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