src/jalview/gui/Preferences.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.gui;
  22
  23 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
  24 import jalview.bin.Cache;
  25 import jalview.gui.Help.HelpId;
  26 import jalview.gui.StructureViewer.ViewerType;
  27 import jalview.hmmer.HmmerCommand;
  28 import jalview.io.FileFormatI;
  29 import jalview.io.JalviewFileChooser;
  30 import jalview.io.JalviewFileView;
  31 import jalview.jbgui.GPreferences;
  32 import jalview.jbgui.GSequenceLink;
  33 import jalview.schemes.ColourSchemeI;
  34 import jalview.schemes.ColourSchemes;
  35 import jalview.schemes.ResidueColourScheme;
  36 import jalview.urls.UrlLinkTableModel;
  37 import jalview.urls.api.UrlProviderFactoryI;
  38 import jalview.urls.api.UrlProviderI;
  39 import jalview.urls.desktop.DesktopUrlProviderFactory;
  40 import jalview.util.MessageManager;
  41 import jalview.util.Platform;
  42 import jalview.util.UrlConstants;
  43 import jalview.ws.sifts.SiftsSettings;
  44
  45 import java.awt.BorderLayout;
  46 import java.awt.Color;
  47 import java.awt.Component;
  48 import java.awt.Dimension;
  49 import java.awt.Font;
  50 import java.awt.event.ActionEvent;
  51 import java.awt.event.ActionListener;
  52 import java.awt.event.FocusAdapter;
  53 import java.awt.event.FocusEvent;
  54 import java.awt.event.MouseEvent;
  55 import java.io.File;
  56 import java.util.ArrayList;
  57 import java.util.List;
  58
  59 import javax.help.HelpSetException;
  60 import javax.swing.JColorChooser;
  61 import javax.swing.JFileChooser;
  62 import javax.swing.JInternalFrame;
  63 import javax.swing.JPanel;
  64 import javax.swing.ListSelectionModel;
  65 import javax.swing.RowFilter;
  66 import javax.swing.RowSorter;
  67 import javax.swing.SortOrder;
  68 import javax.swing.event.DocumentEvent;
  69 import javax.swing.event.DocumentListener;
  70 import javax.swing.event.ListSelectionEvent;
  71 import javax.swing.event.ListSelectionListener;
  72 import javax.swing.table.TableCellRenderer;
  73 import javax.swing.table.TableColumn;
  74 import javax.swing.table.TableModel;
  75 import javax.swing.table.TableRowSorter;
  76
  77 import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
  78
  79 /**
  80  * DOCUMENT ME!
  81  *
  82  * @author $author$
  83  * @version $Revision$
  84  */
  85 public class Preferences extends GPreferences
  86 {
  87   public static final String ENABLE_SPLIT_FRAME = "ENABLE_SPLIT_FRAME";
  88
  89   public static final String SCALE_PROTEIN_TO_CDNA = "SCALE_PROTEIN_TO_CDNA";
  90
  91   public static final String DEFAULT_COLOUR = "DEFAULT_COLOUR";
  92
  93   public static final String DEFAULT_COLOUR_PROT = "DEFAULT_COLOUR_PROT";
  94
  95   public static final String DEFAULT_COLOUR_NUC = "DEFAULT_COLOUR_NUC";
  96
  97   public static final String ADD_TEMPFACT_ANN = "ADD_TEMPFACT_ANN";
  98
  99   public static final String ADD_SS_ANN = "ADD_SS_ANN";
 100
 101   public static final String USE_RNAVIEW = "USE_RNAVIEW";
 102
 103   public static final String STRUCT_FROM_PDB = "STRUCT_FROM_PDB";
 104
 105   public static final String STRUCTURE_DISPLAY = "STRUCTURE_DISPLAY";
 106
 107   public static final String CHIMERA_PATH = "CHIMERA_PATH";
 108
 109   public static final String HMMER_PATH = "HMMER_PATH";
 110
 111   public static final String HMMSEARCH_DB_PATHS = "HMMSEARCH_DB_PATHS";
 112
 113   public static final String HMMSEARCH_DBS = "HMMSEARCH_DBS";
 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     hmmrTrimTermini.setSelected(Cache.getDefault("TRIM_TERMINI", false));
 214     if (Cache.getDefault("USE_UNIPROT", false))
 215     {
 216       hmmerBackgroundUniprot.setSelected(true);
 217     }
 218     else
 219     {
 220       hmmerBackgroundAlignment.setSelected(true);
 221     }
 222     hmmerSequenceCount
 223             .setText(Cache.getProperty("SEQUENCES_TO_KEEP"));
 224     hmmerPath.setText(Cache.getProperty(HMMER_PATH));
 225     hmmerPath.addActionListener(new ActionListener()
 226     {
 227       @Override
 228       public void actionPerformed(ActionEvent e)
 229       {
 230         validateHMMERPath(true);
 231       }
 232     });
 233     hmmerPath.addFocusListener(new FocusAdapter()
 234     {
 235       @Override
 236       public void focusLost(FocusEvent e)
 237       {
 238         validateHMMERPath(true);
 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(hmmrTrimTermini.isSelected()));
 686     Cache.applicationProperties.setProperty("USE_UNIPROT",
 687             Boolean.toString(hmmerBackgroundUniprot.isSelected()));
 688     Cache.applicationProperties.setProperty("SEQUENCES_TO_KEEP",
 689             hmmerSequenceCount.getText());
 690     Cache.applicationProperties.setProperty(HMMER_PATH,
 691             hmmerPath.getText());
 692     AlignFrame[] frames = Desktop.getAlignFrames();
 693     if (frames != null && frames.length > 0)
 694     {
 695       for (AlignFrame f : frames)
 696       {
 697         f.updateHMMERStatus();
 698       }
 699     }
 700
 701     hmmrTrimTermini.setSelected(Cache.getDefault("TRIM_TERMINI", false));
 702     if (Cache.getDefault("USE_UNIPROT", false))
 703     {
 704       hmmerBackgroundUniprot.setSelected(true);
 705     }
 706     else
 707     {
 708       hmmerBackgroundAlignment.setSelected(true);
 709     }
 710     hmmerSequenceCount
 711             .setText(Cache.getProperty("SEQUENCES_TO_KEEP"));
 712     hmmerPath.setText(Cache.getProperty(HMMER_PATH));
 713
 714     /*
 715      * Save Structure settings
 716      */
 717     Cache.applicationProperties.setProperty(ADD_TEMPFACT_ANN,
 718             Boolean.toString(addTempFactor.isSelected()));
 719     Cache.applicationProperties.setProperty(ADD_SS_ANN,
 720             Boolean.toString(addSecondaryStructure.isSelected()));
 721     Cache.applicationProperties.setProperty(USE_RNAVIEW,
 722             Boolean.toString(useRnaView.isSelected()));
 723     Cache.applicationProperties.setProperty(STRUCT_FROM_PDB,
 724             Boolean.toString(structFromPdb.isSelected()));
 725     Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY,
 726             structViewer.getSelectedItem().toString());
 727     Cache.setOrRemove(CHIMERA_PATH, chimeraPath.getText());
 728     Cache.applicationProperties.setProperty("MAP_WITH_SIFTS",
 729             Boolean.toString(siftsMapping.isSelected()));
 730     SiftsSettings.setMapWithSifts(siftsMapping.isSelected());
 731
 732     /*
 733      * Save Output settings
 734      */
 735     Cache.applicationProperties.setProperty("EPS_RENDERING",
 736             ((OptionsParam) epsRendering.getSelectedItem()).getCode());
 737
 738     /*
 739      * Save Connections settings
 740      */
 741     Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText());
 742
 743     jalview.util.BrowserLauncher.resetBrowser();
 744
 745     // save user-defined and selected links
 746     String menuLinks = sequenceUrlLinks.writeUrlsAsString(true);
 747     if (menuLinks.isEmpty())
 748     {
 749       Cache.applicationProperties.remove("SEQUENCE_LINKS");
 750     }
 751     else
 752     {
 753       Cache.applicationProperties.setProperty("SEQUENCE_LINKS",
 754               menuLinks.toString());
 755     }
 756
 757     String nonMenuLinks = sequenceUrlLinks.writeUrlsAsString(false);
 758     if (nonMenuLinks.isEmpty())
 759     {
 760       Cache.applicationProperties.remove("STORED_LINKS");
 761     }
 762     else
 763     {
 764       Cache.applicationProperties.setProperty("STORED_LINKS",
 765               nonMenuLinks.toString());
 766     }
 767
 768     Cache.applicationProperties.setProperty("DEFAULT_URL",
 769             sequenceUrlLinks.getPrimaryUrlId());
 770
 771     Cache.applicationProperties.setProperty("USE_PROXY",
 772             Boolean.toString(useProxy.isSelected()));
 773
 774     Cache.setOrRemove("PROXY_SERVER", proxyServerTB.getText());
 775
 776     Cache.setOrRemove("PROXY_PORT", proxyPortTB.getText());
 777
 778     if (useProxy.isSelected())
 779     {
 780       System.setProperty("http.proxyHost", proxyServerTB.getText());
 781       System.setProperty("http.proxyPort", proxyPortTB.getText());
 782     }
 783     else
 784     {
 785       System.setProperty("http.proxyHost", "");
 786       System.setProperty("http.proxyPort", "");
 787     }
 788     Cache.setProperty("VERSION_CHECK",
 789             Boolean.toString(versioncheck.isSelected()));
 790     if (Cache.getProperty("USAGESTATS") != null || usagestats.isSelected())
 791     {
 792       // default is false - we only set this if the user has actively agreed
 793       Cache.setProperty("USAGESTATS",
 794               Boolean.toString(usagestats.isSelected()));
 795     }
 796     if (!questionnaire.isSelected())
 797     {
 798       Cache.setProperty("NOQUESTIONNAIRES", "true");
 799     }
 800     else
 801     {
 802       // special - made easy to edit a property file to disable questionnaires
 803       // by just adding the given line
 804       Cache.removeProperty("NOQUESTIONNAIRES");
 805     }
 806
 807     /*
 808      * Save Output settings
 809      */
 810     Cache.applicationProperties.setProperty("BLC_JVSUFFIX",
 811             Boolean.toString(blcjv.isSelected()));
 812     Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX",
 813             Boolean.toString(clustaljv.isSelected()));
 814     Cache.applicationProperties.setProperty("FASTA_JVSUFFIX",
 815             Boolean.toString(fastajv.isSelected()));
 816     Cache.applicationProperties.setProperty("MSF_JVSUFFIX",
 817             Boolean.toString(msfjv.isSelected()));
 818     Cache.applicationProperties.setProperty("PFAM_JVSUFFIX",
 819             Boolean.toString(pfamjv.isSelected()));
 820     Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX",
 821             Boolean.toString(pileupjv.isSelected()));
 822     Cache.applicationProperties.setProperty("PIR_JVSUFFIX",
 823             Boolean.toString(pirjv.isSelected()));
 824     Cache.applicationProperties.setProperty("PIR_MODELLER",
 825             Boolean.toString(modellerOutput.isSelected()));
 826     Cache.applicationProperties.setProperty("EXPORT_EMBBED_BIOJSON",
 827             Boolean.toString(embbedBioJSON.isSelected()));
 828     jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
 829
 830     Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH",
 831             Boolean.toString(autoIdWidth.isSelected()));
 832     userIdWidth_actionPerformed();
 833     Cache.applicationProperties.setProperty("FIGURE_USERIDWIDTH",
 834             userIdWidth.getText());
 835
 836     /*
 837      * Save Editing settings
 838      */
 839     Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
 840             Boolean.toString(autoCalculateConsCheck.isSelected()));
 841     Cache.applicationProperties.setProperty("SORT_BY_TREE",
 842             Boolean.toString(sortByTree.isSelected()));
 843     Cache.applicationProperties.setProperty("PAD_GAPS",
 844             Boolean.toString(padGaps.isSelected()));
 845
 846     dasSource.saveProperties(Cache.applicationProperties);
 847     wsPrefs.updateAndRefreshWsMenuConfig(false);
 848     Cache.saveProperties();
 849     Desktop.instance.doConfigureStructurePrefs();
 850     try
 851     {
 852       frame.setClosed(true);
 853     } catch (Exception ex)
 854     {
 855     }
 856   }
 857
 858   /**
 859    * Do any necessary validation before saving settings. Return focus to the
 860    * first tab which fails validation.
 861    *
 862    * @return
 863    */
 864   private boolean validateSettings()
 865   {
 866     if (!validateStructure())
 867     {
 868       structureTab.requestFocusInWindow();
 869       return false;
 870     }
 871     return true;
 872   }
 873
 874   @Override
 875   protected boolean validateStructure()
 876   {
 877     return validateChimeraPath();
 878
 879   }
 880
 881   /**
 882    * DOCUMENT ME!
 883    */
 884   @Override
 885   public void startupFileTextfield_mouseClicked()
 886   {
 887     String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
 888     JalviewFileChooser chooser = JalviewFileChooser
 889             .forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat);
 890     chooser.setFileView(new JalviewFileView());
 891     chooser.setDialogTitle(
 892             MessageManager.getString("label.select_startup_file"));
 893
 894     int value = chooser.showOpenDialog(this);
 895
 896     if (value == JalviewFileChooser.APPROVE_OPTION)
 897     {
 898       FileFormatI format = chooser.getSelectedFormat();
 899       if (format != null)
 900       {
 901         Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT",
 902                 format.getName());
 903       }
 904       startupFileTextfield
 905               .setText(chooser.getSelectedFile().getAbsolutePath());
 906     }
 907   }
 908
 909   /**
 910    * DOCUMENT ME!
 911    *
 912    * @param e
 913    *          DOCUMENT ME!
 914    */
 915   @Override
 916   public void cancel_actionPerformed(ActionEvent e)
 917   {
 918     try
 919     {
 920       wsPrefs.updateWsMenuConfig(true);
 921       wsPrefs.refreshWs_actionPerformed(e);
 922       frame.setClosed(true);
 923     } catch (Exception ex)
 924     {
 925     }
 926   }
 927
 928   /**
 929    * DOCUMENT ME!
 930    *
 931    * @param e
 932    *          DOCUMENT ME!
 933    */
 934   @Override
 935   public void annotations_actionPerformed(ActionEvent e)
 936   {
 937     conservation.setEnabled(annotations.isSelected());
 938     quality.setEnabled(annotations.isSelected());
 939     identity.setEnabled(annotations.isSelected());
 940     showOccupancy.setEnabled(annotations.isSelected());
 941     showGroupConsensus.setEnabled(annotations.isSelected());
 942     showGroupConservation.setEnabled(annotations.isSelected());
 943     showConsensHistogram.setEnabled(annotations.isSelected()
 944             && (identity.isSelected() || showGroupConsensus.isSelected()));
 945     showConsensLogo.setEnabled(annotations.isSelected()
 946             && (identity.isSelected() || showGroupConsensus.isSelected()));
 947     showInformationHistogram.setEnabled(annotations.isSelected());
 948     showHMMLogo.setEnabled(annotations.isSelected());
 949   }
 950
 951   @Override
 952   public void newLink_actionPerformed(ActionEvent e)
 953   {
 954     GSequenceLink link = new GSequenceLink();
 955     boolean valid = false;
 956     while (!valid)
 957     {
 958       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 959               MessageManager.getString("label.new_sequence_url_link"),
 960               JvOptionPane.OK_CANCEL_OPTION, -1,
 961               null) == JvOptionPane.OK_OPTION)
 962       {
 963         if (link.checkValid())
 964         {
 965           if (((UrlLinkTableModel) linkUrlTable.getModel())
 966                   .isUniqueName(link.getName()))
 967           {
 968             ((UrlLinkTableModel) linkUrlTable.getModel())
 969                     .insertRow(link.getName(), link.getURL());
 970             valid = true;
 971           }
 972           else
 973           {
 974             link.notifyDuplicate();
 975             continue;
 976           }
 977         }
 978       }
 979       else
 980       {
 981         break;
 982       }
 983     }
 984   }
 985
 986   @Override
 987   public void editLink_actionPerformed(ActionEvent e)
 988   {
 989     GSequenceLink link = new GSequenceLink();
 990
 991     int index = linkUrlTable.getSelectedRow();
 992     if (index == -1)
 993     {
 994       // button no longer enabled if row is not selected
 995       Cache.log.debug("Edit with no row selected in linkUrlTable");
 996       return;
 997     }
 998
 999     int nameCol = ((UrlLinkTableModel) linkUrlTable.getModel())
1000             .getNameColumn();
1001     int urlCol = ((UrlLinkTableModel) linkUrlTable.getModel())
1002             .getUrlColumn();
1003     String oldName = linkUrlTable.getValueAt(index, nameCol).toString();
1004     link.setName(oldName);
1005     link.setURL(linkUrlTable.getValueAt(index, urlCol).toString());
1006
1007     boolean valid = false;
1008     while (!valid)
1009     {
1010       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
1011               MessageManager.getString("label.edit_sequence_url_link"),
1012               JvOptionPane.OK_CANCEL_OPTION, -1,
1013               null) == JvOptionPane.OK_OPTION)
1014       {
1015         if (link.checkValid())
1016         {
1017           if ((oldName.equals(link.getName()))
1018                   || (((UrlLinkTableModel) linkUrlTable.getModel())
1019                           .isUniqueName(link.getName())))
1020           {
1021             linkUrlTable.setValueAt(link.getName(), index, nameCol);
1022             linkUrlTable.setValueAt(link.getURL(), index, urlCol);
1023             valid = true;
1024           }
1025           else
1026           {
1027             link.notifyDuplicate();
1028             continue;
1029           }
1030         }
1031       }
1032       else
1033       {
1034         break;
1035       }
1036     }
1037   }
1038
1039   @Override
1040   public void deleteLink_actionPerformed(ActionEvent e)
1041   {
1042     int index = linkUrlTable.getSelectedRow();
1043     int modelIndex = -1;
1044     if (index == -1)
1045     {
1046       // button no longer enabled if row is not selected
1047       Cache.log.debug("Delete with no row selected in linkUrlTable");
1048       return;
1049     }
1050     else
1051     {
1052       modelIndex = linkUrlTable.convertRowIndexToModel(index);
1053     }
1054
1055     // make sure we use the model index to delete, and not the table index
1056     ((UrlLinkTableModel) linkUrlTable.getModel()).removeRow(modelIndex);
1057   }
1058
1059   @Override
1060   public void defaultBrowser_mouseClicked(MouseEvent e)
1061   {
1062     JFileChooser chooser = new JFileChooser(".");
1063     chooser.setDialogTitle(
1064             MessageManager.getString("label.select_default_browser"));
1065
1066     int value = chooser.showOpenDialog(this);
1067
1068     if (value == JFileChooser.APPROVE_OPTION)
1069     {
1070       defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
1071     }
1072
1073   }
1074
1075   /*
1076    * (non-Javadoc)
1077    *
1078    * @see
1079    * jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event
1080    * .ActionEvent)
1081    */
1082   @Override
1083   protected void showunconserved_actionPerformed(ActionEvent e)
1084   {
1085     // TODO Auto-generated method stub
1086     super.showunconserved_actionPerformed(e);
1087   }
1088
1089   public static List<String> getGroupURLLinks()
1090   {
1091     return groupURLLinks;
1092   }
1093
1094   @Override
1095   public void minColour_actionPerformed(JPanel panel)
1096   {
1097     Color col = JColorChooser.showDialog(this,
1098             MessageManager.getString("label.select_colour_minimum_value"),
1099             minColour.getBackground());
1100     if (col != null)
1101     {
1102       panel.setBackground(col);
1103     }
1104     panel.repaint();
1105   }
1106
1107   @Override
1108   public void maxColour_actionPerformed(JPanel panel)
1109   {
1110     Color col = JColorChooser.showDialog(this,
1111             MessageManager.getString("label.select_colour_maximum_value"),
1112             maxColour.getBackground());
1113     if (col != null)
1114     {
1115       panel.setBackground(col);
1116     }
1117     panel.repaint();
1118   }
1119
1120   @Override
1121   protected void userIdWidth_actionPerformed()
1122   {
1123     try
1124     {
1125       String val = userIdWidth.getText().trim();
1126       if (val.length() > 0)
1127       {
1128         Integer iw = Integer.parseInt(val);
1129         if (iw.intValue() < 12)
1130         {
1131           throw new NumberFormatException();
1132         }
1133         userIdWidth.setText(iw.toString());
1134       }
1135     } catch (NumberFormatException x)
1136     {
1137       JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1138               MessageManager
1139                       .getString("warn.user_defined_width_requirements"),
1140               MessageManager.getString("label.invalid_id_column_width"),
1141               JvOptionPane.WARNING_MESSAGE);
1142       userIdWidth.setText("");
1143     }
1144   }
1145
1146   @Override
1147   protected void autoIdWidth_actionPerformed()
1148   {
1149     userIdWidth.setEnabled(!autoIdWidth.isSelected());
1150     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
1151   }
1152
1153   /**
1154    * Returns true if chimera path is to a valid executable, else show an error
1155    * dialog.
1156    */
1157   private boolean validateChimeraPath()
1158   {
1159     if (chimeraPath.getText().trim().length() > 0)
1160     {
1161       File f = new File(chimeraPath.getText());
1162       if (!f.canExecute())
1163       {
1164         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1165                 MessageManager.getString("label.invalid_chimera_path"),
1166                 MessageManager.getString("label.invalid_name"),
1167                 JvOptionPane.ERROR_MESSAGE);
1168         return false;
1169       }
1170     }
1171     return true;
1172   }
1173
1174   /**
1175    * Returns true if hmmer path is to a folder that contains an executable
1176    * hmmbuild or hmmbuild.exe, else false (optionally after showing a warning
1177    * dialog)
1178    */
1179   @Override
1180   protected boolean validateHMMERPath(boolean showWarning)
1181   {
1182     String folder = hmmerPath.getText().trim();
1183
1184     if (HmmerCommand.getExecutable(HmmerCommand.HMMBUILD, folder) != null)
1185     {
1186       return true;
1187     }
1188     if (showWarning && folder.length() > 0)
1189     {
1190       JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1191               MessageManager.getString("label.hmmbuild_not_found"),
1192               MessageManager.getString("label.invalid_folder"),
1193               JvOptionPane.ERROR_MESSAGE);
1194     }
1195     return false;
1196   }
1197
1198   /**
1199    * Checks if a file can be executed
1200    *
1201    * @param path
1202    *          the path to the file
1203    * @return
1204    */
1205   public boolean canExecute(String path)
1206   {
1207     File file = new File(path);
1208     if (!file.canExecute())
1209     {
1210       file = new File(path + ".exe");
1211       {
1212         if (!file.canExecute())
1213         {
1214           return false;
1215         }
1216       }
1217     }
1218     return true;
1219   }
1220
1221   /**
1222    * If Chimera is selected, check it can be found on default or user-specified
1223    * path, if not show a warning/help dialog.
1224    */
1225   @Override
1226   protected void structureViewer_actionPerformed(String selectedItem)
1227   {
1228     if (!selectedItem.equals(ViewerType.CHIMERA.name()))
1229     {
1230       return;
1231     }
1232     boolean found = false;
1233
1234     /*
1235      * Try user-specified and standard paths for Chimera executable.
1236      */
1237     List<String> paths = StructureManager.getChimeraPaths();
1238     paths.add(0, chimeraPath.getText());
1239     for (String path : paths)
1240     {
1241       if (new File(path.trim()).canExecute())
1242       {
1243         found = true;
1244         break;
1245       }
1246     }
1247     if (!found)
1248     {
1249       String[] options = { "OK", "Help" };
1250       int showHelp = JvOptionPane.showInternalOptionDialog(Desktop.desktop,
1251               JvSwingUtils.wrapTooltip(true,
1252                       MessageManager.getString("label.chimera_missing")),
1253               "", JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE,
1254               null, options, options[0]);
1255       if (showHelp == JvOptionPane.NO_OPTION)
1256       {
1257         try
1258         {
1259           Help.showHelpWindow(HelpId.StructureViewer);
1260         } catch (HelpSetException e)
1261         {
1262           e.printStackTrace();
1263         }
1264       }
1265     }
1266   }
1267
1268   public class OptionsParam
1269   {
1270     private String name;
1271
1272     private String code;
1273
1274     public OptionsParam(String name, String code)
1275     {
1276       this.name = name;
1277       this.code = code;
1278     }
1279
1280     public String getName()
1281     {
1282       return name;
1283     }
1284
1285     public void setName(String name)
1286     {
1287       this.name = name;
1288     }
1289
1290     public String getCode()
1291     {
1292       return code;
1293     }
1294
1295     public void setCode(String code)
1296     {
1297       this.code = code;
1298     }
1299
1300     @Override
1301     public String toString()
1302     {
1303       return name;
1304     }
1305
1306     @Override
1307     public boolean equals(Object that)
1308     {
1309       if (!(that instanceof OptionsParam))
1310       {
1311         return false;
1312       }
1313       return this.code.equalsIgnoreCase(((OptionsParam) that).code);
1314     }
1315
1316     @Override
1317     public int hashCode()
1318     {
1319       return name.hashCode() + code.hashCode();
1320     }
1321   }
1322
1323   private class UrlListSelectionHandler implements ListSelectionListener
1324   {
1325
1326     @Override
1327     public void valueChanged(ListSelectionEvent e)
1328     {
1329       ListSelectionModel lsm = (ListSelectionModel) e.getSource();
1330
1331       int index = lsm.getMinSelectionIndex();
1332       if (index == -1)
1333       {
1334         // no selection, so disable delete/edit buttons
1335         editLink.setEnabled(false);
1336         deleteLink.setEnabled(false);
1337         return;
1338       }
1339       int modelIndex = linkUrlTable.convertRowIndexToModel(index);
1340
1341       // enable/disable edit and delete link buttons
1342       if (((UrlLinkTableModel) linkUrlTable.getModel())
1343               .isRowDeletable(modelIndex))
1344       {
1345         deleteLink.setEnabled(true);
1346       }
1347       else
1348       {
1349         deleteLink.setEnabled(false);
1350       }
1351
1352       if (((UrlLinkTableModel) linkUrlTable.getModel())
1353               .isRowEditable(modelIndex))
1354       {
1355         editLink.setEnabled(true);
1356       }
1357       else
1358       {
1359         editLink.setEnabled(false);
1360       }
1361     }
1362   }
1363 }