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