src/jalview/gui/Preferences.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.gui;
  22
  23 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
  24 import jalview.bin.Cache;
  25 import jalview.gui.Help.HelpId;
  26 import jalview.gui.StructureViewer.ViewerType;
  27 import jalview.io.JalviewFileChooser;
  28 import jalview.io.JalviewFileView;
  29 import jalview.jbgui.GPreferences;
  30 import jalview.jbgui.GSequenceLink;
  31 import jalview.schemes.ColourSchemeProperty;
  32 import jalview.util.MessageManager;
  33 import jalview.util.Platform;
  34 import jalview.ws.sifts.SiftsSettings;
  35
  36 import java.awt.BorderLayout;
  37 import java.awt.Color;
  38 import java.awt.Dimension;
  39 import java.awt.Font;
  40 import java.awt.event.ActionEvent;
  41 import java.awt.event.ActionListener;
  42 import java.awt.event.MouseEvent;
  43 import java.io.File;
  44 import java.util.ArrayList;
  45 import java.util.List;
  46 import java.util.StringTokenizer;
  47 import java.util.Vector;
  48
  49 import javax.help.HelpSetException;
  50 import javax.swing.JColorChooser;
  51 import javax.swing.JFileChooser;
  52 import javax.swing.JInternalFrame;
  53 import javax.swing.JOptionPane;
  54 import javax.swing.JPanel;
  55
  56 import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
  57
  58 /**
  59  * DOCUMENT ME!
  60  *
  61  * @author $author$
  62  * @version $Revision$
  63  */
  64 public class Preferences extends GPreferences
  65 {
  66   public static final String ENABLE_SPLIT_FRAME = "ENABLE_SPLIT_FRAME";
  67
  68   public static final String SCALE_PROTEIN_TO_CDNA = "SCALE_PROTEIN_TO_CDNA";
  69
  70   public static final String DEFAULT_COLOUR = "DEFAULT_COLOUR";
  71
  72   public static final String DEFAULT_COLOUR_PROT = "DEFAULT_COLOUR_PROT";
  73
  74   public static final String DEFAULT_COLOUR_NUC = "DEFAULT_COLOUR_NUC";
  75
  76   public static final String ADD_TEMPFACT_ANN = "ADD_TEMPFACT_ANN";
  77
  78   public static final String ADD_SS_ANN = "ADD_SS_ANN";
  79
  80   public static final String USE_RNAVIEW = "USE_RNAVIEW";
  81
  82   public static final String STRUCT_FROM_PDB = "STRUCT_FROM_PDB";
  83
  84   public static final String STRUCTURE_DISPLAY = "STRUCTURE_DISPLAY";
  85
  86   public static final String CHIMERA_PATH = "CHIMERA_PATH";
  87
  88   public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS";
  89
  90   public static final String SHOW_AUTOCALC_ABOVE = "SHOW_AUTOCALC_ABOVE";
  91
  92   private static final int MIN_FONT_SIZE = 1;
  93
  94   private static final int MAX_FONT_SIZE = 30;
  95
  96   /**
  97    * Holds name and link separated with | character. Sequence ID must be
  98    * $SEQUENCE_ID$ or $SEQUENCE_ID=/.possible | chars ./=$
  99    */
 100   public static Vector<String> sequenceURLLinks;
 101
 102   /**
 103    * Holds name and link separated with | character. Sequence IDS and Sequences
 104    * must be $SEQUENCEIDS$ or $SEQUENCEIDS=/.possible | chars ./=$ and
 105    * $SEQUENCES$ or $SEQUENCES=/.possible | chars ./=$ and separation character
 106    * for first and second token specified after a pipe character at end |,|.
 107    * (TODO: proper escape for using | to separate ids or sequences
 108    */
 109
 110   public static List<String> groupURLLinks;
 111   static
 112   {
 113     String string = Cache
 114             .getDefault(
 115                     "SEQUENCE_LINKS",
 116                     "EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$");
 117     sequenceURLLinks = new Vector<String>();
 118
 119     try
 120     {
 121       StringTokenizer st = new StringTokenizer(string, "|");
 122       while (st.hasMoreElements())
 123       {
 124         String name = st.nextToken();
 125         String url = st.nextToken();
 126         // check for '|' within a regex
 127         int rxstart = url.indexOf("$SEQUENCE_ID$");
 128         while (rxstart == -1 && url.indexOf("/=$") == -1)
 129         {
 130           url = url + "|" + st.nextToken();
 131         }
 132         sequenceURLLinks.addElement(name + "|" + url);
 133       }
 134     } catch (Exception ex)
 135     {
 136       System.out.println(ex + "\nError parsing sequence links");
 137     }
 138     {
 139       // upgrade old SRS link
 140       int srsPos = sequenceURLLinks
 141               .indexOf("SRS|http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$SEQUENCE_ID$]))+-view+SwissEntry");
 142       if (srsPos > -1)
 143       {
 144         sequenceURLLinks
 145                 .setElementAt(
 146                         "EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$",
 147                         srsPos);
 148       }
 149     }
 150
 151     /**
 152      * TODO: reformulate groupURL encoding so two or more can be stored in the
 153      * .properties file as '|' separated strings
 154      */
 155
 156     groupURLLinks = new ArrayList<String>();
 157   }
 158
 159   Vector<String> nameLinks, urlLinks;
 160
 161   JInternalFrame frame;
 162
 163   DasSourceBrowser dasSource;
 164
 165   private WsPreferences wsPrefs;
 166
 167   private OptionsParam promptEachTimeOpt = new OptionsParam(
 168           MessageManager.getString("label.prompt_each_time"),
 169           "Prompt each time");
 170
 171   private OptionsParam lineArtOpt = new OptionsParam(
 172           MessageManager.getString("label.lineart"), "Lineart");
 173
 174   private OptionsParam textOpt = new OptionsParam(
 175           MessageManager.getString("action.text"), "Text");
 176
 177   /**
 178    * Creates a new Preferences object.
 179    */
 180   public Preferences()
 181   {
 182     super();
 183     frame = new JInternalFrame();
 184     frame.setContentPane(this);
 185     dasSource = new DasSourceBrowser();
 186     dasTab.add(dasSource, BorderLayout.CENTER);
 187     wsPrefs = new WsPreferences();
 188     wsTab.add(wsPrefs, BorderLayout.CENTER);
 189     int width = 500, height = 450;
 190     new jalview.util.Platform();
 191     if (Platform.isAMac())
 192     {
 193       width = 570;
 194       height = 480;
 195     }
 196
 197     Desktop.addInternalFrame(frame,
 198             MessageManager.getString("label.preferences"), width, height);
 199     frame.setMinimumSize(new Dimension(width, height));
 200
 201     /*
 202      * Set Visual tab defaults
 203      */
 204     seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));
 205     rightAlign.setSelected(Cache.getDefault("RIGHT_ALIGN_IDS", false));
 206     fullScreen.setSelected(Cache.getDefault("SHOW_FULLSCREEN", false));
 207     annotations.setSelected(Cache.getDefault("SHOW_ANNOTATIONS", true));
 208
 209     conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));
 210     quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));
 211     identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));
 212     openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false));
 213     showUnconserved
 214             .setSelected(Cache.getDefault("SHOW_UNCONSERVED", false));
 215     showGroupConsensus.setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS",
 216             false));
 217     showGroupConservation.setSelected(Cache.getDefault(
 218             "SHOW_GROUP_CONSERVATION", false));
 219     showConsensHistogram.setSelected(Cache.getDefault(
 220             "SHOW_CONSENSUS_HISTOGRAM", true));
 221     showConsensLogo.setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO",
 222             false));
 223     showNpTooltip.setSelected(Cache
 224             .getDefault("SHOW_NPFEATS_TOOLTIP", true));
 225     showDbRefTooltip.setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP",
 226             true));
 227
 228     String[] fonts = java.awt.GraphicsEnvironment
 229             .getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
 230     for (int i = 0; i < fonts.length; i++)
 231     {
 232       fontNameCB.addItem(fonts[i]);
 233     }
 234
 235     for (int i = MIN_FONT_SIZE; i <= MAX_FONT_SIZE; i++)
 236     {
 237       fontSizeCB.addItem(i + "");
 238     }
 239
 240     fontStyleCB.addItem("plain");
 241     fontStyleCB.addItem("bold");
 242     fontStyleCB.addItem("italic");
 243
 244     fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
 245     fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
 246     fontStyleCB.setSelectedItem(Cache.getDefault("FONT_STYLE", Font.PLAIN
 247             + ""));
 248
 249     smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));
 250     scaleProteinToCdna.setSelected(Cache.getDefault(SCALE_PROTEIN_TO_CDNA,
 251             false));
 252
 253     idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
 254
 255     wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
 256
 257     gapSymbolCB.addItem("-");
 258     gapSymbolCB.addItem(".");
 259
 260     gapSymbolCB.setSelectedItem(Cache.getDefault("GAP_SYMBOL", "-"));
 261
 262     sortby.addItem("No sort");
 263     sortby.addItem("Id");
 264     sortby.addItem("Pairwise Identity");
 265     sortby.setSelectedItem(Cache.getDefault("SORT_ALIGNMENT", "No sort"));
 266
 267     sortAnnBy.addItem(SequenceAnnotationOrder.NONE.toString());
 268     sortAnnBy
 269             .addItem(SequenceAnnotationOrder.SEQUENCE_AND_LABEL.toString());
 270     sortAnnBy
 271             .addItem(SequenceAnnotationOrder.LABEL_AND_SEQUENCE.toString());
 272     SequenceAnnotationOrder savedSort = SequenceAnnotationOrder
 273             .valueOf(Cache.getDefault(SORT_ANNOTATIONS,
 274                     SequenceAnnotationOrder.NONE.name()));
 275     sortAnnBy.setSelectedItem(savedSort.toString());
 276
 277     sortAutocalc.addItem("Autocalculated first");
 278     sortAutocalc.addItem("Autocalculated last");
 279     final boolean showAbove = Cache.getDefault(SHOW_AUTOCALC_ABOVE, true);
 280     sortAutocalc.setSelectedItem(showAbove ? sortAutocalc.getItemAt(0)
 281             : sortAutocalc.getItemAt(1));
 282     startupCheckbox
 283             .setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
 284     startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
 285             Cache.getDefault("www.jalview.org", "http://www.jalview.org")
 286                     + "/examples/exampleFile_2_3.jar"));
 287
 288     /*
 289      * Set Colours tab defaults
 290      */
 291     for (int i = ColourSchemeProperty.FIRST_COLOUR; i <= ColourSchemeProperty.LAST_COLOUR; i++)
 292     {
 293       protColour.addItem(ColourSchemeProperty.getColourName(i));
 294       nucColour.addItem(ColourSchemeProperty.getColourName(i));
 295     }
 296     String oldProp = Cache.getDefault(DEFAULT_COLOUR, "None");
 297     String newProp = Cache.getDefault(DEFAULT_COLOUR_PROT, null);
 298     protColour.setSelectedItem(newProp != null ? newProp : oldProp);
 299     newProp = Cache.getDefault(DEFAULT_COLOUR_NUC, null);
 300     nucColour.setSelectedItem(newProp != null ? newProp : oldProp);
 301     minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN",
 302             Color.orange));
 303     maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX",
 304             Color.red));
 305
 306     /*
 307      * Set Structure tab defaults.
 308      */
 309     final boolean structSelected = Cache.getDefault(STRUCT_FROM_PDB, false);
 310     structFromPdb.setSelected(structSelected);
 311     useRnaView.setSelected(Cache.getDefault(USE_RNAVIEW, false));
 312     useRnaView.setEnabled(structSelected);
 313     addSecondaryStructure.setSelected(Cache.getDefault(ADD_SS_ANN, false));
 314     addSecondaryStructure.setEnabled(structSelected);
 315     addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, false));
 316     addTempFactor.setEnabled(structSelected);
 317     structViewer.setSelectedItem(Cache.getDefault(STRUCTURE_DISPLAY,
 318             ViewerType.JMOL.name()));
 319     chimeraPath.setText(Cache.getDefault(CHIMERA_PATH, ""));
 320     chimeraPath.addActionListener(new ActionListener()
 321     {
 322       @Override
 323       public void actionPerformed(ActionEvent e)
 324       {
 325         validateChimeraPath();
 326       }
 327     });
 328
 329     if (Cache.getDefault("MAP_WITH_SIFTS", false))
 330     {
 331       siftsMapping.setSelected(true);
 332     }
 333     else
 334     {
 335       nwMapping.setSelected(true);
 336     }
 337
 338     SiftsSettings
 339             .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
 340
 341     /*
 342      * Set Connections tab defaults
 343      */
 344     nameLinks = new Vector<String>();
 345     urlLinks = new Vector<String>();
 346     for (int i = 0; i < sequenceURLLinks.size(); i++)
 347     {
 348       String link = sequenceURLLinks.elementAt(i).toString();
 349       nameLinks.addElement(link.substring(0, link.indexOf("|")));
 350       urlLinks.addElement(link.substring(link.indexOf("|") + 1));
 351     }
 352
 353     updateLinkData();
 354
 355     useProxy.setSelected(Cache.getDefault("USE_PROXY", false));
 356     proxyServerTB.setEnabled(useProxy.isSelected());
 357     proxyPortTB.setEnabled(useProxy.isSelected());
 358     proxyServerTB.setText(Cache.getDefault("PROXY_SERVER", ""));
 359     proxyPortTB.setText(Cache.getDefault("PROXY_PORT", ""));
 360
 361     defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", ""));
 362
 363     usagestats.setSelected(Cache.getDefault("USAGESTATS", false));
 364     // note antisense here: default is true
 365     questionnaire
 366             .setSelected(Cache.getProperty("NOQUESTIONNAIRES") == null);
 367     versioncheck.setSelected(Cache.getDefault("VERSION_CHECK", true));
 368
 369     /*
 370      * Set Output tab defaults
 371      */
 372     epsRendering.addItem(promptEachTimeOpt);
 373     epsRendering.addItem(lineArtOpt);
 374     epsRendering.addItem(textOpt);
 375     String defaultEPS = Cache.getDefault("EPS_RENDERING",
 376             "Prompt each time");
 377     if (defaultEPS.equalsIgnoreCase("Text"))
 378     {
 379       epsRendering.setSelectedItem(textOpt);
 380     }
 381     else if (defaultEPS.equalsIgnoreCase("Lineart"))
 382     {
 383       epsRendering.setSelectedItem(lineArtOpt);
 384     }
 385     else
 386     {
 387       epsRendering.setSelectedItem(promptEachTimeOpt);
 388     }
 389     autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false));
 390     userIdWidth.setEnabled(!autoIdWidth.isSelected());
 391     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
 392     Integer wi = Cache.getIntegerProperty("FIGURE_USERIDWIDTH");
 393     userIdWidth.setText(wi == null ? "" : wi.toString());
 394     blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
 395     clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
 396     fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
 397     msfjv.setSelected(Cache.getDefault("MSF_JVSUFFIX", true));
 398     pfamjv.setSelected(Cache.getDefault("PFAM_JVSUFFIX", true));
 399     pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
 400     pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
 401     modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
 402     embbedBioJSON.setSelected(Cache.getDefault("EXPORT_EMBBED_BIOJSON",
 403             true));
 404
 405     /*
 406      * Set Editing tab defaults
 407      */
 408     autoCalculateConsCheck.setSelected(Cache.getDefault(
 409             "AUTO_CALC_CONSENSUS", true));
 410     padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
 411     sortByTree.setSelected(Cache.getDefault("SORT_BY_TREE", false));
 412
 413     annotations_actionPerformed(null); // update the display of the annotation
 414                                        // settings
 415   }
 416
 417   /**
 418    * Save user selections on the Preferences tabs to the Cache and write out to
 419    * file.
 420    *
 421    * @param e
 422    */
 423   @Override
 424   public void ok_actionPerformed(ActionEvent e)
 425   {
 426     if (!validateSettings())
 427     {
 428       return;
 429     }
 430
 431     /*
 432      * Save Visual settings
 433      */
 434     Cache.applicationProperties.setProperty("SHOW_JVSUFFIX",
 435             Boolean.toString(seqLimit.isSelected()));
 436     Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS",
 437             Boolean.toString(rightAlign.isSelected()));
 438     Cache.applicationProperties.setProperty("SHOW_FULLSCREEN",
 439             Boolean.toString(fullScreen.isSelected()));
 440     Cache.applicationProperties.setProperty("SHOW_OVERVIEW",
 441             Boolean.toString(openoverv.isSelected()));
 442     Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
 443             Boolean.toString(annotations.isSelected()));
 444     Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
 445             Boolean.toString(conservation.isSelected()));
 446     Cache.applicationProperties.setProperty("SHOW_QUALITY",
 447             Boolean.toString(quality.isSelected()));
 448     Cache.applicationProperties.setProperty("SHOW_IDENTITY",
 449             Boolean.toString(identity.isSelected()));
 450
 451     Cache.applicationProperties.setProperty("GAP_SYMBOL", gapSymbolCB
 452             .getSelectedItem().toString());
 453
 454     Cache.applicationProperties.setProperty("FONT_NAME", fontNameCB
 455             .getSelectedItem().toString());
 456     Cache.applicationProperties.setProperty("FONT_STYLE", fontStyleCB
 457             .getSelectedItem().toString());
 458     Cache.applicationProperties.setProperty("FONT_SIZE", fontSizeCB
 459             .getSelectedItem().toString());
 460
 461     Cache.applicationProperties.setProperty("ID_ITALICS",
 462             Boolean.toString(idItalics.isSelected()));
 463     Cache.applicationProperties.setProperty("SHOW_UNCONSERVED",
 464             Boolean.toString(showUnconserved.isSelected()));
 465     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS",
 466             Boolean.toString(showGroupConsensus.isSelected()));
 467     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION",
 468             Boolean.toString(showGroupConservation.isSelected()));
 469     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_HISTOGRAM",
 470             Boolean.toString(showConsensHistogram.isSelected()));
 471     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO",
 472             Boolean.toString(showConsensLogo.isSelected()));
 473     Cache.applicationProperties.setProperty("ANTI_ALIAS",
 474             Boolean.toString(smoothFont.isSelected()));
 475     Cache.applicationProperties.setProperty(SCALE_PROTEIN_TO_CDNA,
 476             Boolean.toString(scaleProteinToCdna.isSelected()));
 477     Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP",
 478             Boolean.toString(showNpTooltip.isSelected()));
 479     Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP",
 480             Boolean.toString(showDbRefTooltip.isSelected()));
 481
 482     Cache.applicationProperties.setProperty("WRAP_ALIGNMENT",
 483             Boolean.toString(wrap.isSelected()));
 484
 485     Cache.applicationProperties.setProperty("STARTUP_FILE",
 486             startupFileTextfield.getText());
 487     Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",
 488             Boolean.toString(startupCheckbox.isSelected()));
 489
 490     Cache.applicationProperties.setProperty("SORT_ALIGNMENT", sortby
 491             .getSelectedItem().toString());
 492
 493     // convert description of sort order to enum name for save
 494     SequenceAnnotationOrder annSortOrder = SequenceAnnotationOrder
 495             .forDescription(sortAnnBy.getSelectedItem().toString());
 496     if (annSortOrder != null)
 497     {
 498       Cache.applicationProperties.setProperty(SORT_ANNOTATIONS,
 499               annSortOrder.name());
 500     }
 501
 502     final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
 503     Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE, Boolean
 504             .valueOf(showAutocalcFirst).toString());
 505
 506     /*
 507      * Save Colours settings
 508      */
 509     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_PROT, protColour
 510             .getSelectedItem().toString());
 511     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_NUC, nucColour
 512             .getSelectedItem().toString());
 513     Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
 514             minColour.getBackground());
 515     Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
 516             maxColour.getBackground());
 517
 518     /*
 519      * Save Structure settings
 520      */
 521     Cache.applicationProperties.setProperty(ADD_TEMPFACT_ANN,
 522             Boolean.toString(addTempFactor.isSelected()));
 523     Cache.applicationProperties.setProperty(ADD_SS_ANN,
 524             Boolean.toString(addSecondaryStructure.isSelected()));
 525     Cache.applicationProperties.setProperty(USE_RNAVIEW,
 526             Boolean.toString(useRnaView.isSelected()));
 527     Cache.applicationProperties.setProperty(STRUCT_FROM_PDB,
 528             Boolean.toString(structFromPdb.isSelected()));
 529     Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY, structViewer
 530             .getSelectedItem().toString());
 531     Cache.setOrRemove(CHIMERA_PATH, chimeraPath.getText());
 532     Cache.applicationProperties.setProperty("MAP_WITH_SIFTS",
 533             Boolean.toString(siftsMapping.isSelected()));
 534     SiftsSettings.setMapWithSifts(siftsMapping.isSelected());
 535
 536     /*
 537      * Save Output settings
 538      */
 539       Cache.applicationProperties.setProperty("EPS_RENDERING",
 540               ((OptionsParam) epsRendering.getSelectedItem()).getCode());
 541
 542     /*
 543      * Save Connections settings
 544      */
 545     Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText());
 546
 547     jalview.util.BrowserLauncher.resetBrowser();
 548
 549     if (nameLinks.size() > 0)
 550     {
 551       StringBuffer links = new StringBuffer();
 552       sequenceURLLinks = new Vector<String>();
 553       for (int i = 0; i < nameLinks.size(); i++)
 554       {
 555         sequenceURLLinks.addElement(nameLinks.elementAt(i) + "|"
 556                 + urlLinks.elementAt(i));
 557         links.append(sequenceURLLinks.elementAt(i).toString());
 558         links.append("|");
 559       }
 560       // remove last "|"
 561       links.setLength(links.length() - 1);
 562       Cache.applicationProperties.setProperty("SEQUENCE_LINKS",
 563               links.toString());
 564     }
 565     else
 566     {
 567       Cache.applicationProperties.remove("SEQUENCE_LINKS");
 568     }
 569
 570     Cache.applicationProperties.setProperty("USE_PROXY",
 571             Boolean.toString(useProxy.isSelected()));
 572
 573     Cache.setOrRemove("PROXY_SERVER", proxyServerTB.getText());
 574
 575     Cache.setOrRemove("PROXY_PORT", proxyPortTB.getText());
 576
 577     if (useProxy.isSelected())
 578     {
 579       System.setProperty("http.proxyHost", proxyServerTB.getText());
 580       System.setProperty("http.proxyPort", proxyPortTB.getText());
 581     }
 582     else
 583     {
 584       System.setProperty("http.proxyHost", "");
 585       System.setProperty("http.proxyPort", "");
 586     }
 587     Cache.setProperty("VERSION_CHECK",
 588             Boolean.toString(versioncheck.isSelected()));
 589     if (Cache.getProperty("USAGESTATS") != null || usagestats.isSelected())
 590     {
 591       // default is false - we only set this if the user has actively agreed
 592       Cache.setProperty("USAGESTATS",
 593               Boolean.toString(usagestats.isSelected()));
 594     }
 595     if (!questionnaire.isSelected())
 596     {
 597       Cache.setProperty("NOQUESTIONNAIRES", "true");
 598     }
 599     else
 600     {
 601       // special - made easy to edit a property file to disable questionnaires
 602       // by just adding the given line
 603       Cache.removeProperty("NOQUESTIONNAIRES");
 604     }
 605
 606     /*
 607      * Save Output settings
 608      */
 609     Cache.applicationProperties.setProperty("BLC_JVSUFFIX",
 610             Boolean.toString(blcjv.isSelected()));
 611     Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX",
 612             Boolean.toString(clustaljv.isSelected()));
 613     Cache.applicationProperties.setProperty("FASTA_JVSUFFIX",
 614             Boolean.toString(fastajv.isSelected()));
 615     Cache.applicationProperties.setProperty("MSF_JVSUFFIX",
 616             Boolean.toString(msfjv.isSelected()));
 617     Cache.applicationProperties.setProperty("PFAM_JVSUFFIX",
 618             Boolean.toString(pfamjv.isSelected()));
 619     Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX",
 620             Boolean.toString(pileupjv.isSelected()));
 621     Cache.applicationProperties.setProperty("PIR_JVSUFFIX",
 622             Boolean.toString(pirjv.isSelected()));
 623     Cache.applicationProperties.setProperty("PIR_MODELLER",
 624             Boolean.toString(modellerOutput.isSelected()));
 625     Cache.applicationProperties.setProperty("EXPORT_EMBBED_BIOJSON",
 626             Boolean.toString(embbedBioJSON.isSelected()));
 627     jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
 628
 629     Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH",
 630             Boolean.toString(autoIdWidth.isSelected()));
 631     userIdWidth_actionPerformed();
 632     Cache.applicationProperties.setProperty("FIGURE_USERIDWIDTH",
 633             userIdWidth.getText());
 634
 635     /*
 636      * Save Editing settings
 637      */
 638     Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
 639             Boolean.toString(autoCalculateConsCheck.isSelected()));
 640     Cache.applicationProperties.setProperty("SORT_BY_TREE",
 641             Boolean.toString(sortByTree.isSelected()));
 642     Cache.applicationProperties.setProperty("PAD_GAPS",
 643             Boolean.toString(padGaps.isSelected()));
 644
 645     dasSource.saveProperties(Cache.applicationProperties);
 646     wsPrefs.updateAndRefreshWsMenuConfig(false);
 647     Cache.saveProperties();
 648     Desktop.instance.doConfigureStructurePrefs();
 649     try
 650     {
 651       frame.setClosed(true);
 652     } catch (Exception ex)
 653     {
 654     }
 655   }
 656
 657   /**
 658    * Do any necessary validation before saving settings. Return focus to the
 659    * first tab which fails validation.
 660    *
 661    * @return
 662    */
 663   private boolean validateSettings()
 664   {
 665     if (!validateStructure())
 666     {
 667       structureTab.requestFocusInWindow();
 668       return false;
 669     }
 670     return true;
 671   }
 672
 673   @Override
 674   protected boolean validateStructure()
 675   {
 676     return validateChimeraPath();
 677
 678   }
 679
 680   /**
 681    * DOCUMENT ME!
 682    */
 683   @Override
 684   public void startupFileTextfield_mouseClicked()
 685   {
 686     JalviewFileChooser chooser = new JalviewFileChooser(
 687             Cache.getProperty("LAST_DIRECTORY"), new String[] {
 688                 "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",
 689                 "jar" }, new String[] { "Fasta", "Clustal", "PFAM", "MSF",
 690                 "PIR", "BLC", "Jalview" },
 691             Cache.getProperty("DEFAULT_FILE_FORMAT"));
 692     chooser.setFileView(new JalviewFileView());
 693     chooser.setDialogTitle(MessageManager
 694             .getString("label.select_startup_file"));
 695
 696     int value = chooser.showOpenDialog(this);
 697
 698     if (value == JalviewFileChooser.APPROVE_OPTION)
 699     {
 700       Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT",
 701               chooser
 702                       .getSelectedFormat().toString());
 703       startupFileTextfield.setText(chooser.getSelectedFile()
 704               .getAbsolutePath());
 705     }
 706   }
 707
 708   /**
 709    * DOCUMENT ME!
 710    *
 711    * @param e
 712    *          DOCUMENT ME!
 713    */
 714   @Override
 715   public void cancel_actionPerformed(ActionEvent e)
 716   {
 717     try
 718     {
 719       wsPrefs.updateWsMenuConfig(true);
 720       wsPrefs.refreshWs_actionPerformed(e);
 721       frame.setClosed(true);
 722     } catch (Exception ex)
 723     {
 724     }
 725   }
 726
 727   /**
 728    * DOCUMENT ME!
 729    *
 730    * @param e
 731    *          DOCUMENT ME!
 732    */
 733   @Override
 734   public void annotations_actionPerformed(ActionEvent e)
 735   {
 736     conservation.setEnabled(annotations.isSelected());
 737     quality.setEnabled(annotations.isSelected());
 738     identity.setEnabled(annotations.isSelected());
 739     showGroupConsensus.setEnabled(annotations.isSelected());
 740     showGroupConservation.setEnabled(annotations.isSelected());
 741     showConsensHistogram.setEnabled(annotations.isSelected()
 742             && (identity.isSelected() || showGroupConsensus.isSelected()));
 743     showConsensLogo.setEnabled(annotations.isSelected()
 744             && (identity.isSelected() || showGroupConsensus.isSelected()));
 745   }
 746
 747   @Override
 748   public void newLink_actionPerformed(ActionEvent e)
 749   {
 750
 751     GSequenceLink link = new GSequenceLink();
 752     boolean valid = false;
 753     while (!valid)
 754     {
 755       if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 756               MessageManager.getString("label.new_sequence_url_link"),
 757               JOptionPane.OK_CANCEL_OPTION, -1, null) == JOptionPane.OK_OPTION)
 758       {
 759         if (link.checkValid())
 760         {
 761           nameLinks.addElement(link.getName());
 762           urlLinks.addElement(link.getURL());
 763           updateLinkData();
 764           valid = true;
 765         }
 766       }
 767       else
 768       {
 769         break;
 770       }
 771     }
 772   }
 773
 774   @Override
 775   public void editLink_actionPerformed(ActionEvent e)
 776   {
 777     GSequenceLink link = new GSequenceLink();
 778
 779     int index = linkNameList.getSelectedIndex();
 780     if (index == -1)
 781     {
 782       JOptionPane.showInternalMessageDialog(Desktop.desktop,
 783               MessageManager.getString("label.no_link_selected"),
 784               MessageManager.getString("label.no_link_selected"),
 785               JOptionPane.WARNING_MESSAGE);
 786       return;
 787     }
 788
 789     link.setName(nameLinks.elementAt(index).toString());
 790     link.setURL(urlLinks.elementAt(index).toString());
 791
 792     boolean valid = false;
 793     while (!valid)
 794     {
 795
 796       if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 797               MessageManager.getString("label.new_sequence_url_link"),
 798               JOptionPane.OK_CANCEL_OPTION, -1, null) == JOptionPane.OK_OPTION)
 799       {
 800         if (link.checkValid())
 801         {
 802           nameLinks.setElementAt(link.getName(), index);
 803           urlLinks.setElementAt(link.getURL(), index);
 804           updateLinkData();
 805           valid = true;
 806         }
 807       }
 808
 809       else
 810       {
 811         break;
 812       }
 813     }
 814   }
 815
 816   @Override
 817   public void deleteLink_actionPerformed(ActionEvent e)
 818   {
 819     int index = linkNameList.getSelectedIndex();
 820     if (index == -1)
 821     {
 822       JOptionPane.showInternalMessageDialog(Desktop.desktop,
 823               MessageManager.getString("label.no_link_selected"),
 824               MessageManager.getString("label.no_link_selected"),
 825               JOptionPane.WARNING_MESSAGE);
 826       return;
 827     }
 828     nameLinks.removeElementAt(index);
 829     urlLinks.removeElementAt(index);
 830     updateLinkData();
 831   }
 832
 833   void updateLinkData()
 834   {
 835     linkNameList.setListData(nameLinks);
 836     linkURLList.setListData(urlLinks);
 837   }
 838
 839   @Override
 840   public void defaultBrowser_mouseClicked(MouseEvent e)
 841   {
 842     JFileChooser chooser = new JFileChooser(".");
 843     chooser.setDialogTitle(MessageManager
 844             .getString("label.select_default_browser"));
 845
 846     int value = chooser.showOpenDialog(this);
 847
 848     if (value == JFileChooser.APPROVE_OPTION)
 849     {
 850       defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
 851     }
 852
 853   }
 854
 855   /*
 856    * (non-Javadoc)
 857    *
 858    * @see
 859    * jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event
 860    * .ActionEvent)
 861    */
 862   @Override
 863   protected void showunconserved_actionPerformed(ActionEvent e)
 864   {
 865     // TODO Auto-generated method stub
 866     super.showunconserved_actionPerformed(e);
 867   }
 868
 869   public static List<String> getGroupURLLinks()
 870   {
 871     return groupURLLinks;
 872   }
 873
 874   @Override
 875   public void minColour_actionPerformed(JPanel panel)
 876   {
 877     Color col = JColorChooser.showDialog(this,
 878             MessageManager.getString("label.select_colour_minimum_value"),
 879             minColour.getBackground());
 880     if (col != null)
 881     {
 882       panel.setBackground(col);
 883     }
 884     panel.repaint();
 885   }
 886
 887   @Override
 888   public void maxColour_actionPerformed(JPanel panel)
 889   {
 890     Color col = JColorChooser.showDialog(this,
 891             MessageManager.getString("label.select_colour_maximum_value"),
 892             maxColour.getBackground());
 893     if (col != null)
 894     {
 895       panel.setBackground(col);
 896     }
 897     panel.repaint();
 898   }
 899
 900   @Override
 901   protected void userIdWidth_actionPerformed()
 902   {
 903     try
 904     {
 905       String val = userIdWidth.getText().trim();
 906       if (val.length() > 0)
 907       {
 908         Integer iw = Integer.parseInt(val);
 909         if (iw.intValue() < 12)
 910         {
 911           throw new NumberFormatException();
 912         }
 913         userIdWidth.setText(iw.toString());
 914       }
 915     } catch (NumberFormatException x)
 916     {
 917       JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
 918               .getString("warn.user_defined_width_requirements"),
 919               MessageManager.getString("label.invalid_id_column_width"),
 920               JOptionPane.WARNING_MESSAGE);
 921       userIdWidth.setText("");
 922     }
 923   }
 924
 925   @Override
 926   protected void autoIdWidth_actionPerformed()
 927   {
 928     userIdWidth.setEnabled(!autoIdWidth.isSelected());
 929     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
 930   }
 931
 932   /**
 933    * Returns true if chimera path is to a valid executable, else show an error
 934    * dialog.
 935    */
 936   private boolean validateChimeraPath()
 937   {
 938     if (chimeraPath.getText().trim().length() > 0)
 939     {
 940       File f = new File(chimeraPath.getText());
 941       if (!f.canExecute())
 942       {
 943         JOptionPane.showInternalMessageDialog(Desktop.desktop,
 944                 MessageManager.getString("label.invalid_chimera_path"),
 945                 MessageManager.getString("label.invalid_name"),
 946                 JOptionPane.ERROR_MESSAGE);
 947         return false;
 948       }
 949     }
 950     return true;
 951   }
 952
 953   /**
 954    * If Chimera is selected, check it can be found on default or user-specified
 955    * path, if not show a warning/help dialog.
 956    */
 957   @Override
 958   protected void structureViewer_actionPerformed(String selectedItem)
 959   {
 960     if (!selectedItem.equals(ViewerType.CHIMERA.name()))
 961     {
 962       return;
 963     }
 964     boolean found = false;
 965
 966     /*
 967      * Try user-specified and standard paths for Chimera executable.
 968      */
 969     List<String> paths = StructureManager.getChimeraPaths();
 970     paths.add(0, chimeraPath.getText());
 971     for (String path : paths)
 972     {
 973       if (new File(path.trim()).canExecute())
 974       {
 975         found = true;
 976         break;
 977       }
 978     }
 979     if (!found)
 980     {
 981       String[] options = { "OK", "Help" };
 982       int showHelp = JOptionPane.showInternalOptionDialog(
 983               Desktop.desktop,
 984               JvSwingUtils.wrapTooltip(true,
 985                       MessageManager.getString("label.chimera_missing")),
 986               "", JOptionPane.YES_NO_OPTION, JOptionPane.WARNING_MESSAGE,
 987               null, options, options[0]);
 988       if (showHelp == JOptionPane.NO_OPTION)
 989       {
 990         try
 991         {
 992           Help.showHelpWindow(HelpId.StructureViewer);
 993         } catch (HelpSetException e)
 994         {
 995           e.printStackTrace();
 996         }
 997       }
 998     }
 999   }
1000
1001   public class OptionsParam
1002   {
1003     private String name;
1004
1005     private String code;
1006
1007     public OptionsParam(String name, String code)
1008     {
1009       this.name = name;
1010       this.code = code;
1011     }
1012
1013     public String getName()
1014     {
1015       return name;
1016     }
1017
1018     public void setName(String name)
1019     {
1020       this.name = name;
1021     }
1022
1023     public String getCode()
1024     {
1025       return code;
1026     }
1027
1028     public void setCode(String code)
1029     {
1030       this.code = code;
1031     }
1032
1033     @Override
1034     public String toString()
1035     {
1036       return name;
1037     }
1038
1039     @Override
1040     public boolean equals(Object that)
1041     {
1042       if (!(that instanceof OptionsParam))
1043       {
1044         return false;
1045       }
1046       return this.code.equalsIgnoreCase(((OptionsParam) that).code);
1047     }
1048
1049     @Override
1050     public int hashCode(){
1051       return name.hashCode() + code.hashCode();
1052     }
1053   }
1054 }