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 HMMSEARCH_DB_PATHS = "HMMSEARCH_DB_PATHS";
 116
 117   public static final String HMMSEARCH_DBS = "HMMSEARCH_DBS";
 118
 119   public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS";
 120
 121   public static final String SHOW_AUTOCALC_ABOVE = "SHOW_AUTOCALC_ABOVE";
 122
 123   public static final String SHOW_OCCUPANCY = "SHOW_OCCUPANCY";
 124
 125   private static final int MIN_FONT_SIZE = 1;
 126
 127   private static final int MAX_FONT_SIZE = 30;
 128
 129   /**
 130    * Holds name and link separated with | character. Sequence ID must be
 131    * $SEQUENCE_ID$ or $SEQUENCE_ID=/.possible | chars ./=$
 132    */
 133   public static UrlProviderI sequenceUrlLinks;
 134
 135   public static UrlLinkTableModel dataModel;
 136
 137   /**
 138    * Holds name and link separated with | character. Sequence IDS and Sequences
 139    * must be $SEQUENCEIDS$ or $SEQUENCEIDS=/.possible | chars ./=$ and
 140    * $SEQUENCES$ or $SEQUENCES=/.possible | chars ./=$ and separation character
 141    * for first and second token specified after a pipe character at end |,|.
 142    * (TODO: proper escape for using | to separate ids or sequences
 143    */
 144
 145   public static List<String> groupURLLinks;
 146   static
 147   {
 148     // get links selected to be in the menu (SEQUENCE_LINKS)
 149     // and links entered by the user but not selected (STORED_LINKS)
 150     String inMenuString = Cache.getDefault("SEQUENCE_LINKS", "");
 151     String notInMenuString = Cache.getDefault("STORED_LINKS", "");
 152     String defaultUrl = Cache.getDefault("DEFAULT_URL",
 153             UrlConstants.DEFAULT_LABEL);
 154
 155     // if both links lists are empty, add the DEFAULT_URL link
 156     // otherwise we assume the default link is in one of the lists
 157     if (inMenuString.isEmpty() && notInMenuString.isEmpty())
 158     {
 159       inMenuString = UrlConstants.DEFAULT_STRING;
 160     }
 161     UrlProviderFactoryI factory = new DesktopUrlProviderFactory(defaultUrl,
 162             inMenuString, notInMenuString);
 163     sequenceUrlLinks = factory.createUrlProvider();
 164     dataModel = new UrlLinkTableModel(sequenceUrlLinks);
 165
 166     /**
 167      * TODO: reformulate groupURL encoding so two or more can be stored in the
 168      * .properties file as '|' separated strings
 169      */
 170
 171     groupURLLinks = new ArrayList<>();
 172   }
 173
 174   JInternalFrame frame;
 175
 176   DasSourceBrowser dasSource;
 177
 178   private WsPreferences wsPrefs;
 179
 180   private OptionsParam promptEachTimeOpt = new OptionsParam(
 181           MessageManager.getString("label.prompt_each_time"),
 182           "Prompt each time");
 183
 184   private OptionsParam lineArtOpt = new OptionsParam(
 185           MessageManager.getString("label.lineart"), "Lineart");
 186
 187   private OptionsParam textOpt = new OptionsParam(
 188           MessageManager.getString("action.text"), "Text");
 189
 190   /**
 191    * Creates a new Preferences object.
 192    */
 193   public Preferences()
 194   {
 195     super();
 196     frame = new JInternalFrame();
 197     frame.setContentPane(this);
 198     dasSource = new DasSourceBrowser();
 199     dasTab.add(dasSource, BorderLayout.CENTER);
 200     wsPrefs = new WsPreferences();
 201     wsTab.add(wsPrefs, BorderLayout.CENTER);
 202     int width = 500, height = 450;
 203     new jalview.util.Platform();
 204     if (Platform.isAMac())
 205     {
 206       width = 570;
 207       height = 480;
 208     }
 209
 210     Desktop.addInternalFrame(frame,
 211             MessageManager.getString("label.preferences"), width, height);
 212     frame.setMinimumSize(new Dimension(width, height));
 213
 214     /*
 215      * Set HMMER tab defaults
 216      */
 217     trimTermini.setSelected(Cache.getDefault("TRIM_TERMINI", false));
 218     isHMMERInstalled
 219             .setSelected(Cache.getDefault("HMMER_INSTALLED", false));
 220     if (Cache.getDefault("USE_UNIPROT", false))
 221     {
 222       uniprot.setSelected(true);
 223     }
 224     else
 225     {
 226       alignment.setSelected(true);
 227     }
 228     numberOfSequencesToKeepField
 229             .setText(Cache.getProperty("SEQUENCES_TO_KEEP"));
 230     installationLocation.setEnabled(isHMMERInstalled.isSelected());
 231     hmmerPath.setEnabled(isHMMERInstalled.isSelected());
 232     hmmerPath.setText(Cache.getProperty(HMMER_PATH));
 233     hmmerPath.addActionListener(new ActionListener()
 234     {
 235       @Override
 236       public void actionPerformed(ActionEvent e)
 237       {
 238         validateHMMERPath();
 239       }
 240     });
 241
 242     /*
 243      * Set Visual tab defaults
 244      */
 245     seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));
 246     rightAlign.setSelected(Cache.getDefault("RIGHT_ALIGN_IDS", false));
 247     fullScreen.setSelected(Cache.getDefault("SHOW_FULLSCREEN", false));
 248     annotations.setSelected(Cache.getDefault("SHOW_ANNOTATIONS", true));
 249
 250     conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));
 251     quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));
 252     identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));
 253     openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false));
 254     showUnconserved
 255             .setSelected(Cache.getDefault("SHOW_UNCONSERVED", false));
 256     showOccupancy.setSelected(Cache.getDefault(SHOW_OCCUPANCY, false));
 257     showGroupConsensus
 258             .setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS", false));
 259     showGroupConservation.setSelected(
 260             Cache.getDefault("SHOW_GROUP_CONSERVATION", false));
 261     showConsensHistogram.setSelected(
 262             Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM", true));
 263     showConsensLogo
 264             .setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO", false));
 265     showInformationHistogram.setSelected(
 266             Cache.getDefault("SHOW_INFORMATION_HISTOGRAM", true));
 267     showHMMLogo.setSelected(Cache.getDefault("SHOW_HMM_LOGO", false));
 268     showNpTooltip
 269             .setSelected(Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true));
 270     showDbRefTooltip
 271             .setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP", true));
 272
 273     String[] fonts = java.awt.GraphicsEnvironment
 274             .getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
 275     for (int i = 0; i < fonts.length; i++)
 276     {
 277       fontNameCB.addItem(fonts[i]);
 278     }
 279
 280     for (int i = MIN_FONT_SIZE; i <= MAX_FONT_SIZE; i++)
 281     {
 282       fontSizeCB.addItem(i + "");
 283     }
 284
 285     fontStyleCB.addItem("plain");
 286     fontStyleCB.addItem("bold");
 287     fontStyleCB.addItem("italic");
 288
 289     fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
 290     fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
 291     fontStyleCB.setSelectedItem(
 292             Cache.getDefault("FONT_STYLE", Font.PLAIN + ""));
 293
 294     smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));
 295     scaleProteinToCdna
 296             .setSelected(Cache.getDefault(SCALE_PROTEIN_TO_CDNA, false));
 297
 298     idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
 299
 300     wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
 301
 302     gapSymbolCB.addItem("-");
 303     gapSymbolCB.addItem(".");
 304
 305     gapSymbolCB.setSelectedItem(Cache.getDefault("GAP_SYMBOL", "-"));
 306
 307     sortby.addItem("No sort");
 308     sortby.addItem("Id");
 309     sortby.addItem("Pairwise Identity");
 310     sortby.setSelectedItem(Cache.getDefault("SORT_ALIGNMENT", "No sort"));
 311
 312     sortAnnBy.addItem(SequenceAnnotationOrder.NONE.toString());
 313     sortAnnBy
 314             .addItem(SequenceAnnotationOrder.SEQUENCE_AND_LABEL.toString());
 315     sortAnnBy
 316             .addItem(SequenceAnnotationOrder.LABEL_AND_SEQUENCE.toString());
 317     SequenceAnnotationOrder savedSort = SequenceAnnotationOrder
 318             .valueOf(Cache.getDefault(SORT_ANNOTATIONS,
 319                     SequenceAnnotationOrder.NONE.name()));
 320     sortAnnBy.setSelectedItem(savedSort.toString());
 321
 322     sortAutocalc.addItem("Autocalculated first");
 323     sortAutocalc.addItem("Autocalculated last");
 324     final boolean showAbove = Cache.getDefault(SHOW_AUTOCALC_ABOVE, true);
 325     sortAutocalc.setSelectedItem(showAbove ? sortAutocalc.getItemAt(0)
 326             : sortAutocalc.getItemAt(1));
 327     startupCheckbox
 328             .setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
 329     startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
 330             Cache.getDefault("www.jalview.org", "http://www.jalview.org")
 331                     + "/examples/exampleFile_2_3.jar"));
 332
 333     /*
 334      * Set Colours tab defaults
 335      */
 336     protColour.addItem(ResidueColourScheme.NONE);
 337     nucColour.addItem(ResidueColourScheme.NONE);
 338     for (ColourSchemeI cs : ColourSchemes.getInstance().getColourSchemes())
 339     {
 340       String name = cs.getSchemeName();
 341       protColour.addItem(name);
 342       nucColour.addItem(name);
 343     }
 344     String oldProp = Cache.getDefault(DEFAULT_COLOUR,
 345             ResidueColourScheme.NONE);
 346     String newProp = Cache.getDefault(DEFAULT_COLOUR_PROT, null);
 347     protColour.setSelectedItem(newProp != null ? newProp : oldProp);
 348     newProp = Cache.getDefault(DEFAULT_COLOUR_NUC, null);
 349     nucColour.setSelectedItem(newProp != null ? newProp : oldProp);
 350     minColour.setBackground(
 351             Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN", Color.orange));
 352     maxColour.setBackground(
 353             Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", Color.red));
 354
 355     /*
 356      * Set Structure tab defaults.
 357      */
 358     final boolean structSelected = Cache.getDefault(STRUCT_FROM_PDB, false);
 359     structFromPdb.setSelected(structSelected);
 360     useRnaView.setSelected(Cache.getDefault(USE_RNAVIEW, false));
 361     useRnaView.setEnabled(structSelected);
 362     addSecondaryStructure.setSelected(Cache.getDefault(ADD_SS_ANN, false));
 363     addSecondaryStructure.setEnabled(structSelected);
 364     addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, false));
 365     addTempFactor.setEnabled(structSelected);
 366     structViewer.setSelectedItem(
 367             Cache.getDefault(STRUCTURE_DISPLAY, ViewerType.JMOL.name()));
 368     chimeraPath.setText(Cache.getDefault(CHIMERA_PATH, ""));
 369     chimeraPath.addActionListener(new ActionListener()
 370     {
 371       @Override
 372       public void actionPerformed(ActionEvent e)
 373       {
 374         validateChimeraPath();
 375       }
 376     });
 377
 378     if (Cache.getDefault("MAP_WITH_SIFTS", false))
 379     {
 380       siftsMapping.setSelected(true);
 381     }
 382     else
 383     {
 384       nwMapping.setSelected(true);
 385     }
 386
 387     SiftsSettings
 388             .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
 389
 390     /*
 391      * Set Connections tab defaults
 392      */
 393
 394     // set up sorting
 395     linkUrlTable.setModel(dataModel);
 396     final TableRowSorter<TableModel> sorter = new TableRowSorter<>(
 397             linkUrlTable.getModel());
 398     linkUrlTable.setRowSorter(sorter);
 399     List<RowSorter.SortKey> sortKeys = new ArrayList<>();
 400
 401     UrlLinkTableModel m = (UrlLinkTableModel) linkUrlTable.getModel();
 402     sortKeys.add(new RowSorter.SortKey(m.getPrimaryColumn(),
 403             SortOrder.DESCENDING));
 404     sortKeys.add(new RowSorter.SortKey(m.getSelectedColumn(),
 405             SortOrder.DESCENDING));
 406     sortKeys.add(
 407             new RowSorter.SortKey(m.getNameColumn(), SortOrder.ASCENDING));
 408
 409     sorter.setSortKeys(sortKeys);
 410     sorter.sort();
 411
 412     // set up filtering
 413     ActionListener onReset;
 414     onReset = new ActionListener()
 415     {
 416       @Override
 417       public void actionPerformed(ActionEvent e)
 418       {
 419         filterTB.setText("");
 420         sorter.setRowFilter(RowFilter.regexFilter(""));
 421       }
 422
 423     };
 424     doReset.addActionListener(onReset);
 425
 426     // filter to display only custom urls
 427     final RowFilter<TableModel, Object> customUrlFilter = new RowFilter<TableModel, Object>()
 428     {
 429       @Override
 430       public boolean include(
 431               Entry<? extends TableModel, ? extends Object> entry)
 432       {
 433         return ((UrlLinkTableModel) entry.getModel()).isUserEntry(entry);
 434       }
 435     };
 436
 437     final TableRowSorter<TableModel> customSorter = new TableRowSorter<>(
 438             linkUrlTable.getModel());
 439     customSorter.setRowFilter(customUrlFilter);
 440
 441     ActionListener onCustomOnly;
 442     onCustomOnly = new ActionListener()
 443     {
 444       @Override
 445       public void actionPerformed(ActionEvent e)
 446       {
 447         filterTB.setText("");
 448         sorter.setRowFilter(customUrlFilter);
 449       }
 450     };
 451     userOnly.addActionListener(onCustomOnly);
 452
 453     filterTB.getDocument().addDocumentListener(new DocumentListener()
 454     {
 455       String caseInsensitiveFlag = "(?i)";
 456
 457       @Override
 458       public void changedUpdate(DocumentEvent e)
 459       {
 460         sorter.setRowFilter(RowFilter
 461                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 462       }
 463
 464       @Override
 465       public void removeUpdate(DocumentEvent e)
 466       {
 467         sorter.setRowFilter(RowFilter
 468                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 469       }
 470
 471       @Override
 472       public void insertUpdate(DocumentEvent e)
 473       {
 474         sorter.setRowFilter(RowFilter
 475                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 476       }
 477     });
 478
 479     // set up list selection functionality
 480     linkUrlTable.getSelectionModel()
 481             .addListSelectionListener(new UrlListSelectionHandler());
 482
 483     // set up radio buttons
 484     int onClickCol = ((UrlLinkTableModel) linkUrlTable.getModel())
 485             .getPrimaryColumn();
 486     String onClickName = linkUrlTable.getColumnName(onClickCol);
 487     linkUrlTable.getColumn(onClickName)
 488             .setCellRenderer(new RadioButtonRenderer());
 489     linkUrlTable.getColumn(onClickName)
 490             .setCellEditor(new RadioButtonEditor());
 491
 492     // get boolean columns and resize those to min possible
 493     for (int column = 0; column < linkUrlTable.getColumnCount(); column++)
 494     {
 495       if (linkUrlTable.getModel().getColumnClass(column)
 496               .equals(Boolean.class))
 497       {
 498         TableColumn tableColumn = linkUrlTable.getColumnModel()
 499                 .getColumn(column);
 500         int preferredWidth = tableColumn.getMinWidth();
 501
 502         TableCellRenderer cellRenderer = linkUrlTable.getCellRenderer(0,
 503                 column);
 504         Component c = linkUrlTable.prepareRenderer(cellRenderer, 0, column);
 505         int cwidth = c.getPreferredSize().width
 506                 + linkUrlTable.getIntercellSpacing().width;
 507         preferredWidth = Math.max(preferredWidth, cwidth);
 508
 509         tableColumn.setPreferredWidth(preferredWidth);
 510       }
 511     }
 512
 513     useProxy.setSelected(Cache.getDefault("USE_PROXY", false));
 514     useProxy_actionPerformed(); // make sure useProxy is correctly initialised
 515     proxyServerTB.setText(Cache.getDefault("PROXY_SERVER", ""));
 516     proxyPortTB.setText(Cache.getDefault("PROXY_PORT", ""));
 517
 518     defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", ""));
 519
 520     usagestats.setSelected(Cache.getDefault("USAGESTATS", false));
 521     // note antisense here: default is true
 522     questionnaire
 523             .setSelected(Cache.getProperty("NOQUESTIONNAIRES") == null);
 524     versioncheck.setSelected(Cache.getDefault("VERSION_CHECK", true));
 525
 526     /*
 527      * Set Output tab defaults
 528      */
 529     epsRendering.addItem(promptEachTimeOpt);
 530     epsRendering.addItem(lineArtOpt);
 531     epsRendering.addItem(textOpt);
 532     String defaultEPS = Cache.getDefault("EPS_RENDERING",
 533             "Prompt each time");
 534     if (defaultEPS.equalsIgnoreCase("Text"))
 535     {
 536       epsRendering.setSelectedItem(textOpt);
 537     }
 538     else if (defaultEPS.equalsIgnoreCase("Lineart"))
 539     {
 540       epsRendering.setSelectedItem(lineArtOpt);
 541     }
 542     else
 543     {
 544       epsRendering.setSelectedItem(promptEachTimeOpt);
 545     }
 546     autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false));
 547     userIdWidth.setEnabled(!autoIdWidth.isSelected());
 548     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
 549     Integer wi = Cache.getIntegerProperty("FIGURE_USERIDWIDTH");
 550     userIdWidth.setText(wi == null ? "" : wi.toString());
 551     blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
 552     clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
 553     fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
 554     msfjv.setSelected(Cache.getDefault("MSF_JVSUFFIX", true));
 555     pfamjv.setSelected(Cache.getDefault("PFAM_JVSUFFIX", true));
 556     pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
 557     pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
 558     modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
 559     embbedBioJSON
 560             .setSelected(Cache.getDefault("EXPORT_EMBBED_BIOJSON", true));
 561
 562     /*
 563      * Set Editing tab defaults
 564      */
 565     autoCalculateConsCheck
 566             .setSelected(Cache.getDefault("AUTO_CALC_CONSENSUS", true));
 567     padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
 568     sortByTree.setSelected(Cache.getDefault("SORT_BY_TREE", false));
 569
 570     annotations_actionPerformed(null); // update the display of the annotation
 571                                        // settings
 572   }
 573
 574   /**
 575    * Save user selections on the Preferences tabs to the Cache and write out to
 576    * file.
 577    *
 578    * @param e
 579    */
 580   @Override
 581   public void ok_actionPerformed(ActionEvent e)
 582   {
 583     if (!validateSettings())
 584     {
 585       return;
 586     }
 587
 588     /*
 589      * Save Visual settings
 590      */
 591     Cache.applicationProperties.setProperty("SHOW_JVSUFFIX",
 592             Boolean.toString(seqLimit.isSelected()));
 593     Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS",
 594             Boolean.toString(rightAlign.isSelected()));
 595     Cache.applicationProperties.setProperty("SHOW_FULLSCREEN",
 596             Boolean.toString(fullScreen.isSelected()));
 597     Cache.applicationProperties.setProperty("SHOW_OVERVIEW",
 598             Boolean.toString(openoverv.isSelected()));
 599     Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
 600             Boolean.toString(annotations.isSelected()));
 601     Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
 602             Boolean.toString(conservation.isSelected()));
 603     Cache.applicationProperties.setProperty("SHOW_QUALITY",
 604             Boolean.toString(quality.isSelected()));
 605     Cache.applicationProperties.setProperty("SHOW_IDENTITY",
 606             Boolean.toString(identity.isSelected()));
 607
 608     Cache.applicationProperties.setProperty("GAP_SYMBOL",
 609             gapSymbolCB.getSelectedItem().toString());
 610
 611     Cache.applicationProperties.setProperty("FONT_NAME",
 612             fontNameCB.getSelectedItem().toString());
 613     Cache.applicationProperties.setProperty("FONT_STYLE",
 614             fontStyleCB.getSelectedItem().toString());
 615     Cache.applicationProperties.setProperty("FONT_SIZE",
 616             fontSizeCB.getSelectedItem().toString());
 617
 618     Cache.applicationProperties.setProperty("ID_ITALICS",
 619             Boolean.toString(idItalics.isSelected()));
 620     Cache.applicationProperties.setProperty("SHOW_UNCONSERVED",
 621             Boolean.toString(showUnconserved.isSelected()));
 622     Cache.applicationProperties.setProperty(SHOW_OCCUPANCY,
 623             Boolean.toString(showOccupancy.isSelected()));
 624     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS",
 625             Boolean.toString(showGroupConsensus.isSelected()));
 626     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION",
 627             Boolean.toString(showGroupConservation.isSelected()));
 628     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_HISTOGRAM",
 629             Boolean.toString(showConsensHistogram.isSelected()));
 630     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO",
 631             Boolean.toString(showConsensLogo.isSelected()));
 632     Cache.applicationProperties.setProperty("SHOW_INFORMATION_HISTOGRAM",
 633             Boolean.toString(showConsensHistogram.isSelected()));
 634     Cache.applicationProperties.setProperty("SHOW_HMM_LOGO",
 635             Boolean.toString(showHMMLogo.isSelected()));
 636     Cache.applicationProperties.setProperty("ANTI_ALIAS",
 637             Boolean.toString(smoothFont.isSelected()));
 638     Cache.applicationProperties.setProperty(SCALE_PROTEIN_TO_CDNA,
 639             Boolean.toString(scaleProteinToCdna.isSelected()));
 640     Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP",
 641             Boolean.toString(showNpTooltip.isSelected()));
 642     Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP",
 643             Boolean.toString(showDbRefTooltip.isSelected()));
 644
 645     Cache.applicationProperties.setProperty("WRAP_ALIGNMENT",
 646             Boolean.toString(wrap.isSelected()));
 647
 648     Cache.applicationProperties.setProperty("STARTUP_FILE",
 649             startupFileTextfield.getText());
 650     Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",
 651             Boolean.toString(startupCheckbox.isSelected()));
 652
 653     Cache.applicationProperties.setProperty("SORT_ALIGNMENT",
 654             sortby.getSelectedItem().toString());
 655
 656     // convert description of sort order to enum name for save
 657     SequenceAnnotationOrder annSortOrder = SequenceAnnotationOrder
 658             .forDescription(sortAnnBy.getSelectedItem().toString());
 659     if (annSortOrder != null)
 660     {
 661       Cache.applicationProperties.setProperty(SORT_ANNOTATIONS,
 662               annSortOrder.name());
 663     }
 664
 665     final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
 666     Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE,
 667             Boolean.valueOf(showAutocalcFirst).toString());
 668
 669     /*
 670      * Save Colours settings
 671      */
 672     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_PROT,
 673             protColour.getSelectedItem().toString());
 674     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_NUC,
 675             nucColour.getSelectedItem().toString());
 676     Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
 677             minColour.getBackground());
 678     Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
 679             maxColour.getBackground());
 680
 681     /*
 682      * Save HMMER settings
 683      */
 684     Cache.applicationProperties.setProperty("TRIM_TERMINI",
 685             Boolean.toString(trimTermini.isSelected()));
 686     Cache.applicationProperties.setProperty("USE_UNIPROT",
 687             Boolean.toString(uniprot.isSelected()));
 688     Cache.applicationProperties.setProperty("SEQUENCES_TO_KEEP",
 689             numberOfSequencesToKeepField.getText());
 690     Cache.applicationProperties.setProperty(HMMER_PATH,
 691             hmmerPath.getText());
 692     boolean hmmerInstalled = isHMMERInstalled.isSelected();
 693     Cache.applicationProperties.setProperty("HMMER_INSTALLED",
 694             Boolean.toString(hmmerInstalled));
 695     boolean hmmerFunctioning = validateHMMERPath(false);
 696     Cache.applicationProperties.setProperty("HMMER_FUNCTIONING",
 697             Boolean.toString(hmmerFunctioning));
 698     AlignFrame[] frames = Desktop.getAlignFrames();
 699     boolean hmmerStatus = hmmerFunctioning && hmmerInstalled ? true : false;
 700     if (frames != null && frames.length > 0)
 701     {
 702       for (AlignFrame frame : frames)
 703       {
 704         frame.updateHMMERStatus(hmmerStatus);
 705       }
 706     }
 707
 708     trimTermini.setSelected(Cache.getDefault("TRIM_TERMINI", false));
 709     if (Cache.getDefault("USE_UNIPROT", false))
 710     {
 711       uniprot.setSelected(true);
 712     }
 713     else
 714     {
 715       alignment.setSelected(true);
 716     }
 717     numberOfSequencesToKeepField
 718             .setText(Cache.getProperty("SEQUENCES_TO_KEEP"));
 719     hmmerPath.setText(Cache.getProperty(HMMER_PATH));
 720
 721     /*
 722      * Save Structure settings
 723      */
 724     Cache.applicationProperties.setProperty(ADD_TEMPFACT_ANN,
 725             Boolean.toString(addTempFactor.isSelected()));
 726     Cache.applicationProperties.setProperty(ADD_SS_ANN,
 727             Boolean.toString(addSecondaryStructure.isSelected()));
 728     Cache.applicationProperties.setProperty(USE_RNAVIEW,
 729             Boolean.toString(useRnaView.isSelected()));
 730     Cache.applicationProperties.setProperty(STRUCT_FROM_PDB,
 731             Boolean.toString(structFromPdb.isSelected()));
 732     Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY,
 733             structViewer.getSelectedItem().toString());
 734     Cache.setOrRemove(CHIMERA_PATH, chimeraPath.getText());
 735     Cache.applicationProperties.setProperty("MAP_WITH_SIFTS",
 736             Boolean.toString(siftsMapping.isSelected()));
 737     SiftsSettings.setMapWithSifts(siftsMapping.isSelected());
 738
 739     /*
 740      * Save Output settings
 741      */
 742     Cache.applicationProperties.setProperty("EPS_RENDERING",
 743             ((OptionsParam) epsRendering.getSelectedItem()).getCode());
 744
 745     /*
 746      * Save Connections settings
 747      */
 748     Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText());
 749
 750     jalview.util.BrowserLauncher.resetBrowser();
 751
 752     // save user-defined and selected links
 753     String menuLinks = sequenceUrlLinks.writeUrlsAsString(true);
 754     if (menuLinks.isEmpty())
 755     {
 756       Cache.applicationProperties.remove("SEQUENCE_LINKS");
 757     }
 758     else
 759     {
 760       Cache.applicationProperties.setProperty("SEQUENCE_LINKS",
 761               menuLinks.toString());
 762     }
 763
 764     String nonMenuLinks = sequenceUrlLinks.writeUrlsAsString(false);
 765     if (nonMenuLinks.isEmpty())
 766     {
 767       Cache.applicationProperties.remove("STORED_LINKS");
 768     }
 769     else
 770     {
 771       Cache.applicationProperties.setProperty("STORED_LINKS",
 772               nonMenuLinks.toString());
 773     }
 774
 775     Cache.applicationProperties.setProperty("DEFAULT_URL",
 776             sequenceUrlLinks.getPrimaryUrlId());
 777
 778     Cache.applicationProperties.setProperty("USE_PROXY",
 779             Boolean.toString(useProxy.isSelected()));
 780
 781     Cache.setOrRemove("PROXY_SERVER", proxyServerTB.getText());
 782
 783     Cache.setOrRemove("PROXY_PORT", proxyPortTB.getText());
 784
 785     if (useProxy.isSelected())
 786     {
 787       System.setProperty("http.proxyHost", proxyServerTB.getText());
 788       System.setProperty("http.proxyPort", proxyPortTB.getText());
 789     }
 790     else
 791     {
 792       System.setProperty("http.proxyHost", "");
 793       System.setProperty("http.proxyPort", "");
 794     }
 795     Cache.setProperty("VERSION_CHECK",
 796             Boolean.toString(versioncheck.isSelected()));
 797     if (Cache.getProperty("USAGESTATS") != null || usagestats.isSelected())
 798     {
 799       // default is false - we only set this if the user has actively agreed
 800       Cache.setProperty("USAGESTATS",
 801               Boolean.toString(usagestats.isSelected()));
 802     }
 803     if (!questionnaire.isSelected())
 804     {
 805       Cache.setProperty("NOQUESTIONNAIRES", "true");
 806     }
 807     else
 808     {
 809       // special - made easy to edit a property file to disable questionnaires
 810       // by just adding the given line
 811       Cache.removeProperty("NOQUESTIONNAIRES");
 812     }
 813
 814     /*
 815      * Save Output settings
 816      */
 817     Cache.applicationProperties.setProperty("BLC_JVSUFFIX",
 818             Boolean.toString(blcjv.isSelected()));
 819     Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX",
 820             Boolean.toString(clustaljv.isSelected()));
 821     Cache.applicationProperties.setProperty("FASTA_JVSUFFIX",
 822             Boolean.toString(fastajv.isSelected()));
 823     Cache.applicationProperties.setProperty("MSF_JVSUFFIX",
 824             Boolean.toString(msfjv.isSelected()));
 825     Cache.applicationProperties.setProperty("PFAM_JVSUFFIX",
 826             Boolean.toString(pfamjv.isSelected()));
 827     Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX",
 828             Boolean.toString(pileupjv.isSelected()));
 829     Cache.applicationProperties.setProperty("PIR_JVSUFFIX",
 830             Boolean.toString(pirjv.isSelected()));
 831     Cache.applicationProperties.setProperty("PIR_MODELLER",
 832             Boolean.toString(modellerOutput.isSelected()));
 833     Cache.applicationProperties.setProperty("EXPORT_EMBBED_BIOJSON",
 834             Boolean.toString(embbedBioJSON.isSelected()));
 835     jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
 836
 837     Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH",
 838             Boolean.toString(autoIdWidth.isSelected()));
 839     userIdWidth_actionPerformed();
 840     Cache.applicationProperties.setProperty("FIGURE_USERIDWIDTH",
 841             userIdWidth.getText());
 842
 843     /*
 844      * Save Editing settings
 845      */
 846     Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
 847             Boolean.toString(autoCalculateConsCheck.isSelected()));
 848     Cache.applicationProperties.setProperty("SORT_BY_TREE",
 849             Boolean.toString(sortByTree.isSelected()));
 850     Cache.applicationProperties.setProperty("PAD_GAPS",
 851             Boolean.toString(padGaps.isSelected()));
 852
 853     dasSource.saveProperties(Cache.applicationProperties);
 854     wsPrefs.updateAndRefreshWsMenuConfig(false);
 855     Cache.saveProperties();
 856     Desktop.instance.doConfigureStructurePrefs();
 857     try
 858     {
 859       frame.setClosed(true);
 860     } catch (Exception ex)
 861     {
 862     }
 863   }
 864
 865   /**
 866    * Do any necessary validation before saving settings. Return focus to the
 867    * first tab which fails validation.
 868    *
 869    * @return
 870    */
 871   private boolean validateSettings()
 872   {
 873     if (!validateStructure())
 874     {
 875       structureTab.requestFocusInWindow();
 876       return false;
 877     }
 878     if (isHMMERInstalled.isSelected())
 879     {
 880       if (!validateHMMER())
 881       {
 882         hmmerTab.requestFocusInWindow();
 883         return false;
 884       }
 885     }
 886     return true;
 887   }
 888
 889   @Override
 890   protected boolean validateStructure()
 891   {
 892     return validateChimeraPath();
 893
 894   }
 895
 896   @Override
 897   protected boolean validateHMMER()
 898   {
 899     return validateHMMERPath();
 900
 901   }
 902
 903   /**
 904    * DOCUMENT ME!
 905    */
 906   @Override
 907   public void startupFileTextfield_mouseClicked()
 908   {
 909     String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
 910     JalviewFileChooser chooser = JalviewFileChooser
 911             .forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat);
 912     chooser.setFileView(new JalviewFileView());
 913     chooser.setDialogTitle(
 914             MessageManager.getString("label.select_startup_file"));
 915
 916     int value = chooser.showOpenDialog(this);
 917
 918     if (value == JalviewFileChooser.APPROVE_OPTION)
 919     {
 920       FileFormatI format = chooser.getSelectedFormat();
 921       if (format != null)
 922       {
 923         Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT",
 924                 format.getName());
 925       }
 926       startupFileTextfield
 927               .setText(chooser.getSelectedFile().getAbsolutePath());
 928     }
 929   }
 930
 931   /**
 932    * DOCUMENT ME!
 933    *
 934    * @param e
 935    *          DOCUMENT ME!
 936    */
 937   @Override
 938   public void cancel_actionPerformed(ActionEvent e)
 939   {
 940     try
 941     {
 942       wsPrefs.updateWsMenuConfig(true);
 943       wsPrefs.refreshWs_actionPerformed(e);
 944       frame.setClosed(true);
 945     } catch (Exception ex)
 946     {
 947     }
 948   }
 949
 950   /**
 951    * DOCUMENT ME!
 952    *
 953    * @param e
 954    *          DOCUMENT ME!
 955    */
 956   @Override
 957   public void annotations_actionPerformed(ActionEvent e)
 958   {
 959     conservation.setEnabled(annotations.isSelected());
 960     quality.setEnabled(annotations.isSelected());
 961     identity.setEnabled(annotations.isSelected());
 962     showOccupancy.setEnabled(annotations.isSelected());
 963     showGroupConsensus.setEnabled(annotations.isSelected());
 964     showGroupConservation.setEnabled(annotations.isSelected());
 965     showConsensHistogram.setEnabled(annotations.isSelected()
 966             && (identity.isSelected() || showGroupConsensus.isSelected()));
 967     showConsensLogo.setEnabled(annotations.isSelected()
 968             && (identity.isSelected() || showGroupConsensus.isSelected()));
 969     showInformationHistogram.setEnabled(annotations.isSelected());
 970     showHMMLogo.setEnabled(annotations.isSelected());
 971   }
 972
 973   @Override
 974   public void newLink_actionPerformed(ActionEvent e)
 975   {
 976     GSequenceLink link = new GSequenceLink();
 977     boolean valid = false;
 978     while (!valid)
 979     {
 980       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 981               MessageManager.getString("label.new_sequence_url_link"),
 982               JvOptionPane.OK_CANCEL_OPTION, -1,
 983               null) == JvOptionPane.OK_OPTION)
 984       {
 985         if (link.checkValid())
 986         {
 987           if (((UrlLinkTableModel) linkUrlTable.getModel())
 988                   .isUniqueName(link.getName()))
 989           {
 990             ((UrlLinkTableModel) linkUrlTable.getModel())
 991                     .insertRow(link.getName(), link.getURL());
 992             valid = true;
 993           }
 994           else
 995           {
 996             link.notifyDuplicate();
 997             continue;
 998           }
 999         }
1000       }
1001       else
1002       {
1003         break;
1004       }
1005     }
1006   }
1007
1008   @Override
1009   public void editLink_actionPerformed(ActionEvent e)
1010   {
1011     GSequenceLink link = new GSequenceLink();
1012
1013     int index = linkUrlTable.getSelectedRow();
1014     if (index == -1)
1015     {
1016       // button no longer enabled if row is not selected
1017       Cache.log.debug("Edit with no row selected in linkUrlTable");
1018       return;
1019     }
1020
1021     int nameCol = ((UrlLinkTableModel) linkUrlTable.getModel())
1022             .getNameColumn();
1023     int urlCol = ((UrlLinkTableModel) linkUrlTable.getModel())
1024             .getUrlColumn();
1025     String oldName = linkUrlTable.getValueAt(index, nameCol).toString();
1026     link.setName(oldName);
1027     link.setURL(linkUrlTable.getValueAt(index, urlCol).toString());
1028
1029     boolean valid = false;
1030     while (!valid)
1031     {
1032       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
1033               MessageManager.getString("label.edit_sequence_url_link"),
1034               JvOptionPane.OK_CANCEL_OPTION, -1,
1035               null) == JvOptionPane.OK_OPTION)
1036       {
1037         if (link.checkValid())
1038         {
1039           if ((oldName.equals(link.getName()))
1040                   || (((UrlLinkTableModel) linkUrlTable.getModel())
1041                           .isUniqueName(link.getName())))
1042           {
1043             linkUrlTable.setValueAt(link.getName(), index, nameCol);
1044             linkUrlTable.setValueAt(link.getURL(), index, urlCol);
1045             valid = true;
1046           }
1047           else
1048           {
1049             link.notifyDuplicate();
1050             continue;
1051           }
1052         }
1053       }
1054       else
1055       {
1056         break;
1057       }
1058     }
1059   }
1060
1061   @Override
1062   public void deleteLink_actionPerformed(ActionEvent e)
1063   {
1064     int index = linkUrlTable.getSelectedRow();
1065     int modelIndex = -1;
1066     if (index == -1)
1067     {
1068       // button no longer enabled if row is not selected
1069       Cache.log.debug("Delete with no row selected in linkUrlTable");
1070       return;
1071     }
1072     else
1073     {
1074       modelIndex = linkUrlTable.convertRowIndexToModel(index);
1075     }
1076
1077     // make sure we use the model index to delete, and not the table index
1078     ((UrlLinkTableModel) linkUrlTable.getModel()).removeRow(modelIndex);
1079   }
1080
1081   @Override
1082   public void defaultBrowser_mouseClicked(MouseEvent e)
1083   {
1084     JFileChooser chooser = new JFileChooser(".");
1085     chooser.setDialogTitle(
1086             MessageManager.getString("label.select_default_browser"));
1087
1088     int value = chooser.showOpenDialog(this);
1089
1090     if (value == JFileChooser.APPROVE_OPTION)
1091     {
1092       defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
1093     }
1094
1095   }
1096
1097   /*
1098    * (non-Javadoc)
1099    *
1100    * @see
1101    * jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event
1102    * .ActionEvent)
1103    */
1104   @Override
1105   protected void showunconserved_actionPerformed(ActionEvent e)
1106   {
1107     // TODO Auto-generated method stub
1108     super.showunconserved_actionPerformed(e);
1109   }
1110
1111   public static List<String> getGroupURLLinks()
1112   {
1113     return groupURLLinks;
1114   }
1115
1116   @Override
1117   public void minColour_actionPerformed(JPanel panel)
1118   {
1119     Color col = JColorChooser.showDialog(this,
1120             MessageManager.getString("label.select_colour_minimum_value"),
1121             minColour.getBackground());
1122     if (col != null)
1123     {
1124       panel.setBackground(col);
1125     }
1126     panel.repaint();
1127   }
1128
1129   @Override
1130   public void maxColour_actionPerformed(JPanel panel)
1131   {
1132     Color col = JColorChooser.showDialog(this,
1133             MessageManager.getString("label.select_colour_maximum_value"),
1134             maxColour.getBackground());
1135     if (col != null)
1136     {
1137       panel.setBackground(col);
1138     }
1139     panel.repaint();
1140   }
1141
1142   @Override
1143   protected void userIdWidth_actionPerformed()
1144   {
1145     try
1146     {
1147       String val = userIdWidth.getText().trim();
1148       if (val.length() > 0)
1149       {
1150         Integer iw = Integer.parseInt(val);
1151         if (iw.intValue() < 12)
1152         {
1153           throw new NumberFormatException();
1154         }
1155         userIdWidth.setText(iw.toString());
1156       }
1157     } catch (NumberFormatException x)
1158     {
1159       JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1160               MessageManager
1161                       .getString("warn.user_defined_width_requirements"),
1162               MessageManager.getString("label.invalid_id_column_width"),
1163               JvOptionPane.WARNING_MESSAGE);
1164       userIdWidth.setText("");
1165     }
1166   }
1167
1168   @Override
1169   protected void autoIdWidth_actionPerformed()
1170   {
1171     userIdWidth.setEnabled(!autoIdWidth.isSelected());
1172     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
1173   }
1174
1175   /**
1176    * Returns true if chimera path is to a valid executable, else show an error
1177    * dialog.
1178    */
1179   private boolean validateChimeraPath()
1180   {
1181     if (chimeraPath.getText().trim().length() > 0)
1182     {
1183       File f = new File(chimeraPath.getText());
1184       if (!f.canExecute())
1185       {
1186         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1187                 MessageManager.getString("label.invalid_chimera_path"),
1188                 MessageManager.getString("label.invalid_name"),
1189                 JvOptionPane.ERROR_MESSAGE);
1190         return false;
1191       }
1192     }
1193     return true;
1194   }
1195
1196   /**
1197    * Returns true if hmmer path contains the necessary valid executables, else
1198    * show an error dialog (if showing dialog).
1199    */
1200   private boolean validateHMMERPath(boolean showDialog)
1201   {
1202     int missing = 0;
1203     String message = "";
1204     String folder = hmmerPath.getText().trim();
1205     if (folder.length() > 0)
1206     {
1207       File f = new File(folder);
1208       if (!f.exists())
1209       {
1210         if (showDialog)
1211         {
1212           JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1213                 MessageManager.getString("label.folder_not_exists"),
1214                 MessageManager.getString("label.invalid_folder"),
1215                 JvOptionPane.ERROR_MESSAGE);
1216         }
1217         return false;
1218       }
1219       AlignmentI alignment = new Alignment(
1220               new SequenceI[]
1221       { new Sequence("test", "WLWL", 0, 3) });
1222       if (canExecute(folder + "/hmmbuild"))
1223         {
1224         validateHMMBuild(alignment);
1225         }
1226       else
1227       {
1228         message += MessageManager.getString("label.hmmbuild_not_found")
1229                 + "\n";
1230         missing++;
1231       }
1232
1233
1234       if (canExecute(folder + "/hmmalign"))
1235         {
1236
1237         }
1238       else
1239       {
1240         message += MessageManager.getString("label.hmmalign_not_found")
1241                 + "\n";
1242         missing++;
1243       }
1244
1245
1246       if (canExecute(folder + "/hmmsearch"))
1247         {
1248
1249         }
1250       else
1251       {
1252         message += MessageManager.getString("label.hmmsearch_not_found")
1253                 + "\n";
1254         missing++;
1255       }
1256       }
1257
1258       if (missing > 0)
1259       {
1260         if (missing < 3)
1261         {
1262           if (showDialog)
1263           {
1264             JvOptionPane.showInternalMessageDialog(Desktop.desktop, message,
1265                   MessageManager.getString("label.invalid_folder"),
1266                   JvOptionPane.ERROR_MESSAGE);
1267           }
1268           return false;
1269         }
1270         else
1271         {
1272           if (showDialog)
1273           {
1274             JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1275                   MessageManager.getString("label.no_binaries"),
1276                   MessageManager.getString("label.invalid_folder"),
1277                   JvOptionPane.ERROR_MESSAGE);
1278           }
1279
1280           return false;
1281         }
1282       }
1283
1284     return true;
1285   }
1286
1287   /**
1288    * Checks if a file can be executed
1289    *
1290    * @param path
1291    *          the path to the file
1292    * @return
1293    */
1294   public boolean canExecute(String path)
1295   {
1296     File file = new File(path);
1297     if (!file.canExecute())
1298     {
1299       file = new File(path + ".exe");
1300       {
1301         if (!file.canExecute())
1302         {
1303           return false;
1304         }
1305       }
1306     }
1307     return true;
1308   }
1309
1310   /**
1311    * Runs hmmbuild to check if it is working. While doing this it parses the
1312    * version of HMMER.
1313    *
1314    * @param frame
1315    * @return
1316    */
1317   public boolean validateHMMBuild(AlignmentI alignment)
1318   {
1319     HMMBuildThread hmmbuild = new HMMBuildThread(alignment);
1320     hmmbuild.hmmbuildWaitTillComplete();
1321     SequenceI hmmSeq = alignment.getSequenceAt(0);
1322     HiddenMarkovModel hmm;
1323     if (hmmSeq.isHMMConsensusSequence() && hmmSeq.getHMM() != null)
1324     {
1325       hmm = hmmSeq.getHMM();
1326
1327       if (hmm.getNumberOfSymbols() < 1)
1328       {
1329         return false;
1330       }
1331     }
1332     else
1333     {
1334       return false;
1335     }
1336
1337     String header = hmm.getFileHeader();
1338     if (header == null)
1339     {
1340       return false;
1341     }
1342     else
1343     {
1344       Scanner scanner = new Scanner(header);
1345       scanner.next();
1346       String string = scanner.next();
1347       String version = string.substring(1);
1348       Cache.setProperty("HMMER_VERSION", version);
1349       scanner.close();
1350
1351     }
1352     return true;
1353   }
1354
1355
1356   private boolean validateHMMERPath()
1357   {
1358     return validateHMMERPath(true);
1359   }
1360
1361   /**
1362    * If Chimera is selected, check it can be found on default or user-specified
1363    * path, if not show a warning/help dialog.
1364    */
1365   @Override
1366   protected void structureViewer_actionPerformed(String selectedItem)
1367   {
1368     if (!selectedItem.equals(ViewerType.CHIMERA.name()))
1369     {
1370       return;
1371     }
1372     boolean found = false;
1373
1374     /*
1375      * Try user-specified and standard paths for Chimera executable.
1376      */
1377     List<String> paths = StructureManager.getChimeraPaths();
1378     paths.add(0, chimeraPath.getText());
1379     for (String path : paths)
1380     {
1381       if (new File(path.trim()).canExecute())
1382       {
1383         found = true;
1384         break;
1385       }
1386     }
1387     if (!found)
1388     {
1389       String[] options = { "OK", "Help" };
1390       int showHelp = JvOptionPane.showInternalOptionDialog(Desktop.desktop,
1391               JvSwingUtils.wrapTooltip(true,
1392                       MessageManager.getString("label.chimera_missing")),
1393               "", JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE,
1394               null, options, options[0]);
1395       if (showHelp == JvOptionPane.NO_OPTION)
1396       {
1397         try
1398         {
1399           Help.showHelpWindow(HelpId.StructureViewer);
1400         } catch (HelpSetException e)
1401         {
1402           e.printStackTrace();
1403         }
1404       }
1405     }
1406   }
1407
1408   public class OptionsParam
1409   {
1410     private String name;
1411
1412     private String code;
1413
1414     public OptionsParam(String name, String code)
1415     {
1416       this.name = name;
1417       this.code = code;
1418     }
1419
1420     public String getName()
1421     {
1422       return name;
1423     }
1424
1425     public void setName(String name)
1426     {
1427       this.name = name;
1428     }
1429
1430     public String getCode()
1431     {
1432       return code;
1433     }
1434
1435     public void setCode(String code)
1436     {
1437       this.code = code;
1438     }
1439
1440     @Override
1441     public String toString()
1442     {
1443       return name;
1444     }
1445
1446     @Override
1447     public boolean equals(Object that)
1448     {
1449       if (!(that instanceof OptionsParam))
1450       {
1451         return false;
1452       }
1453       return this.code.equalsIgnoreCase(((OptionsParam) that).code);
1454     }
1455
1456     @Override
1457     public int hashCode()
1458     {
1459       return name.hashCode() + code.hashCode();
1460     }
1461   }
1462
1463   private class UrlListSelectionHandler implements ListSelectionListener
1464   {
1465
1466     @Override
1467     public void valueChanged(ListSelectionEvent e)
1468     {
1469       ListSelectionModel lsm = (ListSelectionModel) e.getSource();
1470
1471       int index = lsm.getMinSelectionIndex();
1472       if (index == -1)
1473       {
1474         // no selection, so disable delete/edit buttons
1475         editLink.setEnabled(false);
1476         deleteLink.setEnabled(false);
1477         return;
1478       }
1479       int modelIndex = linkUrlTable.convertRowIndexToModel(index);
1480
1481       // enable/disable edit and delete link buttons
1482       if (((UrlLinkTableModel) linkUrlTable.getModel())
1483               .isRowDeletable(modelIndex))
1484       {
1485         deleteLink.setEnabled(true);
1486       }
1487       else
1488       {
1489         deleteLink.setEnabled(false);
1490       }
1491
1492       if (((UrlLinkTableModel) linkUrlTable.getModel())
1493               .isRowEditable(modelIndex))
1494       {
1495         editLink.setEnabled(true);
1496       }
1497       else
1498       {
1499         editLink.setEnabled(false);
1500       }
1501     }
1502   }
1503 }