src/jalview/gui/Preferences.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
   3  * Copyright (C) 2014 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.StructureViewer.Viewer;
  26 import jalview.io.JalviewFileChooser;
  27 import jalview.io.JalviewFileView;
  28 import jalview.jbgui.GPreferences;
  29 import jalview.jbgui.GSequenceLink;
  30 import jalview.schemes.ColourSchemeProperty;
  31 import jalview.util.MessageManager;
  32
  33 import java.awt.BorderLayout;
  34 import java.awt.Color;
  35 import java.awt.Dimension;
  36 import java.awt.Font;
  37 import java.awt.event.ActionEvent;
  38 import java.awt.event.ActionListener;
  39 import java.awt.event.MouseEvent;
  40 import java.io.File;
  41 import java.util.Collection;
  42 import java.util.StringTokenizer;
  43 import java.util.Vector;
  44
  45 import javax.swing.JColorChooser;
  46 import javax.swing.JFileChooser;
  47 import javax.swing.JInternalFrame;
  48 import javax.swing.JOptionPane;
  49 import javax.swing.JPanel;
  50
  51 /**
  52  * DOCUMENT ME!
  53  *
  54  * @author $author$
  55  * @version $Revision$
  56  */
  57 public class Preferences extends GPreferences
  58 {
  59
  60   public static final String ADD_TEMPFACT_ANN = "ADD_TEMPFACT_ANN";
  61
  62   public static final String ADD_SS_ANN = "ADD_SS_ANN";
  63
  64   public static final String USE_RNAVIEW = "USE_RNAVIEW";
  65
  66   public static final String STRUCT_FROM_PDB = "STRUCT_FROM_PDB";
  67
  68   public static final String STRUCTURE_DISPLAY = "STRUCTURE_DISPLAY";
  69
  70   public static final String CHIMERA_PATH = "CHIMERA_PATH";
  71
  72   public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS";
  73
  74   public static final String SHOW_AUTOCALC_ABOVE = "SHOW_AUTOCALC_ABOVE";
  75
  76   private static final int MIN_FONT_SIZE = 1;
  77
  78   private static final int MAX_FONT_SIZE = 30;
  79
  80   /**
  81    * Holds name and link separated with | character. Sequence ID must be
  82    * $SEQUENCE_ID$ or $SEQUENCE_ID=/.possible | chars ./=$
  83    */
  84   public static Vector sequenceURLLinks;
  85
  86   /**
  87    * Holds name and link separated with | character. Sequence IDS and Sequences
  88    * must be $SEQUENCEIDS$ or $SEQUENCEIDS=/.possible | chars ./=$ and
  89    * $SEQUENCES$ or $SEQUENCES=/.possible | chars ./=$ and separation character
  90    * for first and second token specified after a pipe character at end |,|.
  91    * (TODO: proper escape for using | to separate ids or sequences
  92    */
  93
  94   public static Vector groupURLLinks;
  95   static
  96   {
  97     String string = Cache
  98             .getDefault(
  99                     "SEQUENCE_LINKS",
 100                     "EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$");
 101     sequenceURLLinks = new Vector();
 102
 103     try
 104     {
 105       StringTokenizer st = new StringTokenizer(string, "|");
 106       while (st.hasMoreElements())
 107       {
 108         String name = st.nextToken();
 109         String url = st.nextToken();
 110         // check for '|' within a regex
 111         int rxstart = url.indexOf("$SEQUENCE_ID$");
 112         while (rxstart == -1 && url.indexOf("/=$") == -1)
 113         {
 114           url = url + "|" + st.nextToken();
 115         }
 116         sequenceURLLinks.addElement(name + "|" + url);
 117       }
 118     } catch (Exception ex)
 119     {
 120       System.out.println(ex + "\nError parsing sequence links");
 121     }
 122     {
 123       // upgrade old SRS link
 124       int srsPos = sequenceURLLinks
 125               .indexOf("SRS|http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$SEQUENCE_ID$]))+-view+SwissEntry");
 126       if (srsPos > -1)
 127       {
 128         sequenceURLLinks
 129                 .setElementAt(
 130                         "EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$",
 131                         srsPos);
 132       }
 133     }
 134
 135     /**
 136      * TODO: reformulate groupURL encoding so two or more can be stored in the
 137      * .properties file as '|' separated strings
 138      */
 139
 140     groupURLLinks = new Vector();
 141   }
 142
 143   Vector nameLinks, urlLinks;
 144
 145   JInternalFrame frame;
 146
 147   DasSourceBrowser dasSource;
 148
 149   private WsPreferences wsPrefs;
 150
 151   /**
 152    * Creates a new Preferences object.
 153    */
 154   public Preferences()
 155   {
 156     super();
 157     frame = new JInternalFrame();
 158     frame.setContentPane(this);
 159     dasSource = new DasSourceBrowser();
 160     dasTab.add(dasSource, BorderLayout.CENTER);
 161     wsPrefs = new WsPreferences();
 162     wsTab.add(wsPrefs, BorderLayout.CENTER);
 163     int width = 500, height = 420;
 164     if (new jalview.util.Platform().isAMac())
 165     {
 166       width = 570;
 167       height = 460;
 168     }
 169
 170     Desktop.addInternalFrame(frame,
 171             MessageManager.getString("label.preferences"), width, height);
 172     frame.setMinimumSize(new Dimension(width, height));
 173
 174     /*
 175      * Set Visual tab defaults
 176      */
 177     seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));
 178     rightAlign.setSelected(Cache.getDefault("RIGHT_ALIGN_IDS", false));
 179     fullScreen.setSelected(Cache.getDefault("SHOW_FULLSCREEN", false));
 180     annotations.setSelected(Cache.getDefault("SHOW_ANNOTATIONS", true));
 181
 182     conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));
 183     quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));
 184     identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));
 185     openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false));
 186     showUnconserved
 187             .setSelected(Cache.getDefault("SHOW_UNCONSERVED", false));
 188     showGroupConsensus.setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS",
 189             false));
 190     showGroupConservation.setSelected(Cache.getDefault(
 191             "SHOW_GROUP_CONSERVATION", false));
 192     showConsensHistogram.setSelected(Cache.getDefault(
 193             "SHOW_CONSENSUS_HISTOGRAM", true));
 194     showConsensLogo.setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO",
 195             false));
 196     showNpTooltip.setSelected(Cache
 197             .getDefault("SHOW_NPFEATS_TOOLTIP", true));
 198     showDbRefTooltip.setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP",
 199             true));
 200
 201     String[] fonts = java.awt.GraphicsEnvironment
 202             .getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
 203     for (int i = 0; i < fonts.length; i++)
 204     {
 205       fontNameCB.addItem(fonts[i]);
 206     }
 207
 208     for (int i = MIN_FONT_SIZE; i <= MAX_FONT_SIZE; i++)
 209     {
 210       fontSizeCB.addItem(i + "");
 211     }
 212
 213     fontStyleCB.addItem("plain");
 214     fontStyleCB.addItem("bold");
 215     fontStyleCB.addItem("italic");
 216
 217     fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
 218     fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
 219     fontStyleCB.setSelectedItem(Cache.getDefault("FONT_STYLE", Font.PLAIN
 220             + ""));
 221
 222     smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));
 223
 224     idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
 225
 226     wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
 227
 228     gapSymbolCB.addItem("-");
 229     gapSymbolCB.addItem(".");
 230
 231     gapSymbolCB.setSelectedItem(Cache.getDefault("GAP_SYMBOL", "-"));
 232
 233     sortby.addItem("No sort");
 234     sortby.addItem("Id");
 235     sortby.addItem("Pairwise Identity");
 236     sortby.setSelectedItem(Cache.getDefault("SORT_ALIGNMENT", "No sort"));
 237
 238     sortAnnBy.addItem(SequenceAnnotationOrder.NONE.toString());
 239     sortAnnBy
 240             .addItem(SequenceAnnotationOrder.SEQUENCE_AND_LABEL.toString());
 241     sortAnnBy
 242             .addItem(SequenceAnnotationOrder.LABEL_AND_SEQUENCE.toString());
 243     SequenceAnnotationOrder savedSort = SequenceAnnotationOrder
 244             .valueOf(Cache.getDefault(SORT_ANNOTATIONS,
 245                     SequenceAnnotationOrder.NONE.name()));
 246     sortAnnBy.setSelectedItem(savedSort.toString());
 247
 248     sortAutocalc.addItem("Autocalculated first");
 249     sortAutocalc.addItem("Autocalculated last");
 250     final boolean showAbove = Cache.getDefault(SHOW_AUTOCALC_ABOVE,
 251             true);
 252     sortAutocalc.setSelectedItem(showAbove ? sortAutocalc.getItemAt(0)
 253             : sortAutocalc.getItemAt(1));
 254     startupCheckbox
 255             .setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
 256     startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
 257             Cache.getDefault("www.jalview.org", "http://www.jalview.org")
 258                     + "/examples/exampleFile_2_3.jar"));
 259
 260     /*
 261      * Set Colours tab defaults
 262      */
 263     for (int i = ColourSchemeProperty.FIRST_COLOUR; i <= ColourSchemeProperty.LAST_COLOUR; i++)
 264     {
 265       colour.addItem(ColourSchemeProperty.getColourName(i));
 266     }
 267     String string = Cache.getDefault("DEFAULT_COLOUR", "None");
 268     colour.setSelectedItem(string);
 269     minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN",
 270             Color.orange));
 271     maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX",
 272             Color.red));
 273
 274     /*
 275      * Set Structure tab defaults.
 276      */
 277     final boolean structSelected = Cache.getDefault(STRUCT_FROM_PDB, false);
 278     structFromPdb.setSelected(structSelected);
 279     useRnaView.setSelected(Cache.getDefault(USE_RNAVIEW, false));
 280     useRnaView.setEnabled(structSelected);
 281     addSecondaryStructure
 282             .setSelected(Cache.getDefault(ADD_SS_ANN, false));
 283     addSecondaryStructure.setEnabled(structSelected);
 284     addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, false));
 285     addTempFactor.setEnabled(structSelected);
 286     structViewer.setSelectedItem(Cache.getDefault(STRUCTURE_DISPLAY,
 287             Viewer.JMOL.name()));
 288     chimeraPath.setText(Cache.getDefault(CHIMERA_PATH, ""));
 289     chimeraPath.addActionListener(new ActionListener()
 290     {
 291       @Override
 292       public void actionPerformed(ActionEvent e)
 293       {
 294         validateChimeraPath();
 295       }
 296     });
 297
 298     /*
 299      * Set Connections tab defaults
 300      */
 301     nameLinks = new Vector();
 302     urlLinks = new Vector();
 303     for (int i = 0; i < sequenceURLLinks.size(); i++)
 304     {
 305       String link = sequenceURLLinks.elementAt(i).toString();
 306       nameLinks.addElement(link.substring(0, link.indexOf("|")));
 307       urlLinks.addElement(link.substring(link.indexOf("|") + 1));
 308     }
 309
 310     updateLinkData();
 311
 312     useProxy.setSelected(Cache.getDefault("USE_PROXY", false));
 313     proxyServerTB.setEnabled(useProxy.isSelected());
 314     proxyPortTB.setEnabled(useProxy.isSelected());
 315     proxyServerTB.setText(Cache.getDefault("PROXY_SERVER", ""));
 316     proxyPortTB.setText(Cache.getDefault("PROXY_PORT", ""));
 317
 318     defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", ""));
 319
 320     usagestats.setSelected(Cache.getDefault("USAGESTATS", false));
 321     // note antisense here: default is true
 322     questionnaire
 323             .setSelected(Cache.getProperty("NOQUESTIONNAIRES") == null);
 324     versioncheck.setSelected(Cache.getDefault("VERSION_CHECK", true));
 325
 326     /*
 327      * Set Output tab defaults
 328      */
 329     epsRendering
 330             .addItem(MessageManager.getString("label.prompt_each_time"));
 331     epsRendering.addItem(MessageManager.getString("label.lineart"));
 332     epsRendering.addItem(MessageManager.getString("action.text"));
 333     epsRendering.setSelectedItem(Cache.getDefault("EPS_RENDERING",
 334             "Prompt each time"));
 335     autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false));
 336     userIdWidth.setEnabled(autoIdWidth.isSelected());
 337     userIdWidthlabel.setEnabled(autoIdWidth.isSelected());
 338     Integer wi = Cache.getIntegerProperty("FIGURE_USERIDWIDTH");
 339     userIdWidth.setText(wi == null ? "" : wi.toString());
 340     blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
 341     clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
 342     fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
 343     msfjv.setSelected(Cache.getDefault("MSF_JVSUFFIX", true));
 344     pfamjv.setSelected(Cache.getDefault("PFAM_JVSUFFIX", true));
 345     pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
 346     pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
 347     modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
 348
 349     /*
 350      * Set Editing tab defaults
 351      */
 352     autoCalculateConsCheck.setSelected(Cache.getDefault(
 353             "AUTO_CALC_CONSENSUS", true));
 354     padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
 355     sortByTree.setSelected(Cache.getDefault("SORT_BY_TREE", false));
 356
 357     annotations_actionPerformed(null); // update the display of the annotation
 358                                        // settings
 359   }
 360
 361   /**
 362    * Save user selections on the Preferences tabs to the Cache and write out to
 363    * file.
 364    *
 365    * @param e
 366    */
 367   public void ok_actionPerformed(ActionEvent e)
 368   {
 369     if (!validateSettings())
 370     {
 371       return;
 372     }
 373
 374     /*
 375      * Save Visual settings
 376      */
 377     Cache.applicationProperties.setProperty("SHOW_JVSUFFIX",
 378             Boolean.toString(seqLimit.isSelected()));
 379     Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS",
 380             Boolean.toString(rightAlign.isSelected()));
 381     Cache.applicationProperties.setProperty("SHOW_FULLSCREEN",
 382             Boolean.toString(fullScreen.isSelected()));
 383     Cache.applicationProperties.setProperty("SHOW_OVERVIEW",
 384             Boolean.toString(openoverv.isSelected()));
 385     Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
 386             Boolean.toString(annotations.isSelected()));
 387     Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
 388             Boolean.toString(conservation.isSelected()));
 389     Cache.applicationProperties.setProperty("SHOW_QUALITY",
 390             Boolean.toString(quality.isSelected()));
 391     Cache.applicationProperties.setProperty("SHOW_IDENTITY",
 392             Boolean.toString(identity.isSelected()));
 393
 394     Cache.applicationProperties.setProperty("GAP_SYMBOL", gapSymbolCB
 395             .getSelectedItem().toString());
 396
 397     Cache.applicationProperties.setProperty("FONT_NAME", fontNameCB
 398             .getSelectedItem().toString());
 399     Cache.applicationProperties.setProperty("FONT_STYLE", fontStyleCB
 400             .getSelectedItem().toString());
 401     Cache.applicationProperties.setProperty("FONT_SIZE", fontSizeCB
 402             .getSelectedItem().toString());
 403
 404     Cache.applicationProperties.setProperty("ID_ITALICS",
 405             Boolean.toString(idItalics.isSelected()));
 406     Cache.applicationProperties.setProperty("SHOW_UNCONSERVED",
 407             Boolean.toString(showUnconserved.isSelected()));
 408     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS",
 409             Boolean.toString(showGroupConsensus.isSelected()));
 410     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION",
 411             Boolean.toString(showGroupConservation.isSelected()));
 412     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_HISTOGRAM",
 413             Boolean.toString(showConsensHistogram.isSelected()));
 414     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO",
 415             Boolean.toString(showConsensLogo.isSelected()));
 416     Cache.applicationProperties.setProperty("ANTI_ALIAS",
 417             Boolean.toString(smoothFont.isSelected()));
 418     Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP",
 419             Boolean.toString(showNpTooltip.isSelected()));
 420     Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP",
 421             Boolean.toString(showDbRefTooltip.isSelected()));
 422
 423     Cache.applicationProperties.setProperty("WRAP_ALIGNMENT",
 424             Boolean.toString(wrap.isSelected()));
 425
 426     Cache.applicationProperties.setProperty("STARTUP_FILE",
 427             startupFileTextfield.getText());
 428     Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",
 429             Boolean.toString(startupCheckbox.isSelected()));
 430
 431     Cache.applicationProperties.setProperty("SORT_ALIGNMENT", sortby
 432             .getSelectedItem().toString());
 433
 434     // convert description of sort order to enum name for save
 435     SequenceAnnotationOrder annSortOrder = SequenceAnnotationOrder
 436             .forDescription(sortAnnBy.getSelectedItem().toString());
 437     if (annSortOrder != null)
 438     {
 439       Cache.applicationProperties.setProperty(SORT_ANNOTATIONS,
 440               annSortOrder.name());
 441     }
 442
 443     final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
 444     Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE,
 445             Boolean.valueOf(showAutocalcFirst).toString());
 446
 447     /*
 448      * Save Colours settings
 449      */
 450     Cache.applicationProperties.setProperty("DEFAULT_COLOUR", colour
 451             .getSelectedItem().toString());
 452     Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
 453             minColour.getBackground());
 454     Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
 455             maxColour.getBackground());
 456
 457     /*
 458      * Save Structure settings
 459      */
 460     Cache.applicationProperties.setProperty(ADD_TEMPFACT_ANN,
 461             Boolean.toString(addTempFactor.isSelected()));
 462     Cache.applicationProperties.setProperty(ADD_SS_ANN,
 463             Boolean.toString(addSecondaryStructure.isSelected()));
 464     Cache.applicationProperties.setProperty(USE_RNAVIEW,
 465             Boolean.toString(useRnaView.isSelected()));
 466     Cache.applicationProperties.setProperty(STRUCT_FROM_PDB,
 467             Boolean.toString(structFromPdb.isSelected()));
 468     Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY, structViewer
 469             .getSelectedItem().toString());
 470     Cache.setOrRemove(CHIMERA_PATH, chimeraPath.getText());
 471
 472     /*
 473      * Save Output settings
 474      */
 475     if (epsRendering.getSelectedItem().equals("Prompt each time"))
 476     {
 477       Cache.applicationProperties.remove("EPS_RENDERING");
 478     }
 479     else
 480     {
 481       Cache.applicationProperties.setProperty("EPS_RENDERING", epsRendering
 482               .getSelectedItem().toString());
 483     }
 484
 485     /*
 486      * Save Connections settings
 487      */
 488     Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText());
 489
 490     jalview.util.BrowserLauncher.resetBrowser();
 491
 492     if (nameLinks.size() > 0)
 493     {
 494       StringBuffer links = new StringBuffer();
 495       sequenceURLLinks = new Vector();
 496       for (int i = 0; i < nameLinks.size(); i++)
 497       {
 498         sequenceURLLinks.addElement(nameLinks.elementAt(i) + "|"
 499                 + urlLinks.elementAt(i));
 500         links.append(sequenceURLLinks.elementAt(i).toString());
 501         links.append("|");
 502       }
 503       // remove last "|"
 504       links.setLength(links.length() - 1);
 505       Cache.applicationProperties.setProperty("SEQUENCE_LINKS",
 506               links.toString());
 507     }
 508     else
 509     {
 510       Cache.applicationProperties.remove("SEQUENCE_LINKS");
 511     }
 512
 513     Cache.applicationProperties.setProperty("USE_PROXY",
 514             Boolean.toString(useProxy.isSelected()));
 515
 516     Cache.setOrRemove("PROXY_SERVER", proxyServerTB.getText());
 517
 518     Cache.setOrRemove("PROXY_PORT", proxyPortTB.getText());
 519
 520     if (useProxy.isSelected())
 521     {
 522       System.setProperty("http.proxyHost", proxyServerTB.getText());
 523       System.setProperty("http.proxyPort", proxyPortTB.getText());
 524     }
 525     else
 526     {
 527       System.setProperty("http.proxyHost", "");
 528       System.setProperty("http.proxyPort", "");
 529     }
 530     Cache.setProperty("VERSION_CHECK",
 531             Boolean.toString(versioncheck.isSelected()));
 532     if (Cache.getProperty("USAGESTATS") != null || usagestats.isSelected())
 533     {
 534       // default is false - we only set this if the user has actively agreed
 535       Cache.setProperty("USAGESTATS",
 536               Boolean.toString(usagestats.isSelected()));
 537     }
 538     if (!questionnaire.isSelected())
 539     {
 540       Cache.setProperty("NOQUESTIONNAIRES", "true");
 541     }
 542     else
 543     {
 544       // special - made easy to edit a property file to disable questionnaires
 545       // by just adding the given line
 546       Cache.removeProperty("NOQUESTIONNAIRES");
 547     }
 548
 549     /*
 550      * Save Output settings
 551      */
 552     Cache.applicationProperties.setProperty("BLC_JVSUFFIX",
 553             Boolean.toString(blcjv.isSelected()));
 554     Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX",
 555             Boolean.toString(clustaljv.isSelected()));
 556     Cache.applicationProperties.setProperty("FASTA_JVSUFFIX",
 557             Boolean.toString(fastajv.isSelected()));
 558     Cache.applicationProperties.setProperty("MSF_JVSUFFIX",
 559             Boolean.toString(msfjv.isSelected()));
 560     Cache.applicationProperties.setProperty("PFAM_JVSUFFIX",
 561             Boolean.toString(pfamjv.isSelected()));
 562     Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX",
 563             Boolean.toString(pileupjv.isSelected()));
 564     Cache.applicationProperties.setProperty("PIR_JVSUFFIX",
 565             Boolean.toString(pirjv.isSelected()));
 566     Cache.applicationProperties.setProperty("PIR_MODELLER",
 567             Boolean.toString(modellerOutput.isSelected()));
 568     jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
 569
 570     Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH",
 571             Boolean.toString(autoIdWidth.isSelected()));
 572     userIdWidth_actionPerformed();
 573     Cache.applicationProperties.setProperty("FIGURE_USERIDWIDTH",
 574             userIdWidth.getText());
 575
 576     /*
 577      * Save Editing settings
 578      */
 579     Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
 580             Boolean.toString(autoCalculateConsCheck.isSelected()));
 581     Cache.applicationProperties.setProperty("SORT_BY_TREE",
 582             Boolean.toString(sortByTree.isSelected()));
 583     Cache.applicationProperties.setProperty("PAD_GAPS",
 584             Boolean.toString(padGaps.isSelected()));
 585
 586     dasSource.saveProperties(Cache.applicationProperties);
 587     wsPrefs.updateAndRefreshWsMenuConfig(false);
 588     Cache.saveProperties();
 589     Desktop.instance.doConfigureStructurePrefs();
 590     try
 591     {
 592       frame.setClosed(true);
 593     } catch (Exception ex)
 594     {
 595     }
 596   }
 597
 598   /**
 599    * Do any necessary validation before saving settings.
 600    *
 601    * @return
 602    */
 603   private boolean validateSettings()
 604   {
 605     if (!validateStructure())
 606     {
 607       structureTab.requestFocusInWindow();
 608       return false;
 609     }
 610     return true;
 611   }
 612
 613   @Override
 614   protected boolean validateStructure()
 615   {
 616     return validateChimeraPath();
 617
 618   }
 619   /**
 620    * DOCUMENT ME!
 621    */
 622   public void startupFileTextfield_mouseClicked()
 623   {
 624     JalviewFileChooser chooser = new JalviewFileChooser(
 625             jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
 626             new String[]
 627             { "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc", "jar" },
 628             new String[]
 629             { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview" },
 630             jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));
 631     chooser.setFileView(new JalviewFileView());
 632     chooser.setDialogTitle(MessageManager.getString("label.select_startup_file"));
 633
 634     int value = chooser.showOpenDialog(this);
 635
 636     if (value == JalviewFileChooser.APPROVE_OPTION)
 637     {
 638       jalview.bin.Cache.applicationProperties.setProperty(
 639               "DEFAULT_FILE_FORMAT", chooser.getSelectedFormat());
 640       startupFileTextfield.setText(chooser.getSelectedFile()
 641               .getAbsolutePath());
 642     }
 643   }
 644
 645   /**
 646    * DOCUMENT ME!
 647    *
 648    * @param e
 649    *          DOCUMENT ME!
 650    */
 651   public void cancel_actionPerformed(ActionEvent e)
 652   {
 653     try
 654     {
 655       wsPrefs.updateWsMenuConfig(true);
 656       wsPrefs.refreshWs_actionPerformed(e);
 657       frame.setClosed(true);
 658     } catch (Exception ex)
 659     {
 660     }
 661   }
 662
 663   /**
 664    * DOCUMENT ME!
 665    *
 666    * @param e
 667    *          DOCUMENT ME!
 668    */
 669   public void annotations_actionPerformed(ActionEvent e)
 670   {
 671     conservation.setEnabled(annotations.isSelected());
 672     quality.setEnabled(annotations.isSelected());
 673     identity.setEnabled(annotations.isSelected());
 674     showGroupConsensus.setEnabled(annotations.isSelected());
 675     showGroupConservation.setEnabled(annotations.isSelected());
 676     showConsensHistogram.setEnabled(annotations.isSelected()
 677             && (identity.isSelected() || showGroupConsensus.isSelected()));
 678     showConsensLogo.setEnabled(annotations.isSelected()
 679             && (identity.isSelected() || showGroupConsensus.isSelected()));
 680   }
 681
 682   public void newLink_actionPerformed(ActionEvent e)
 683   {
 684
 685     GSequenceLink link = new GSequenceLink();
 686     boolean valid = false;
 687     while (!valid)
 688     {
 689       if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 690               MessageManager.getString("label.new_sequence_url_link"),
 691               JOptionPane.OK_CANCEL_OPTION, -1, null) == JOptionPane.OK_OPTION)
 692       {
 693         if (link.checkValid())
 694         {
 695           nameLinks.addElement(link.getName());
 696           urlLinks.addElement(link.getURL());
 697           updateLinkData();
 698           valid = true;
 699         }
 700       }
 701       else
 702       {
 703         break;
 704       }
 705     }
 706   }
 707
 708   public void editLink_actionPerformed(ActionEvent e)
 709   {
 710     GSequenceLink link = new GSequenceLink();
 711
 712     int index = linkNameList.getSelectedIndex();
 713     if (index == -1)
 714     {
 715       JOptionPane.showInternalMessageDialog(Desktop.desktop,
 716               MessageManager.getString("label.no_link_selected"),
 717               MessageManager.getString("label.no_link_selected"),
 718               JOptionPane.WARNING_MESSAGE);
 719       return;
 720     }
 721
 722     link.setName(nameLinks.elementAt(index).toString());
 723     link.setURL(urlLinks.elementAt(index).toString());
 724
 725     boolean valid = false;
 726     while (!valid)
 727     {
 728
 729       if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 730               MessageManager.getString("label.new_sequence_url_link"),
 731               JOptionPane.OK_CANCEL_OPTION, -1, null) == JOptionPane.OK_OPTION)
 732       {
 733         if (link.checkValid())
 734         {
 735           nameLinks.setElementAt(link.getName(), index);
 736           urlLinks.setElementAt(link.getURL(), index);
 737           updateLinkData();
 738           valid = true;
 739         }
 740       }
 741
 742       else
 743       {
 744         break;
 745       }
 746     }
 747   }
 748
 749   public void deleteLink_actionPerformed(ActionEvent e)
 750   {
 751     int index = linkNameList.getSelectedIndex();
 752     if (index == -1)
 753     {
 754       JOptionPane.showInternalMessageDialog(Desktop.desktop,
 755               MessageManager.getString("label.no_link_selected"),
 756               MessageManager.getString("label.no_link_selected"),
 757               JOptionPane.WARNING_MESSAGE);
 758       return;
 759     }
 760     nameLinks.removeElementAt(index);
 761     urlLinks.removeElementAt(index);
 762     updateLinkData();
 763   }
 764
 765   void updateLinkData()
 766   {
 767     linkNameList.setListData(nameLinks);
 768     linkURLList.setListData(urlLinks);
 769   }
 770
 771   public void defaultBrowser_mouseClicked(MouseEvent e)
 772   {
 773     JFileChooser chooser = new JFileChooser(".");
 774     chooser.setDialogTitle(MessageManager.getString("label.select_default_browser"));
 775
 776     int value = chooser.showOpenDialog(this);
 777
 778     if (value == JFileChooser.APPROVE_OPTION)
 779     {
 780       defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
 781     }
 782
 783   }
 784
 785   /*
 786    * (non-Javadoc)
 787    *
 788    * @see
 789    * jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event
 790    * .ActionEvent)
 791    */
 792   protected void showunconserved_actionPerformed(ActionEvent e)
 793   {
 794     // TODO Auto-generated method stub
 795     super.showunconserved_actionPerformed(e);
 796   }
 797
 798   public static Collection getGroupURLLinks()
 799   {
 800     return groupURLLinks;
 801   }
 802
 803   @Override
 804   public void minColour_actionPerformed(JPanel panel)
 805   {
 806     Color col = JColorChooser.showDialog(this,
 807             MessageManager.getString("label.select_colour_minimum_value"), minColour.getBackground());
 808     if (col != null)
 809     {
 810       panel.setBackground(col);
 811     }
 812     panel.repaint();
 813   }
 814
 815   @Override
 816   public void maxColour_actionPerformed(JPanel panel)
 817   {
 818     Color col = JColorChooser.showDialog(this,
 819             MessageManager.getString("label.select_colour_maximum_value"), maxColour.getBackground());
 820     if (col != null)
 821     {
 822       panel.setBackground(col);
 823     }
 824     panel.repaint();
 825   }
 826
 827   @Override
 828   protected void userIdWidth_actionPerformed()
 829   {
 830     try
 831     {
 832       String val = userIdWidth.getText().trim();
 833       if (val.length() > 0)
 834       {
 835         Integer iw = Integer.parseInt(val);
 836         if (iw.intValue() < 12)
 837         {
 838           throw new NumberFormatException();
 839         }
 840         userIdWidth.setText(iw.toString());
 841       }
 842     } catch (NumberFormatException x)
 843     {
 844       JOptionPane
 845               .showInternalMessageDialog(
 846                       Desktop.desktop,
 847                       MessageManager.getString("warn.user_defined_width_requirements"),
 848                       MessageManager.getString("label.invalid_id_column_width"),
 849                       JOptionPane.WARNING_MESSAGE);
 850       userIdWidth.setText("");
 851     }
 852   }
 853
 854   @Override
 855   protected void autoIdWidth_actionPerformed()
 856   {
 857     userIdWidth.setEnabled(!autoIdWidth.isSelected());
 858     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
 859   }
 860
 861   /**
 862    * Returns true if chimera path is to a valid executable, else show an error
 863    * dialog.
 864    */
 865   private boolean validateChimeraPath()
 866   {
 867     if (chimeraPath.getText().trim().length() > 0)
 868     {
 869       File f = new File(chimeraPath.getText());
 870       if (!f.canExecute())
 871       {
 872         JOptionPane.showInternalMessageDialog(Desktop.desktop,
 873                 MessageManager.getString("label.invalid_chimera_path"),
 874                 MessageManager.getString("label.invalid_name"),
 875                 JOptionPane.ERROR_MESSAGE);
 876         return false;
 877       }
 878     }
 879     return true;
 880   }
 881
 882 }