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.datamodel.Alignment;
  26 import jalview.datamodel.AlignmentI;
  27 import jalview.datamodel.HiddenMarkovModel;
  28 import jalview.datamodel.Sequence;
  29 import jalview.datamodel.SequenceI;
  30 import jalview.gui.Help.HelpId;
  31 import jalview.gui.StructureViewer.ViewerType;
  32 import jalview.hmmer.HMMBuildThread;
  33 import jalview.io.FileFormatI;
  34 import jalview.io.JalviewFileChooser;
  35 import jalview.io.JalviewFileView;
  36 import jalview.jbgui.GPreferences;
  37 import jalview.jbgui.GSequenceLink;
  38 import jalview.schemes.ColourSchemeI;
  39 import jalview.schemes.ColourSchemes;
  40 import jalview.schemes.ResidueColourScheme;
  41 import jalview.urls.UrlLinkTableModel;
  42 import jalview.urls.api.UrlProviderFactoryI;
  43 import jalview.urls.api.UrlProviderI;
  44 import jalview.urls.desktop.DesktopUrlProviderFactory;
  45 import jalview.util.MessageManager;
  46 import jalview.util.Platform;
  47 import jalview.util.UrlConstants;
  48 import jalview.ws.sifts.SiftsSettings;
  49
  50 import java.awt.BorderLayout;
  51 import java.awt.Color;
  52 import java.awt.Component;
  53 import java.awt.Dimension;
  54 import java.awt.Font;
  55 import java.awt.event.ActionEvent;
  56 import java.awt.event.ActionListener;
  57 import java.awt.event.MouseEvent;
  58 import java.io.File;
  59 import java.util.ArrayList;
  60 import java.util.List;
  61 import java.util.Scanner;
  62
  63 import javax.help.HelpSetException;
  64 import javax.swing.JColorChooser;
  65 import javax.swing.JFileChooser;
  66 import javax.swing.JInternalFrame;
  67 import javax.swing.JPanel;
  68 import javax.swing.ListSelectionModel;
  69 import javax.swing.RowFilter;
  70 import javax.swing.RowSorter;
  71 import javax.swing.SortOrder;
  72 import javax.swing.event.DocumentEvent;
  73 import javax.swing.event.DocumentListener;
  74 import javax.swing.event.ListSelectionEvent;
  75 import javax.swing.event.ListSelectionListener;
  76 import javax.swing.table.TableCellRenderer;
  77 import javax.swing.table.TableColumn;
  78 import javax.swing.table.TableModel;
  79 import javax.swing.table.TableRowSorter;
  80
  81 import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
  82
  83 /**
  84  * DOCUMENT ME!
  85  *
  86  * @author $author$
  87  * @version $Revision$
  88  */
  89 public class Preferences extends GPreferences
  90 {
  91   public static final String ENABLE_SPLIT_FRAME = "ENABLE_SPLIT_FRAME";
  92
  93   public static final String SCALE_PROTEIN_TO_CDNA = "SCALE_PROTEIN_TO_CDNA";
  94
  95   public static final String DEFAULT_COLOUR = "DEFAULT_COLOUR";
  96
  97   public static final String DEFAULT_COLOUR_PROT = "DEFAULT_COLOUR_PROT";
  98
  99   public static final String DEFAULT_COLOUR_NUC = "DEFAULT_COLOUR_NUC";
 100
 101   public static final String ADD_TEMPFACT_ANN = "ADD_TEMPFACT_ANN";
 102
 103   public static final String ADD_SS_ANN = "ADD_SS_ANN";
 104
 105   public static final String USE_RNAVIEW = "USE_RNAVIEW";
 106
 107   public static final String STRUCT_FROM_PDB = "STRUCT_FROM_PDB";
 108
 109   public static final String STRUCTURE_DISPLAY = "STRUCTURE_DISPLAY";
 110
 111   public static final String CHIMERA_PATH = "CHIMERA_PATH";
 112
 113   public static final String HMMER_PATH = "HMMER_PATH";
 114
 115   public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS";
 116
 117   public static final String SHOW_AUTOCALC_ABOVE = "SHOW_AUTOCALC_ABOVE";
 118
 119   public static final String SHOW_OCCUPANCY = "SHOW_OCCUPANCY";
 120
 121   private static final int MIN_FONT_SIZE = 1;
 122
 123   private static final int MAX_FONT_SIZE = 30;
 124
 125   /**
 126    * Holds name and link separated with | character. Sequence ID must be
 127    * $SEQUENCE_ID$ or $SEQUENCE_ID=/.possible | chars ./=$
 128    */
 129   public static UrlProviderI sequenceUrlLinks;
 130
 131   public static UrlLinkTableModel dataModel;
 132
 133   /**
 134    * Holds name and link separated with | character. Sequence IDS and Sequences
 135    * must be $SEQUENCEIDS$ or $SEQUENCEIDS=/.possible | chars ./=$ and
 136    * $SEQUENCES$ or $SEQUENCES=/.possible | chars ./=$ and separation character
 137    * for first and second token specified after a pipe character at end |,|.
 138    * (TODO: proper escape for using | to separate ids or sequences
 139    */
 140
 141   public static List<String> groupURLLinks;
 142   static
 143   {
 144     // get links selected to be in the menu (SEQUENCE_LINKS)
 145     // and links entered by the user but not selected (STORED_LINKS)
 146     String inMenuString = Cache.getDefault("SEQUENCE_LINKS", "");
 147     String notInMenuString = Cache.getDefault("STORED_LINKS", "");
 148     String defaultUrl = Cache.getDefault("DEFAULT_URL",
 149             UrlConstants.DEFAULT_LABEL);
 150
 151     // if both links lists are empty, add the DEFAULT_URL link
 152     // otherwise we assume the default link is in one of the lists
 153     if (inMenuString.isEmpty() && notInMenuString.isEmpty())
 154     {
 155       inMenuString = UrlConstants.DEFAULT_STRING;
 156     }
 157     UrlProviderFactoryI factory = new DesktopUrlProviderFactory(defaultUrl,
 158             inMenuString, notInMenuString);
 159     sequenceUrlLinks = factory.createUrlProvider();
 160     dataModel = new UrlLinkTableModel(sequenceUrlLinks);
 161
 162     /**
 163      * TODO: reformulate groupURL encoding so two or more can be stored in the
 164      * .properties file as '|' separated strings
 165      */
 166
 167     groupURLLinks = new ArrayList<>();
 168   }
 169
 170   JInternalFrame frame;
 171
 172   DasSourceBrowser dasSource;
 173
 174   private WsPreferences wsPrefs;
 175
 176   private OptionsParam promptEachTimeOpt = new OptionsParam(
 177           MessageManager.getString("label.prompt_each_time"),
 178           "Prompt each time");
 179
 180   private OptionsParam lineArtOpt = new OptionsParam(
 181           MessageManager.getString("label.lineart"), "Lineart");
 182
 183   private OptionsParam textOpt = new OptionsParam(
 184           MessageManager.getString("action.text"), "Text");
 185
 186   /**
 187    * Creates a new Preferences object.
 188    */
 189   public Preferences()
 190   {
 191     super();
 192     frame = new JInternalFrame();
 193     frame.setContentPane(this);
 194     dasSource = new DasSourceBrowser();
 195     dasTab.add(dasSource, BorderLayout.CENTER);
 196     wsPrefs = new WsPreferences();
 197     wsTab.add(wsPrefs, BorderLayout.CENTER);
 198     int width = 500, height = 450;
 199     new jalview.util.Platform();
 200     if (Platform.isAMac())
 201     {
 202       width = 570;
 203       height = 480;
 204     }
 205
 206     Desktop.addInternalFrame(frame,
 207             MessageManager.getString("label.preferences"), width, height);
 208     frame.setMinimumSize(new Dimension(width, height));
 209
 210     /*
 211      * Set HMMER tab defaults
 212      */
 213     trimTermini.setSelected(Cache.getDefault("TRIM_TERMINI", false));
 214     isHMMERInstalled
 215             .setSelected(Cache.getDefault("HMMER_INSTALLED", false));
 216     if (Cache.getDefault("USE_UNIPROT", false))
 217     {
 218       uniprot.setSelected(true);
 219     }
 220     else
 221     {
 222       alignment.setSelected(true);
 223     }
 224     numberOfSequencesToKeepField
 225             .setText(Cache.getProperty("SEQUENCES_TO_KEEP"));
 226     installationLocation.setEnabled(isHMMERInstalled.isSelected());
 227     hmmerPath.setEnabled(isHMMERInstalled.isSelected());
 228     hmmerPath.setText(Cache.getProperty(HMMER_PATH));
 229     hmmerPath.addActionListener(new ActionListener()
 230     {
 231       @Override
 232       public void actionPerformed(ActionEvent e)
 233       {
 234         validateHMMERPath();
 235       }
 236     });
 237
 238     /*
 239      * Set Visual tab defaults
 240      */
 241     seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));
 242     rightAlign.setSelected(Cache.getDefault("RIGHT_ALIGN_IDS", false));
 243     fullScreen.setSelected(Cache.getDefault("SHOW_FULLSCREEN", false));
 244     annotations.setSelected(Cache.getDefault("SHOW_ANNOTATIONS", true));
 245
 246     conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));
 247     quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));
 248     identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));
 249     openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false));
 250     showUnconserved
 251             .setSelected(Cache.getDefault("SHOW_UNCONSERVED", false));
 252     showOccupancy.setSelected(Cache.getDefault(SHOW_OCCUPANCY, false));
 253     showGroupConsensus
 254             .setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS", false));
 255     showGroupConservation.setSelected(
 256             Cache.getDefault("SHOW_GROUP_CONSERVATION", false));
 257     showConsensHistogram.setSelected(
 258             Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM", true));
 259     showConsensLogo
 260             .setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO", false));
 261     showInformationHistogram.setSelected(
 262             Cache.getDefault("SHOW_INFORMATION_HISTOGRAM", true));
 263     showHMMLogo.setSelected(Cache.getDefault("SHOW_HMM_LOGO", false));
 264     showNpTooltip
 265             .setSelected(Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true));
 266     showDbRefTooltip
 267             .setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP", true));
 268
 269     String[] fonts = java.awt.GraphicsEnvironment
 270             .getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
 271     for (int i = 0; i < fonts.length; i++)
 272     {
 273       fontNameCB.addItem(fonts[i]);
 274     }
 275
 276     for (int i = MIN_FONT_SIZE; i <= MAX_FONT_SIZE; i++)
 277     {
 278       fontSizeCB.addItem(i + "");
 279     }
 280
 281     fontStyleCB.addItem("plain");
 282     fontStyleCB.addItem("bold");
 283     fontStyleCB.addItem("italic");
 284
 285     fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
 286     fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
 287     fontStyleCB.setSelectedItem(
 288             Cache.getDefault("FONT_STYLE", Font.PLAIN + ""));
 289
 290     smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));
 291     scaleProteinToCdna
 292             .setSelected(Cache.getDefault(SCALE_PROTEIN_TO_CDNA, false));
 293
 294     idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
 295
 296     wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
 297
 298     gapSymbolCB.addItem("-");
 299     gapSymbolCB.addItem(".");
 300
 301     gapSymbolCB.setSelectedItem(Cache.getDefault("GAP_SYMBOL", "-"));
 302
 303     sortby.addItem("No sort");
 304     sortby.addItem("Id");
 305     sortby.addItem("Pairwise Identity");
 306     sortby.setSelectedItem(Cache.getDefault("SORT_ALIGNMENT", "No sort"));
 307
 308     sortAnnBy.addItem(SequenceAnnotationOrder.NONE.toString());
 309     sortAnnBy
 310             .addItem(SequenceAnnotationOrder.SEQUENCE_AND_LABEL.toString());
 311     sortAnnBy
 312             .addItem(SequenceAnnotationOrder.LABEL_AND_SEQUENCE.toString());
 313     SequenceAnnotationOrder savedSort = SequenceAnnotationOrder
 314             .valueOf(Cache.getDefault(SORT_ANNOTATIONS,
 315                     SequenceAnnotationOrder.NONE.name()));
 316     sortAnnBy.setSelectedItem(savedSort.toString());
 317
 318     sortAutocalc.addItem("Autocalculated first");
 319     sortAutocalc.addItem("Autocalculated last");
 320     final boolean showAbove = Cache.getDefault(SHOW_AUTOCALC_ABOVE, true);
 321     sortAutocalc.setSelectedItem(showAbove ? sortAutocalc.getItemAt(0)
 322             : sortAutocalc.getItemAt(1));
 323     startupCheckbox
 324             .setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
 325     startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
 326             Cache.getDefault("www.jalview.org", "http://www.jalview.org")
 327                     + "/examples/exampleFile_2_3.jar"));
 328
 329     /*
 330      * Set Colours tab defaults
 331      */
 332     protColour.addItem(ResidueColourScheme.NONE);
 333     nucColour.addItem(ResidueColourScheme.NONE);
 334     for (ColourSchemeI cs : ColourSchemes.getInstance().getColourSchemes())
 335     {
 336       String name = cs.getSchemeName();
 337       protColour.addItem(name);
 338       nucColour.addItem(name);
 339     }
 340     String oldProp = Cache.getDefault(DEFAULT_COLOUR,
 341             ResidueColourScheme.NONE);
 342     String newProp = Cache.getDefault(DEFAULT_COLOUR_PROT, null);
 343     protColour.setSelectedItem(newProp != null ? newProp : oldProp);
 344     newProp = Cache.getDefault(DEFAULT_COLOUR_NUC, null);
 345     nucColour.setSelectedItem(newProp != null ? newProp : oldProp);
 346     minColour.setBackground(
 347             Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN", Color.orange));
 348     maxColour.setBackground(
 349             Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", Color.red));
 350
 351     /*
 352      * Set Structure tab defaults.
 353      */
 354     final boolean structSelected = Cache.getDefault(STRUCT_FROM_PDB, false);
 355     structFromPdb.setSelected(structSelected);
 356     useRnaView.setSelected(Cache.getDefault(USE_RNAVIEW, false));
 357     useRnaView.setEnabled(structSelected);
 358     addSecondaryStructure.setSelected(Cache.getDefault(ADD_SS_ANN, false));
 359     addSecondaryStructure.setEnabled(structSelected);
 360     addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, false));
 361     addTempFactor.setEnabled(structSelected);
 362     structViewer.setSelectedItem(
 363             Cache.getDefault(STRUCTURE_DISPLAY, ViewerType.JMOL.name()));
 364     chimeraPath.setText(Cache.getDefault(CHIMERA_PATH, ""));
 365     chimeraPath.addActionListener(new ActionListener()
 366     {
 367       @Override
 368       public void actionPerformed(ActionEvent e)
 369       {
 370         validateChimeraPath();
 371       }
 372     });
 373
 374     if (Cache.getDefault("MAP_WITH_SIFTS", false))
 375     {
 376       siftsMapping.setSelected(true);
 377     }
 378     else
 379     {
 380       nwMapping.setSelected(true);
 381     }
 382
 383     SiftsSettings
 384             .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
 385
 386     /*
 387      * Set Connections tab defaults
 388      */
 389
 390     // set up sorting
 391     linkUrlTable.setModel(dataModel);
 392     final TableRowSorter<TableModel> sorter = new TableRowSorter<>(
 393             linkUrlTable.getModel());
 394     linkUrlTable.setRowSorter(sorter);
 395     List<RowSorter.SortKey> sortKeys = new ArrayList<>();
 396
 397     UrlLinkTableModel m = (UrlLinkTableModel) linkUrlTable.getModel();
 398     sortKeys.add(new RowSorter.SortKey(m.getPrimaryColumn(),
 399             SortOrder.DESCENDING));
 400     sortKeys.add(new RowSorter.SortKey(m.getSelectedColumn(),
 401             SortOrder.DESCENDING));
 402     sortKeys.add(
 403             new RowSorter.SortKey(m.getNameColumn(), SortOrder.ASCENDING));
 404
 405     sorter.setSortKeys(sortKeys);
 406     sorter.sort();
 407
 408     // set up filtering
 409     ActionListener onReset;
 410     onReset = new ActionListener()
 411     {
 412       @Override
 413       public void actionPerformed(ActionEvent e)
 414       {
 415         filterTB.setText("");
 416         sorter.setRowFilter(RowFilter.regexFilter(""));
 417       }
 418
 419     };
 420     doReset.addActionListener(onReset);
 421
 422     // filter to display only custom urls
 423     final RowFilter<TableModel, Object> customUrlFilter = new RowFilter<TableModel, Object>()
 424     {
 425       @Override
 426       public boolean include(
 427               Entry<? extends TableModel, ? extends Object> entry)
 428       {
 429         return ((UrlLinkTableModel) entry.getModel()).isUserEntry(entry);
 430       }
 431     };
 432
 433     final TableRowSorter<TableModel> customSorter = new TableRowSorter<>(
 434             linkUrlTable.getModel());
 435     customSorter.setRowFilter(customUrlFilter);
 436
 437     ActionListener onCustomOnly;
 438     onCustomOnly = new ActionListener()
 439     {
 440       @Override
 441       public void actionPerformed(ActionEvent e)
 442       {
 443         filterTB.setText("");
 444         sorter.setRowFilter(customUrlFilter);
 445       }
 446     };
 447     userOnly.addActionListener(onCustomOnly);
 448
 449     filterTB.getDocument().addDocumentListener(new DocumentListener()
 450     {
 451       String caseInsensitiveFlag = "(?i)";
 452
 453       @Override
 454       public void changedUpdate(DocumentEvent e)
 455       {
 456         sorter.setRowFilter(RowFilter
 457                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 458       }
 459
 460       @Override
 461       public void removeUpdate(DocumentEvent e)
 462       {
 463         sorter.setRowFilter(RowFilter
 464                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 465       }
 466
 467       @Override
 468       public void insertUpdate(DocumentEvent e)
 469       {
 470         sorter.setRowFilter(RowFilter
 471                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 472       }
 473     });
 474
 475     // set up list selection functionality
 476     linkUrlTable.getSelectionModel()
 477             .addListSelectionListener(new UrlListSelectionHandler());
 478
 479     // set up radio buttons
 480     int onClickCol = ((UrlLinkTableModel) linkUrlTable.getModel())
 481             .getPrimaryColumn();
 482     String onClickName = linkUrlTable.getColumnName(onClickCol);
 483     linkUrlTable.getColumn(onClickName)
 484             .setCellRenderer(new RadioButtonRenderer());
 485     linkUrlTable.getColumn(onClickName)
 486             .setCellEditor(new RadioButtonEditor());
 487
 488     // get boolean columns and resize those to min possible
 489     for (int column = 0; column < linkUrlTable.getColumnCount(); column++)
 490     {
 491       if (linkUrlTable.getModel().getColumnClass(column)
 492               .equals(Boolean.class))
 493       {
 494         TableColumn tableColumn = linkUrlTable.getColumnModel()
 495                 .getColumn(column);
 496         int preferredWidth = tableColumn.getMinWidth();
 497
 498         TableCellRenderer cellRenderer = linkUrlTable.getCellRenderer(0,
 499                 column);
 500         Component c = linkUrlTable.prepareRenderer(cellRenderer, 0, column);
 501         int cwidth = c.getPreferredSize().width
 502                 + linkUrlTable.getIntercellSpacing().width;
 503         preferredWidth = Math.max(preferredWidth, cwidth);
 504
 505         tableColumn.setPreferredWidth(preferredWidth);
 506       }
 507     }
 508
 509     useProxy.setSelected(Cache.getDefault("USE_PROXY", false));
 510     useProxy_actionPerformed(); // make sure useProxy is correctly initialised
 511     proxyServerTB.setText(Cache.getDefault("PROXY_SERVER", ""));
 512     proxyPortTB.setText(Cache.getDefault("PROXY_PORT", ""));
 513
 514     defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", ""));
 515
 516     usagestats.setSelected(Cache.getDefault("USAGESTATS", false));
 517     // note antisense here: default is true
 518     questionnaire
 519             .setSelected(Cache.getProperty("NOQUESTIONNAIRES") == null);
 520     versioncheck.setSelected(Cache.getDefault("VERSION_CHECK", true));
 521
 522     /*
 523      * Set Output tab defaults
 524      */
 525     epsRendering.addItem(promptEachTimeOpt);
 526     epsRendering.addItem(lineArtOpt);
 527     epsRendering.addItem(textOpt);
 528     String defaultEPS = Cache.getDefault("EPS_RENDERING",
 529             "Prompt each time");
 530     if (defaultEPS.equalsIgnoreCase("Text"))
 531     {
 532       epsRendering.setSelectedItem(textOpt);
 533     }
 534     else if (defaultEPS.equalsIgnoreCase("Lineart"))
 535     {
 536       epsRendering.setSelectedItem(lineArtOpt);
 537     }
 538     else
 539     {
 540       epsRendering.setSelectedItem(promptEachTimeOpt);
 541     }
 542     autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false));
 543     userIdWidth.setEnabled(!autoIdWidth.isSelected());
 544     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
 545     Integer wi = Cache.getIntegerProperty("FIGURE_USERIDWIDTH");
 546     userIdWidth.setText(wi == null ? "" : wi.toString());
 547     blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
 548     clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
 549     fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
 550     msfjv.setSelected(Cache.getDefault("MSF_JVSUFFIX", true));
 551     pfamjv.setSelected(Cache.getDefault("PFAM_JVSUFFIX", true));
 552     pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
 553     pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
 554     modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
 555     embbedBioJSON
 556             .setSelected(Cache.getDefault("EXPORT_EMBBED_BIOJSON", true));
 557
 558     /*
 559      * Set Editing tab defaults
 560      */
 561     autoCalculateConsCheck
 562             .setSelected(Cache.getDefault("AUTO_CALC_CONSENSUS", true));
 563     padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
 564     sortByTree.setSelected(Cache.getDefault("SORT_BY_TREE", false));
 565
 566     annotations_actionPerformed(null); // update the display of the annotation
 567                                        // settings
 568   }
 569
 570   /**
 571    * Save user selections on the Preferences tabs to the Cache and write out to
 572    * file.
 573    *
 574    * @param e
 575    */
 576   @Override
 577   public void ok_actionPerformed(ActionEvent e)
 578   {
 579     if (!validateSettings())
 580     {
 581       return;
 582     }
 583
 584     /*
 585      * Save Visual settings
 586      */
 587     Cache.applicationProperties.setProperty("SHOW_JVSUFFIX",
 588             Boolean.toString(seqLimit.isSelected()));
 589     Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS",
 590             Boolean.toString(rightAlign.isSelected()));
 591     Cache.applicationProperties.setProperty("SHOW_FULLSCREEN",
 592             Boolean.toString(fullScreen.isSelected()));
 593     Cache.applicationProperties.setProperty("SHOW_OVERVIEW",
 594             Boolean.toString(openoverv.isSelected()));
 595     Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
 596             Boolean.toString(annotations.isSelected()));
 597     Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
 598             Boolean.toString(conservation.isSelected()));
 599     Cache.applicationProperties.setProperty("SHOW_QUALITY",
 600             Boolean.toString(quality.isSelected()));
 601     Cache.applicationProperties.setProperty("SHOW_IDENTITY",
 602             Boolean.toString(identity.isSelected()));
 603
 604     Cache.applicationProperties.setProperty("GAP_SYMBOL",
 605             gapSymbolCB.getSelectedItem().toString());
 606
 607     Cache.applicationProperties.setProperty("FONT_NAME",
 608             fontNameCB.getSelectedItem().toString());
 609     Cache.applicationProperties.setProperty("FONT_STYLE",
 610             fontStyleCB.getSelectedItem().toString());
 611     Cache.applicationProperties.setProperty("FONT_SIZE",
 612             fontSizeCB.getSelectedItem().toString());
 613
 614     Cache.applicationProperties.setProperty("ID_ITALICS",
 615             Boolean.toString(idItalics.isSelected()));
 616     Cache.applicationProperties.setProperty("SHOW_UNCONSERVED",
 617             Boolean.toString(showUnconserved.isSelected()));
 618     Cache.applicationProperties.setProperty(SHOW_OCCUPANCY,
 619             Boolean.toString(showOccupancy.isSelected()));
 620     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS",
 621             Boolean.toString(showGroupConsensus.isSelected()));
 622     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION",
 623             Boolean.toString(showGroupConservation.isSelected()));
 624     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_HISTOGRAM",
 625             Boolean.toString(showConsensHistogram.isSelected()));
 626     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO",
 627             Boolean.toString(showConsensLogo.isSelected()));
 628     Cache.applicationProperties.setProperty("SHOW_INFORMATION_HISTOGRAM",
 629             Boolean.toString(showConsensHistogram.isSelected()));
 630     Cache.applicationProperties.setProperty("SHOW_HMM_LOGO",
 631             Boolean.toString(showHMMLogo.isSelected()));
 632     Cache.applicationProperties.setProperty("ANTI_ALIAS",
 633             Boolean.toString(smoothFont.isSelected()));
 634     Cache.applicationProperties.setProperty(SCALE_PROTEIN_TO_CDNA,
 635             Boolean.toString(scaleProteinToCdna.isSelected()));
 636     Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP",
 637             Boolean.toString(showNpTooltip.isSelected()));
 638     Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP",
 639             Boolean.toString(showDbRefTooltip.isSelected()));
 640
 641     Cache.applicationProperties.setProperty("WRAP_ALIGNMENT",
 642             Boolean.toString(wrap.isSelected()));
 643
 644     Cache.applicationProperties.setProperty("STARTUP_FILE",
 645             startupFileTextfield.getText());
 646     Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",
 647             Boolean.toString(startupCheckbox.isSelected()));
 648
 649     Cache.applicationProperties.setProperty("SORT_ALIGNMENT",
 650             sortby.getSelectedItem().toString());
 651
 652     // convert description of sort order to enum name for save
 653     SequenceAnnotationOrder annSortOrder = SequenceAnnotationOrder
 654             .forDescription(sortAnnBy.getSelectedItem().toString());
 655     if (annSortOrder != null)
 656     {
 657       Cache.applicationProperties.setProperty(SORT_ANNOTATIONS,
 658               annSortOrder.name());
 659     }
 660
 661     final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
 662     Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE,
 663             Boolean.valueOf(showAutocalcFirst).toString());
 664
 665     /*
 666      * Save Colours settings
 667      */
 668     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_PROT,
 669             protColour.getSelectedItem().toString());
 670     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_NUC,
 671             nucColour.getSelectedItem().toString());
 672     Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
 673             minColour.getBackground());
 674     Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
 675             maxColour.getBackground());
 676
 677     /*
 678      * Save HMMER settings
 679      */
 680     Cache.applicationProperties.setProperty("TRIM_TERMINI",
 681             Boolean.toString(trimTermini.isSelected()));
 682     Cache.applicationProperties.setProperty("USE_UNIPROT",
 683             Boolean.toString(uniprot.isSelected()));
 684     Cache.applicationProperties.setProperty("SEQUENCES_TO_KEEP",
 685             numberOfSequencesToKeepField.getText());
 686     Cache.applicationProperties.setProperty(HMMER_PATH,
 687             hmmerPath.getText());
 688     boolean hmmerInstalled = isHMMERInstalled.isSelected();
 689     Cache.applicationProperties.setProperty("HMMER_INSTALLED",
 690             Boolean.toString(hmmerInstalled));
 691     boolean hmmerFunctioning = validateHMMERPath(false);
 692     Cache.applicationProperties.setProperty("HMMER_FUNCTIONING",
 693             Boolean.toString(hmmerFunctioning));
 694     AlignFrame[] frames = Desktop.getAlignFrames();
 695     boolean hmmerStatus = hmmerFunctioning && hmmerInstalled ? true : false;
 696     for (AlignFrame frame : frames)
 697     {
 698       frame.updateHMMERStatus(hmmerStatus);
 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,
 727             structViewer.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
 905             .forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat);
 906     chooser.setFileView(new JalviewFileView());
 907     chooser.setDialogTitle(
 908             MessageManager.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
 921               .setText(chooser.getSelectedFile().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,
 977               null) == JvOptionPane.OK_OPTION)
 978       {
 979         if (link.checkValid())
 980         {
 981           if (((UrlLinkTableModel) linkUrlTable.getModel())
 982                   .isUniqueName(link.getName()))
 983           {
 984             ((UrlLinkTableModel) linkUrlTable.getModel())
 985                     .insertRow(link.getName(), link.getURL());
 986             valid = true;
 987           }
 988           else
 989           {
 990             link.notifyDuplicate();
 991             continue;
 992           }
 993         }
 994       }
 995       else
 996       {
 997         break;
 998       }
 999     }
1000   }
1001
1002   @Override
1003   public void editLink_actionPerformed(ActionEvent e)
1004   {
1005     GSequenceLink link = new GSequenceLink();
1006
1007     int index = linkUrlTable.getSelectedRow();
1008     if (index == -1)
1009     {
1010       // button no longer enabled if row is not selected
1011       Cache.log.debug("Edit with no row selected in linkUrlTable");
1012       return;
1013     }
1014
1015     int nameCol = ((UrlLinkTableModel) linkUrlTable.getModel())
1016             .getNameColumn();
1017     int urlCol = ((UrlLinkTableModel) linkUrlTable.getModel())
1018             .getUrlColumn();
1019     String oldName = linkUrlTable.getValueAt(index, nameCol).toString();
1020     link.setName(oldName);
1021     link.setURL(linkUrlTable.getValueAt(index, urlCol).toString());
1022
1023     boolean valid = false;
1024     while (!valid)
1025     {
1026       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
1027               MessageManager.getString("label.edit_sequence_url_link"),
1028               JvOptionPane.OK_CANCEL_OPTION, -1,
1029               null) == JvOptionPane.OK_OPTION)
1030       {
1031         if (link.checkValid())
1032         {
1033           if ((oldName.equals(link.getName()))
1034                   || (((UrlLinkTableModel) linkUrlTable.getModel())
1035                           .isUniqueName(link.getName())))
1036           {
1037             linkUrlTable.setValueAt(link.getName(), index, nameCol);
1038             linkUrlTable.setValueAt(link.getURL(), index, urlCol);
1039             valid = true;
1040           }
1041           else
1042           {
1043             link.notifyDuplicate();
1044             continue;
1045           }
1046         }
1047       }
1048       else
1049       {
1050         break;
1051       }
1052     }
1053   }
1054
1055   @Override
1056   public void deleteLink_actionPerformed(ActionEvent e)
1057   {
1058     int index = linkUrlTable.getSelectedRow();
1059     int modelIndex = -1;
1060     if (index == -1)
1061     {
1062       // button no longer enabled if row is not selected
1063       Cache.log.debug("Delete with no row selected in linkUrlTable");
1064       return;
1065     }
1066     else
1067     {
1068       modelIndex = linkUrlTable.convertRowIndexToModel(index);
1069     }
1070
1071     // make sure we use the model index to delete, and not the table index
1072     ((UrlLinkTableModel) linkUrlTable.getModel()).removeRow(modelIndex);
1073   }
1074
1075   @Override
1076   public void defaultBrowser_mouseClicked(MouseEvent e)
1077   {
1078     JFileChooser chooser = new JFileChooser(".");
1079     chooser.setDialogTitle(
1080             MessageManager.getString("label.select_default_browser"));
1081
1082     int value = chooser.showOpenDialog(this);
1083
1084     if (value == JFileChooser.APPROVE_OPTION)
1085     {
1086       defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
1087     }
1088
1089   }
1090
1091   /*
1092    * (non-Javadoc)
1093    *
1094    * @see
1095    * jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event
1096    * .ActionEvent)
1097    */
1098   @Override
1099   protected void showunconserved_actionPerformed(ActionEvent e)
1100   {
1101     // TODO Auto-generated method stub
1102     super.showunconserved_actionPerformed(e);
1103   }
1104
1105   public static List<String> getGroupURLLinks()
1106   {
1107     return groupURLLinks;
1108   }
1109
1110   @Override
1111   public void minColour_actionPerformed(JPanel panel)
1112   {
1113     Color col = JColorChooser.showDialog(this,
1114             MessageManager.getString("label.select_colour_minimum_value"),
1115             minColour.getBackground());
1116     if (col != null)
1117     {
1118       panel.setBackground(col);
1119     }
1120     panel.repaint();
1121   }
1122
1123   @Override
1124   public void maxColour_actionPerformed(JPanel panel)
1125   {
1126     Color col = JColorChooser.showDialog(this,
1127             MessageManager.getString("label.select_colour_maximum_value"),
1128             maxColour.getBackground());
1129     if (col != null)
1130     {
1131       panel.setBackground(col);
1132     }
1133     panel.repaint();
1134   }
1135
1136   @Override
1137   protected void userIdWidth_actionPerformed()
1138   {
1139     try
1140     {
1141       String val = userIdWidth.getText().trim();
1142       if (val.length() > 0)
1143       {
1144         Integer iw = Integer.parseInt(val);
1145         if (iw.intValue() < 12)
1146         {
1147           throw new NumberFormatException();
1148         }
1149         userIdWidth.setText(iw.toString());
1150       }
1151     } catch (NumberFormatException x)
1152     {
1153       JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1154               MessageManager
1155                       .getString("warn.user_defined_width_requirements"),
1156               MessageManager.getString("label.invalid_id_column_width"),
1157               JvOptionPane.WARNING_MESSAGE);
1158       userIdWidth.setText("");
1159     }
1160   }
1161
1162   @Override
1163   protected void autoIdWidth_actionPerformed()
1164   {
1165     userIdWidth.setEnabled(!autoIdWidth.isSelected());
1166     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
1167   }
1168
1169   /**
1170    * Returns true if chimera path is to a valid executable, else show an error
1171    * dialog.
1172    */
1173   private boolean validateChimeraPath()
1174   {
1175     if (chimeraPath.getText().trim().length() > 0)
1176     {
1177       File f = new File(chimeraPath.getText());
1178       if (!f.canExecute())
1179       {
1180         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1181                 MessageManager.getString("label.invalid_chimera_path"),
1182                 MessageManager.getString("label.invalid_name"),
1183                 JvOptionPane.ERROR_MESSAGE);
1184         return false;
1185       }
1186     }
1187     return true;
1188   }
1189
1190   /**
1191    * Returns true if hmmer path contains the necessary valid executables, else
1192    * show an error dialog (if showing dialog).
1193    */
1194   private boolean validateHMMERPath(boolean showDialog)
1195   {
1196     int missing = 0;
1197     String message = "";
1198     String folder = hmmerPath.getText().trim();
1199     if (folder.length() > 0)
1200     {
1201       File f = new File(folder);
1202       if (!f.exists())
1203       {
1204         if (showDialog)
1205         {
1206           JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1207                 MessageManager.getString("label.folder_not_exists"),
1208                 MessageManager.getString("label.invalid_folder"),
1209                 JvOptionPane.ERROR_MESSAGE);
1210         }
1211         return false;
1212       }
1213       AlignmentI alignment = new Alignment(
1214               new SequenceI[]
1215       { new Sequence("test", "WLWL", 0, 3) });
1216       if (canExecute(folder + "/hmmbuild"))
1217         {
1218         validateHMMBuild(alignment);
1219         }
1220       else
1221       {
1222         message += MessageManager.getString("label.hmmbuild_not_found")
1223                 + "\n";
1224         missing++;
1225       }
1226
1227
1228       if (canExecute(folder + "/hmmalign"))
1229         {
1230
1231         }
1232       else
1233       {
1234         message += MessageManager.getString("label.hmmalign_not_found")
1235                 + "\n";
1236         missing++;
1237       }
1238
1239
1240       if (canExecute(folder + "/hmmsearch"))
1241         {
1242
1243         }
1244       else
1245       {
1246         message += MessageManager.getString("label.hmmsearch_not_found")
1247                 + "\n";
1248         missing++;
1249       }
1250       }
1251
1252       if (missing > 0)
1253       {
1254         if (missing < 3)
1255         {
1256           if (showDialog)
1257           {
1258             JvOptionPane.showInternalMessageDialog(Desktop.desktop, message,
1259                   MessageManager.getString("label.invalid_folder"),
1260                   JvOptionPane.ERROR_MESSAGE);
1261           }
1262           return false;
1263         }
1264         else
1265         {
1266           if (showDialog)
1267           {
1268             JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1269                   MessageManager.getString("label.no_binaries"),
1270                   MessageManager.getString("label.invalid_folder"),
1271                   JvOptionPane.ERROR_MESSAGE);
1272           }
1273
1274           return false;
1275         }
1276       }
1277
1278     return true;
1279   }
1280
1281   /**
1282    * Checks if a file can be executed
1283    *
1284    * @param path
1285    *          the path to the file
1286    * @return
1287    */
1288   public boolean canExecute(String path)
1289   {
1290     File file = new File(path);
1291     if (!file.canExecute())
1292     {
1293       file = new File(path + ".exe");
1294       {
1295         if (!file.canExecute())
1296         {
1297           return false;
1298         }
1299       }
1300     }
1301     return true;
1302   }
1303
1304   /**
1305    * Runs hmmbuild to check if it is working. While doing this it parses the
1306    * version of HMMER.
1307    *
1308    * @param frame
1309    * @return
1310    */
1311   public boolean validateHMMBuild(AlignmentI alignment)
1312   {
1313     HMMBuildThread hmmbuild = new HMMBuildThread(alignment);
1314     hmmbuild.hmmbuildWaitTillComplete();
1315     SequenceI hmmSeq = alignment.getSequenceAt(1);
1316     HiddenMarkovModel hmm;
1317     if (hmmSeq.isHMMConsensusSequence() && hmmSeq.getHMM() != null)
1318     {
1319       hmm = hmmSeq.getHMM();
1320
1321       if (hmm.getNumberOfSymbols() < 1)
1322       {
1323         return false;
1324       }
1325     }
1326     else
1327     {
1328       return false;
1329     }
1330
1331     String header = hmm.getFileHeader();
1332     if (header == null)
1333     {
1334       return false;
1335     }
1336     else
1337     {
1338       Scanner scanner = new Scanner(header);
1339       scanner.next();
1340       String string = scanner.next();
1341       String version = string.substring(1);
1342       Cache.setProperty("HMMER_VERSION", version);
1343       scanner.close();
1344
1345     }
1346     return true;
1347   }
1348
1349
1350   private boolean validateHMMERPath()
1351   {
1352     return validateHMMERPath(true);
1353   }
1354
1355   /**
1356    * If Chimera is selected, check it can be found on default or user-specified
1357    * path, if not show a warning/help dialog.
1358    */
1359   @Override
1360   protected void structureViewer_actionPerformed(String selectedItem)
1361   {
1362     if (!selectedItem.equals(ViewerType.CHIMERA.name()))
1363     {
1364       return;
1365     }
1366     boolean found = false;
1367
1368     /*
1369      * Try user-specified and standard paths for Chimera executable.
1370      */
1371     List<String> paths = StructureManager.getChimeraPaths();
1372     paths.add(0, chimeraPath.getText());
1373     for (String path : paths)
1374     {
1375       if (new File(path.trim()).canExecute())
1376       {
1377         found = true;
1378         break;
1379       }
1380     }
1381     if (!found)
1382     {
1383       String[] options = { "OK", "Help" };
1384       int showHelp = JvOptionPane.showInternalOptionDialog(Desktop.desktop,
1385               JvSwingUtils.wrapTooltip(true,
1386                       MessageManager.getString("label.chimera_missing")),
1387               "", JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE,
1388               null, options, options[0]);
1389       if (showHelp == JvOptionPane.NO_OPTION)
1390       {
1391         try
1392         {
1393           Help.showHelpWindow(HelpId.StructureViewer);
1394         } catch (HelpSetException e)
1395         {
1396           e.printStackTrace();
1397         }
1398       }
1399     }
1400   }
1401
1402   public class OptionsParam
1403   {
1404     private String name;
1405
1406     private String code;
1407
1408     public OptionsParam(String name, String code)
1409     {
1410       this.name = name;
1411       this.code = code;
1412     }
1413
1414     public String getName()
1415     {
1416       return name;
1417     }
1418
1419     public void setName(String name)
1420     {
1421       this.name = name;
1422     }
1423
1424     public String getCode()
1425     {
1426       return code;
1427     }
1428
1429     public void setCode(String code)
1430     {
1431       this.code = code;
1432     }
1433
1434     @Override
1435     public String toString()
1436     {
1437       return name;
1438     }
1439
1440     @Override
1441     public boolean equals(Object that)
1442     {
1443       if (!(that instanceof OptionsParam))
1444       {
1445         return false;
1446       }
1447       return this.code.equalsIgnoreCase(((OptionsParam) that).code);
1448     }
1449
1450     @Override
1451     public int hashCode()
1452     {
1453       return name.hashCode() + code.hashCode();
1454     }
1455   }
1456
1457   private class UrlListSelectionHandler implements ListSelectionListener
1458   {
1459
1460     @Override
1461     public void valueChanged(ListSelectionEvent e)
1462     {
1463       ListSelectionModel lsm = (ListSelectionModel) e.getSource();
1464
1465       int index = lsm.getMinSelectionIndex();
1466       if (index == -1)
1467       {
1468         // no selection, so disable delete/edit buttons
1469         editLink.setEnabled(false);
1470         deleteLink.setEnabled(false);
1471         return;
1472       }
1473       int modelIndex = linkUrlTable.convertRowIndexToModel(index);
1474
1475       // enable/disable edit and delete link buttons
1476       if (((UrlLinkTableModel) linkUrlTable.getModel())
1477               .isRowDeletable(modelIndex))
1478       {
1479         deleteLink.setEnabled(true);
1480       }
1481       else
1482       {
1483         deleteLink.setEnabled(false);
1484       }
1485
1486       if (((UrlLinkTableModel) linkUrlTable.getModel())
1487               .isRowEditable(modelIndex))
1488       {
1489         editLink.setEnabled(true);
1490       }
1491       else
1492       {
1493         editLink.setEnabled(false);
1494       }
1495     }
1496   }
1497 }