 = new GridBagConstraints();
1025     c2.fill = GridBagConstraints.HORIZONTAL;
1026     c2.gridx = 1;
1027     c2.gridy = 0;
1028     c2.insets = new Insets(0, 5, 0, 5);
1029     overviewPanel.add(gapLabel, c2);
1030
1031     GridBagConstraints c3 = new GridBagConstraints();
1032     c3.fill = GridBagConstraints.HORIZONTAL;
1033     c3.gridx = 2;
1034     c3.gridy = 0;
1035     overviewPanel.add(gapColour, c3);
1036
1037     GridBagConstraints c4 = new GridBagConstraints();
1038     c4.fill = GridBagConstraints.HORIZONTAL;
1039     c4.gridx = 0;
1040     c4.gridy = 1;
1041     c4.weightx = 1;
1042     overviewPanel.add(hiddenSetting, c4);
1043
1044     GridBagConstraints c5 = new GridBagConstraints();
1045     c5.fill = GridBagConstraints.HORIZONTAL;
1046     c5.gridx = 1;
1047     c5.gridy = 1;
1048     c5.insets = new Insets(0, 5, 0, 5);
1049     overviewPanel.add(hiddenLabel, c5);
1050
1051     GridBagConstraints c6 = new GridBagConstraints();
1052     c6.fill = GridBagConstraints.HORIZONTAL;
1053     c6.gridx = 2;
1054     c6.gridy = 1;
1055     overviewPanel.add(hiddenColour, c6);
1056
1057     // Add padding so the panel doesn't look ridiculous
1058     JPanel spacePanel = new JPanel();
1059     overviewPanel.add(spacePanel,
1060             new GridBagConstraints(0, 2, 1, 1, 1.0, 1.0,
1061                     GridBagConstraints.WEST, GridBagConstraints.BOTH,
1062                     new Insets(0, 0, 0, 5), 0, 0));
1063
1064     coloursTab.setLayout(new GridLayout(2, 1));
1065     coloursTab.add(alignmentPanel);
1066     coloursTab.add(overviewPanel);
1067     return coloursTab;
1068   }
1069
1070   /**
1071    * Initialises the Structure tabbed panel.
1072    *
1073    * @return
1074    */
1075   private JPanel initStructureTab()
1076   {
1077     structureTab = new JPanel();
1078
1079     structureTab.setBorder(new TitledBorder(
1080             MessageManager.getString("label.structure_options")));
1081     structureTab.setLayout(null);
1082     final int width = 400;
1083     final int height = 22;
1084     final int lineSpacing = 25;
1085     int ypos = 15;
1086
1087     structFromPdb.setFont(LABEL_FONT);
1088     structFromPdb
1089             .setText(MessageManager.getString("label.struct_from_pdb"));
1090     structFromPdb.setBounds(new Rectangle(5, ypos, width, height));
1091     structFromPdb.addActionListener(new ActionListener()
1092     {
1093       @Override
1094       public void actionPerformed(ActionEvent e)
1095       {
1096         boolean selected = structFromPdb.isSelected();
1097         // enable other options only when the first is checked
1098         useRnaView.setEnabled(selected);
1099         addSecondaryStructure.setEnabled(selected);
1100         addTempFactor.setEnabled(selected);
1101       }
1102     });
1103     structureTab.add(structFromPdb);
1104
1105     // indent checkboxes that are conditional on the first one
1106     ypos += lineSpacing;
1107     useRnaView.setFont(LABEL_FONT);
1108     useRnaView.setText(MessageManager.getString("label.use_rnaview"));
1109     useRnaView.setBounds(new Rectangle(25, ypos, width, height));
1110     structureTab.add(useRnaView);
1111
1112     ypos += lineSpacing;
1113     addSecondaryStructure.setFont(LABEL_FONT);
1114     addSecondaryStructure
1115             .setText(MessageManager.getString("label.autoadd_secstr"));
1116     addSecondaryStructure.setBounds(new Rectangle(25, ypos, width, height));
1117     structureTab.add(addSecondaryStructure);
1118
1119     ypos += lineSpacing;
1120     addTempFactor.setFont(LABEL_FONT);
1121     addTempFactor.setText(MessageManager.getString("label.autoadd_temp"));
1122     addTempFactor.setBounds(new Rectangle(25, ypos, width, height));
1123     structureTab.add(addTempFactor);
1124
1125     ypos += lineSpacing;
1126     JLabel viewerLabel = new JLabel();
1127     viewerLabel.setFont(LABEL_FONT);
1128     viewerLabel.setHorizontalAlignment(SwingConstants.LEFT);
1129     viewerLabel.setText(MessageManager.getString("label.structure_viewer"));
1130     viewerLabel.setBounds(new Rectangle(10, ypos, 200, height));
1131     structureTab.add(viewerLabel);
1132
1133     structViewer.setFont(LABEL_FONT);
1134     structViewer.setBounds(new Rectangle(160, ypos, 120, height));
1135     structViewer.addItem(ViewerType.JMOL.name());
1136     structViewer.addItem(ViewerType.CHIMERA.name());
1137     structViewer.addActionListener(new ActionListener()
1138     {
1139       @Override
1140       public void actionPerformed(ActionEvent e)
1141       {
1142         structureViewer_actionPerformed(
1143                 (String) structViewer.getSelectedItem());
1144       }
1145     });
1146     structureTab.add(structViewer);
1147
1148     ypos += lineSpacing;
1149     JLabel pathLabel = new JLabel();
1150     pathLabel.setFont(new java.awt.Font("SansSerif", 0, 11));
1151     pathLabel.setHorizontalAlignment(SwingConstants.LEFT);
1152     pathLabel.setText(MessageManager.getString("label.chimera_path"));
1153     final String tooltip = JvSwingUtils.wrapTooltip(true,
1154             MessageManager.getString("label.chimera_path_tip"));
1155     pathLabel.setToolTipText(tooltip);
1156     pathLabel.setBounds(new Rectangle(10, ypos, 140, height));
1157     structureTab.add(pathLabel);
1158
1159     chimeraPath.setFont(LABEL_FONT);
1160     chimeraPath.setText("");
1161     chimeraPath.setBounds(new Rectangle(160, ypos, 300, height));
1162     chimeraPath.addMouseListener(new MouseAdapter()
1163     {
1164       @Override
1165       public void mouseClicked(MouseEvent e)
1166       {
1167         if (e.getClickCount() == 2)
1168         {
1169           String chosen = openFileChooser();
1170           if (chosen != null)
1171           {
1172             chimeraPath.setText(chosen);
1173           }
1174         }
1175       }
1176     });
1177     structureTab.add(chimeraPath);
1178
1179     ypos += lineSpacing;
1180     nwMapping.setFont(LABEL_FONT);
1181     nwMapping.setText(MessageManager.getString("label.nw_mapping"));
1182     siftsMapping.setFont(LABEL_FONT);
1183     siftsMapping.setText(MessageManager.getString("label.sifts_mapping"));
1184     mappingMethod.add(nwMapping);
1185     mappingMethod.add(siftsMapping);
1186     JPanel mappingPanel = new JPanel();
1187     mappingPanel.setFont(LABEL_FONT);
1188     TitledBorder mmTitledBorder = new TitledBorder(
1189             MessageManager.getString("label.mapping_method"));
1190     mmTitledBorder.setTitleFont(LABEL_FONT);
1191     mappingPanel.setBorder(mmTitledBorder);
1192     mappingPanel.setBounds(new Rectangle(10, ypos, 452, 45));
1193     // GridLayout mappingLayout = new GridLayout();
1194     mappingPanel.setLayout(new GridLayout());
1195     mappingPanel.add(nwMapping);
1196     mappingPanel.add(siftsMapping);
1197     structureTab.add(mappingPanel);
1198
1199     ypos += lineSpacing;
1200     ypos += lineSpacing;
1201     FTSDataColumnPreferences docFieldPref = new FTSDataColumnPreferences(
1202             PreferenceSource.PREFERENCES, PDBFTSRestClient.getInstance());
1203     docFieldPref.setBounds(new Rectangle(10, ypos, 450, 120));
1204     structureTab.add(docFieldPref);
1205
1206     return structureTab;
1207   }
1208
1209   /**
1210    * Action on choosing a structure viewer from combobox options.
1211    *
1212    * @param selectedItem
1213    */
1214   protected void structureViewer_actionPerformed(String selectedItem)
1215   {
1216   }
1217
1218   /**
1219    * Show a dialog for the user to choose a file. Returns the chosen path, or
1220    * null on Cancel.
1221    *
1222    * @return
1223    */
1224   protected String openFileChooser()
1225   {
1226     String choice = null;
1227     JFileChooser chooser = new JFileChooser();
1228
1229     // chooser.setFileView(new JalviewFileView());
1230     chooser.setDialogTitle(
1231             MessageManager.getString("label.open_local_file"));
1232     chooser.setToolTipText(MessageManager.getString("action.open"));
1233
1234     int value = chooser.showOpenDialog(this);
1235
1236     if (value == JFileChooser.APPROVE_OPTION)
1237     {
1238       choice = chooser.getSelectedFile().getPath();
1239     }
1240     return choice;
1241   }
1242
1243   /**
1244    * Validate the structure tab preferences; if invalid, set focus on this tab.
1245    *
1246    * @param e
1247    */
1248   protected boolean validateStructure(FocusEvent e)
1249   {
1250     if (!validateStructure())
1251     {
1252       e.getComponent().requestFocusInWindow();
1253       return false;
1254     }
1255     return true;
1256   }
1257
1258   protected boolean validateStructure()
1259   {
1260     return false;
1261   }
1262
1263   /**
1264    * Initialises the Visual tabbed panel.
1265    *
1266    * @return
1267    */
1268   private JPanel initVisualTab()
1269   {
1270     JPanel visualTab = new JPanel();
1271     visualTab.setBorder(new TitledBorder(
1272             MessageManager.getString("action.open_new_alignment")));
1273     visualTab.setLayout(null);
1274     fullScreen.setFont(LABEL_FONT);
1275     fullScreen.setHorizontalAlignment(SwingConstants.RIGHT);
1276     fullScreen.setHorizontalTextPosition(SwingConstants.LEFT);
1277     fullScreen.setText(MessageManager.getString("label.maximize_window"));
1278     quality.setEnabled(false);
1279     quality.setFont(LABEL_FONT);
1280     quality.setHorizontalAlignment(SwingConstants.RIGHT);
1281     quality.setHorizontalTextPosition(SwingConstants.LEFT);
1282     quality.setSelected(true);
1283     quality.setText(MessageManager.getString("label.quality"));
1284     conservation.setEnabled(false);
1285     conservation.setFont(LABEL_FONT);
1286     conservation.setHorizontalAlignment(SwingConstants.RIGHT);
1287     conservation.setHorizontalTextPosition(SwingConstants.LEFT);
1288     conservation.setSelected(true);
1289     conservation.setText(MessageManager.getString("label.conservation"));
1290     identity.setEnabled(false);
1291     identity.setFont(LABEL_FONT);
1292     identity.setHorizontalAlignment(SwingConstants.RIGHT);
1293     identity.setHorizontalTextPosition(SwingConstants.LEFT);
1294     identity.setSelected(true);
1295     identity.setText(MessageManager.getString("label.consensus"));
1296     showOccupancy.setFont(LABEL_FONT);
1297     showOccupancy.setEnabled(false);
1298     showOccupancy.setHorizontalAlignment(SwingConstants.RIGHT);
1299     showOccupancy.setHorizontalTextPosition(SwingConstants.LEFT);
1300     showOccupancy.setSelected(true);
1301     showOccupancy.setText(MessageManager.getString("label.occupancy"));
1302
1303     JLabel showGroupbits = new JLabel();
1304     showGroupbits.setFont(LABEL_FONT);
1305     showGroupbits.setHorizontalAlignment(SwingConstants.RIGHT);
1306     showGroupbits.setHorizontalTextPosition(SwingConstants.LEFT);
1307     showGroupbits
1308             .setText(MessageManager.getString("action.show_group") + ":");
1309     JLabel showConsensbits = new JLabel();
1310     showConsensbits.setFont(LABEL_FONT);
1311     showConsensbits.setHorizontalAlignment(SwingConstants.RIGHT);
1312     showConsensbits.setHorizontalTextPosition(SwingConstants.LEFT);
1313     showConsensbits
1314             .setText(MessageManager.getString("label.consensus") + ":");
1315     showConsensHistogram.setEnabled(false);
1316     showConsensHistogram.setFont(LABEL_FONT);
1317     showConsensHistogram.setHorizontalAlignment(SwingConstants.RIGHT);
1318     showConsensHistogram.setHorizontalTextPosition(SwingConstants.LEFT);
1319     showConsensHistogram.setSelected(true);
1320     showConsensHistogram
1321             .setText(MessageManager.getString("label.histogram"));
1322     showConsensLogo.setEnabled(false);
1323     showConsensLogo.setFont(LABEL_FONT);
1324     showConsensLogo.setHorizontalAlignment(SwingConstants.RIGHT);
1325     showConsensLogo.setHorizontalTextPosition(SwingConstants.LEFT);
1326     showConsensLogo.setSelected(true);
1327     showConsensLogo.setText(MessageManager.getString("label.logo"));
1328     showGroupConsensus.setEnabled(false);
1329     showGroupConsensus.setFont(LABEL_FONT);
1330     showGroupConsensus.setHorizontalAlignment(SwingConstants.RIGHT);
1331     showGroupConsensus.setHorizontalTextPosition(SwingConstants.LEFT);
1332     showGroupConsensus.setSelected(true);
1333     showGroupConsensus.setText(MessageManager.getString("label.consensus"));
1334     showGroupConservation.setEnabled(false);
1335     showGroupConservation.setFont(LABEL_FONT);
1336     showGroupConservation.setHorizontalAlignment(SwingConstants.RIGHT);
1337     showGroupConservation.setHorizontalTextPosition(SwingConstants.LEFT);
1338     showGroupConservation.setSelected(true);
1339     showGroupConservation
1340             .setText(MessageManager.getString("label.conservation"));
1341     showNpTooltip.setEnabled(true);
1342     showNpTooltip.setFont(LABEL_FONT);
1343     showNpTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
1344     showNpTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
1345     showNpTooltip.setSelected(true);
1346     showNpTooltip.setText(
1347             MessageManager.getString("label.non_positional_features"));
1348     showDbRefTooltip.setEnabled(true);
1349     showDbRefTooltip.setFont(LABEL_FONT);
1350     showDbRefTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
1351     showDbRefTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
1352     showDbRefTooltip.setSelected(true);
1353     showDbRefTooltip
1354             .setText(MessageManager.getString("label.database_references"));
1355     annotations.setFont(LABEL_FONT);
1356     annotations.setHorizontalAlignment(SwingConstants.RIGHT);
1357     annotations.setHorizontalTextPosition(SwingConstants.LEFT);
1358     annotations.setSelected(true);
1359     annotations.setText(MessageManager.getString("label.show_annotations"));
1360     // annotations.setBounds(new Rectangle(169, 12, 200, 23));
1361     annotations.addActionListener(new ActionListener()
1362     {
1363       @Override
1364       public void actionPerformed(ActionEvent e)
1365       {
1366         annotations_actionPerformed(e);
1367       }
1368     });
1369     identity.addActionListener(new ActionListener()
1370     {
1371       @Override
1372       public void actionPerformed(ActionEvent e)
1373       {
1374         annotations_actionPerformed(e);
1375       }
1376     });
1377     showGroupConsensus.addActionListener(new ActionListener()
1378     {
1379       @Override
1380       public void actionPerformed(ActionEvent e)
1381       {
1382         annotations_actionPerformed(e);
1383       }
1384     });
1385     showUnconserved.setFont(LABEL_FONT);
1386     showUnconserved.setHorizontalAlignment(SwingConstants.RIGHT);
1387     showUnconserved.setHorizontalTextPosition(SwingConstants.LEFT);
1388     showUnconserved.setSelected(true);
1389     showUnconserved
1390             .setText(MessageManager.getString("action.show_unconserved"));
1391     showUnconserved.addActionListener(new ActionListener()
1392     {
1393       @Override
1394       public void actionPerformed(ActionEvent e)
1395       {
1396         showunconserved_actionPerformed(e);
1397       }
1398     });
1399
1400     // TODO these are not yet added to / action from Preferences
1401     // JCheckBox shareSelections = new JCheckBox();
1402     // shareSelections.setFont(verdana11);
1403     // shareSelections.setHorizontalAlignment(SwingConstants.RIGHT);
1404     // shareSelections.setHorizontalTextPosition(SwingConstants.LEFT);
1405     // shareSelections.setSelected(true);
1406     // shareSelections.setText(MessageManager
1407     // .getString("label.share_selection_across_views"));
1408     // JCheckBox followHighlight = new JCheckBox();
1409     // followHighlight.setFont(verdana11);
1410     // followHighlight.setHorizontalAlignment(SwingConstants.RIGHT);
1411     // followHighlight.setHorizontalTextPosition(SwingConstants.LEFT);
1412     // // showUnconserved.setBounds(new Rectangle(169, 40, 200, 23));
1413     // followHighlight.setSelected(true);
1414     // followHighlight.setText(MessageManager
1415     // .getString("label.scroll_highlighted_regions"));
1416
1417     seqLimit.setFont(LABEL_FONT);
1418     seqLimit.setHorizontalAlignment(SwingConstants.RIGHT);
1419     seqLimit.setHorizontalTextPosition(SwingConstants.LEFT);
1420     seqLimit.setText(MessageManager.getString("label.full_sequence_id"));
1421     smoothFont.setFont(LABEL_FONT);
1422     smoothFont.setHorizontalAlignment(SwingConstants.RIGHT);
1423     smoothFont.setHorizontalTextPosition(SwingConstants.LEADING);
1424     smoothFont.setText(MessageManager.getString("label.smooth_font"));
1425     scaleProteinToCdna.setFont(LABEL_FONT);
1426     scaleProteinToCdna.setHorizontalAlignment(SwingConstants.RIGHT);
1427     scaleProteinToCdna.setHorizontalTextPosition(SwingConstants.LEADING);
1428     scaleProteinToCdna.setText(
1429             MessageManager.getString("label.scale_protein_to_cdna"));
1430     scaleProteinToCdna.setToolTipText(
1431             MessageManager.getString("label.scale_protein_to_cdna_tip"));
1432     JLabel gapLabel = new JLabel();
1433     gapLabel.setFont(LABEL_FONT);
1434     gapLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1435     gapLabel.setText(MessageManager.getString("label.gap_symbol") + " ");
1436     JLabel fontLabel = new JLabel();
1437     fontLabel.setFont(LABEL_FONT);
1438     fontLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1439     fontLabel.setText(MessageManager.getString("label.font"));
1440     fontSizeCB.setFont(LABEL_FONT);
1441     fontSizeCB.setBounds(new Rectangle(320, 112, 65, 23));
1442     fontStyleCB.setFont(LABEL_FONT);
1443     fontStyleCB.setBounds(new Rectangle(382, 112, 80, 23));
1444     fontNameCB.setFont(LABEL_FONT);
1445     fontNameCB.setBounds(new Rectangle(172, 112, 147, 23));
1446     gapSymbolCB.setFont(LABEL_FONT);
1447     gapSymbolCB.setBounds(new Rectangle(172, 215, 69, 23));
1448     DefaultListCellRenderer dlcr = new DefaultListCellRenderer();
1449     dlcr.setHorizontalAlignment(DefaultListCellRenderer.CENTER);
1450     gapSymbolCB.setRenderer(dlcr);
1451
1452     startupCheckbox.setText(MessageManager.getString("action.open_file"));
1453     startupCheckbox.setFont(LABEL_FONT);
1454     startupCheckbox.setHorizontalAlignment(SwingConstants.RIGHT);
1455     startupCheckbox.setHorizontalTextPosition(SwingConstants.LEFT);
1456     startupCheckbox.setSelected(true);
1457     startupFileTextfield.setFont(LABEL_FONT);
1458     startupFileTextfield.setBounds(new Rectangle(172, 310, 330, 20));
1459     startupFileTextfield.addMouseListener(new MouseAdapter()
1460     {
1461       @Override
1462       public void mouseClicked(MouseEvent e)
1463       {
1464         if (e.getClickCount() > 1)
1465         {
1466           startupFileTextfield_mouseClicked();
1467         }
1468       }
1469     });
1470
1471     sortby.setFont(LABEL_FONT);
1472     sortby.setBounds(new Rectangle(172, 260, 155, 21));
1473     JLabel sortLabel = new JLabel();
1474     sortLabel.setFont(LABEL_FONT);
1475     sortLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1476     sortLabel.setText(MessageManager.getString("label.sort_by"));
1477     sortAnnBy.setFont(LABEL_FONT);
1478     sortAnnBy.setBounds(new Rectangle(172, 285, 110, 21));
1479     JLabel sortAnnLabel = new JLabel();
1480     sortAnnLabel.setFont(LABEL_FONT);
1481     sortAnnLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1482     sortAnnLabel.setText(MessageManager.getString("label.sort_ann_by"));
1483     sortAutocalc.setFont(LABEL_FONT);
1484     sortAutocalc.setBounds(new Rectangle(290, 285, 165, 21));
1485
1486     JPanel annsettingsPanel = new JPanel();
1487     annsettingsPanel.setBounds(new Rectangle(173, 13, 320, 96));
1488     annsettingsPanel.setLayout(new FlowLayout(FlowLayout.LEFT, 0, 0));
1489     annsettingsPanel.setBorder(new EtchedBorder());
1490     visualTab.add(annsettingsPanel);
1491     Border jb = new EmptyBorder(1, 1, 4, 5);
1492     annotations.setBorder(jb);
1493     showOccupancy.setBorder(jb);
1494     quality.setBorder(jb);
1495     conservation.setBorder(jb);
1496     identity.setBorder(jb);
1497     showConsensbits.setBorder(jb);
1498     showGroupbits.setBorder(jb);
1499     showGroupConsensus.setBorder(jb);
1500     showGroupConservation.setBorder(jb);
1501     showConsensHistogram.setBorder(jb);
1502     showConsensLogo.setBorder(jb);
1503
1504     JPanel autoAnnotSettings = new JPanel();
1505     annsettingsPanel.add(autoAnnotSettings);
1506     autoAnnotSettings.setLayout(new GridLayout(0, 2));
1507     autoAnnotSettings.add(annotations);
1508     autoAnnotSettings.add(quality);
1509     // second row of autoannotation box
1510     autoAnnotSettings = new JPanel();
1511     annsettingsPanel.add(autoAnnotSettings);
1512
1513     autoAnnotSettings.setLayout(new GridLayout(0, 3));
1514     autoAnnotSettings.add(conservation);
1515     autoAnnotSettings.add(identity);
1516     autoAnnotSettings.add(showOccupancy);
1517     autoAnnotSettings.add(showGroupbits);
1518     autoAnnotSettings.add(showGroupConservation);
1519     autoAnnotSettings.add(showGroupConsensus);
1520     autoAnnotSettings.add(showConsensbits);
1521     autoAnnotSettings.add(showConsensHistogram);
1522     autoAnnotSettings.add(showConsensLogo);
1523
1524     JPanel tooltipSettings = new JPanel();
1525     tooltipSettings.setBorder(new TitledBorder(
1526             MessageManager.getString("label.sequence_id_tooltip")));
1527     tooltipSettings.setBounds(173, 140, 220, 62);
1528     tooltipSettings.setLayout(new GridLayout(2, 1));
1529     tooltipSettings.add(showDbRefTooltip);
1530     tooltipSettings.add(showNpTooltip);
1531     visualTab.add(tooltipSettings);
1532
1533     wrap.setFont(LABEL_FONT);
1534     wrap.setHorizontalAlignment(SwingConstants.TRAILING);
1535     wrap.setHorizontalTextPosition(SwingConstants.LEADING);
1536     wrap.setText(MessageManager.getString("label.wrap_alignment"));
1537     rightAlign.setFont(LABEL_FONT);
1538     rightAlign.setForeground(Color.black);
1539     rightAlign.setHorizontalAlignment(SwingConstants.RIGHT);
1540     rightAlign.setHorizontalTextPosition(SwingConstants.LEFT);
1541     rightAlign.setText(MessageManager.getString("label.right_align_ids"));
1542     idItalics.setFont(LABEL_FONT_ITALIC);
1543     idItalics.setHorizontalAlignment(SwingConstants.RIGHT);
1544     idItalics.setHorizontalTextPosition(SwingConstants.LEADING);
1545     idItalics.setText(
1546             MessageManager.getString("label.sequence_name_italics"));
1547     openoverv.setFont(LABEL_FONT);
1548     openoverv.setActionCommand(
1549             MessageManager.getString("label.open_overview"));
1550     openoverv.setHorizontalAlignment(SwingConstants.RIGHT);
1551     openoverv.setHorizontalTextPosition(SwingConstants.LEFT);
1552     openoverv.setText(MessageManager.getString("label.open_overview"));
1553     JPanel jPanel2 = new JPanel();
1554     jPanel2.setBounds(new Rectangle(7, 17, 158, 310));
1555     jPanel2.setLayout(new GridLayout(14, 1));
1556     jPanel2.add(fullScreen);
1557     jPanel2.add(openoverv);
1558     jPanel2.add(seqLimit);
1559     jPanel2.add(rightAlign);
1560     jPanel2.add(fontLabel);
1561     jPanel2.add(showUnconserved);
1562     jPanel2.add(idItalics);
1563     jPanel2.add(smoothFont);
1564     jPanel2.add(scaleProteinToCdna);
1565     jPanel2.add(gapLabel);
1566     jPanel2.add(wrap);
1567     jPanel2.add(sortLabel);
1568     jPanel2.add(sortAnnLabel);
1569     jPanel2.add(startupCheckbox);
1570     visualTab.add(jPanel2);
1571     visualTab.add(startupFileTextfield);
1572     visualTab.add(sortby);
1573     visualTab.add(sortAnnBy);
1574     visualTab.add(sortAutocalc);
1575     visualTab.add(gapSymbolCB);
1576     visualTab.add(fontNameCB);
1577     visualTab.add(fontSizeCB);
1578     visualTab.add(fontStyleCB);
1579     return visualTab;
1580   }
1581
1582   protected void autoIdWidth_actionPerformed()
1583   {
1584     // TODO Auto-generated method stub
1585
1586   }
1587
1588   protected void userIdWidth_actionPerformed()
1589   {
1590     // TODO Auto-generated method stub
1591
1592   }
1593
1594   protected void maxColour_actionPerformed(JPanel panel)
1595   {
1596   }
1597
1598   protected void minColour_actionPerformed(JPanel panel)
1599   {
1600   }
1601
1602   protected void gapColour_actionPerformed(JButton btn)
1603   {
1604   }
1605
1606   protected void hiddenColour_actionPerformed(JButton btn)
1607   {
1608   }
1609
1610   protected void showunconserved_actionPerformed(ActionEvent e)
1611   {
1612     // TODO Auto-generated method stub
1613
1614   }
1615
1616   /**
1617    * DOCUMENT ME!
1618    *
1619    * @param e
1620    *          DOCUMENT ME!
1621    */
1622   public void ok_actionPerformed(ActionEvent e)
1623   {
1624   }
1625
1626   /**
1627    * DOCUMENT ME!
1628    *
1629    * @param e
1630    *          DOCUMENT ME!
1631    */
1632   public void cancel_actionPerformed(ActionEvent e)
1633   {
1634   }
1635
1636   /**
1637    * DOCUMENT ME!
1638    *
1639    * @param e
1640    *          DOCUMENT ME!
1641    */
1642   public void annotations_actionPerformed(ActionEvent e)
1643   {
1644   }
1645
1646   /**
1647    * DOCUMENT ME!
1648    */
1649   public void startupFileTextfield_mouseClicked()
1650   {
1651   }
1652
1653   public void newLink_actionPerformed(ActionEvent e)
1654   {
1655
1656   }
1657
1658   public void editLink_actionPerformed(ActionEvent e)
1659   {
1660
1661   }
1662
1663   public void deleteLink_actionPerformed(ActionEvent e)
1664   {
1665
1666   }
1667
1668   public void defaultBrowser_mouseClicked(MouseEvent e)
1669   {
1670
1671   }
1672
1673   public void linkURLList_keyTyped(KeyEvent e)
1674   {
1675
1676   }
1677
1678   public void useProxy_actionPerformed()
1679   {
1680     boolean enabled = useProxy.isSelected();
1681     portLabel.setEnabled(enabled);
1682     serverLabel.setEnabled(enabled);
1683     proxyServerTB.setEnabled(enabled);
1684     proxyPortTB.setEnabled(enabled);
1685   }
1686
1687   /**
1688    * Customer renderer for JTable: supports column of radio buttons
1689    */
1690   public class RadioButtonRenderer extends JRadioButton
1691           implements TableCellRenderer
1692   {
1693     public RadioButtonRenderer()
1694     {
1695       setHorizontalAlignment(CENTER);
1696       setToolTipText(MessageManager.getString("label.urltooltip"));
1697     }
1698
1699     @Override
1700     public Component getTableCellRendererComponent(JTable table,
1701             Object value, boolean isSelected, boolean hasFocus, int row,
1702             int column)
1703     {
1704       setSelected((boolean) value);
1705
1706       // set colours to match rest of table
1707       if (isSelected)
1708       {
1709         setBackground(table.getSelectionBackground());
1710         setForeground(table.getSelectionForeground());
1711       }
1712       else
1713       {
1714         setBackground(table.getBackground());
1715         setForeground(table.getForeground());
1716       }
1717       return this;
1718     }
1719   }
1720
1721   /**
1722    * Customer cell editor for JTable: supports column of radio buttons in
1723    * conjunction with renderer
1724    */
1725   public class RadioButtonEditor extends AbstractCellEditor
1726           implements TableCellEditor
1727   {
1728     private JRadioButton button = new JRadioButton();
1729
1730     public RadioButtonEditor()
1731     {
1732       button.setHorizontalAlignment(SwingConstants.CENTER);
1733       this.button.addActionListener(new ActionListener()
1734       {
1735         @Override
1736         public void actionPerformed(ActionEvent e)
1737         {
1738           fireEditingStopped();
1739         }
1740       });
1741     }
1742
1743     @Override
1744     public Component getTableCellEditorComponent(JTable table, Object value,
1745             boolean isSelected, int row, int column)
1746     {
1747       button.setSelected((boolean) value);
1748       return button;
1749     }
1750
1751     @Override
1752     public Object getCellEditorValue()
1753     {
1754       return button.isSelected();
1755     }
1756
1757   }
1758 }