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.FileUtils;
  41 import jalview.util.MessageManager;
  42 import jalview.util.Platform;
  43 import jalview.util.UrlConstants;
  44 import jalview.ws.sifts.SiftsSettings;
  45
  46 import java.awt.BorderLayout;
  47 import java.awt.Color;
  48 import java.awt.Component;
  49 import java.awt.Dimension;
  50 import java.awt.Font;
  51 import java.awt.event.ActionEvent;
  52 import java.awt.event.ActionListener;
  53 import java.awt.event.FocusAdapter;
  54 import java.awt.event.FocusEvent;
  55 import java.awt.event.MouseEvent;
  56 import java.io.File;
  57 import java.util.ArrayList;
  58 import java.util.List;
  59
  60 import javax.help.HelpSetException;
  61 import javax.swing.JColorChooser;
  62 import javax.swing.JFileChooser;
  63 import javax.swing.JInternalFrame;
  64 import javax.swing.JPanel;
  65 import javax.swing.JTextField;
  66 import javax.swing.ListSelectionModel;
  67 import javax.swing.RowFilter;
  68 import javax.swing.RowSorter;
  69 import javax.swing.SortOrder;
  70 import javax.swing.event.DocumentEvent;
  71 import javax.swing.event.DocumentListener;
  72 import javax.swing.event.ListSelectionEvent;
  73 import javax.swing.event.ListSelectionListener;
  74 import javax.swing.table.TableCellRenderer;
  75 import javax.swing.table.TableColumn;
  76 import javax.swing.table.TableModel;
  77 import javax.swing.table.TableRowSorter;
  78
  79 import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
  80
  81 /**
  82  * DOCUMENT ME!
  83  *
  84  * @author $author$
  85  * @version $Revision$
  86  */
  87 public class Preferences extends GPreferences
  88 {
  89   // suggested list delimiter character
  90   public static final String COMMA = ",";
  91
  92   public static final String HMMSEARCH_SEQCOUNT = "HMMSEARCH_SEQCOUNT";
  93
  94   public static final String HMMINFO_GLOBAL_BACKGROUND = "HMMINFO_GLOBAL_BACKGROUND";
  95
  96   public static final String HMMALIGN_TRIM_TERMINI = "HMMALIGN_TRIM_TERMINI";
  97
  98   public static final String ENABLE_SPLIT_FRAME = "ENABLE_SPLIT_FRAME";
  99
 100   public static final String SCALE_PROTEIN_TO_CDNA = "SCALE_PROTEIN_TO_CDNA";
 101
 102   public static final String DEFAULT_COLOUR = "DEFAULT_COLOUR";
 103
 104   public static final String DEFAULT_COLOUR_PROT = "DEFAULT_COLOUR_PROT";
 105
 106   public static final String DEFAULT_COLOUR_NUC = "DEFAULT_COLOUR_NUC";
 107
 108   public static final String ADD_TEMPFACT_ANN = "ADD_TEMPFACT_ANN";
 109
 110   public static final String ADD_SS_ANN = "ADD_SS_ANN";
 111
 112   public static final String USE_RNAVIEW = "USE_RNAVIEW";
 113
 114   public static final String STRUCT_FROM_PDB = "STRUCT_FROM_PDB";
 115
 116   public static final String STRUCTURE_DISPLAY = "STRUCTURE_DISPLAY";
 117
 118   public static final String CHIMERA_PATH = "CHIMERA_PATH";
 119
 120   public static final String HMMER_PATH = "HMMER_PATH";
 121
 122   public static final String CYGWIN_PATH = "CYGWIN_PATH";
 123
 124   public static final String HMMSEARCH_DBS = "HMMSEARCH_DBS";
 125
 126   public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS";
 127
 128   public static final String SHOW_AUTOCALC_ABOVE = "SHOW_AUTOCALC_ABOVE";
 129
 130   public static final String SHOW_OCCUPANCY = "SHOW_OCCUPANCY";
 131
 132   public static final String SHOW_OV_HIDDEN_AT_START = "SHOW_OV_HIDDEN_AT_START";
 133
 134   public static final String USE_LEGACY_GAP = "USE_LEGACY_GAP";
 135
 136   public static final String GAP_COLOUR = "GAP_COLOUR";
 137
 138   public static final String HIDDEN_COLOUR = "HIDDEN_COLOUR";
 139
 140   private static final int MIN_FONT_SIZE = 1;
 141
 142   private static final int MAX_FONT_SIZE = 30;
 143
 144   /**
 145    * Holds name and link separated with | character. Sequence ID must be
 146    * $SEQUENCE_ID$ or $SEQUENCE_ID=/.possible | chars ./=$
 147    */
 148   public static UrlProviderI sequenceUrlLinks;
 149
 150   public static UrlLinkTableModel dataModel;
 151
 152   /**
 153    * Holds name and link separated with | character. Sequence IDS and Sequences
 154    * must be $SEQUENCEIDS$ or $SEQUENCEIDS=/.possible | chars ./=$ and
 155    * $SEQUENCES$ or $SEQUENCES=/.possible | chars ./=$ and separation character
 156    * for first and second token specified after a pipe character at end |,|.
 157    * (TODO: proper escape for using | to separate ids or sequences
 158    */
 159
 160   public static List<String> groupURLLinks;
 161   static
 162   {
 163     // get links selected to be in the menu (SEQUENCE_LINKS)
 164     // and links entered by the user but not selected (STORED_LINKS)
 165     String inMenuString = Cache.getDefault("SEQUENCE_LINKS", "");
 166     String notInMenuString = Cache.getDefault("STORED_LINKS", "");
 167     String defaultUrl = Cache.getDefault("DEFAULT_URL",
 168             UrlConstants.DEFAULT_LABEL);
 169
 170     // if both links lists are empty, add the DEFAULT_URL link
 171     // otherwise we assume the default link is in one of the lists
 172     if (inMenuString.isEmpty() && notInMenuString.isEmpty())
 173     {
 174       inMenuString = UrlConstants.DEFAULT_STRING;
 175     }
 176     UrlProviderFactoryI factory = new DesktopUrlProviderFactory(defaultUrl,
 177             inMenuString, notInMenuString);
 178     sequenceUrlLinks = factory.createUrlProvider();
 179     dataModel = new UrlLinkTableModel(sequenceUrlLinks);
 180
 181     /**
 182      * TODO: reformulate groupURL encoding so two or more can be stored in the
 183      * .properties file as '|' separated strings
 184      */
 185
 186     groupURLLinks = new ArrayList<>();
 187   }
 188
 189   JInternalFrame frame;
 190
 191   DasSourceBrowser dasSource;
 192
 193   private WsPreferences wsPrefs;
 194
 195   private OptionsParam promptEachTimeOpt = new OptionsParam(
 196           MessageManager.getString("label.prompt_each_time"),
 197           "Prompt each time");
 198
 199   private OptionsParam lineArtOpt = new OptionsParam(
 200           MessageManager.getString("label.lineart"), "Lineart");
 201
 202   private OptionsParam textOpt = new OptionsParam(
 203           MessageManager.getString("action.text"), "Text");
 204
 205   /**
 206    * Creates a new Preferences object.
 207    */
 208   public Preferences()
 209   {
 210     super();
 211     frame = new JInternalFrame();
 212     frame.setContentPane(this);
 213     dasSource = new DasSourceBrowser();
 214     dasTab.add(dasSource, BorderLayout.CENTER);
 215     wsPrefs = new WsPreferences();
 216     wsTab.add(wsPrefs, BorderLayout.CENTER);
 217     int width = 500, height = 450;
 218     new jalview.util.Platform();
 219     if (Platform.isAMac())
 220     {
 221       width = 570;
 222       height = 480;
 223     }
 224
 225     Desktop.addInternalFrame(frame,
 226             MessageManager.getString("label.preferences"), width, height);
 227     frame.setMinimumSize(new Dimension(width, height));
 228
 229     /*
 230      * Set HMMER tab defaults
 231      */
 232     hmmrTrimTermini.setSelected(Cache.getDefault(HMMALIGN_TRIM_TERMINI, false));
 233     if (Cache.getDefault(HMMINFO_GLOBAL_BACKGROUND, false))
 234     {
 235       hmmerBackgroundUniprot.setSelected(true);
 236     }
 237     else
 238     {
 239       hmmerBackgroundAlignment.setSelected(true);
 240     }
 241     hmmerSequenceCount
 242             .setText(Cache.getProperty(HMMSEARCH_SEQCOUNT));
 243     hmmerPath.setText(Cache.getProperty(HMMER_PATH));
 244     hmmerPath.addActionListener(new ActionListener()
 245     {
 246       @Override
 247       public void actionPerformed(ActionEvent e)
 248       {
 249         validateHmmerPath();
 250       }
 251     });
 252     hmmerPath.addFocusListener(new FocusAdapter()
 253     {
 254       @Override
 255       public void focusLost(FocusEvent e)
 256       {
 257         validateHmmerPath();
 258       }
 259     });
 260     if (cygwinPath != null)
 261     {
 262       String path = Cache.getProperty(CYGWIN_PATH);
 263       if (path == null)
 264       {
 265         path = FileUtils.getPathTo("bash");
 266       }
 267       cygwinPath.setText(path);
 268       cygwinPath.addActionListener(new ActionListener()
 269       {
 270         @Override
 271         public void actionPerformed(ActionEvent e)
 272         {
 273           validateCygwinPath();
 274         }
 275       });
 276       cygwinPath.addFocusListener(new FocusAdapter()
 277       {
 278         @Override
 279         public void focusLost(FocusEvent e)
 280         {
 281           validateCygwinPath();
 282         }
 283       });
 284     }
 285
 286     /*
 287      * Set Visual tab defaults
 288      */
 289     seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));
 290     rightAlign.setSelected(Cache.getDefault("RIGHT_ALIGN_IDS", false));
 291     fullScreen.setSelected(Cache.getDefault("SHOW_FULLSCREEN", false));
 292     annotations.setSelected(Cache.getDefault("SHOW_ANNOTATIONS", true));
 293
 294     conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));
 295     quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));
 296     identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));
 297     openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false));
 298     showUnconserved
 299             .setSelected(Cache.getDefault("SHOW_UNCONSERVED", false));
 300     showOccupancy.setSelected(Cache.getDefault(SHOW_OCCUPANCY, false));
 301     showGroupConsensus
 302             .setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS", false));
 303     showGroupConservation.setSelected(
 304             Cache.getDefault("SHOW_GROUP_CONSERVATION", false));
 305     showConsensHistogram.setSelected(
 306             Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM", true));
 307     showConsensLogo
 308             .setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO", false));
 309     showInformationHistogram.setSelected(
 310             Cache.getDefault("SHOW_INFORMATION_HISTOGRAM", true));
 311     showHMMLogo.setSelected(Cache.getDefault("SHOW_HMM_LOGO", false));
 312     showNpTooltip
 313             .setSelected(Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true));
 314     showDbRefTooltip
 315             .setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP", true));
 316
 317     String[] fonts = java.awt.GraphicsEnvironment
 318             .getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
 319     for (int i = 0; i < fonts.length; i++)
 320     {
 321       fontNameCB.addItem(fonts[i]);
 322     }
 323
 324     for (int i = MIN_FONT_SIZE; i <= MAX_FONT_SIZE; i++)
 325     {
 326       fontSizeCB.addItem(i + "");
 327     }
 328
 329     fontStyleCB.addItem("plain");
 330     fontStyleCB.addItem("bold");
 331     fontStyleCB.addItem("italic");
 332
 333     fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
 334     fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
 335     fontStyleCB.setSelectedItem(
 336             Cache.getDefault("FONT_STYLE", Font.PLAIN + ""));
 337
 338     smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));
 339     scaleProteinToCdna
 340             .setSelected(Cache.getDefault(SCALE_PROTEIN_TO_CDNA, false));
 341
 342     idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
 343
 344     wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
 345
 346     gapSymbolCB.addItem("-");
 347     gapSymbolCB.addItem(".");
 348
 349     gapSymbolCB.setSelectedItem(Cache.getDefault("GAP_SYMBOL", "-"));
 350
 351     sortby.addItem("No sort");
 352     sortby.addItem("Id");
 353     sortby.addItem("Pairwise Identity");
 354     sortby.setSelectedItem(Cache.getDefault("SORT_ALIGNMENT", "No sort"));
 355
 356     sortAnnBy.addItem(SequenceAnnotationOrder.NONE.toString());
 357     sortAnnBy
 358             .addItem(SequenceAnnotationOrder.SEQUENCE_AND_LABEL.toString());
 359     sortAnnBy
 360             .addItem(SequenceAnnotationOrder.LABEL_AND_SEQUENCE.toString());
 361     SequenceAnnotationOrder savedSort = SequenceAnnotationOrder
 362             .valueOf(Cache.getDefault(SORT_ANNOTATIONS,
 363                     SequenceAnnotationOrder.NONE.name()));
 364     sortAnnBy.setSelectedItem(savedSort.toString());
 365
 366     sortAutocalc.addItem("Autocalculated first");
 367     sortAutocalc.addItem("Autocalculated last");
 368     final boolean showAbove = Cache.getDefault(SHOW_AUTOCALC_ABOVE, true);
 369     sortAutocalc.setSelectedItem(showAbove ? sortAutocalc.getItemAt(0)
 370             : sortAutocalc.getItemAt(1));
 371     startupCheckbox
 372             .setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
 373     startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
 374             Cache.getDefault("www.jalview.org", "http://www.jalview.org")
 375                     + "/examples/exampleFile_2_3.jar"));
 376
 377     /*
 378      * Set Colours tab defaults
 379      */
 380     protColour.addItem(ResidueColourScheme.NONE);
 381     nucColour.addItem(ResidueColourScheme.NONE);
 382     for (ColourSchemeI cs : ColourSchemes.getInstance().getColourSchemes())
 383     {
 384       String name = cs.getSchemeName();
 385       protColour.addItem(name);
 386       nucColour.addItem(name);
 387     }
 388     String oldProp = Cache.getDefault(DEFAULT_COLOUR,
 389             ResidueColourScheme.NONE);
 390     String newProp = Cache.getDefault(DEFAULT_COLOUR_PROT, null);
 391     protColour.setSelectedItem(newProp != null ? newProp : oldProp);
 392     newProp = Cache.getDefault(DEFAULT_COLOUR_NUC, null);
 393     nucColour.setSelectedItem(newProp != null ? newProp : oldProp);
 394     minColour.setBackground(
 395             Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN", Color.orange));
 396     maxColour.setBackground(
 397             Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", Color.red));
 398
 399     /*
 400      * Set overview panel defaults
 401      */
 402     gapColour.setBackground(
 403             Cache.getDefaultColour(GAP_COLOUR,
 404                     jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP));
 405     hiddenColour.setBackground(
 406             Cache.getDefaultColour(HIDDEN_COLOUR,
 407                     jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN));
 408     useLegacyGap.setSelected(Cache.getDefault(USE_LEGACY_GAP, false));
 409     gapLabel.setEnabled(!useLegacyGap.isSelected());
 410     gapColour.setEnabled(!useLegacyGap.isSelected());
 411     showHiddenAtStart
 412             .setSelected(Cache.getDefault(SHOW_OV_HIDDEN_AT_START, true));
 413
 414     /*
 415      * Set Structure tab defaults.
 416      */
 417     final boolean structSelected = Cache.getDefault(STRUCT_FROM_PDB, false);
 418     structFromPdb.setSelected(structSelected);
 419     useRnaView.setSelected(Cache.getDefault(USE_RNAVIEW, false));
 420     useRnaView.setEnabled(structSelected);
 421     addSecondaryStructure.setSelected(Cache.getDefault(ADD_SS_ANN, false));
 422     addSecondaryStructure.setEnabled(structSelected);
 423     addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, false));
 424     addTempFactor.setEnabled(structSelected);
 425     structViewer.setSelectedItem(
 426             Cache.getDefault(STRUCTURE_DISPLAY, ViewerType.JMOL.name()));
 427     chimeraPath.setText(Cache.getDefault(CHIMERA_PATH, ""));
 428     chimeraPath.addActionListener(new ActionListener()
 429     {
 430       @Override
 431       public void actionPerformed(ActionEvent e)
 432       {
 433         validateChimeraPath();
 434       }
 435     });
 436
 437     if (Cache.getDefault("MAP_WITH_SIFTS", false))
 438     {
 439       siftsMapping.setSelected(true);
 440     }
 441     else
 442     {
 443       nwMapping.setSelected(true);
 444     }
 445
 446     SiftsSettings
 447             .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
 448
 449     /*
 450      * Set Connections tab defaults
 451      */
 452
 453     // set up sorting
 454     linkUrlTable.setModel(dataModel);
 455     final TableRowSorter<TableModel> sorter = new TableRowSorter<>(
 456             linkUrlTable.getModel());
 457     linkUrlTable.setRowSorter(sorter);
 458     List<RowSorter.SortKey> sortKeys = new ArrayList<>();
 459
 460     UrlLinkTableModel m = (UrlLinkTableModel) linkUrlTable.getModel();
 461     sortKeys.add(new RowSorter.SortKey(m.getPrimaryColumn(),
 462             SortOrder.DESCENDING));
 463     sortKeys.add(new RowSorter.SortKey(m.getSelectedColumn(),
 464             SortOrder.DESCENDING));
 465     sortKeys.add(
 466             new RowSorter.SortKey(m.getNameColumn(), SortOrder.ASCENDING));
 467
 468     sorter.setSortKeys(sortKeys);
 469     sorter.sort();
 470
 471     // set up filtering
 472     ActionListener onReset;
 473     onReset = new ActionListener()
 474     {
 475       @Override
 476       public void actionPerformed(ActionEvent e)
 477       {
 478         filterTB.setText("");
 479         sorter.setRowFilter(RowFilter.regexFilter(""));
 480       }
 481
 482     };
 483     doReset.addActionListener(onReset);
 484
 485     // filter to display only custom urls
 486     final RowFilter<TableModel, Object> customUrlFilter = new RowFilter<TableModel, Object>()
 487     {
 488       @Override
 489       public boolean include(
 490               Entry<? extends TableModel, ? extends Object> entry)
 491       {
 492         return ((UrlLinkTableModel) entry.getModel()).isUserEntry(entry);
 493       }
 494     };
 495
 496     final TableRowSorter<TableModel> customSorter = new TableRowSorter<>(
 497             linkUrlTable.getModel());
 498     customSorter.setRowFilter(customUrlFilter);
 499
 500     ActionListener onCustomOnly;
 501     onCustomOnly = new ActionListener()
 502     {
 503       @Override
 504       public void actionPerformed(ActionEvent e)
 505       {
 506         filterTB.setText("");
 507         sorter.setRowFilter(customUrlFilter);
 508       }
 509     };
 510     userOnly.addActionListener(onCustomOnly);
 511
 512     filterTB.getDocument().addDocumentListener(new DocumentListener()
 513     {
 514       String caseInsensitiveFlag = "(?i)";
 515
 516       @Override
 517       public void changedUpdate(DocumentEvent e)
 518       {
 519         sorter.setRowFilter(RowFilter
 520                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 521       }
 522
 523       @Override
 524       public void removeUpdate(DocumentEvent e)
 525       {
 526         sorter.setRowFilter(RowFilter
 527                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 528       }
 529
 530       @Override
 531       public void insertUpdate(DocumentEvent e)
 532       {
 533         sorter.setRowFilter(RowFilter
 534                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 535       }
 536     });
 537
 538     // set up list selection functionality
 539     linkUrlTable.getSelectionModel()
 540             .addListSelectionListener(new UrlListSelectionHandler());
 541
 542     // set up radio buttons
 543     int onClickCol = ((UrlLinkTableModel) linkUrlTable.getModel())
 544             .getPrimaryColumn();
 545     String onClickName = linkUrlTable.getColumnName(onClickCol);
 546     linkUrlTable.getColumn(onClickName)
 547             .setCellRenderer(new RadioButtonRenderer());
 548     linkUrlTable.getColumn(onClickName)
 549             .setCellEditor(new RadioButtonEditor());
 550
 551     // get boolean columns and resize those to min possible
 552     for (int column = 0; column < linkUrlTable.getColumnCount(); column++)
 553     {
 554       if (linkUrlTable.getModel().getColumnClass(column)
 555               .equals(Boolean.class))
 556       {
 557         TableColumn tableColumn = linkUrlTable.getColumnModel()
 558                 .getColumn(column);
 559         int preferredWidth = tableColumn.getMinWidth();
 560
 561         TableCellRenderer cellRenderer = linkUrlTable.getCellRenderer(0,
 562                 column);
 563         Component c = linkUrlTable.prepareRenderer(cellRenderer, 0, column);
 564         int cwidth = c.getPreferredSize().width
 565                 + linkUrlTable.getIntercellSpacing().width;
 566         preferredWidth = Math.max(preferredWidth, cwidth);
 567
 568         tableColumn.setPreferredWidth(preferredWidth);
 569       }
 570     }
 571
 572     useProxy.setSelected(Cache.getDefault("USE_PROXY", false));
 573     useProxy_actionPerformed(); // make sure useProxy is correctly initialised
 574     proxyServerTB.setText(Cache.getDefault("PROXY_SERVER", ""));
 575     proxyPortTB.setText(Cache.getDefault("PROXY_PORT", ""));
 576
 577     defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", ""));
 578
 579     usagestats.setSelected(Cache.getDefault("USAGESTATS", false));
 580     // note antisense here: default is true
 581     questionnaire
 582             .setSelected(Cache.getProperty("NOQUESTIONNAIRES") == null);
 583     versioncheck.setSelected(Cache.getDefault("VERSION_CHECK", true));
 584
 585     /*
 586      * Set Output tab defaults
 587      */
 588     epsRendering.addItem(promptEachTimeOpt);
 589     epsRendering.addItem(lineArtOpt);
 590     epsRendering.addItem(textOpt);
 591     String defaultEPS = Cache.getDefault("EPS_RENDERING",
 592             "Prompt each time");
 593     if (defaultEPS.equalsIgnoreCase("Text"))
 594     {
 595       epsRendering.setSelectedItem(textOpt);
 596     }
 597     else if (defaultEPS.equalsIgnoreCase("Lineart"))
 598     {
 599       epsRendering.setSelectedItem(lineArtOpt);
 600     }
 601     else
 602     {
 603       epsRendering.setSelectedItem(promptEachTimeOpt);
 604     }
 605     autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false));
 606     userIdWidth.setEnabled(!autoIdWidth.isSelected());
 607     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
 608     Integer wi = Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH");
 609     userIdWidth.setText(wi == null ? "" : wi.toString());
 610     // TODO: refactor to use common enum via FormatAdapter and allow extension
 611     // for new flat file formats
 612     blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
 613     clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
 614     fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
 615     msfjv.setSelected(Cache.getDefault("MSF_JVSUFFIX", true));
 616     pfamjv.setSelected(Cache.getDefault("PFAM_JVSUFFIX", true));
 617     pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
 618     pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
 619     modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
 620     embbedBioJSON
 621             .setSelected(Cache.getDefault("EXPORT_EMBBED_BIOJSON", true));
 622
 623     /*
 624      * Set Editing tab defaults
 625      */
 626     autoCalculateConsCheck
 627             .setSelected(Cache.getDefault("AUTO_CALC_CONSENSUS", true));
 628     padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
 629     sortByTree.setSelected(Cache.getDefault("SORT_BY_TREE", false));
 630
 631     annotations_actionPerformed(null); // update the display of the annotation
 632                                        // settings
 633   }
 634
 635   /**
 636    * Save user selections on the Preferences tabs to the Cache and write out to
 637    * file.
 638    *
 639    * @param e
 640    */
 641   @Override
 642   public void ok_actionPerformed(ActionEvent e)
 643   {
 644     if (!validateSettings())
 645     {
 646       return;
 647     }
 648
 649     /*
 650      * Save Visual settings
 651      */
 652     Cache.applicationProperties.setProperty("SHOW_JVSUFFIX",
 653             Boolean.toString(seqLimit.isSelected()));
 654     Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS",
 655             Boolean.toString(rightAlign.isSelected()));
 656     Cache.applicationProperties.setProperty("SHOW_FULLSCREEN",
 657             Boolean.toString(fullScreen.isSelected()));
 658     Cache.applicationProperties.setProperty("SHOW_OVERVIEW",
 659             Boolean.toString(openoverv.isSelected()));
 660     Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
 661             Boolean.toString(annotations.isSelected()));
 662     Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
 663             Boolean.toString(conservation.isSelected()));
 664     Cache.applicationProperties.setProperty("SHOW_QUALITY",
 665             Boolean.toString(quality.isSelected()));
 666     Cache.applicationProperties.setProperty("SHOW_IDENTITY",
 667             Boolean.toString(identity.isSelected()));
 668
 669     Cache.applicationProperties.setProperty("GAP_SYMBOL",
 670             gapSymbolCB.getSelectedItem().toString());
 671
 672     Cache.applicationProperties.setProperty("FONT_NAME",
 673             fontNameCB.getSelectedItem().toString());
 674     Cache.applicationProperties.setProperty("FONT_STYLE",
 675             fontStyleCB.getSelectedItem().toString());
 676     Cache.applicationProperties.setProperty("FONT_SIZE",
 677             fontSizeCB.getSelectedItem().toString());
 678
 679     Cache.applicationProperties.setProperty("ID_ITALICS",
 680             Boolean.toString(idItalics.isSelected()));
 681     Cache.applicationProperties.setProperty("SHOW_UNCONSERVED",
 682             Boolean.toString(showUnconserved.isSelected()));
 683     Cache.applicationProperties.setProperty(SHOW_OCCUPANCY,
 684             Boolean.toString(showOccupancy.isSelected()));
 685     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS",
 686             Boolean.toString(showGroupConsensus.isSelected()));
 687     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION",
 688             Boolean.toString(showGroupConservation.isSelected()));
 689     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_HISTOGRAM",
 690             Boolean.toString(showConsensHistogram.isSelected()));
 691     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO",
 692             Boolean.toString(showConsensLogo.isSelected()));
 693     Cache.applicationProperties.setProperty("SHOW_INFORMATION_HISTOGRAM",
 694             Boolean.toString(showConsensHistogram.isSelected()));
 695     Cache.applicationProperties.setProperty("SHOW_HMM_LOGO",
 696             Boolean.toString(showHMMLogo.isSelected()));
 697     Cache.applicationProperties.setProperty("ANTI_ALIAS",
 698             Boolean.toString(smoothFont.isSelected()));
 699     Cache.applicationProperties.setProperty(SCALE_PROTEIN_TO_CDNA,
 700             Boolean.toString(scaleProteinToCdna.isSelected()));
 701     Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP",
 702             Boolean.toString(showNpTooltip.isSelected()));
 703     Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP",
 704             Boolean.toString(showDbRefTooltip.isSelected()));
 705
 706     Cache.applicationProperties.setProperty("WRAP_ALIGNMENT",
 707             Boolean.toString(wrap.isSelected()));
 708
 709     Cache.applicationProperties.setProperty("STARTUP_FILE",
 710             startupFileTextfield.getText());
 711     Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",
 712             Boolean.toString(startupCheckbox.isSelected()));
 713
 714     Cache.applicationProperties.setProperty("SORT_ALIGNMENT",
 715             sortby.getSelectedItem().toString());
 716
 717     // convert description of sort order to enum name for save
 718     SequenceAnnotationOrder annSortOrder = SequenceAnnotationOrder
 719             .forDescription(sortAnnBy.getSelectedItem().toString());
 720     if (annSortOrder != null)
 721     {
 722       Cache.applicationProperties.setProperty(SORT_ANNOTATIONS,
 723               annSortOrder.name());
 724     }
 725
 726     final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
 727     Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE,
 728             Boolean.valueOf(showAutocalcFirst).toString());
 729
 730     /*
 731      * Save Colours settings
 732      */
 733     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_PROT,
 734             protColour.getSelectedItem().toString());
 735     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_NUC,
 736             nucColour.getSelectedItem().toString());
 737     Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
 738             minColour.getBackground());
 739     Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
 740             maxColour.getBackground());
 741
 742     /*
 743      * Save HMMER settings
 744      */
 745     Cache.applicationProperties.setProperty(HMMALIGN_TRIM_TERMINI,
 746             Boolean.toString(hmmrTrimTermini.isSelected()));
 747     Cache.applicationProperties.setProperty(HMMINFO_GLOBAL_BACKGROUND,
 748             Boolean.toString(hmmerBackgroundUniprot.isSelected()));
 749     Cache.applicationProperties.setProperty(HMMSEARCH_SEQCOUNT,
 750             hmmerSequenceCount.getText());
 751     Cache.setOrRemove(HMMER_PATH, hmmerPath.getText());
 752     if (cygwinPath != null)
 753     {
 754       Cache.setOrRemove(CYGWIN_PATH, cygwinPath.getText());
 755     }
 756     AlignFrame[] frames = Desktop.getAlignFrames();
 757     if (frames != null && frames.length > 0)
 758     {
 759       for (AlignFrame f : frames)
 760       {
 761         f.updateHMMERStatus();
 762       }
 763     }
 764
 765     hmmrTrimTermini.setSelected(Cache.getDefault(HMMALIGN_TRIM_TERMINI, false));
 766     if (Cache.getDefault(HMMINFO_GLOBAL_BACKGROUND, false))
 767     {
 768       hmmerBackgroundUniprot.setSelected(true);
 769     }
 770     else
 771     {
 772       hmmerBackgroundAlignment.setSelected(true);
 773     }
 774     hmmerSequenceCount
 775             .setText(Cache.getProperty(HMMSEARCH_SEQCOUNT));
 776     hmmerPath.setText(Cache.getProperty(HMMER_PATH));
 777
 778     /*
 779      * Save Overview settings
 780      */
 781     Cache.setColourProperty(GAP_COLOUR, gapColour.getBackground());
 782     Cache.setColourProperty(HIDDEN_COLOUR, hiddenColour.getBackground());
 783     Cache.applicationProperties.setProperty(USE_LEGACY_GAP,
 784             Boolean.toString(useLegacyGap.isSelected()));
 785     Cache.applicationProperties.setProperty(SHOW_OV_HIDDEN_AT_START,
 786             Boolean.toString(showHiddenAtStart.isSelected()));
 787
 788     /*
 789      * Save Structure settings
 790      */
 791     Cache.applicationProperties.setProperty(ADD_TEMPFACT_ANN,
 792             Boolean.toString(addTempFactor.isSelected()));
 793     Cache.applicationProperties.setProperty(ADD_SS_ANN,
 794             Boolean.toString(addSecondaryStructure.isSelected()));
 795     Cache.applicationProperties.setProperty(USE_RNAVIEW,
 796             Boolean.toString(useRnaView.isSelected()));
 797     Cache.applicationProperties.setProperty(STRUCT_FROM_PDB,
 798             Boolean.toString(structFromPdb.isSelected()));
 799     Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY,
 800             structViewer.getSelectedItem().toString());
 801     Cache.setOrRemove(CHIMERA_PATH, chimeraPath.getText());
 802     Cache.applicationProperties.setProperty("MAP_WITH_SIFTS",
 803             Boolean.toString(siftsMapping.isSelected()));
 804     SiftsSettings.setMapWithSifts(siftsMapping.isSelected());
 805
 806     /*
 807      * Save Output settings
 808      */
 809     Cache.applicationProperties.setProperty("EPS_RENDERING",
 810             ((OptionsParam) epsRendering.getSelectedItem()).getCode());
 811
 812     /*
 813      * Save Connections settings
 814      */
 815     Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText());
 816
 817     jalview.util.BrowserLauncher.resetBrowser();
 818
 819     // save user-defined and selected links
 820     String menuLinks = sequenceUrlLinks.writeUrlsAsString(true);
 821     if (menuLinks.isEmpty())
 822     {
 823       Cache.applicationProperties.remove("SEQUENCE_LINKS");
 824     }
 825     else
 826     {
 827       Cache.applicationProperties.setProperty("SEQUENCE_LINKS",
 828               menuLinks.toString());
 829     }
 830
 831     String nonMenuLinks = sequenceUrlLinks.writeUrlsAsString(false);
 832     if (nonMenuLinks.isEmpty())
 833     {
 834       Cache.applicationProperties.remove("STORED_LINKS");
 835     }
 836     else
 837     {
 838       Cache.applicationProperties.setProperty("STORED_LINKS",
 839               nonMenuLinks.toString());
 840     }
 841
 842     Cache.applicationProperties.setProperty("DEFAULT_URL",
 843             sequenceUrlLinks.getPrimaryUrlId());
 844
 845     Cache.applicationProperties.setProperty("USE_PROXY",
 846             Boolean.toString(useProxy.isSelected()));
 847
 848     Cache.setOrRemove("PROXY_SERVER", proxyServerTB.getText());
 849
 850     Cache.setOrRemove("PROXY_PORT", proxyPortTB.getText());
 851
 852     if (useProxy.isSelected())
 853     {
 854       System.setProperty("http.proxyHost", proxyServerTB.getText());
 855       System.setProperty("http.proxyPort", proxyPortTB.getText());
 856     }
 857     else
 858     {
 859       System.setProperty("http.proxyHost", "");
 860       System.setProperty("http.proxyPort", "");
 861     }
 862     Cache.setProperty("VERSION_CHECK",
 863             Boolean.toString(versioncheck.isSelected()));
 864     if (Cache.getProperty("USAGESTATS") != null || usagestats.isSelected())
 865     {
 866       // default is false - we only set this if the user has actively agreed
 867       Cache.setProperty("USAGESTATS",
 868               Boolean.toString(usagestats.isSelected()));
 869     }
 870     if (!questionnaire.isSelected())
 871     {
 872       Cache.setProperty("NOQUESTIONNAIRES", "true");
 873     }
 874     else
 875     {
 876       // special - made easy to edit a property file to disable questionnaires
 877       // by just adding the given line
 878       Cache.removeProperty("NOQUESTIONNAIRES");
 879     }
 880
 881     /*
 882      * Save Output settings
 883      */
 884     Cache.applicationProperties.setProperty("BLC_JVSUFFIX",
 885             Boolean.toString(blcjv.isSelected()));
 886     Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX",
 887             Boolean.toString(clustaljv.isSelected()));
 888     Cache.applicationProperties.setProperty("FASTA_JVSUFFIX",
 889             Boolean.toString(fastajv.isSelected()));
 890     Cache.applicationProperties.setProperty("MSF_JVSUFFIX",
 891             Boolean.toString(msfjv.isSelected()));
 892     Cache.applicationProperties.setProperty("PFAM_JVSUFFIX",
 893             Boolean.toString(pfamjv.isSelected()));
 894     Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX",
 895             Boolean.toString(pileupjv.isSelected()));
 896     Cache.applicationProperties.setProperty("PIR_JVSUFFIX",
 897             Boolean.toString(pirjv.isSelected()));
 898     Cache.applicationProperties.setProperty("PIR_MODELLER",
 899             Boolean.toString(modellerOutput.isSelected()));
 900     Cache.applicationProperties.setProperty("EXPORT_EMBBED_BIOJSON",
 901             Boolean.toString(embbedBioJSON.isSelected()));
 902     jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
 903
 904     Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH",
 905             Boolean.toString(autoIdWidth.isSelected()));
 906     userIdWidth_actionPerformed();
 907     Cache.applicationProperties.setProperty("FIGURE_FIXEDIDWIDTH",
 908             userIdWidth.getText());
 909
 910     /*
 911      * Save Editing settings
 912      */
 913     Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
 914             Boolean.toString(autoCalculateConsCheck.isSelected()));
 915     Cache.applicationProperties.setProperty("SORT_BY_TREE",
 916             Boolean.toString(sortByTree.isSelected()));
 917     Cache.applicationProperties.setProperty("PAD_GAPS",
 918             Boolean.toString(padGaps.isSelected()));
 919
 920     dasSource.saveProperties(Cache.applicationProperties);
 921     wsPrefs.updateAndRefreshWsMenuConfig(false);
 922     Cache.saveProperties();
 923     Desktop.instance.doConfigureStructurePrefs();
 924     try
 925     {
 926       frame.setClosed(true);
 927     } catch (Exception ex)
 928     {
 929     }
 930   }
 931
 932   /**
 933    * Do any necessary validation before saving settings. Return focus to the
 934    * first tab which fails validation.
 935    *
 936    * @return
 937    */
 938   private boolean validateSettings()
 939   {
 940     if (!validateStructure())
 941     {
 942       structureTab.requestFocusInWindow();
 943       return false;
 944     }
 945     return true;
 946   }
 947
 948   @Override
 949   protected boolean validateStructure()
 950   {
 951     return validateChimeraPath();
 952
 953   }
 954
 955   /**
 956    * DOCUMENT ME!
 957    */
 958   @Override
 959   public void startupFileTextfield_mouseClicked()
 960   {
 961     String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
 962     JalviewFileChooser chooser = JalviewFileChooser
 963             .forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat);
 964     chooser.setFileView(new JalviewFileView());
 965     chooser.setDialogTitle(
 966             MessageManager.getString("label.select_startup_file"));
 967
 968     int value = chooser.showOpenDialog(this);
 969
 970     if (value == JalviewFileChooser.APPROVE_OPTION)
 971     {
 972       FileFormatI format = chooser.getSelectedFormat();
 973       if (format != null)
 974       {
 975         Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT",
 976                 format.getName());
 977       }
 978       startupFileTextfield
 979               .setText(chooser.getSelectedFile().getAbsolutePath());
 980     }
 981   }
 982
 983   /**
 984    * DOCUMENT ME!
 985    *
 986    * @param e
 987    *          DOCUMENT ME!
 988    */
 989   @Override
 990   public void cancel_actionPerformed(ActionEvent e)
 991   {
 992     try
 993     {
 994       wsPrefs.updateWsMenuConfig(true);
 995       wsPrefs.refreshWs_actionPerformed(e);
 996       frame.setClosed(true);
 997     } catch (Exception ex)
 998     {
 999     }
1000   }
1001
1002   /**
1003    * DOCUMENT ME!
1004    *
1005    * @param e
1006    *          DOCUMENT ME!
1007    */
1008   @Override
1009   public void annotations_actionPerformed(ActionEvent e)
1010   {
1011     conservation.setEnabled(annotations.isSelected());
1012     quality.setEnabled(annotations.isSelected());
1013     identity.setEnabled(annotations.isSelected());
1014     showOccupancy.setEnabled(annotations.isSelected());
1015     showGroupConsensus.setEnabled(annotations.isSelected());
1016     showGroupConservation.setEnabled(annotations.isSelected());
1017     showConsensHistogram.setEnabled(annotations.isSelected()
1018             && (identity.isSelected() || showGroupConsensus.isSelected()));
1019     showConsensLogo.setEnabled(annotations.isSelected()
1020             && (identity.isSelected() || showGroupConsensus.isSelected()));
1021     showInformationHistogram.setEnabled(annotations.isSelected());
1022     showHMMLogo.setEnabled(annotations.isSelected());
1023   }
1024
1025   @Override
1026   public void newLink_actionPerformed(ActionEvent e)
1027   {
1028     GSequenceLink link = new GSequenceLink();
1029     boolean valid = false;
1030     while (!valid)
1031     {
1032       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
1033               MessageManager.getString("label.new_sequence_url_link"),
1034               JvOptionPane.OK_CANCEL_OPTION, -1,
1035               null) == JvOptionPane.OK_OPTION)
1036       {
1037         if (link.checkValid())
1038         {
1039           if (((UrlLinkTableModel) linkUrlTable.getModel())
1040                   .isUniqueName(link.getName()))
1041           {
1042             ((UrlLinkTableModel) linkUrlTable.getModel())
1043                     .insertRow(link.getName(), link.getURL());
1044             valid = true;
1045           }
1046           else
1047           {
1048             link.notifyDuplicate();
1049             continue;
1050           }
1051         }
1052       }
1053       else
1054       {
1055         break;
1056       }
1057     }
1058   }
1059
1060   @Override
1061   public void editLink_actionPerformed(ActionEvent e)
1062   {
1063     GSequenceLink link = new GSequenceLink();
1064
1065     int index = linkUrlTable.getSelectedRow();
1066     if (index == -1)
1067     {
1068       // button no longer enabled if row is not selected
1069       Cache.log.debug("Edit with no row selected in linkUrlTable");
1070       return;
1071     }
1072
1073     int nameCol = ((UrlLinkTableModel) linkUrlTable.getModel())
1074             .getNameColumn();
1075     int urlCol = ((UrlLinkTableModel) linkUrlTable.getModel())
1076             .getUrlColumn();
1077     String oldName = linkUrlTable.getValueAt(index, nameCol).toString();
1078     link.setName(oldName);
1079     link.setURL(linkUrlTable.getValueAt(index, urlCol).toString());
1080
1081     boolean valid = false;
1082     while (!valid)
1083     {
1084       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
1085               MessageManager.getString("label.edit_sequence_url_link"),
1086               JvOptionPane.OK_CANCEL_OPTION, -1,
1087               null) == JvOptionPane.OK_OPTION)
1088       {
1089         if (link.checkValid())
1090         {
1091           if ((oldName.equals(link.getName()))
1092                   || (((UrlLinkTableModel) linkUrlTable.getModel())
1093                           .isUniqueName(link.getName())))
1094           {
1095             linkUrlTable.setValueAt(link.getName(), index, nameCol);
1096             linkUrlTable.setValueAt(link.getURL(), index, urlCol);
1097             valid = true;
1098           }
1099           else
1100           {
1101             link.notifyDuplicate();
1102             continue;
1103           }
1104         }
1105       }
1106       else
1107       {
1108         break;
1109       }
1110     }
1111   }
1112
1113   @Override
1114   public void deleteLink_actionPerformed(ActionEvent e)
1115   {
1116     int index = linkUrlTable.getSelectedRow();
1117     int modelIndex = -1;
1118     if (index == -1)
1119     {
1120       // button no longer enabled if row is not selected
1121       Cache.log.debug("Delete with no row selected in linkUrlTable");
1122       return;
1123     }
1124     else
1125     {
1126       modelIndex = linkUrlTable.convertRowIndexToModel(index);
1127     }
1128
1129     // make sure we use the model index to delete, and not the table index
1130     ((UrlLinkTableModel) linkUrlTable.getModel()).removeRow(modelIndex);
1131   }
1132
1133   @Override
1134   public void defaultBrowser_mouseClicked(MouseEvent e)
1135   {
1136     JFileChooser chooser = new JFileChooser(".");
1137     chooser.setDialogTitle(
1138             MessageManager.getString("label.select_default_browser"));
1139
1140     int value = chooser.showOpenDialog(this);
1141
1142     if (value == JFileChooser.APPROVE_OPTION)
1143     {
1144       defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
1145     }
1146
1147   }
1148
1149   /*
1150    * (non-Javadoc)
1151    *
1152    * @see
1153    * jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event
1154    * .ActionEvent)
1155    */
1156   @Override
1157   protected void showunconserved_actionPerformed(ActionEvent e)
1158   {
1159     // TODO Auto-generated method stub
1160     super.showunconserved_actionPerformed(e);
1161   }
1162
1163   public static List<String> getGroupURLLinks()
1164   {
1165     return groupURLLinks;
1166   }
1167
1168   @Override
1169   public void minColour_actionPerformed(JPanel panel)
1170   {
1171     Color col = JColorChooser.showDialog(this,
1172             MessageManager.getString("label.select_colour_minimum_value"),
1173             minColour.getBackground());
1174     if (col != null)
1175     {
1176       panel.setBackground(col);
1177     }
1178     panel.repaint();
1179   }
1180
1181   @Override
1182   public void maxColour_actionPerformed(JPanel panel)
1183   {
1184     Color col = JColorChooser.showDialog(this,
1185             MessageManager.getString("label.select_colour_maximum_value"),
1186             maxColour.getBackground());
1187     if (col != null)
1188     {
1189       panel.setBackground(col);
1190     }
1191     panel.repaint();
1192   }
1193
1194   @Override
1195   public void gapColour_actionPerformed(JPanel gap)
1196   {
1197     if (!useLegacyGap.isSelected())
1198     {
1199       Color col = JColorChooser.showDialog(this,
1200               MessageManager.getString("label.select_gap_colour"),
1201               gapColour.getBackground());
1202       if (col != null)
1203       {
1204         gap.setBackground(col);
1205       }
1206       gap.repaint();
1207     }
1208   }
1209
1210   @Override
1211   public void hiddenColour_actionPerformed(JPanel hidden)
1212   {
1213     Color col = JColorChooser.showDialog(this,
1214             MessageManager.getString("label.select_hidden_colour"),
1215             hiddenColour.getBackground());
1216     if (col != null)
1217     {
1218       hidden.setBackground(col);
1219     }
1220     hidden.repaint();
1221   }
1222
1223   @Override
1224   protected void useLegacyGaps_actionPerformed(ActionEvent e)
1225   {
1226     boolean enabled = useLegacyGap.isSelected();
1227     if (enabled)
1228     {
1229       gapColour.setBackground(
1230               jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_LEGACY_GAP);
1231     }
1232     else
1233     {
1234       gapColour.setBackground(
1235               jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP);
1236     }
1237     gapColour.setEnabled(!enabled);
1238     gapLabel.setEnabled(!enabled);
1239   }
1240
1241   @Override
1242   protected void resetOvDefaults_actionPerformed(ActionEvent e)
1243   {
1244     useLegacyGap.setSelected(false);
1245     useLegacyGaps_actionPerformed(null);
1246     showHiddenAtStart.setSelected(true);
1247     hiddenColour.setBackground(
1248             jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN);
1249   }
1250
1251   @Override
1252   protected void userIdWidth_actionPerformed()
1253   {
1254     try
1255     {
1256       String val = userIdWidth.getText().trim();
1257       if (val.length() > 0)
1258       {
1259         Integer iw = Integer.parseInt(val);
1260         if (iw.intValue() < 12)
1261         {
1262           throw new NumberFormatException();
1263         }
1264         userIdWidth.setText(iw.toString());
1265       }
1266     } catch (NumberFormatException x)
1267     {
1268       JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1269               MessageManager
1270                       .getString("warn.user_defined_width_requirements"),
1271               MessageManager.getString("label.invalid_id_column_width"),
1272               JvOptionPane.WARNING_MESSAGE);
1273       userIdWidth.setText("");
1274     }
1275   }
1276
1277   @Override
1278   protected void autoIdWidth_actionPerformed()
1279   {
1280     userIdWidth.setEnabled(!autoIdWidth.isSelected());
1281     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
1282   }
1283
1284   /**
1285    * Returns true if chimera path is to a valid executable, else show an error
1286    * dialog.
1287    */
1288   private boolean validateChimeraPath()
1289   {
1290     if (chimeraPath.getText().trim().length() > 0)
1291     {
1292       File f = new File(chimeraPath.getText());
1293       if (!f.canExecute())
1294       {
1295         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1296                 MessageManager.getString("label.invalid_chimera_path"),
1297                 MessageManager.getString("label.invalid_name"),
1298                 JvOptionPane.ERROR_MESSAGE);
1299         return false;
1300       }
1301     }
1302     return true;
1303   }
1304
1305   /**
1306    * Returns true if the given text field contains a path to a folder that
1307    * contains an executable with the given name, else false (after showing a
1308    * warning dialog). The executable name will be tried with .exe appended if not
1309    * found.
1310    *
1311    * @param textField
1312    * @param executable
1313    */
1314   protected boolean validateExecutablePath(JTextField textField, String executable)
1315   {
1316     String folder = textField.getText().trim();
1317
1318     if (FileUtils.getExecutable(executable, folder) != null)
1319     {
1320       return true;
1321     }
1322     if (folder.length() > 0)
1323     {
1324       JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1325               MessageManager.formatMessage("label.executable_not_found",
1326                       executable),
1327               MessageManager.getString("label.invalid_folder"),
1328               JvOptionPane.ERROR_MESSAGE);
1329     }
1330     return false;
1331   }
1332
1333   /**
1334    * Checks if a file can be executed
1335    *
1336    * @param path
1337    *          the path to the file
1338    * @return
1339    */
1340   public boolean canExecute(String path)
1341   {
1342     File file = new File(path);
1343     if (!file.canExecute())
1344     {
1345       file = new File(path + ".exe");
1346       {
1347         if (!file.canExecute())
1348         {
1349           return false;
1350         }
1351       }
1352     }
1353     return true;
1354   }
1355
1356   /**
1357    * If Chimera is selected, check it can be found on default or user-specified
1358    * path, if not show a warning/help dialog.
1359    */
1360   @Override
1361   protected void structureViewer_actionPerformed(String selectedItem)
1362   {
1363     if (!selectedItem.equals(ViewerType.CHIMERA.name()))
1364     {
1365       return;
1366     }
1367     boolean found = false;
1368
1369     /*
1370      * Try user-specified and standard paths for Chimera executable.
1371      */
1372     List<String> paths = StructureManager.getChimeraPaths();
1373     paths.add(0, chimeraPath.getText());
1374     for (String path : paths)
1375     {
1376       if (new File(path.trim()).canExecute())
1377       {
1378         found = true;
1379         break;
1380       }
1381     }
1382     if (!found)
1383     {
1384       String[] options = { "OK", "Help" };
1385       int showHelp = JvOptionPane.showInternalOptionDialog(Desktop.desktop,
1386               JvSwingUtils.wrapTooltip(true,
1387                       MessageManager.getString("label.chimera_missing")),
1388               "", JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE,
1389               null, options, options[0]);
1390       if (showHelp == JvOptionPane.NO_OPTION)
1391       {
1392         try
1393         {
1394           Help.showHelpWindow(HelpId.StructureViewer);
1395         } catch (HelpSetException e)
1396         {
1397           e.printStackTrace();
1398         }
1399       }
1400     }
1401   }
1402
1403   @Override
1404   protected void validateHmmerPath()
1405   {
1406     validateExecutablePath(hmmerPath, HmmerCommand.HMMBUILD);
1407   }
1408
1409   @Override
1410   protected void validateCygwinPath()
1411   {
1412     validateExecutablePath(cygwinPath, "run");
1413   }
1414
1415   public class OptionsParam
1416   {
1417     private String name;
1418
1419     private String code;
1420
1421     public OptionsParam(String name, String code)
1422     {
1423       this.name = name;
1424       this.code = code;
1425     }
1426
1427     public String getName()
1428     {
1429       return name;
1430     }
1431
1432     public void setName(String name)
1433     {
1434       this.name = name;
1435     }
1436
1437     public String getCode()
1438     {
1439       return code;
1440     }
1441
1442     public void setCode(String code)
1443     {
1444       this.code = code;
1445     }
1446
1447     @Override
1448     public String toString()
1449     {
1450       return name;
1451     }
1452
1453     @Override
1454     public boolean equals(Object that)
1455     {
1456       if (!(that instanceof OptionsParam))
1457       {
1458         return false;
1459       }
1460       return this.code.equalsIgnoreCase(((OptionsParam) that).code);
1461     }
1462
1463     @Override
1464     public int hashCode()
1465     {
1466       return name.hashCode() + code.hashCode();
1467     }
1468   }
1469
1470   private class UrlListSelectionHandler implements ListSelectionListener
1471   {
1472
1473     @Override
1474     public void valueChanged(ListSelectionEvent e)
1475     {
1476       ListSelectionModel lsm = (ListSelectionModel) e.getSource();
1477
1478       int index = lsm.getMinSelectionIndex();
1479       if (index == -1)
1480       {
1481         // no selection, so disable delete/edit buttons
1482         editLink.setEnabled(false);
1483         deleteLink.setEnabled(false);
1484         return;
1485       }
1486       int modelIndex = linkUrlTable.convertRowIndexToModel(index);
1487
1488       // enable/disable edit and delete link buttons
1489       if (((UrlLinkTableModel) linkUrlTable.getModel())
1490               .isRowDeletable(modelIndex))
1491       {
1492         deleteLink.setEnabled(true);
1493       }
1494       else
1495       {
1496         deleteLink.setEnabled(false);
1497       }
1498
1499       if (((UrlLinkTableModel) linkUrlTable.getModel())
1500               .isRowEditable(modelIndex))
1501       {
1502         editLink.setEnabled(true);
1503       }
1504       else
1505       {
1506         editLink.setEnabled(false);
1507       }
1508     }
1509   }
1510 }