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