src/jalview/gui/Preferences.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.gui;
  22
  23 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
  24 import jalview.bin.Cache;
  25 import jalview.gui.Help.HelpId;
  26 import jalview.gui.StructureViewer.ViewerType;
  27 import jalview.io.FileFormatI;
  28 import jalview.io.JalviewFileChooser;
  29 import jalview.io.JalviewFileView;
  30 import jalview.jbgui.GPreferences;
  31 import jalview.jbgui.GSequenceLink;
  32 import jalview.schemes.ColourSchemeI;
  33 import jalview.schemes.ColourSchemes;
  34 import jalview.schemes.ResidueColourScheme;
  35 import jalview.urls.UrlLinkTableModel;
  36 import jalview.urls.api.UrlProviderFactoryI;
  37 import jalview.urls.api.UrlProviderI;
  38 import jalview.urls.desktop.DesktopUrlProviderFactory;
  39 import jalview.util.MessageManager;
  40 import jalview.util.Platform;
  41 import jalview.util.UrlConstants;
  42 import jalview.ws.sifts.SiftsSettings;
  43
  44 import java.awt.BorderLayout;
  45 import java.awt.Color;
  46 import java.awt.Component;
  47 import java.awt.Dimension;
  48 import java.awt.Font;
  49 import java.awt.event.ActionEvent;
  50 import java.awt.event.ActionListener;
  51 import java.awt.event.MouseEvent;
  52 import java.io.File;
  53 import java.util.ArrayList;
  54 import java.util.List;
  55
  56 import javax.help.HelpSetException;
  57 import javax.swing.JColorChooser;
  58 import javax.swing.JFileChooser;
  59 import javax.swing.JInternalFrame;
  60 import javax.swing.JPanel;
  61 import javax.swing.ListSelectionModel;
  62 import javax.swing.RowFilter;
  63 import javax.swing.RowSorter;
  64 import javax.swing.SortOrder;
  65 import javax.swing.event.DocumentEvent;
  66 import javax.swing.event.DocumentListener;
  67 import javax.swing.event.ListSelectionEvent;
  68 import javax.swing.event.ListSelectionListener;
  69 import javax.swing.table.TableCellRenderer;
  70 import javax.swing.table.TableColumn;
  71 import javax.swing.table.TableModel;
  72 import javax.swing.table.TableRowSorter;
  73
  74 import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
  75
  76 /**
  77  * DOCUMENT ME!
  78  *
  79  * @author $author$
  80  * @version $Revision$
  81  */
  82 public class Preferences extends GPreferences
  83 {
  84   public static final String ENABLE_SPLIT_FRAME = "ENABLE_SPLIT_FRAME";
  85
  86   public static final String SCALE_PROTEIN_TO_CDNA = "SCALE_PROTEIN_TO_CDNA";
  87
  88   public static final String DEFAULT_COLOUR = "DEFAULT_COLOUR";
  89
  90   public static final String DEFAULT_COLOUR_PROT = "DEFAULT_COLOUR_PROT";
  91
  92   public static final String DEFAULT_COLOUR_NUC = "DEFAULT_COLOUR_NUC";
  93
  94   public static final String ADD_TEMPFACT_ANN = "ADD_TEMPFACT_ANN";
  95
  96   public static final String ADD_SS_ANN = "ADD_SS_ANN";
  97
  98   public static final String USE_RNAVIEW = "USE_RNAVIEW";
  99
 100   public static final String STRUCT_FROM_PDB = "STRUCT_FROM_PDB";
 101
 102   public static final String STRUCTURE_DISPLAY = "STRUCTURE_DISPLAY";
 103
 104   public static final String CHIMERA_PATH = "CHIMERA_PATH";
 105
 106   public static final String HMMER_PATH = "HMMER_PATH";
 107
 108   public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS";
 109
 110   public static final String SHOW_AUTOCALC_ABOVE = "SHOW_AUTOCALC_ABOVE";
 111
 112   public static final String SHOW_OCCUPANCY = "SHOW_OCCUPANCY";
 113
 114   private static final int MIN_FONT_SIZE = 1;
 115
 116   private static final int MAX_FONT_SIZE = 30;
 117
 118   /**
 119    * Holds name and link separated with | character. Sequence ID must be
 120    * $SEQUENCE_ID$ or $SEQUENCE_ID=/.possible | chars ./=$
 121    */
 122   public static UrlProviderI sequenceUrlLinks;
 123
 124   public static UrlLinkTableModel dataModel;
 125
 126   /**
 127    * Holds name and link separated with | character. Sequence IDS and Sequences
 128    * must be $SEQUENCEIDS$ or $SEQUENCEIDS=/.possible | chars ./=$ and
 129    * $SEQUENCES$ or $SEQUENCES=/.possible | chars ./=$ and separation character
 130    * for first and second token specified after a pipe character at end |,|.
 131    * (TODO: proper escape for using | to separate ids or sequences
 132    */
 133
 134   public static List<String> groupURLLinks;
 135   static
 136   {
 137     // get links selected to be in the menu (SEQUENCE_LINKS)
 138     // and links entered by the user but not selected (STORED_LINKS)
 139     String inMenuString = Cache.getDefault("SEQUENCE_LINKS", "");
 140     String notInMenuString = Cache.getDefault("STORED_LINKS", "");
 141     String defaultUrl = Cache.getDefault("DEFAULT_URL",
 142             UrlConstants.DEFAULT_LABEL);
 143
 144     // if both links lists are empty, add the DEFAULT_URL link
 145     // otherwise we assume the default link is in one of the lists
 146     if (inMenuString.isEmpty() && notInMenuString.isEmpty())
 147     {
 148       inMenuString = UrlConstants.DEFAULT_STRING;
 149     }
 150     UrlProviderFactoryI factory = new DesktopUrlProviderFactory(defaultUrl,
 151             inMenuString, notInMenuString);
 152     sequenceUrlLinks = factory.createUrlProvider();
 153     dataModel = new UrlLinkTableModel(sequenceUrlLinks);
 154
 155     /**
 156      * TODO: reformulate groupURL encoding so two or more can be stored in the
 157      * .properties file as '|' separated strings
 158      */
 159
 160     groupURLLinks = new ArrayList<>();
 161   }
 162
 163   JInternalFrame frame;
 164
 165   DasSourceBrowser dasSource;
 166
 167   private WsPreferences wsPrefs;
 168
 169   private OptionsParam promptEachTimeOpt = new OptionsParam(
 170           MessageManager.getString("label.prompt_each_time"),
 171           "Prompt each time");
 172
 173   private OptionsParam lineArtOpt = new OptionsParam(
 174           MessageManager.getString("label.lineart"), "Lineart");
 175
 176   private OptionsParam textOpt = new OptionsParam(
 177           MessageManager.getString("action.text"), "Text");
 178
 179   /**
 180    * Creates a new Preferences object.
 181    */
 182   public Preferences()
 183   {
 184     super();
 185     frame = new JInternalFrame();
 186     frame.setContentPane(this);
 187     dasSource = new DasSourceBrowser();
 188     dasTab.add(dasSource, BorderLayout.CENTER);
 189     wsPrefs = new WsPreferences();
 190     wsTab.add(wsPrefs, BorderLayout.CENTER);
 191     int width = 500, height = 450;
 192     new jalview.util.Platform();
 193     if (Platform.isAMac())
 194     {
 195       width = 570;
 196       height = 480;
 197     }
 198
 199     Desktop.addInternalFrame(frame,
 200             MessageManager.getString("label.preferences"), width, height);
 201     frame.setMinimumSize(new Dimension(width, height));
 202
 203     /*
 204      * Set HMMER tab defaults
 205      */
 206     trimTermini.setSelected(Cache.getDefault("TRIM_TERMINI", false));
 207     isHMMERInstalled
 208             .setSelected(Cache.getDefault("HMMER_INSTALLED", false));
 209     if (Cache.getDefault("USE_UNIPROT", false))
 210     {
 211       uniprot.setSelected(true);
 212     }
 213     else
 214     {
 215       alignment.setSelected(true);
 216     }
 217     numberOfSequencesToKeepField
 218             .setText(Cache.getProperty("SEQUENCES_TO_KEEP"));
 219     installationLocation.setEnabled(isHMMERInstalled.isSelected());
 220     hmmerPath.setEnabled(isHMMERInstalled.isSelected());
 221     hmmerPath.setText(Cache.getProperty(HMMER_PATH));
 222     hmmerPath.addActionListener(new ActionListener()
 223     {
 224       @Override
 225       public void actionPerformed(ActionEvent e)
 226       {
 227         validateHMMERPath();
 228       }
 229     });
 230
 231     /*
 232      * Set Visual tab defaults
 233      */
 234     seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));
 235     rightAlign.setSelected(Cache.getDefault("RIGHT_ALIGN_IDS", false));
 236     fullScreen.setSelected(Cache.getDefault("SHOW_FULLSCREEN", false));
 237     annotations.setSelected(Cache.getDefault("SHOW_ANNOTATIONS", true));
 238
 239     conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));
 240     quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));
 241     identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));
 242     openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false));
 243     showUnconserved
 244             .setSelected(Cache.getDefault("SHOW_UNCONSERVED", false));
 245     showOccupancy.setSelected(Cache.getDefault(SHOW_OCCUPANCY, false));
 246     showGroupConsensus.setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS",
 247             false));
 248     showGroupConservation.setSelected(Cache.getDefault(
 249             "SHOW_GROUP_CONSERVATION", false));
 250     showConsensHistogram.setSelected(Cache.getDefault(
 251             "SHOW_CONSENSUS_HISTOGRAM", true));
 252     showConsensLogo.setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO",
 253             false));
 254     showInformationHistogram.setSelected(
 255             Cache.getDefault("SHOW_INFORMATION_HISTOGRAM", true));
 256     showHMMLogo.setSelected(Cache.getDefault("SHOW_HMM_LOGO", false));
 257     showNpTooltip.setSelected(Cache
 258             .getDefault("SHOW_NPFEATS_TOOLTIP", true));
 259     showDbRefTooltip.setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP",
 260             true));
 261
 262     String[] fonts = java.awt.GraphicsEnvironment
 263             .getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
 264     for (int i = 0; i < fonts.length; i++)
 265     {
 266       fontNameCB.addItem(fonts[i]);
 267     }
 268
 269     for (int i = MIN_FONT_SIZE; i <= MAX_FONT_SIZE; i++)
 270     {
 271       fontSizeCB.addItem(i + "");
 272     }
 273
 274     fontStyleCB.addItem("plain");
 275     fontStyleCB.addItem("bold");
 276     fontStyleCB.addItem("italic");
 277
 278     fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
 279     fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
 280     fontStyleCB.setSelectedItem(Cache.getDefault("FONT_STYLE", Font.PLAIN
 281             + ""));
 282
 283     smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));
 284     scaleProteinToCdna.setSelected(Cache.getDefault(SCALE_PROTEIN_TO_CDNA,
 285             false));
 286
 287     idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
 288
 289     wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
 290
 291     gapSymbolCB.addItem("-");
 292     gapSymbolCB.addItem(".");
 293
 294     gapSymbolCB.setSelectedItem(Cache.getDefault("GAP_SYMBOL", "-"));
 295
 296     sortby.addItem("No sort");
 297     sortby.addItem("Id");
 298     sortby.addItem("Pairwise Identity");
 299     sortby.setSelectedItem(Cache.getDefault("SORT_ALIGNMENT", "No sort"));
 300
 301     sortAnnBy.addItem(SequenceAnnotationOrder.NONE.toString());
 302     sortAnnBy
 303             .addItem(SequenceAnnotationOrder.SEQUENCE_AND_LABEL.toString());
 304     sortAnnBy
 305             .addItem(SequenceAnnotationOrder.LABEL_AND_SEQUENCE.toString());
 306     SequenceAnnotationOrder savedSort = SequenceAnnotationOrder
 307             .valueOf(Cache.getDefault(SORT_ANNOTATIONS,
 308                     SequenceAnnotationOrder.NONE.name()));
 309     sortAnnBy.setSelectedItem(savedSort.toString());
 310
 311     sortAutocalc.addItem("Autocalculated first");
 312     sortAutocalc.addItem("Autocalculated last");
 313     final boolean showAbove = Cache.getDefault(SHOW_AUTOCALC_ABOVE, true);
 314     sortAutocalc.setSelectedItem(showAbove ? sortAutocalc.getItemAt(0)
 315             : sortAutocalc.getItemAt(1));
 316     startupCheckbox
 317             .setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
 318     startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
 319             Cache.getDefault("www.jalview.org", "http://www.jalview.org")
 320                     + "/examples/exampleFile_2_3.jar"));
 321
 322     /*
 323      * Set Colours tab defaults
 324      */
 325     protColour.addItem(ResidueColourScheme.NONE);
 326     nucColour.addItem(ResidueColourScheme.NONE);
 327     for (ColourSchemeI cs : ColourSchemes.getInstance().getColourSchemes())
 328     {
 329       String name = cs.getSchemeName();
 330       protColour.addItem(name);
 331       nucColour.addItem(name);
 332     }
 333     String oldProp = Cache.getDefault(DEFAULT_COLOUR,
 334             ResidueColourScheme.NONE);
 335     String newProp = Cache.getDefault(DEFAULT_COLOUR_PROT, null);
 336     protColour.setSelectedItem(newProp != null ? newProp : oldProp);
 337     newProp = Cache.getDefault(DEFAULT_COLOUR_NUC, null);
 338     nucColour.setSelectedItem(newProp != null ? newProp : oldProp);
 339     minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN",
 340             Color.orange));
 341     maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX",
 342             Color.red));
 343
 344     /*
 345      * Set Structure tab defaults.
 346      */
 347     final boolean structSelected = Cache.getDefault(STRUCT_FROM_PDB, false);
 348     structFromPdb.setSelected(structSelected);
 349     useRnaView.setSelected(Cache.getDefault(USE_RNAVIEW, false));
 350     useRnaView.setEnabled(structSelected);
 351     addSecondaryStructure.setSelected(Cache.getDefault(ADD_SS_ANN, false));
 352     addSecondaryStructure.setEnabled(structSelected);
 353     addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, false));
 354     addTempFactor.setEnabled(structSelected);
 355     structViewer.setSelectedItem(Cache.getDefault(STRUCTURE_DISPLAY,
 356             ViewerType.JMOL.name()));
 357     chimeraPath.setText(Cache.getDefault(CHIMERA_PATH, ""));
 358     chimeraPath.addActionListener(new ActionListener()
 359     {
 360       @Override
 361       public void actionPerformed(ActionEvent e)
 362       {
 363         validateChimeraPath();
 364       }
 365     });
 366
 367     if (Cache.getDefault("MAP_WITH_SIFTS", false))
 368     {
 369       siftsMapping.setSelected(true);
 370     }
 371     else
 372     {
 373       nwMapping.setSelected(true);
 374     }
 375
 376     SiftsSettings
 377             .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
 378
 379     /*
 380      * Set Connections tab defaults
 381      */
 382
 383     // set up sorting
 384     linkUrlTable.setModel(dataModel);
 385     final TableRowSorter<TableModel> sorter = new TableRowSorter<>(
 386             linkUrlTable.getModel());
 387     linkUrlTable.setRowSorter(sorter);
 388     List<RowSorter.SortKey> sortKeys = new ArrayList<>();
 389
 390     UrlLinkTableModel m = (UrlLinkTableModel) linkUrlTable.getModel();
 391     sortKeys.add(new RowSorter.SortKey(m.getPrimaryColumn(),
 392             SortOrder.DESCENDING));
 393     sortKeys.add(new RowSorter.SortKey(m.getSelectedColumn(),
 394             SortOrder.DESCENDING));
 395     sortKeys.add(new RowSorter.SortKey(m.getNameColumn(),
 396             SortOrder.ASCENDING));
 397
 398     sorter.setSortKeys(sortKeys);
 399     sorter.sort();
 400
 401     // set up filtering
 402     ActionListener onReset;
 403     onReset = new ActionListener()
 404     {
 405       @Override
 406       public void actionPerformed(ActionEvent e)
 407       {
 408         filterTB.setText("");
 409         sorter.setRowFilter(RowFilter.regexFilter(""));
 410       }
 411
 412     };
 413     doReset.addActionListener(onReset);
 414
 415     // filter to display only custom urls
 416     final RowFilter<TableModel, Object> customUrlFilter = new RowFilter<TableModel, Object>()
 417     {
 418       @Override
 419       public boolean include(
 420               Entry<? extends TableModel, ? extends Object> entry)
 421       {
 422         return ((UrlLinkTableModel) entry.getModel()).isUserEntry(entry);
 423       }
 424     };
 425
 426     final TableRowSorter<TableModel> customSorter = new TableRowSorter<>(
 427             linkUrlTable.getModel());
 428     customSorter.setRowFilter(customUrlFilter);
 429
 430     ActionListener onCustomOnly;
 431     onCustomOnly = new ActionListener()
 432     {
 433       @Override
 434       public void actionPerformed(ActionEvent e)
 435       {
 436         filterTB.setText("");
 437         sorter.setRowFilter(customUrlFilter);
 438       }
 439     };
 440     userOnly.addActionListener(onCustomOnly);
 441
 442     filterTB.getDocument().addDocumentListener(new DocumentListener()
 443     {
 444       String caseInsensitiveFlag = "(?i)";
 445
 446       @Override
 447       public void changedUpdate(DocumentEvent e)
 448       {
 449         sorter.setRowFilter(RowFilter.regexFilter(caseInsensitiveFlag
 450                 + filterTB.getText()));
 451       }
 452
 453       @Override
 454       public void removeUpdate(DocumentEvent e)
 455       {
 456         sorter.setRowFilter(RowFilter.regexFilter(caseInsensitiveFlag
 457                 + filterTB.getText()));
 458       }
 459
 460       @Override
 461       public void insertUpdate(DocumentEvent e)
 462       {
 463         sorter.setRowFilter(RowFilter.regexFilter(caseInsensitiveFlag
 464                 + filterTB.getText()));
 465       }
 466     });
 467
 468     // set up list selection functionality
 469     linkUrlTable.getSelectionModel().addListSelectionListener(
 470             new UrlListSelectionHandler());
 471
 472     // set up radio buttons
 473     int onClickCol = ((UrlLinkTableModel) linkUrlTable.getModel())
 474             .getPrimaryColumn();
 475     String onClickName = linkUrlTable.getColumnName(onClickCol);
 476     linkUrlTable.getColumn(onClickName).setCellRenderer(
 477                new RadioButtonRenderer());
 478     linkUrlTable.getColumn(onClickName)
 479             .setCellEditor(new RadioButtonEditor());
 480
 481     // get boolean columns and resize those to min possible
 482     for (int column = 0; column < linkUrlTable.getColumnCount(); column++)
 483     {
 484       if (linkUrlTable.getModel().getColumnClass(column)
 485               .equals(Boolean.class))
 486       {
 487         TableColumn tableColumn = linkUrlTable.getColumnModel().getColumn(
 488                 column);
 489         int preferredWidth = tableColumn.getMinWidth();
 490
 491         TableCellRenderer cellRenderer = linkUrlTable.getCellRenderer(0,
 492                 column);
 493         Component c = linkUrlTable.prepareRenderer(cellRenderer, 0, column);
 494         int cwidth = c.getPreferredSize().width
 495                 + linkUrlTable.getIntercellSpacing().width;
 496         preferredWidth = Math.max(preferredWidth, cwidth);
 497
 498         tableColumn.setPreferredWidth(preferredWidth);
 499       }
 500     }
 501
 502     useProxy.setSelected(Cache.getDefault("USE_PROXY", false));
 503     useProxy_actionPerformed(); // make sure useProxy is correctly initialised
 504     proxyServerTB.setText(Cache.getDefault("PROXY_SERVER", ""));
 505     proxyPortTB.setText(Cache.getDefault("PROXY_PORT", ""));
 506
 507     defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", ""));
 508
 509     usagestats.setSelected(Cache.getDefault("USAGESTATS", false));
 510     // note antisense here: default is true
 511     questionnaire
 512             .setSelected(Cache.getProperty("NOQUESTIONNAIRES") == null);
 513     versioncheck.setSelected(Cache.getDefault("VERSION_CHECK", true));
 514
 515     /*
 516      * Set Output tab defaults
 517      */
 518     epsRendering.addItem(promptEachTimeOpt);
 519     epsRendering.addItem(lineArtOpt);
 520     epsRendering.addItem(textOpt);
 521     String defaultEPS = Cache.getDefault("EPS_RENDERING",
 522             "Prompt each time");
 523     if (defaultEPS.equalsIgnoreCase("Text"))
 524     {
 525       epsRendering.setSelectedItem(textOpt);
 526     }
 527     else if (defaultEPS.equalsIgnoreCase("Lineart"))
 528     {
 529       epsRendering.setSelectedItem(lineArtOpt);
 530     }
 531     else
 532     {
 533       epsRendering.setSelectedItem(promptEachTimeOpt);
 534     }
 535     autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false));
 536     userIdWidth.setEnabled(!autoIdWidth.isSelected());
 537     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
 538     Integer wi = Cache.getIntegerProperty("FIGURE_USERIDWIDTH");
 539     userIdWidth.setText(wi == null ? "" : wi.toString());
 540     blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
 541     clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
 542     fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
 543     msfjv.setSelected(Cache.getDefault("MSF_JVSUFFIX", true));
 544     pfamjv.setSelected(Cache.getDefault("PFAM_JVSUFFIX", true));
 545     pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
 546     pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
 547     modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
 548     embbedBioJSON.setSelected(Cache.getDefault("EXPORT_EMBBED_BIOJSON",
 549             true));
 550
 551     /*
 552      * Set Editing tab defaults
 553      */
 554     autoCalculateConsCheck.setSelected(Cache.getDefault(
 555             "AUTO_CALC_CONSENSUS", true));
 556     padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
 557     sortByTree.setSelected(Cache.getDefault("SORT_BY_TREE", false));
 558
 559     annotations_actionPerformed(null); // update the display of the annotation
 560                                        // settings
 561   }
 562
 563   /**
 564    * Save user selections on the Preferences tabs to the Cache and write out to
 565    * file.
 566    *
 567    * @param e
 568    */
 569   @Override
 570   public void ok_actionPerformed(ActionEvent e)
 571   {
 572     if (!validateSettings())
 573     {
 574       return;
 575     }
 576
 577     /*
 578      * Save Visual settings
 579      */
 580     Cache.applicationProperties.setProperty("SHOW_JVSUFFIX",
 581             Boolean.toString(seqLimit.isSelected()));
 582     Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS",
 583             Boolean.toString(rightAlign.isSelected()));
 584     Cache.applicationProperties.setProperty("SHOW_FULLSCREEN",
 585             Boolean.toString(fullScreen.isSelected()));
 586     Cache.applicationProperties.setProperty("SHOW_OVERVIEW",
 587             Boolean.toString(openoverv.isSelected()));
 588     Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
 589             Boolean.toString(annotations.isSelected()));
 590     Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
 591             Boolean.toString(conservation.isSelected()));
 592     Cache.applicationProperties.setProperty("SHOW_QUALITY",
 593             Boolean.toString(quality.isSelected()));
 594     Cache.applicationProperties.setProperty("SHOW_IDENTITY",
 595             Boolean.toString(identity.isSelected()));
 596
 597     Cache.applicationProperties.setProperty("GAP_SYMBOL", gapSymbolCB
 598             .getSelectedItem().toString());
 599
 600     Cache.applicationProperties.setProperty("FONT_NAME", fontNameCB
 601             .getSelectedItem().toString());
 602     Cache.applicationProperties.setProperty("FONT_STYLE", fontStyleCB
 603             .getSelectedItem().toString());
 604     Cache.applicationProperties.setProperty("FONT_SIZE", fontSizeCB
 605             .getSelectedItem().toString());
 606
 607     Cache.applicationProperties.setProperty("ID_ITALICS",
 608             Boolean.toString(idItalics.isSelected()));
 609     Cache.applicationProperties.setProperty("SHOW_UNCONSERVED",
 610             Boolean.toString(showUnconserved.isSelected()));
 611     Cache.applicationProperties.setProperty(SHOW_OCCUPANCY,
 612             Boolean.toString(showOccupancy.isSelected()));
 613     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS",
 614             Boolean.toString(showGroupConsensus.isSelected()));
 615     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION",
 616             Boolean.toString(showGroupConservation.isSelected()));
 617     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_HISTOGRAM",
 618             Boolean.toString(showConsensHistogram.isSelected()));
 619     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO",
 620             Boolean.toString(showConsensLogo.isSelected()));
 621     Cache.applicationProperties.setProperty("SHOW_INFORMATION_HISTOGRAM",
 622             Boolean.toString(showConsensHistogram.isSelected()));
 623     Cache.applicationProperties.setProperty("SHOW_HMM_LOGO",
 624             Boolean.toString(showHMMLogo.isSelected()));
 625     Cache.applicationProperties.setProperty("ANTI_ALIAS",
 626             Boolean.toString(smoothFont.isSelected()));
 627     Cache.applicationProperties.setProperty(SCALE_PROTEIN_TO_CDNA,
 628             Boolean.toString(scaleProteinToCdna.isSelected()));
 629     Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP",
 630             Boolean.toString(showNpTooltip.isSelected()));
 631     Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP",
 632             Boolean.toString(showDbRefTooltip.isSelected()));
 633
 634     Cache.applicationProperties.setProperty("WRAP_ALIGNMENT",
 635             Boolean.toString(wrap.isSelected()));
 636
 637     Cache.applicationProperties.setProperty("STARTUP_FILE",
 638             startupFileTextfield.getText());
 639     Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",
 640             Boolean.toString(startupCheckbox.isSelected()));
 641
 642     Cache.applicationProperties.setProperty("SORT_ALIGNMENT", sortby
 643             .getSelectedItem().toString());
 644
 645     // convert description of sort order to enum name for save
 646     SequenceAnnotationOrder annSortOrder = SequenceAnnotationOrder
 647             .forDescription(sortAnnBy.getSelectedItem().toString());
 648     if (annSortOrder != null)
 649     {
 650       Cache.applicationProperties.setProperty(SORT_ANNOTATIONS,
 651               annSortOrder.name());
 652     }
 653
 654     final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
 655     Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE, Boolean
 656             .valueOf(showAutocalcFirst).toString());
 657
 658     /*
 659      * Save Colours settings
 660      */
 661     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_PROT, protColour
 662             .getSelectedItem().toString());
 663     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_NUC, nucColour
 664             .getSelectedItem().toString());
 665     Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
 666             minColour.getBackground());
 667     Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
 668             maxColour.getBackground());
 669
 670     /*
 671      * Save HMMER settings
 672      */
 673     Cache.applicationProperties.setProperty("TRIM_TERMINI",
 674             Boolean.toString(trimTermini.isSelected()));
 675     Cache.applicationProperties.setProperty("USE_UNIPROT",
 676             Boolean.toString(uniprot.isSelected()));
 677     Cache.applicationProperties.setProperty("SEQUENCES_TO_KEEP",
 678             numberOfSequencesToKeepField.getText());
 679     Cache.applicationProperties.setProperty(HMMER_PATH,
 680             hmmerPath.getText());
 681     boolean hmmerInstalled = isHMMERInstalled.isSelected();
 682     Cache.applicationProperties.setProperty("HMMER_INSTALLED",
 683             Boolean.toString(hmmerInstalled));
 684     boolean hmmerFunctioning = validateHMMERPath(false);
 685     Cache.applicationProperties.setProperty("HMMER_FUNCTIONING",
 686             Boolean.toString(hmmerFunctioning));
 687     AlignFrame[] frames = Desktop.getAlignFrames();
 688     boolean hmmerStatus = hmmerFunctioning && hmmerInstalled ? true : false;
 689     for (AlignFrame frame : frames)
 690     {
 691       frame.updateHMMERStatus(hmmerStatus);
 692     }
 693
 694
 695     trimTermini.setSelected(Cache.getDefault("TRIM_TERMINI", false));
 696     if (Cache.getDefault("USE_UNIPROT", false))
 697     {
 698       uniprot.setSelected(true);
 699     }
 700     else
 701     {
 702       alignment.setSelected(true);
 703     }
 704     numberOfSequencesToKeepField
 705             .setText(Cache.getProperty("SEQUENCES_TO_KEEP"));
 706     hmmerPath.setText(Cache.getProperty(HMMER_PATH));
 707
 708     /*
 709      * Save Structure settings
 710      */
 711     Cache.applicationProperties.setProperty(ADD_TEMPFACT_ANN,
 712             Boolean.toString(addTempFactor.isSelected()));
 713     Cache.applicationProperties.setProperty(ADD_SS_ANN,
 714             Boolean.toString(addSecondaryStructure.isSelected()));
 715     Cache.applicationProperties.setProperty(USE_RNAVIEW,
 716             Boolean.toString(useRnaView.isSelected()));
 717     Cache.applicationProperties.setProperty(STRUCT_FROM_PDB,
 718             Boolean.toString(structFromPdb.isSelected()));
 719     Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY, structViewer
 720             .getSelectedItem().toString());
 721     Cache.setOrRemove(CHIMERA_PATH, chimeraPath.getText());
 722     Cache.applicationProperties.setProperty("MAP_WITH_SIFTS",
 723             Boolean.toString(siftsMapping.isSelected()));
 724     SiftsSettings.setMapWithSifts(siftsMapping.isSelected());
 725
 726     /*
 727      * Save Output settings
 728      */
 729     Cache.applicationProperties.setProperty("EPS_RENDERING",
 730             ((OptionsParam) epsRendering.getSelectedItem()).getCode());
 731
 732     /*
 733      * Save Connections settings
 734      */
 735     Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText());
 736
 737     jalview.util.BrowserLauncher.resetBrowser();
 738
 739     // save user-defined and selected links
 740     String menuLinks = sequenceUrlLinks.writeUrlsAsString(true);
 741     if (menuLinks.isEmpty())
 742     {
 743       Cache.applicationProperties.remove("SEQUENCE_LINKS");
 744     }
 745     else
 746     {
 747       Cache.applicationProperties.setProperty("SEQUENCE_LINKS",
 748               menuLinks.toString());
 749     }
 750
 751     String nonMenuLinks = sequenceUrlLinks.writeUrlsAsString(false);
 752     if (nonMenuLinks.isEmpty())
 753     {
 754       Cache.applicationProperties.remove("STORED_LINKS");
 755     }
 756     else
 757     {
 758       Cache.applicationProperties.setProperty("STORED_LINKS",
 759               nonMenuLinks.toString());
 760     }
 761
 762     Cache.applicationProperties.setProperty("DEFAULT_URL",
 763             sequenceUrlLinks.getPrimaryUrlId());
 764
 765     Cache.applicationProperties.setProperty("USE_PROXY",
 766             Boolean.toString(useProxy.isSelected()));
 767
 768     Cache.setOrRemove("PROXY_SERVER", proxyServerTB.getText());
 769
 770     Cache.setOrRemove("PROXY_PORT", proxyPortTB.getText());
 771
 772     if (useProxy.isSelected())
 773     {
 774       System.setProperty("http.proxyHost", proxyServerTB.getText());
 775       System.setProperty("http.proxyPort", proxyPortTB.getText());
 776     }
 777     else
 778     {
 779       System.setProperty("http.proxyHost", "");
 780       System.setProperty("http.proxyPort", "");
 781     }
 782     Cache.setProperty("VERSION_CHECK",
 783             Boolean.toString(versioncheck.isSelected()));
 784     if (Cache.getProperty("USAGESTATS") != null || usagestats.isSelected())
 785     {
 786       // default is false - we only set this if the user has actively agreed
 787       Cache.setProperty("USAGESTATS",
 788               Boolean.toString(usagestats.isSelected()));
 789     }
 790     if (!questionnaire.isSelected())
 791     {
 792       Cache.setProperty("NOQUESTIONNAIRES", "true");
 793     }
 794     else
 795     {
 796       // special - made easy to edit a property file to disable questionnaires
 797       // by just adding the given line
 798       Cache.removeProperty("NOQUESTIONNAIRES");
 799     }
 800
 801     /*
 802      * Save Output settings
 803      */
 804     Cache.applicationProperties.setProperty("BLC_JVSUFFIX",
 805             Boolean.toString(blcjv.isSelected()));
 806     Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX",
 807             Boolean.toString(clustaljv.isSelected()));
 808     Cache.applicationProperties.setProperty("FASTA_JVSUFFIX",
 809             Boolean.toString(fastajv.isSelected()));
 810     Cache.applicationProperties.setProperty("MSF_JVSUFFIX",
 811             Boolean.toString(msfjv.isSelected()));
 812     Cache.applicationProperties.setProperty("PFAM_JVSUFFIX",
 813             Boolean.toString(pfamjv.isSelected()));
 814     Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX",
 815             Boolean.toString(pileupjv.isSelected()));
 816     Cache.applicationProperties.setProperty("PIR_JVSUFFIX",
 817             Boolean.toString(pirjv.isSelected()));
 818     Cache.applicationProperties.setProperty("PIR_MODELLER",
 819             Boolean.toString(modellerOutput.isSelected()));
 820     Cache.applicationProperties.setProperty("EXPORT_EMBBED_BIOJSON",
 821             Boolean.toString(embbedBioJSON.isSelected()));
 822     jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
 823
 824     Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH",
 825             Boolean.toString(autoIdWidth.isSelected()));
 826     userIdWidth_actionPerformed();
 827     Cache.applicationProperties.setProperty("FIGURE_USERIDWIDTH",
 828             userIdWidth.getText());
 829
 830     /*
 831      * Save Editing settings
 832      */
 833     Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
 834             Boolean.toString(autoCalculateConsCheck.isSelected()));
 835     Cache.applicationProperties.setProperty("SORT_BY_TREE",
 836             Boolean.toString(sortByTree.isSelected()));
 837     Cache.applicationProperties.setProperty("PAD_GAPS",
 838             Boolean.toString(padGaps.isSelected()));
 839
 840     dasSource.saveProperties(Cache.applicationProperties);
 841     wsPrefs.updateAndRefreshWsMenuConfig(false);
 842     Cache.saveProperties();
 843     Desktop.instance.doConfigureStructurePrefs();
 844     try
 845     {
 846       frame.setClosed(true);
 847     } catch (Exception ex)
 848     {
 849     }
 850   }
 851
 852   /**
 853    * Do any necessary validation before saving settings. Return focus to the
 854    * first tab which fails validation.
 855    *
 856    * @return
 857    */
 858   private boolean validateSettings()
 859   {
 860     if (!validateStructure())
 861     {
 862       structureTab.requestFocusInWindow();
 863       return false;
 864     }
 865     if (isHMMERInstalled.isSelected())
 866     {
 867       if (!validateHMMER())
 868       {
 869         hmmerTab.requestFocusInWindow();
 870         return false;
 871       }
 872     }
 873     return true;
 874   }
 875
 876   @Override
 877   protected boolean validateStructure()
 878   {
 879     return validateChimeraPath();
 880
 881   }
 882
 883   @Override
 884   protected boolean validateHMMER()
 885   {
 886     return validateHMMERPath();
 887
 888   }
 889
 890   /**
 891    * DOCUMENT ME!
 892    */
 893   @Override
 894   public void startupFileTextfield_mouseClicked()
 895   {
 896     String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
 897     JalviewFileChooser chooser = JalviewFileChooser.forRead(
 898             Cache.getProperty("LAST_DIRECTORY"), fileFormat);
 899     chooser.setFileView(new JalviewFileView());
 900     chooser.setDialogTitle(MessageManager
 901             .getString("label.select_startup_file"));
 902
 903     int value = chooser.showOpenDialog(this);
 904
 905     if (value == JalviewFileChooser.APPROVE_OPTION)
 906     {
 907       FileFormatI format = chooser.getSelectedFormat();
 908       if (format != null)
 909       {
 910         Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT",
 911                 format.getName());
 912       }
 913       startupFileTextfield.setText(chooser.getSelectedFile()
 914               .getAbsolutePath());
 915     }
 916   }
 917
 918   /**
 919    * DOCUMENT ME!
 920    *
 921    * @param e
 922    *          DOCUMENT ME!
 923    */
 924   @Override
 925   public void cancel_actionPerformed(ActionEvent e)
 926   {
 927     try
 928     {
 929       wsPrefs.updateWsMenuConfig(true);
 930       wsPrefs.refreshWs_actionPerformed(e);
 931       frame.setClosed(true);
 932     } catch (Exception ex)
 933     {
 934     }
 935   }
 936
 937   /**
 938    * DOCUMENT ME!
 939    *
 940    * @param e
 941    *          DOCUMENT ME!
 942    */
 943   @Override
 944   public void annotations_actionPerformed(ActionEvent e)
 945   {
 946     conservation.setEnabled(annotations.isSelected());
 947     quality.setEnabled(annotations.isSelected());
 948     identity.setEnabled(annotations.isSelected());
 949     showOccupancy.setEnabled(annotations.isSelected());
 950     showGroupConsensus.setEnabled(annotations.isSelected());
 951     showGroupConservation.setEnabled(annotations.isSelected());
 952     showConsensHistogram.setEnabled(annotations.isSelected()
 953             && (identity.isSelected() || showGroupConsensus.isSelected()));
 954     showConsensLogo.setEnabled(annotations.isSelected()
 955             && (identity.isSelected() || showGroupConsensus.isSelected()));
 956     showInformationHistogram.setEnabled(annotations.isSelected());
 957     showHMMLogo.setEnabled(annotations.isSelected());
 958   }
 959
 960   @Override
 961   public void newLink_actionPerformed(ActionEvent e)
 962   {
 963     GSequenceLink link = new GSequenceLink();
 964     boolean valid = false;
 965     while (!valid)
 966     {
 967       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 968               MessageManager.getString("label.new_sequence_url_link"),
 969               JvOptionPane.OK_CANCEL_OPTION, -1, null) == JvOptionPane.OK_OPTION)
 970       {
 971         if (link.checkValid())
 972         {
 973           if (((UrlLinkTableModel) linkUrlTable.getModel())
 974                   .isUniqueName(link.getName()))
 975           {
 976             ((UrlLinkTableModel) linkUrlTable.getModel()).insertRow(
 977                     link.getName(), link.getURL());
 978             valid = true;
 979           }
 980           else
 981           {
 982             link.notifyDuplicate();
 983             continue;
 984           }
 985         }
 986       }
 987       else
 988       {
 989         break;
 990       }
 991     }
 992   }
 993
 994   @Override
 995   public void editLink_actionPerformed(ActionEvent e)
 996   {
 997     GSequenceLink link = new GSequenceLink();
 998
 999     int index = linkUrlTable.getSelectedRow();
1000     if (index == -1)
1001     {
1002       // button no longer enabled if row is not selected
1003       Cache.log.debug("Edit with no row selected in linkUrlTable");
1004       return;
1005     }
1006
1007     int nameCol = ((UrlLinkTableModel) linkUrlTable.getModel())
1008             .getNameColumn();
1009     int urlCol = ((UrlLinkTableModel) linkUrlTable.getModel())
1010             .getUrlColumn();
1011     String oldName = linkUrlTable.getValueAt(index, nameCol).toString();
1012     link.setName(oldName);
1013     link.setURL(linkUrlTable.getValueAt(index, urlCol).toString());
1014
1015     boolean valid = false;
1016     while (!valid)
1017     {
1018       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
1019               MessageManager.getString("label.edit_sequence_url_link"),
1020               JvOptionPane.OK_CANCEL_OPTION, -1, null) == JvOptionPane.OK_OPTION)
1021       {
1022         if (link.checkValid())
1023         {
1024           if ((oldName.equals(link.getName()))
1025                   || (((UrlLinkTableModel) linkUrlTable.getModel())
1026                           .isUniqueName(link.getName())))
1027           {
1028             linkUrlTable.setValueAt(link.getName(), index, nameCol);
1029             linkUrlTable.setValueAt(link.getURL(), index, urlCol);
1030             valid = true;
1031           }
1032           else
1033           {
1034             link.notifyDuplicate();
1035             continue;
1036           }
1037         }
1038       }
1039       else
1040       {
1041         break;
1042       }
1043     }
1044   }
1045
1046   @Override
1047   public void deleteLink_actionPerformed(ActionEvent e)
1048   {
1049     int index = linkUrlTable.getSelectedRow();
1050     int modelIndex = -1;
1051     if (index == -1)
1052     {
1053       // button no longer enabled if row is not selected
1054       Cache.log.debug("Delete with no row selected in linkUrlTable");
1055       return;
1056     }
1057     else
1058     {
1059       modelIndex = linkUrlTable.convertRowIndexToModel(index);
1060     }
1061
1062     // make sure we use the model index to delete, and not the table index
1063     ((UrlLinkTableModel) linkUrlTable.getModel()).removeRow(modelIndex);
1064   }
1065
1066
1067   @Override
1068   public void defaultBrowser_mouseClicked(MouseEvent e)
1069   {
1070     JFileChooser chooser = new JFileChooser(".");
1071     chooser.setDialogTitle(MessageManager
1072             .getString("label.select_default_browser"));
1073
1074     int value = chooser.showOpenDialog(this);
1075
1076     if (value == JFileChooser.APPROVE_OPTION)
1077     {
1078       defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
1079     }
1080
1081   }
1082
1083   /*
1084    * (non-Javadoc)
1085    *
1086    * @see
1087    * jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event
1088    * .ActionEvent)
1089    */
1090   @Override
1091   protected void showunconserved_actionPerformed(ActionEvent e)
1092   {
1093     // TODO Auto-generated method stub
1094     super.showunconserved_actionPerformed(e);
1095   }
1096
1097   public static List<String> getGroupURLLinks()
1098   {
1099     return groupURLLinks;
1100   }
1101
1102   @Override
1103   public void minColour_actionPerformed(JPanel panel)
1104   {
1105     Color col = JColorChooser.showDialog(this,
1106             MessageManager.getString("label.select_colour_minimum_value"),
1107             minColour.getBackground());
1108     if (col != null)
1109     {
1110       panel.setBackground(col);
1111     }
1112     panel.repaint();
1113   }
1114
1115   @Override
1116   public void maxColour_actionPerformed(JPanel panel)
1117   {
1118     Color col = JColorChooser.showDialog(this,
1119             MessageManager.getString("label.select_colour_maximum_value"),
1120             maxColour.getBackground());
1121     if (col != null)
1122     {
1123       panel.setBackground(col);
1124     }
1125     panel.repaint();
1126   }
1127
1128   @Override
1129   protected void userIdWidth_actionPerformed()
1130   {
1131     try
1132     {
1133       String val = userIdWidth.getText().trim();
1134       if (val.length() > 0)
1135       {
1136         Integer iw = Integer.parseInt(val);
1137         if (iw.intValue() < 12)
1138         {
1139           throw new NumberFormatException();
1140         }
1141         userIdWidth.setText(iw.toString());
1142       }
1143     } catch (NumberFormatException x)
1144     {
1145       JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
1146               .getString("warn.user_defined_width_requirements"),
1147               MessageManager.getString("label.invalid_id_column_width"),
1148               JvOptionPane.WARNING_MESSAGE);
1149       userIdWidth.setText("");
1150     }
1151   }
1152
1153   @Override
1154   protected void autoIdWidth_actionPerformed()
1155   {
1156     userIdWidth.setEnabled(!autoIdWidth.isSelected());
1157     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
1158   }
1159
1160   /**
1161    * Returns true if chimera path is to a valid executable, else show an error
1162    * dialog.
1163    */
1164   private boolean validateChimeraPath()
1165   {
1166     if (chimeraPath.getText().trim().length() > 0)
1167     {
1168       File f = new File(chimeraPath.getText());
1169       if (!f.canExecute())
1170       {
1171         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1172                 MessageManager.getString("label.invalid_chimera_path"),
1173                 MessageManager.getString("label.invalid_name"),
1174                 JvOptionPane.ERROR_MESSAGE);
1175         return false;
1176       }
1177     }
1178     return true;
1179   }
1180
1181   /**
1182    * Returns true if hmmer path contains the necessary valid executables, else
1183    * show an error dialog (if showing dialog).
1184    */
1185   private boolean validateHMMERPath(boolean showDialog)
1186   {
1187     int missing = 0;
1188     String message = "";
1189     String path = hmmerPath.getText().trim();
1190     if (path.length() > 0)
1191     {
1192       File f = new File(path);
1193       if (!f.exists())
1194       {
1195         if (showDialog)
1196         {
1197           JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1198                 MessageManager.getString("label.folder_not_exists"),
1199                 MessageManager.getString("label.invalid_folder"),
1200                 JvOptionPane.ERROR_MESSAGE);
1201         }
1202         return false;
1203       }
1204
1205       File hmmbuild = new File(path + "/binaries/hmmbuild.exe");
1206       {
1207         if (!hmmbuild.canExecute())
1208         {
1209           message += MessageManager.getString("label.hmmbuild_not_found")
1210                   + "\n";
1211           missing++;
1212         }
1213       }
1214
1215       File hmmalign = new File(path + "/binaries/hmmalign.exe");
1216       {
1217         if (!hmmalign.canExecute())
1218         {
1219           message += MessageManager.getString("label.hmmalign_not_found")
1220                   + "\n";
1221           missing++;
1222         }
1223       }
1224
1225       File hmmsearch = new File(path + "/binaries/hmmsearch.exe");
1226       {
1227         if (!hmmsearch.canExecute())
1228         {
1229           message += MessageManager.getString("label.hmmsearch_not_found")
1230                   + "\n";
1231           missing++;
1232         }
1233       }
1234
1235       if (missing > 0)
1236       {
1237         if (missing < 3)
1238         {
1239           if (showDialog)
1240           {
1241             JvOptionPane.showInternalMessageDialog(Desktop.desktop, message,
1242                   MessageManager.getString("label.invalid_folder"),
1243                   JvOptionPane.ERROR_MESSAGE);
1244           }
1245           return false;
1246         }
1247         else
1248         {
1249           if (showDialog)
1250           {
1251             JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1252                   MessageManager.getString("label.no_binaries"),
1253                   MessageManager.getString("label.invalid_folder"),
1254                   JvOptionPane.ERROR_MESSAGE);
1255           }
1256
1257           return false;
1258         }
1259       }
1260
1261     }
1262     return true;
1263   }
1264
1265   private boolean validateHMMERPath()
1266   {
1267     return validateHMMERPath(true);
1268   }
1269
1270   /**
1271    * If Chimera is selected, check it can be found on default or user-specified
1272    * path, if not show a warning/help dialog.
1273    */
1274   @Override
1275   protected void structureViewer_actionPerformed(String selectedItem)
1276   {
1277     if (!selectedItem.equals(ViewerType.CHIMERA.name()))
1278     {
1279       return;
1280     }
1281     boolean found = false;
1282
1283     /*
1284      * Try user-specified and standard paths for Chimera executable.
1285      */
1286     List<String> paths = StructureManager.getChimeraPaths();
1287     paths.add(0, chimeraPath.getText());
1288     for (String path : paths)
1289     {
1290       if (new File(path.trim()).canExecute())
1291       {
1292         found = true;
1293         break;
1294       }
1295     }
1296     if (!found)
1297     {
1298       String[] options = { "OK", "Help" };
1299       int showHelp = JvOptionPane.showInternalOptionDialog(
1300               Desktop.desktop,
1301               JvSwingUtils.wrapTooltip(true,
1302                       MessageManager.getString("label.chimera_missing")),
1303               "", JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE,
1304               null, options, options[0]);
1305       if (showHelp == JvOptionPane.NO_OPTION)
1306       {
1307         try
1308         {
1309           Help.showHelpWindow(HelpId.StructureViewer);
1310         } catch (HelpSetException e)
1311         {
1312           e.printStackTrace();
1313         }
1314       }
1315     }
1316   }
1317
1318   public class OptionsParam
1319   {
1320     private String name;
1321
1322     private String code;
1323
1324     public OptionsParam(String name, String code)
1325     {
1326       this.name = name;
1327       this.code = code;
1328     }
1329
1330     public String getName()
1331     {
1332       return name;
1333     }
1334
1335     public void setName(String name)
1336     {
1337       this.name = name;
1338     }
1339
1340     public String getCode()
1341     {
1342       return code;
1343     }
1344
1345     public void setCode(String code)
1346     {
1347       this.code = code;
1348     }
1349
1350     @Override
1351     public String toString()
1352     {
1353       return name;
1354     }
1355
1356     @Override
1357     public boolean equals(Object that)
1358     {
1359       if (!(that instanceof OptionsParam))
1360       {
1361         return false;
1362       }
1363       return this.code.equalsIgnoreCase(((OptionsParam) that).code);
1364     }
1365
1366     @Override
1367     public int hashCode()
1368     {
1369       return name.hashCode() + code.hashCode();
1370     }
1371   }
1372
1373   private class UrlListSelectionHandler implements ListSelectionListener
1374   {
1375
1376     @Override
1377     public void valueChanged(ListSelectionEvent e)
1378     {
1379       ListSelectionModel lsm = (ListSelectionModel) e.getSource();
1380
1381       int index = lsm.getMinSelectionIndex();
1382       if (index == -1)
1383       {
1384         // no selection, so disable delete/edit buttons
1385         editLink.setEnabled(false);
1386         deleteLink.setEnabled(false);
1387         return;
1388       }
1389       int modelIndex = linkUrlTable.convertRowIndexToModel(index);
1390
1391       // enable/disable edit and delete link buttons
1392       if (((UrlLinkTableModel) linkUrlTable.getModel())
1393               .isRowDeletable(modelIndex))
1394       {
1395         deleteLink.setEnabled(true);
1396       }
1397       else
1398       {
1399         deleteLink.setEnabled(false);
1400       }
1401
1402       if (((UrlLinkTableModel) linkUrlTable.getModel())
1403               .isRowEditable(modelIndex))
1404       {
1405         editLink.setEnabled(true);
1406       }
1407       else
1408       {
1409         editLink.setEnabled(false);
1410       }
1411     }
1412 }
1413 }