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.io.IOException;
  54 import java.util.ArrayList;
  55 import java.util.List;
  56 import java.util.Scanner;
  57
  58 import javax.help.HelpSetException;
  59 import javax.swing.JColorChooser;
  60 import javax.swing.JFileChooser;
  61 import javax.swing.JInternalFrame;
  62 import javax.swing.JPanel;
  63 import javax.swing.ListSelectionModel;
  64 import javax.swing.RowFilter;
  65 import javax.swing.RowSorter;
  66 import javax.swing.SortOrder;
  67 import javax.swing.event.DocumentEvent;
  68 import javax.swing.event.DocumentListener;
  69 import javax.swing.event.ListSelectionEvent;
  70 import javax.swing.event.ListSelectionListener;
  71 import javax.swing.table.TableCellRenderer;
  72 import javax.swing.table.TableColumn;
  73 import javax.swing.table.TableModel;
  74 import javax.swing.table.TableRowSorter;
  75
  76 import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
  77
  78 /**
  79  * DOCUMENT ME!
  80  *
  81  * @author $author$
  82  * @version $Revision$
  83  */
  84 public class Preferences extends GPreferences
  85 {
  86   public static final String ENABLE_SPLIT_FRAME = "ENABLE_SPLIT_FRAME";
  87
  88   public static final String SCALE_PROTEIN_TO_CDNA = "SCALE_PROTEIN_TO_CDNA";
  89
  90   public static final String DEFAULT_COLOUR = "DEFAULT_COLOUR";
  91
  92   public static final String DEFAULT_COLOUR_PROT = "DEFAULT_COLOUR_PROT";
  93
  94   public static final String DEFAULT_COLOUR_NUC = "DEFAULT_COLOUR_NUC";
  95
  96   public static final String ADD_TEMPFACT_ANN = "ADD_TEMPFACT_ANN";
  97
  98   public static final String ADD_SS_ANN = "ADD_SS_ANN";
  99
 100   public static final String USE_RNAVIEW = "USE_RNAVIEW";
 101
 102   public static final String STRUCT_FROM_PDB = "STRUCT_FROM_PDB";
 103
 104   public static final String STRUCTURE_DISPLAY = "STRUCTURE_DISPLAY";
 105
 106   public static final String CHIMERA_PATH = "CHIMERA_PATH";
 107
 108   public static final String HMMER_PATH = "HMMER_PATH";
 109
 110   public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS";
 111
 112   public static final String SHOW_AUTOCALC_ABOVE = "SHOW_AUTOCALC_ABOVE";
 113
 114   public static final String SHOW_OCCUPANCY = "SHOW_OCCUPANCY";
 115
 116   private static final int MIN_FONT_SIZE = 1;
 117
 118   private static final int MAX_FONT_SIZE = 30;
 119
 120   /**
 121    * Holds name and link separated with | character. Sequence ID must be
 122    * $SEQUENCE_ID$ or $SEQUENCE_ID=/.possible | chars ./=$
 123    */
 124   public static UrlProviderI sequenceUrlLinks;
 125
 126   public static UrlLinkTableModel dataModel;
 127
 128   /**
 129    * Holds name and link separated with | character. Sequence IDS and Sequences
 130    * must be $SEQUENCEIDS$ or $SEQUENCEIDS=/.possible | chars ./=$ and
 131    * $SEQUENCES$ or $SEQUENCES=/.possible | chars ./=$ and separation character
 132    * for first and second token specified after a pipe character at end |,|.
 133    * (TODO: proper escape for using | to separate ids or sequences
 134    */
 135
 136   public static List<String> groupURLLinks;
 137   static
 138   {
 139     // get links selected to be in the menu (SEQUENCE_LINKS)
 140     // and links entered by the user but not selected (STORED_LINKS)
 141     String inMenuString = Cache.getDefault("SEQUENCE_LINKS", "");
 142     String notInMenuString = Cache.getDefault("STORED_LINKS", "");
 143     String defaultUrl = Cache.getDefault("DEFAULT_URL",
 144             UrlConstants.DEFAULT_LABEL);
 145
 146     // if both links lists are empty, add the DEFAULT_URL link
 147     // otherwise we assume the default link is in one of the lists
 148     if (inMenuString.isEmpty() && notInMenuString.isEmpty())
 149     {
 150       inMenuString = UrlConstants.DEFAULT_STRING;
 151     }
 152     UrlProviderFactoryI factory = new DesktopUrlProviderFactory(defaultUrl,
 153             inMenuString, notInMenuString);
 154     sequenceUrlLinks = factory.createUrlProvider();
 155     dataModel = new UrlLinkTableModel(sequenceUrlLinks);
 156
 157     /**
 158      * TODO: reformulate groupURL encoding so two or more can be stored in the
 159      * .properties file as '|' separated strings
 160      */
 161
 162     groupURLLinks = new ArrayList<>();
 163   }
 164
 165   JInternalFrame frame;
 166
 167   DasSourceBrowser dasSource;
 168
 169   private WsPreferences wsPrefs;
 170
 171   private OptionsParam promptEachTimeOpt = new OptionsParam(
 172           MessageManager.getString("label.prompt_each_time"),
 173           "Prompt each time");
 174
 175   private OptionsParam lineArtOpt = new OptionsParam(
 176           MessageManager.getString("label.lineart"), "Lineart");
 177
 178   private OptionsParam textOpt = new OptionsParam(
 179           MessageManager.getString("action.text"), "Text");
 180
 181   /**
 182    * Creates a new Preferences object.
 183    */
 184   public Preferences()
 185   {
 186     super();
 187     frame = new JInternalFrame();
 188     frame.setContentPane(this);
 189     dasSource = new DasSourceBrowser();
 190     dasTab.add(dasSource, BorderLayout.CENTER);
 191     wsPrefs = new WsPreferences();
 192     wsTab.add(wsPrefs, BorderLayout.CENTER);
 193     int width = 500, height = 450;
 194     new jalview.util.Platform();
 195     if (Platform.isAMac())
 196     {
 197       width = 570;
 198       height = 480;
 199     }
 200
 201     Desktop.addInternalFrame(frame,
 202             MessageManager.getString("label.preferences"), width, height);
 203     frame.setMinimumSize(new Dimension(width, height));
 204
 205     /*
 206      * Set HMMER tab defaults
 207      */
 208     trimTermini.setSelected(Cache.getDefault("TRIM_TERMINI", false));
 209     isHMMERInstalled
 210             .setSelected(Cache.getDefault("HMMER_INSTALLED", false));
 211     if (Cache.getDefault("USE_UNIPROT", false))
 212     {
 213       uniprot.setSelected(true);
 214     }
 215     else
 216     {
 217       alignment.setSelected(true);
 218     }
 219     numberOfSequencesToKeepField
 220             .setText(Cache.getProperty("SEQUENCES_TO_KEEP"));
 221     installationLocation.setEnabled(isHMMERInstalled.isSelected());
 222     hmmerPath.setEnabled(isHMMERInstalled.isSelected());
 223     hmmerPath.setText(Cache.getProperty(HMMER_PATH));
 224     hmmerPath.addActionListener(new ActionListener()
 225     {
 226       @Override
 227       public void actionPerformed(ActionEvent e)
 228       {
 229         validateHMMERPath();
 230       }
 231     });
 232
 233     /*
 234      * Set Visual tab defaults
 235      */
 236     seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));
 237     rightAlign.setSelected(Cache.getDefault("RIGHT_ALIGN_IDS", false));
 238     fullScreen.setSelected(Cache.getDefault("SHOW_FULLSCREEN", false));
 239     annotations.setSelected(Cache.getDefault("SHOW_ANNOTATIONS", true));
 240
 241     conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));
 242     quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));
 243     identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));
 244     openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false));
 245     showUnconserved
 246             .setSelected(Cache.getDefault("SHOW_UNCONSERVED", false));
 247     showOccupancy.setSelected(Cache.getDefault(SHOW_OCCUPANCY, false));
 248     showGroupConsensus.setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS",
 249             false));
 250     showGroupConservation.setSelected(Cache.getDefault(
 251             "SHOW_GROUP_CONSERVATION", false));
 252     showConsensHistogram.setSelected(Cache.getDefault(
 253             "SHOW_CONSENSUS_HISTOGRAM", true));
 254     showConsensLogo.setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO",
 255             false));
 256     showInformationHistogram.setSelected(
 257             Cache.getDefault("SHOW_INFORMATION_HISTOGRAM", true));
 258     showHMMLogo.setSelected(Cache.getDefault("SHOW_HMM_LOGO", false));
 259     showNpTooltip.setSelected(Cache
 260             .getDefault("SHOW_NPFEATS_TOOLTIP", true));
 261     showDbRefTooltip.setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP",
 262             true));
 263
 264     String[] fonts = java.awt.GraphicsEnvironment
 265             .getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
 266     for (int i = 0; i < fonts.length; i++)
 267     {
 268       fontNameCB.addItem(fonts[i]);
 269     }
 270
 271     for (int i = MIN_FONT_SIZE; i <= MAX_FONT_SIZE; i++)
 272     {
 273       fontSizeCB.addItem(i + "");
 274     }
 275
 276     fontStyleCB.addItem("plain");
 277     fontStyleCB.addItem("bold");
 278     fontStyleCB.addItem("italic");
 279
 280     fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
 281     fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
 282     fontStyleCB.setSelectedItem(Cache.getDefault("FONT_STYLE", Font.PLAIN
 283             + ""));
 284
 285     smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));
 286     scaleProteinToCdna.setSelected(Cache.getDefault(SCALE_PROTEIN_TO_CDNA,
 287             false));
 288
 289     idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
 290
 291     wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
 292
 293     gapSymbolCB.addItem("-");
 294     gapSymbolCB.addItem(".");
 295
 296     gapSymbolCB.setSelectedItem(Cache.getDefault("GAP_SYMBOL", "-"));
 297
 298     sortby.addItem("No sort");
 299     sortby.addItem("Id");
 300     sortby.addItem("Pairwise Identity");
 301     sortby.setSelectedItem(Cache.getDefault("SORT_ALIGNMENT", "No sort"));
 302
 303     sortAnnBy.addItem(SequenceAnnotationOrder.NONE.toString());
 304     sortAnnBy
 305             .addItem(SequenceAnnotationOrder.SEQUENCE_AND_LABEL.toString());
 306     sortAnnBy
 307             .addItem(SequenceAnnotationOrder.LABEL_AND_SEQUENCE.toString());
 308     SequenceAnnotationOrder savedSort = SequenceAnnotationOrder
 309             .valueOf(Cache.getDefault(SORT_ANNOTATIONS,
 310                     SequenceAnnotationOrder.NONE.name()));
 311     sortAnnBy.setSelectedItem(savedSort.toString());
 312
 313     sortAutocalc.addItem("Autocalculated first");
 314     sortAutocalc.addItem("Autocalculated last");
 315     final boolean showAbove = Cache.getDefault(SHOW_AUTOCALC_ABOVE, true);
 316     sortAutocalc.setSelectedItem(showAbove ? sortAutocalc.getItemAt(0)
 317             : sortAutocalc.getItemAt(1));
 318     startupCheckbox
 319             .setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
 320     startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
 321             Cache.getDefault("www.jalview.org", "http://www.jalview.org")
 322                     + "/examples/exampleFile_2_3.jar"));
 323
 324     /*
 325      * Set Colours tab defaults
 326      */
 327     protColour.addItem(ResidueColourScheme.NONE);
 328     nucColour.addItem(ResidueColourScheme.NONE);
 329     for (ColourSchemeI cs : ColourSchemes.getInstance().getColourSchemes())
 330     {
 331       String name = cs.getSchemeName();
 332       protColour.addItem(name);
 333       nucColour.addItem(name);
 334     }
 335     String oldProp = Cache.getDefault(DEFAULT_COLOUR,
 336             ResidueColourScheme.NONE);
 337     String newProp = Cache.getDefault(DEFAULT_COLOUR_PROT, null);
 338     protColour.setSelectedItem(newProp != null ? newProp : oldProp);
 339     newProp = Cache.getDefault(DEFAULT_COLOUR_NUC, null);
 340     nucColour.setSelectedItem(newProp != null ? newProp : oldProp);
 341     minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN",
 342             Color.orange));
 343     maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX",
 344             Color.red));
 345
 346     /*
 347      * Set Structure tab defaults.
 348      */
 349     final boolean structSelected = Cache.getDefault(STRUCT_FROM_PDB, false);
 350     structFromPdb.setSelected(structSelected);
 351     useRnaView.setSelected(Cache.getDefault(USE_RNAVIEW, false));
 352     useRnaView.setEnabled(structSelected);
 353     addSecondaryStructure.setSelected(Cache.getDefault(ADD_SS_ANN, false));
 354     addSecondaryStructure.setEnabled(structSelected);
 355     addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, false));
 356     addTempFactor.setEnabled(structSelected);
 357     structViewer.setSelectedItem(Cache.getDefault(STRUCTURE_DISPLAY,
 358             ViewerType.JMOL.name()));
 359     chimeraPath.setText(Cache.getDefault(CHIMERA_PATH, ""));
 360     chimeraPath.addActionListener(new ActionListener()
 361     {
 362       @Override
 363       public void actionPerformed(ActionEvent e)
 364       {
 365         validateChimeraPath();
 366       }
 367     });
 368
 369     if (Cache.getDefault("MAP_WITH_SIFTS", false))
 370     {
 371       siftsMapping.setSelected(true);
 372     }
 373     else
 374     {
 375       nwMapping.setSelected(true);
 376     }
 377
 378     SiftsSettings
 379             .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
 380
 381     /*
 382      * Set Connections tab defaults
 383      */
 384
 385     // set up sorting
 386     linkUrlTable.setModel(dataModel);
 387     final TableRowSorter<TableModel> sorter = new TableRowSorter<>(
 388             linkUrlTable.getModel());
 389     linkUrlTable.setRowSorter(sorter);
 390     List<RowSorter.SortKey> sortKeys = new ArrayList<>();
 391
 392     UrlLinkTableModel m = (UrlLinkTableModel) linkUrlTable.getModel();
 393     sortKeys.add(new RowSorter.SortKey(m.getPrimaryColumn(),
 394             SortOrder.DESCENDING));
 395     sortKeys.add(new RowSorter.SortKey(m.getSelectedColumn(),
 396             SortOrder.DESCENDING));
 397     sortKeys.add(new RowSorter.SortKey(m.getNameColumn(),
 398             SortOrder.ASCENDING));
 399
 400     sorter.setSortKeys(sortKeys);
 401     sorter.sort();
 402
 403     // set up filtering
 404     ActionListener onReset;
 405     onReset = new ActionListener()
 406     {
 407       @Override
 408       public void actionPerformed(ActionEvent e)
 409       {
 410         filterTB.setText("");
 411         sorter.setRowFilter(RowFilter.regexFilter(""));
 412       }
 413
 414     };
 415     doReset.addActionListener(onReset);
 416
 417     // filter to display only custom urls
 418     final RowFilter<TableModel, Object> customUrlFilter = new RowFilter<TableModel, Object>()
 419     {
 420       @Override
 421       public boolean include(
 422               Entry<? extends TableModel, ? extends Object> entry)
 423       {
 424         return ((UrlLinkTableModel) entry.getModel()).isUserEntry(entry);
 425       }
 426     };
 427
 428     final TableRowSorter<TableModel> customSorter = new TableRowSorter<>(
 429             linkUrlTable.getModel());
 430     customSorter.setRowFilter(customUrlFilter);
 431
 432     ActionListener onCustomOnly;
 433     onCustomOnly = new ActionListener()
 434     {
 435       @Override
 436       public void actionPerformed(ActionEvent e)
 437       {
 438         filterTB.setText("");
 439         sorter.setRowFilter(customUrlFilter);
 440       }
 441     };
 442     userOnly.addActionListener(onCustomOnly);
 443
 444     filterTB.getDocument().addDocumentListener(new DocumentListener()
 445     {
 446       String caseInsensitiveFlag = "(?i)";
 447
 448       @Override
 449       public void changedUpdate(DocumentEvent e)
 450       {
 451         sorter.setRowFilter(RowFilter.regexFilter(caseInsensitiveFlag
 452                 + filterTB.getText()));
 453       }
 454
 455       @Override
 456       public void removeUpdate(DocumentEvent e)
 457       {
 458         sorter.setRowFilter(RowFilter.regexFilter(caseInsensitiveFlag
 459                 + filterTB.getText()));
 460       }
 461
 462       @Override
 463       public void insertUpdate(DocumentEvent e)
 464       {
 465         sorter.setRowFilter(RowFilter.regexFilter(caseInsensitiveFlag
 466                 + filterTB.getText()));
 467       }
 468     });
 469
 470     // set up list selection functionality
 471     linkUrlTable.getSelectionModel().addListSelectionListener(
 472             new UrlListSelectionHandler());
 473
 474     // set up radio buttons
 475     int onClickCol = ((UrlLinkTableModel) linkUrlTable.getModel())
 476             .getPrimaryColumn();
 477     String onClickName = linkUrlTable.getColumnName(onClickCol);
 478     linkUrlTable.getColumn(onClickName).setCellRenderer(
 479                new RadioButtonRenderer());
 480     linkUrlTable.getColumn(onClickName)
 481             .setCellEditor(new RadioButtonEditor());
 482
 483     // get boolean columns and resize those to min possible
 484     for (int column = 0; column < linkUrlTable.getColumnCount(); column++)
 485     {
 486       if (linkUrlTable.getModel().getColumnClass(column)
 487               .equals(Boolean.class))
 488       {
 489         TableColumn tableColumn = linkUrlTable.getColumnModel().getColumn(
 490                 column);
 491         int preferredWidth = tableColumn.getMinWidth();
 492
 493         TableCellRenderer cellRenderer = linkUrlTable.getCellRenderer(0,
 494                 column);
 495         Component c = linkUrlTable.prepareRenderer(cellRenderer, 0, column);
 496         int cwidth = c.getPreferredSize().width
 497                 + linkUrlTable.getIntercellSpacing().width;
 498         preferredWidth = Math.max(preferredWidth, cwidth);
 499
 500         tableColumn.setPreferredWidth(preferredWidth);
 501       }
 502     }
 503
 504     useProxy.setSelected(Cache.getDefault("USE_PROXY", false));
 505     useProxy_actionPerformed(); // make sure useProxy is correctly initialised
 506     proxyServerTB.setText(Cache.getDefault("PROXY_SERVER", ""));
 507     proxyPortTB.setText(Cache.getDefault("PROXY_PORT", ""));
 508
 509     defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", ""));
 510
 511     usagestats.setSelected(Cache.getDefault("USAGESTATS", false));
 512     // note antisense here: default is true
 513     questionnaire
 514             .setSelected(Cache.getProperty("NOQUESTIONNAIRES") == null);
 515     versioncheck.setSelected(Cache.getDefault("VERSION_CHECK", true));
 516
 517     /*
 518      * Set Output tab defaults
 519      */
 520     epsRendering.addItem(promptEachTimeOpt);
 521     epsRendering.addItem(lineArtOpt);
 522     epsRendering.addItem(textOpt);
 523     String defaultEPS = Cache.getDefault("EPS_RENDERING",
 524             "Prompt each time");
 525     if (defaultEPS.equalsIgnoreCase("Text"))
 526     {
 527       epsRendering.setSelectedItem(textOpt);
 528     }
 529     else if (defaultEPS.equalsIgnoreCase("Lineart"))
 530     {
 531       epsRendering.setSelectedItem(lineArtOpt);
 532     }
 533     else
 534     {
 535       epsRendering.setSelectedItem(promptEachTimeOpt);
 536     }
 537     autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false));
 538     userIdWidth.setEnabled(!autoIdWidth.isSelected());
 539     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
 540     Integer wi = Cache.getIntegerProperty("FIGURE_USERIDWIDTH");
 541     userIdWidth.setText(wi == null ? "" : wi.toString());
 542     blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
 543     clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
 544     fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
 545     msfjv.setSelected(Cache.getDefault("MSF_JVSUFFIX", true));
 546     pfamjv.setSelected(Cache.getDefault("PFAM_JVSUFFIX", true));
 547     pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
 548     pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
 549     modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
 550     embbedBioJSON.setSelected(Cache.getDefault("EXPORT_EMBBED_BIOJSON",
 551             true));
 552
 553     /*
 554      * Set Editing tab defaults
 555      */
 556     autoCalculateConsCheck.setSelected(Cache.getDefault(
 557             "AUTO_CALC_CONSENSUS", true));
 558     padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
 559     sortByTree.setSelected(Cache.getDefault("SORT_BY_TREE", false));
 560
 561     annotations_actionPerformed(null); // update the display of the annotation
 562                                        // settings
 563   }
 564
 565   /**
 566    * Save user selections on the Preferences tabs to the Cache and write out to
 567    * file.
 568    *
 569    * @param e
 570    */
 571   @Override
 572   public void ok_actionPerformed(ActionEvent e)
 573   {
 574     if (!validateSettings())
 575     {
 576       return;
 577     }
 578
 579     /*
 580      * Save Visual settings
 581      */
 582     Cache.applicationProperties.setProperty("SHOW_JVSUFFIX",
 583             Boolean.toString(seqLimit.isSelected()));
 584     Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS",
 585             Boolean.toString(rightAlign.isSelected()));
 586     Cache.applicationProperties.setProperty("SHOW_FULLSCREEN",
 587             Boolean.toString(fullScreen.isSelected()));
 588     Cache.applicationProperties.setProperty("SHOW_OVERVIEW",
 589             Boolean.toString(openoverv.isSelected()));
 590     Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
 591             Boolean.toString(annotations.isSelected()));
 592     Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
 593             Boolean.toString(conservation.isSelected()));
 594     Cache.applicationProperties.setProperty("SHOW_QUALITY",
 595             Boolean.toString(quality.isSelected()));
 596     Cache.applicationProperties.setProperty("SHOW_IDENTITY",
 597             Boolean.toString(identity.isSelected()));
 598
 599     Cache.applicationProperties.setProperty("GAP_SYMBOL", gapSymbolCB
 600             .getSelectedItem().toString());
 601
 602     Cache.applicationProperties.setProperty("FONT_NAME", fontNameCB
 603             .getSelectedItem().toString());
 604     Cache.applicationProperties.setProperty("FONT_STYLE", fontStyleCB
 605             .getSelectedItem().toString());
 606     Cache.applicationProperties.setProperty("FONT_SIZE", fontSizeCB
 607             .getSelectedItem().toString());
 608
 609     Cache.applicationProperties.setProperty("ID_ITALICS",
 610             Boolean.toString(idItalics.isSelected()));
 611     Cache.applicationProperties.setProperty("SHOW_UNCONSERVED",
 612             Boolean.toString(showUnconserved.isSelected()));
 613     Cache.applicationProperties.setProperty(SHOW_OCCUPANCY,
 614             Boolean.toString(showOccupancy.isSelected()));
 615     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS",
 616             Boolean.toString(showGroupConsensus.isSelected()));
 617     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION",
 618             Boolean.toString(showGroupConservation.isSelected()));
 619     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_HISTOGRAM",
 620             Boolean.toString(showConsensHistogram.isSelected()));
 621     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO",
 622             Boolean.toString(showConsensLogo.isSelected()));
 623     Cache.applicationProperties.setProperty("SHOW_INFORMATION_HISTOGRAM",
 624             Boolean.toString(showConsensHistogram.isSelected()));
 625     Cache.applicationProperties.setProperty("SHOW_HMM_LOGO",
 626             Boolean.toString(showHMMLogo.isSelected()));
 627     Cache.applicationProperties.setProperty("ANTI_ALIAS",
 628             Boolean.toString(smoothFont.isSelected()));
 629     Cache.applicationProperties.setProperty(SCALE_PROTEIN_TO_CDNA,
 630             Boolean.toString(scaleProteinToCdna.isSelected()));
 631     Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP",
 632             Boolean.toString(showNpTooltip.isSelected()));
 633     Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP",
 634             Boolean.toString(showDbRefTooltip.isSelected()));
 635
 636     Cache.applicationProperties.setProperty("WRAP_ALIGNMENT",
 637             Boolean.toString(wrap.isSelected()));
 638
 639     Cache.applicationProperties.setProperty("STARTUP_FILE",
 640             startupFileTextfield.getText());
 641     Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",
 642             Boolean.toString(startupCheckbox.isSelected()));
 643
 644     Cache.applicationProperties.setProperty("SORT_ALIGNMENT", sortby
 645             .getSelectedItem().toString());
 646
 647     // convert description of sort order to enum name for save
 648     SequenceAnnotationOrder annSortOrder = SequenceAnnotationOrder
 649             .forDescription(sortAnnBy.getSelectedItem().toString());
 650     if (annSortOrder != null)
 651     {
 652       Cache.applicationProperties.setProperty(SORT_ANNOTATIONS,
 653               annSortOrder.name());
 654     }
 655
 656     final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
 657     Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE, Boolean
 658             .valueOf(showAutocalcFirst).toString());
 659
 660     /*
 661      * Save Colours settings
 662      */
 663     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_PROT, protColour
 664             .getSelectedItem().toString());
 665     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_NUC, nucColour
 666             .getSelectedItem().toString());
 667     Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
 668             minColour.getBackground());
 669     Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
 670             maxColour.getBackground());
 671
 672     /*
 673      * Save HMMER settings
 674      */
 675     Cache.applicationProperties.setProperty("TRIM_TERMINI",
 676             Boolean.toString(trimTermini.isSelected()));
 677     Cache.applicationProperties.setProperty("USE_UNIPROT",
 678             Boolean.toString(uniprot.isSelected()));
 679     Cache.applicationProperties.setProperty("SEQUENCES_TO_KEEP",
 680             numberOfSequencesToKeepField.getText());
 681     Cache.applicationProperties.setProperty(HMMER_PATH,
 682             hmmerPath.getText());
 683     boolean hmmerInstalled = isHMMERInstalled.isSelected();
 684     Cache.applicationProperties.setProperty("HMMER_INSTALLED",
 685             Boolean.toString(hmmerInstalled));
 686     boolean hmmerFunctioning = validateHMMERPath(false);
 687     Cache.applicationProperties.setProperty("HMMER_FUNCTIONING",
 688             Boolean.toString(hmmerFunctioning));
 689     AlignFrame[] frames = Desktop.getAlignFrames();
 690     boolean hmmerStatus = hmmerFunctioning && hmmerInstalled ? true : false;
 691     for (AlignFrame frame : frames)
 692     {
 693       frame.updateHMMERStatus(hmmerStatus);
 694     }
 695     if (hmmerStatus)
 696     {
 697       String ver = getHMMERVersion();
 698       Cache.setProperty("HMMER_VERSION", ver);
 699     }
 700
 701
 702     trimTermini.setSelected(Cache.getDefault("TRIM_TERMINI", false));
 703     if (Cache.getDefault("USE_UNIPROT", false))
 704     {
 705       uniprot.setSelected(true);
 706     }
 707     else
 708     {
 709       alignment.setSelected(true);
 710     }
 711     numberOfSequencesToKeepField
 712             .setText(Cache.getProperty("SEQUENCES_TO_KEEP"));
 713     hmmerPath.setText(Cache.getProperty(HMMER_PATH));
 714
 715     /*
 716      * Save Structure settings
 717      */
 718     Cache.applicationProperties.setProperty(ADD_TEMPFACT_ANN,
 719             Boolean.toString(addTempFactor.isSelected()));
 720     Cache.applicationProperties.setProperty(ADD_SS_ANN,
 721             Boolean.toString(addSecondaryStructure.isSelected()));
 722     Cache.applicationProperties.setProperty(USE_RNAVIEW,
 723             Boolean.toString(useRnaView.isSelected()));
 724     Cache.applicationProperties.setProperty(STRUCT_FROM_PDB,
 725             Boolean.toString(structFromPdb.isSelected()));
 726     Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY, structViewer
 727             .getSelectedItem().toString());
 728     Cache.setOrRemove(CHIMERA_PATH, chimeraPath.getText());
 729     Cache.applicationProperties.setProperty("MAP_WITH_SIFTS",
 730             Boolean.toString(siftsMapping.isSelected()));
 731     SiftsSettings.setMapWithSifts(siftsMapping.isSelected());
 732
 733     /*
 734      * Save Output settings
 735      */
 736     Cache.applicationProperties.setProperty("EPS_RENDERING",
 737             ((OptionsParam) epsRendering.getSelectedItem()).getCode());
 738
 739     /*
 740      * Save Connections settings
 741      */
 742     Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText());
 743
 744     jalview.util.BrowserLauncher.resetBrowser();
 745
 746     // save user-defined and selected links
 747     String menuLinks = sequenceUrlLinks.writeUrlsAsString(true);
 748     if (menuLinks.isEmpty())
 749     {
 750       Cache.applicationProperties.remove("SEQUENCE_LINKS");
 751     }
 752     else
 753     {
 754       Cache.applicationProperties.setProperty("SEQUENCE_LINKS",
 755               menuLinks.toString());
 756     }
 757
 758     String nonMenuLinks = sequenceUrlLinks.writeUrlsAsString(false);
 759     if (nonMenuLinks.isEmpty())
 760     {
 761       Cache.applicationProperties.remove("STORED_LINKS");
 762     }
 763     else
 764     {
 765       Cache.applicationProperties.setProperty("STORED_LINKS",
 766               nonMenuLinks.toString());
 767     }
 768
 769     Cache.applicationProperties.setProperty("DEFAULT_URL",
 770             sequenceUrlLinks.getPrimaryUrlId());
 771
 772     Cache.applicationProperties.setProperty("USE_PROXY",
 773             Boolean.toString(useProxy.isSelected()));
 774
 775     Cache.setOrRemove("PROXY_SERVER", proxyServerTB.getText());
 776
 777     Cache.setOrRemove("PROXY_PORT", proxyPortTB.getText());
 778
 779     if (useProxy.isSelected())
 780     {
 781       System.setProperty("http.proxyHost", proxyServerTB.getText());
 782       System.setProperty("http.proxyPort", proxyPortTB.getText());
 783     }
 784     else
 785     {
 786       System.setProperty("http.proxyHost", "");
 787       System.setProperty("http.proxyPort", "");
 788     }
 789     Cache.setProperty("VERSION_CHECK",
 790             Boolean.toString(versioncheck.isSelected()));
 791     if (Cache.getProperty("USAGESTATS") != null || usagestats.isSelected())
 792     {
 793       // default is false - we only set this if the user has actively agreed
 794       Cache.setProperty("USAGESTATS",
 795               Boolean.toString(usagestats.isSelected()));
 796     }
 797     if (!questionnaire.isSelected())
 798     {
 799       Cache.setProperty("NOQUESTIONNAIRES", "true");
 800     }
 801     else
 802     {
 803       // special - made easy to edit a property file to disable questionnaires
 804       // by just adding the given line
 805       Cache.removeProperty("NOQUESTIONNAIRES");
 806     }
 807
 808     /*
 809      * Save Output settings
 810      */
 811     Cache.applicationProperties.setProperty("BLC_JVSUFFIX",
 812             Boolean.toString(blcjv.isSelected()));
 813     Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX",
 814             Boolean.toString(clustaljv.isSelected()));
 815     Cache.applicationProperties.setProperty("FASTA_JVSUFFIX",
 816             Boolean.toString(fastajv.isSelected()));
 817     Cache.applicationProperties.setProperty("MSF_JVSUFFIX",
 818             Boolean.toString(msfjv.isSelected()));
 819     Cache.applicationProperties.setProperty("PFAM_JVSUFFIX",
 820             Boolean.toString(pfamjv.isSelected()));
 821     Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX",
 822             Boolean.toString(pileupjv.isSelected()));
 823     Cache.applicationProperties.setProperty("PIR_JVSUFFIX",
 824             Boolean.toString(pirjv.isSelected()));
 825     Cache.applicationProperties.setProperty("PIR_MODELLER",
 826             Boolean.toString(modellerOutput.isSelected()));
 827     Cache.applicationProperties.setProperty("EXPORT_EMBBED_BIOJSON",
 828             Boolean.toString(embbedBioJSON.isSelected()));
 829     jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
 830
 831     Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH",
 832             Boolean.toString(autoIdWidth.isSelected()));
 833     userIdWidth_actionPerformed();
 834     Cache.applicationProperties.setProperty("FIGURE_USERIDWIDTH",
 835             userIdWidth.getText());
 836
 837     /*
 838      * Save Editing settings
 839      */
 840     Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
 841             Boolean.toString(autoCalculateConsCheck.isSelected()));
 842     Cache.applicationProperties.setProperty("SORT_BY_TREE",
 843             Boolean.toString(sortByTree.isSelected()));
 844     Cache.applicationProperties.setProperty("PAD_GAPS",
 845             Boolean.toString(padGaps.isSelected()));
 846
 847     dasSource.saveProperties(Cache.applicationProperties);
 848     wsPrefs.updateAndRefreshWsMenuConfig(false);
 849     Cache.saveProperties();
 850     Desktop.instance.doConfigureStructurePrefs();
 851     try
 852     {
 853       frame.setClosed(true);
 854     } catch (Exception ex)
 855     {
 856     }
 857   }
 858
 859   /**
 860    * Do any necessary validation before saving settings. Return focus to the
 861    * first tab which fails validation.
 862    *
 863    * @return
 864    */
 865   private boolean validateSettings()
 866   {
 867     if (!validateStructure())
 868     {
 869       structureTab.requestFocusInWindow();
 870       return false;
 871     }
 872     if (isHMMERInstalled.isSelected())
 873     {
 874       if (!validateHMMER())
 875       {
 876         hmmerTab.requestFocusInWindow();
 877         return false;
 878       }
 879     }
 880     return true;
 881   }
 882
 883   @Override
 884   protected boolean validateStructure()
 885   {
 886     return validateChimeraPath();
 887
 888   }
 889
 890   @Override
 891   protected boolean validateHMMER()
 892   {
 893     return validateHMMERPath();
 894
 895   }
 896
 897   /**
 898    * DOCUMENT ME!
 899    */
 900   @Override
 901   public void startupFileTextfield_mouseClicked()
 902   {
 903     String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
 904     JalviewFileChooser chooser = JalviewFileChooser.forRead(
 905             Cache.getProperty("LAST_DIRECTORY"), fileFormat);
 906     chooser.setFileView(new JalviewFileView());
 907     chooser.setDialogTitle(MessageManager
 908             .getString("label.select_startup_file"));
 909
 910     int value = chooser.showOpenDialog(this);
 911
 912     if (value == JalviewFileChooser.APPROVE_OPTION)
 913     {
 914       FileFormatI format = chooser.getSelectedFormat();
 915       if (format != null)
 916       {
 917         Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT",
 918                 format.getName());
 919       }
 920       startupFileTextfield.setText(chooser.getSelectedFile()
 921               .getAbsolutePath());
 922     }
 923   }
 924
 925   /**
 926    * DOCUMENT ME!
 927    *
 928    * @param e
 929    *          DOCUMENT ME!
 930    */
 931   @Override
 932   public void cancel_actionPerformed(ActionEvent e)
 933   {
 934     try
 935     {
 936       wsPrefs.updateWsMenuConfig(true);
 937       wsPrefs.refreshWs_actionPerformed(e);
 938       frame.setClosed(true);
 939     } catch (Exception ex)
 940     {
 941     }
 942   }
 943
 944   /**
 945    * DOCUMENT ME!
 946    *
 947    * @param e
 948    *          DOCUMENT ME!
 949    */
 950   @Override
 951   public void annotations_actionPerformed(ActionEvent e)
 952   {
 953     conservation.setEnabled(annotations.isSelected());
 954     quality.setEnabled(annotations.isSelected());
 955     identity.setEnabled(annotations.isSelected());
 956     showOccupancy.setEnabled(annotations.isSelected());
 957     showGroupConsensus.setEnabled(annotations.isSelected());
 958     showGroupConservation.setEnabled(annotations.isSelected());
 959     showConsensHistogram.setEnabled(annotations.isSelected()
 960             && (identity.isSelected() || showGroupConsensus.isSelected()));
 961     showConsensLogo.setEnabled(annotations.isSelected()
 962             && (identity.isSelected() || showGroupConsensus.isSelected()));
 963     showInformationHistogram.setEnabled(annotations.isSelected());
 964     showHMMLogo.setEnabled(annotations.isSelected());
 965   }
 966
 967   @Override
 968   public void newLink_actionPerformed(ActionEvent e)
 969   {
 970     GSequenceLink link = new GSequenceLink();
 971     boolean valid = false;
 972     while (!valid)
 973     {
 974       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 975               MessageManager.getString("label.new_sequence_url_link"),
 976               JvOptionPane.OK_CANCEL_OPTION, -1, null) == JvOptionPane.OK_OPTION)
 977       {
 978         if (link.checkValid())
 979         {
 980           if (((UrlLinkTableModel) linkUrlTable.getModel())
 981                   .isUniqueName(link.getName()))
 982           {
 983             ((UrlLinkTableModel) linkUrlTable.getModel()).insertRow(
 984                     link.getName(), link.getURL());
 985             valid = true;
 986           }
 987           else
 988           {
 989             link.notifyDuplicate();
 990             continue;
 991           }
 992         }
 993       }
 994       else
 995       {
 996         break;
 997       }
 998     }
 999   }
1000
1001   @Override
1002   public void editLink_actionPerformed(ActionEvent e)
1003   {
1004     GSequenceLink link = new GSequenceLink();
1005
1006     int index = linkUrlTable.getSelectedRow();
1007     if (index == -1)
1008     {
1009       // button no longer enabled if row is not selected
1010       Cache.log.debug("Edit with no row selected in linkUrlTable");
1011       return;
1012     }
1013
1014     int nameCol = ((UrlLinkTableModel) linkUrlTable.getModel())
1015             .getNameColumn();
1016     int urlCol = ((UrlLinkTableModel) linkUrlTable.getModel())
1017             .getUrlColumn();
1018     String oldName = linkUrlTable.getValueAt(index, nameCol).toString();
1019     link.setName(oldName);
1020     link.setURL(linkUrlTable.getValueAt(index, urlCol).toString());
1021
1022     boolean valid = false;
1023     while (!valid)
1024     {
1025       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
1026               MessageManager.getString("label.edit_sequence_url_link"),
1027               JvOptionPane.OK_CANCEL_OPTION, -1, null) == JvOptionPane.OK_OPTION)
1028       {
1029         if (link.checkValid())
1030         {
1031           if ((oldName.equals(link.getName()))
1032                   || (((UrlLinkTableModel) linkUrlTable.getModel())
1033                           .isUniqueName(link.getName())))
1034           {
1035             linkUrlTable.setValueAt(link.getName(), index, nameCol);
1036             linkUrlTable.setValueAt(link.getURL(), index, urlCol);
1037             valid = true;
1038           }
1039           else
1040           {
1041             link.notifyDuplicate();
1042             continue;
1043           }
1044         }
1045       }
1046       else
1047       {
1048         break;
1049       }
1050     }
1051   }
1052
1053   @Override
1054   public void deleteLink_actionPerformed(ActionEvent e)
1055   {
1056     int index = linkUrlTable.getSelectedRow();
1057     int modelIndex = -1;
1058     if (index == -1)
1059     {
1060       // button no longer enabled if row is not selected
1061       Cache.log.debug("Delete with no row selected in linkUrlTable");
1062       return;
1063     }
1064     else
1065     {
1066       modelIndex = linkUrlTable.convertRowIndexToModel(index);
1067     }
1068
1069     // make sure we use the model index to delete, and not the table index
1070     ((UrlLinkTableModel) linkUrlTable.getModel()).removeRow(modelIndex);
1071   }
1072
1073
1074   @Override
1075   public void defaultBrowser_mouseClicked(MouseEvent e)
1076   {
1077     JFileChooser chooser = new JFileChooser(".");
1078     chooser.setDialogTitle(MessageManager
1079             .getString("label.select_default_browser"));
1080
1081     int value = chooser.showOpenDialog(this);
1082
1083     if (value == JFileChooser.APPROVE_OPTION)
1084     {
1085       defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
1086     }
1087
1088   }
1089
1090   /*
1091    * (non-Javadoc)
1092    *
1093    * @see
1094    * jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event
1095    * .ActionEvent)
1096    */
1097   @Override
1098   protected void showunconserved_actionPerformed(ActionEvent e)
1099   {
1100     // TODO Auto-generated method stub
1101     super.showunconserved_actionPerformed(e);
1102   }
1103
1104   public static List<String> getGroupURLLinks()
1105   {
1106     return groupURLLinks;
1107   }
1108
1109   @Override
1110   public void minColour_actionPerformed(JPanel panel)
1111   {
1112     Color col = JColorChooser.showDialog(this,
1113             MessageManager.getString("label.select_colour_minimum_value"),
1114             minColour.getBackground());
1115     if (col != null)
1116     {
1117       panel.setBackground(col);
1118     }
1119     panel.repaint();
1120   }
1121
1122   @Override
1123   public void maxColour_actionPerformed(JPanel panel)
1124   {
1125     Color col = JColorChooser.showDialog(this,
1126             MessageManager.getString("label.select_colour_maximum_value"),
1127             maxColour.getBackground());
1128     if (col != null)
1129     {
1130       panel.setBackground(col);
1131     }
1132     panel.repaint();
1133   }
1134
1135   @Override
1136   protected void userIdWidth_actionPerformed()
1137   {
1138     try
1139     {
1140       String val = userIdWidth.getText().trim();
1141       if (val.length() > 0)
1142       {
1143         Integer iw = Integer.parseInt(val);
1144         if (iw.intValue() < 12)
1145         {
1146           throw new NumberFormatException();
1147         }
1148         userIdWidth.setText(iw.toString());
1149       }
1150     } catch (NumberFormatException x)
1151     {
1152       JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
1153               .getString("warn.user_defined_width_requirements"),
1154               MessageManager.getString("label.invalid_id_column_width"),
1155               JvOptionPane.WARNING_MESSAGE);
1156       userIdWidth.setText("");
1157     }
1158   }
1159
1160   @Override
1161   protected void autoIdWidth_actionPerformed()
1162   {
1163     userIdWidth.setEnabled(!autoIdWidth.isSelected());
1164     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
1165   }
1166
1167   /**
1168    * Returns true if chimera path is to a valid executable, else show an error
1169    * dialog.
1170    */
1171   private boolean validateChimeraPath()
1172   {
1173     if (chimeraPath.getText().trim().length() > 0)
1174     {
1175       File f = new File(chimeraPath.getText());
1176       if (!f.canExecute())
1177       {
1178         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1179                 MessageManager.getString("label.invalid_chimera_path"),
1180                 MessageManager.getString("label.invalid_name"),
1181                 JvOptionPane.ERROR_MESSAGE);
1182         return false;
1183       }
1184     }
1185     return true;
1186   }
1187
1188   /**
1189    * Returns true if hmmer path contains the necessary valid executables, else
1190    * show an error dialog (if showing dialog).
1191    */
1192   private boolean validateHMMERPath(boolean showDialog)
1193   {
1194     int missing = 0;
1195     String message = "";
1196     String path = hmmerPath.getText().trim();
1197     if (path.length() > 0)
1198     {
1199       File f = new File(path);
1200       if (!f.exists())
1201       {
1202         if (showDialog)
1203         {
1204           JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1205                 MessageManager.getString("label.folder_not_exists"),
1206                 MessageManager.getString("label.invalid_folder"),
1207                 JvOptionPane.ERROR_MESSAGE);
1208         }
1209         return false;
1210       }
1211
1212       File hmmbuild = new File(path + "/binaries/hmmbuild.exe");
1213       {
1214         if (!hmmbuild.canExecute())
1215         {
1216           message += MessageManager.getString("label.hmmbuild_not_found")
1217                   + "\n";
1218           missing++;
1219         }
1220       }
1221
1222       File hmmalign = new File(path + "/binaries/hmmalign.exe");
1223       {
1224         if (!hmmalign.canExecute())
1225         {
1226           message += MessageManager.getString("label.hmmalign_not_found")
1227                   + "\n";
1228           missing++;
1229         }
1230       }
1231
1232       File hmmsearch = new File(path + "/binaries/hmmsearch.exe");
1233       {
1234         if (!hmmsearch.canExecute())
1235         {
1236           message += MessageManager.getString("label.hmmsearch_not_found")
1237                   + "\n";
1238           missing++;
1239         }
1240       }
1241
1242       if (missing > 0)
1243       {
1244         if (missing < 3)
1245         {
1246           if (showDialog)
1247           {
1248             JvOptionPane.showInternalMessageDialog(Desktop.desktop, message,
1249                   MessageManager.getString("label.invalid_folder"),
1250                   JvOptionPane.ERROR_MESSAGE);
1251           }
1252           return false;
1253         }
1254         else
1255         {
1256           if (showDialog)
1257           {
1258             JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1259                   MessageManager.getString("label.no_binaries"),
1260                   MessageManager.getString("label.invalid_folder"),
1261                   JvOptionPane.ERROR_MESSAGE);
1262           }
1263
1264           return false;
1265         }
1266       }
1267
1268     }
1269     return true;
1270   }
1271
1272   private String getHMMERVersion()
1273   {
1274     File file = new File(hmmerPath.getText() + "/release-notes.txt");
1275     Scanner scanner = null;
1276     try
1277     {
1278       scanner = new Scanner(file);
1279     } catch (IOException e)
1280     {
1281       e.printStackTrace();
1282       return null;
1283     }
1284     scanner.next();
1285     String res = scanner.next();
1286     scanner.close();
1287     return res;
1288   }
1289
1290   private boolean validateHMMERPath()
1291   {
1292     return validateHMMERPath(true);
1293   }
1294
1295   /**
1296    * If Chimera is selected, check it can be found on default or user-specified
1297    * path, if not show a warning/help dialog.
1298    */
1299   @Override
1300   protected void structureViewer_actionPerformed(String selectedItem)
1301   {
1302     if (!selectedItem.equals(ViewerType.CHIMERA.name()))
1303     {
1304       return;
1305     }
1306     boolean found = false;
1307
1308     /*
1309      * Try user-specified and standard paths for Chimera executable.
1310      */
1311     List<String> paths = StructureManager.getChimeraPaths();
1312     paths.add(0, chimeraPath.getText());
1313     for (String path : paths)
1314     {
1315       if (new File(path.trim()).canExecute())
1316       {
1317         found = true;
1318         break;
1319       }
1320     }
1321     if (!found)
1322     {
1323       String[] options = { "OK", "Help" };
1324       int showHelp = JvOptionPane.showInternalOptionDialog(
1325               Desktop.desktop,
1326               JvSwingUtils.wrapTooltip(true,
1327                       MessageManager.getString("label.chimera_missing")),
1328               "", JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE,
1329               null, options, options[0]);
1330       if (showHelp == JvOptionPane.NO_OPTION)
1331       {
1332         try
1333         {
1334           Help.showHelpWindow(HelpId.StructureViewer);
1335         } catch (HelpSetException e)
1336         {
1337           e.printStackTrace();
1338         }
1339       }
1340     }
1341   }
1342
1343   public class OptionsParam
1344   {
1345     private String name;
1346
1347     private String code;
1348
1349     public OptionsParam(String name, String code)
1350     {
1351       this.name = name;
1352       this.code = code;
1353     }
1354
1355     public String getName()
1356     {
1357       return name;
1358     }
1359
1360     public void setName(String name)
1361     {
1362       this.name = name;
1363     }
1364
1365     public String getCode()
1366     {
1367       return code;
1368     }
1369
1370     public void setCode(String code)
1371     {
1372       this.code = code;
1373     }
1374
1375     @Override
1376     public String toString()
1377     {
1378       return name;
1379     }
1380
1381     @Override
1382     public boolean equals(Object that)
1383     {
1384       if (!(that instanceof OptionsParam))
1385       {
1386         return false;
1387       }
1388       return this.code.equalsIgnoreCase(((OptionsParam) that).code);
1389     }
1390
1391     @Override
1392     public int hashCode()
1393     {
1394       return name.hashCode() + code.hashCode();
1395     }
1396   }
1397
1398   private class UrlListSelectionHandler implements ListSelectionListener
1399   {
1400
1401     @Override
1402     public void valueChanged(ListSelectionEvent e)
1403     {
1404       ListSelectionModel lsm = (ListSelectionModel) e.getSource();
1405
1406       int index = lsm.getMinSelectionIndex();
1407       if (index == -1)
1408       {
1409         // no selection, so disable delete/edit buttons
1410         editLink.setEnabled(false);
1411         deleteLink.setEnabled(false);
1412         return;
1413       }
1414       int modelIndex = linkUrlTable.convertRowIndexToModel(index);
1415
1416       // enable/disable edit and delete link buttons
1417       if (((UrlLinkTableModel) linkUrlTable.getModel())
1418               .isRowDeletable(modelIndex))
1419       {
1420         deleteLink.setEnabled(true);
1421       }
1422       else
1423       {
1424         deleteLink.setEnabled(false);
1425       }
1426
1427       if (((UrlLinkTableModel) linkUrlTable.getModel())
1428               .isRowEditable(modelIndex))
1429       {
1430         editLink.setEnabled(true);
1431       }
1432       else
1433       {
1434         editLink.setEnabled(false);
1435       }
1436     }
1437 }
1438 }