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,
 267             true);
 268     sortAutocalc.setSelectedItem(showAbove ? sortAutocalc.getItemAt(0)
 269             : sortAutocalc.getItemAt(1));
 270     startupCheckbox
 271             .setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
 272     startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
 273             Cache.getDefault("www.jalview.org", "http://www.jalview.org")
 274                     + "/examples/exampleFile_2_3.jar"));
 275
 276     /*
 277      * Set Colours tab defaults
 278      */
 279     for (int i = ColourSchemeProperty.FIRST_COLOUR; i <= ColourSchemeProperty.LAST_COLOUR; i++)
 280     {
 281       protColour.addItem(ColourSchemeProperty.getColourName(i));
 282       nucColour.addItem(ColourSchemeProperty.getColourName(i));
 283     }
 284     String oldProp = Cache.getDefault(DEFAULT_COLOUR, "None");
 285     String newProp = Cache.getDefault(DEFAULT_COLOUR_PROT, null);
 286     protColour.setSelectedItem(newProp != null ? newProp : oldProp);
 287     newProp = Cache.getDefault(DEFAULT_COLOUR_NUC, null);
 288     nucColour.setSelectedItem(newProp != null ? newProp : oldProp);
 289     minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN",
 290             Color.orange));
 291     maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX",
 292             Color.red));
 293
 294     /*
 295      * Set Structure tab defaults.
 296      */
 297     final boolean structSelected = Cache.getDefault(STRUCT_FROM_PDB, false);
 298     structFromPdb.setSelected(structSelected);
 299     useRnaView.setSelected(Cache.getDefault(USE_RNAVIEW, false));
 300     useRnaView.setEnabled(structSelected);
 301     addSecondaryStructure
 302             .setSelected(Cache.getDefault(ADD_SS_ANN, false));
 303     addSecondaryStructure.setEnabled(structSelected);
 304     addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, false));
 305     addTempFactor.setEnabled(structSelected);
 306     structViewer.setSelectedItem(Cache.getDefault(STRUCTURE_DISPLAY,
 307             ViewerType.JMOL.name()));
 308     chimeraPath.setText(Cache.getDefault(CHIMERA_PATH, ""));
 309     chimeraPath.addActionListener(new ActionListener()
 310     {
 311       @Override
 312       public void actionPerformed(ActionEvent e)
 313       {
 314         validateChimeraPath();
 315       }
 316     });
 317
 318     /*
 319      * Set Connections tab defaults
 320      */
 321     nameLinks = new Vector();
 322     urlLinks = new Vector();
 323     for (int i = 0; i < sequenceURLLinks.size(); i++)
 324     {
 325       String link = sequenceURLLinks.elementAt(i).toString();
 326       nameLinks.addElement(link.substring(0, link.indexOf("|")));
 327       urlLinks.addElement(link.substring(link.indexOf("|") + 1));
 328     }
 329
 330     updateLinkData();
 331
 332     useProxy.setSelected(Cache.getDefault("USE_PROXY", false));
 333     proxyServerTB.setEnabled(useProxy.isSelected());
 334     proxyPortTB.setEnabled(useProxy.isSelected());
 335     proxyServerTB.setText(Cache.getDefault("PROXY_SERVER", ""));
 336     proxyPortTB.setText(Cache.getDefault("PROXY_PORT", ""));
 337
 338     defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", ""));
 339
 340     usagestats.setSelected(Cache.getDefault("USAGESTATS", false));
 341     // note antisense here: default is true
 342     questionnaire
 343             .setSelected(Cache.getProperty("NOQUESTIONNAIRES") == null);
 344     versioncheck.setSelected(Cache.getDefault("VERSION_CHECK", true));
 345
 346     /*
 347      * Set Output tab defaults
 348      */
 349     epsRendering
 350             .addItem(MessageManager.getString("label.prompt_each_time"));
 351     epsRendering.addItem(MessageManager.getString("label.lineart"));
 352     epsRendering.addItem(MessageManager.getString("action.text"));
 353     epsRendering.setSelectedItem(Cache.getDefault("EPS_RENDERING",
 354             "Prompt each time"));
 355     autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false));
 356     userIdWidth.setEnabled(autoIdWidth.isSelected());
 357     userIdWidthlabel.setEnabled(autoIdWidth.isSelected());
 358     Integer wi = Cache.getIntegerProperty("FIGURE_USERIDWIDTH");
 359     userIdWidth.setText(wi == null ? "" : wi.toString());
 360     blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
 361     clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
 362     fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
 363     msfjv.setSelected(Cache.getDefault("MSF_JVSUFFIX", true));
 364     pfamjv.setSelected(Cache.getDefault("PFAM_JVSUFFIX", true));
 365     pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
 366     pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
 367     modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
 368     embbedBioJSON.setSelected(Cache.getDefault("EXPORT_EMBBED_BIOJSON",
 369             true));
 370
 371     /*
 372      * Set Editing tab defaults
 373      */
 374     autoCalculateConsCheck.setSelected(Cache.getDefault(
 375             "AUTO_CALC_CONSENSUS", true));
 376     padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
 377     sortByTree.setSelected(Cache.getDefault("SORT_BY_TREE", false));
 378
 379     annotations_actionPerformed(null); // update the display of the annotation
 380                                        // settings
 381   }
 382
 383   /**
 384    * Save user selections on the Preferences tabs to the Cache and write out to
 385    * file.
 386    *
 387    * @param e
 388    */
 389   public void ok_actionPerformed(ActionEvent e)
 390   {
 391     if (!validateSettings())
 392     {
 393       return;
 394     }
 395
 396     /*
 397      * Save Visual settings
 398      */
 399     Cache.applicationProperties.setProperty("SHOW_JVSUFFIX",
 400             Boolean.toString(seqLimit.isSelected()));
 401     Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS",
 402             Boolean.toString(rightAlign.isSelected()));
 403     Cache.applicationProperties.setProperty("SHOW_FULLSCREEN",
 404             Boolean.toString(fullScreen.isSelected()));
 405     Cache.applicationProperties.setProperty("SHOW_OVERVIEW",
 406             Boolean.toString(openoverv.isSelected()));
 407     Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
 408             Boolean.toString(annotations.isSelected()));
 409     Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
 410             Boolean.toString(conservation.isSelected()));
 411     Cache.applicationProperties.setProperty("SHOW_QUALITY",
 412             Boolean.toString(quality.isSelected()));
 413     Cache.applicationProperties.setProperty("SHOW_IDENTITY",
 414             Boolean.toString(identity.isSelected()));
 415
 416     Cache.applicationProperties.setProperty("GAP_SYMBOL", gapSymbolCB
 417             .getSelectedItem().toString());
 418
 419     Cache.applicationProperties.setProperty("FONT_NAME", fontNameCB
 420             .getSelectedItem().toString());
 421     Cache.applicationProperties.setProperty("FONT_STYLE", fontStyleCB
 422             .getSelectedItem().toString());
 423     Cache.applicationProperties.setProperty("FONT_SIZE", fontSizeCB
 424             .getSelectedItem().toString());
 425
 426     Cache.applicationProperties.setProperty("ID_ITALICS",
 427             Boolean.toString(idItalics.isSelected()));
 428     Cache.applicationProperties.setProperty("SHOW_UNCONSERVED",
 429             Boolean.toString(showUnconserved.isSelected()));
 430     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS",
 431             Boolean.toString(showGroupConsensus.isSelected()));
 432     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION",
 433             Boolean.toString(showGroupConservation.isSelected()));
 434     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_HISTOGRAM",
 435             Boolean.toString(showConsensHistogram.isSelected()));
 436     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO",
 437             Boolean.toString(showConsensLogo.isSelected()));
 438     Cache.applicationProperties.setProperty("ANTI_ALIAS",
 439             Boolean.toString(smoothFont.isSelected()));
 440     Cache.applicationProperties.setProperty(SCALE_PROTEIN_TO_CDNA,
 441             Boolean.toString(scaleProteinToCdna.isSelected()));
 442     Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP",
 443             Boolean.toString(showNpTooltip.isSelected()));
 444     Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP",
 445             Boolean.toString(showDbRefTooltip.isSelected()));
 446
 447     Cache.applicationProperties.setProperty("WRAP_ALIGNMENT",
 448             Boolean.toString(wrap.isSelected()));
 449
 450     Cache.applicationProperties.setProperty("STARTUP_FILE",
 451             startupFileTextfield.getText());
 452     Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",
 453             Boolean.toString(startupCheckbox.isSelected()));
 454
 455     Cache.applicationProperties.setProperty("SORT_ALIGNMENT", sortby
 456             .getSelectedItem().toString());
 457
 458     // convert description of sort order to enum name for save
 459     SequenceAnnotationOrder annSortOrder = SequenceAnnotationOrder
 460             .forDescription(sortAnnBy.getSelectedItem().toString());
 461     if (annSortOrder != null)
 462     {
 463       Cache.applicationProperties.setProperty(SORT_ANNOTATIONS,
 464               annSortOrder.name());
 465     }
 466
 467     final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
 468     Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE,
 469             Boolean.valueOf(showAutocalcFirst).toString());
 470
 471     /*
 472      * Save Colours settings
 473      */
 474     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_PROT, protColour
 475             .getSelectedItem().toString());
 476     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_NUC, nucColour
 477             .getSelectedItem().toString());
 478     Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
 479             minColour.getBackground());
 480     Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
 481             maxColour.getBackground());
 482
 483     /*
 484      * Save Structure settings
 485      */
 486     Cache.applicationProperties.setProperty(ADD_TEMPFACT_ANN,
 487             Boolean.toString(addTempFactor.isSelected()));
 488     Cache.applicationProperties.setProperty(ADD_SS_ANN,
 489             Boolean.toString(addSecondaryStructure.isSelected()));
 490     Cache.applicationProperties.setProperty(USE_RNAVIEW,
 491             Boolean.toString(useRnaView.isSelected()));
 492     Cache.applicationProperties.setProperty(STRUCT_FROM_PDB,
 493             Boolean.toString(structFromPdb.isSelected()));
 494     Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY, structViewer
 495             .getSelectedItem().toString());
 496     Cache.setOrRemove(CHIMERA_PATH, chimeraPath.getText());
 497
 498     /*
 499      * Save Output settings
 500      */
 501     if (epsRendering.getSelectedItem().equals("Prompt each time"))
 502     {
 503       Cache.applicationProperties.remove("EPS_RENDERING");
 504     }
 505     else
 506     {
 507       Cache.applicationProperties.setProperty("EPS_RENDERING", epsRendering
 508               .getSelectedItem().toString());
 509     }
 510
 511     /*
 512      * Save Connections settings
 513      */
 514     Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText());
 515
 516     jalview.util.BrowserLauncher.resetBrowser();
 517
 518     if (nameLinks.size() > 0)
 519     {
 520       StringBuffer links = new StringBuffer();
 521       sequenceURLLinks = new Vector();
 522       for (int i = 0; i < nameLinks.size(); i++)
 523       {
 524         sequenceURLLinks.addElement(nameLinks.elementAt(i) + "|"
 525                 + urlLinks.elementAt(i));
 526         links.append(sequenceURLLinks.elementAt(i).toString());
 527         links.append("|");
 528       }
 529       // remove last "|"
 530       links.setLength(links.length() - 1);
 531       Cache.applicationProperties.setProperty("SEQUENCE_LINKS",
 532               links.toString());
 533     }
 534     else
 535     {
 536       Cache.applicationProperties.remove("SEQUENCE_LINKS");
 537     }
 538
 539     Cache.applicationProperties.setProperty("USE_PROXY",
 540             Boolean.toString(useProxy.isSelected()));
 541
 542     Cache.setOrRemove("PROXY_SERVER", proxyServerTB.getText());
 543
 544     Cache.setOrRemove("PROXY_PORT", proxyPortTB.getText());
 545
 546     if (useProxy.isSelected())
 547     {
 548       System.setProperty("http.proxyHost", proxyServerTB.getText());
 549       System.setProperty("http.proxyPort", proxyPortTB.getText());
 550     }
 551     else
 552     {
 553       System.setProperty("http.proxyHost", "");
 554       System.setProperty("http.proxyPort", "");
 555     }
 556     Cache.setProperty("VERSION_CHECK",
 557             Boolean.toString(versioncheck.isSelected()));
 558     if (Cache.getProperty("USAGESTATS") != null || usagestats.isSelected())
 559     {
 560       // default is false - we only set this if the user has actively agreed
 561       Cache.setProperty("USAGESTATS",
 562               Boolean.toString(usagestats.isSelected()));
 563     }
 564     if (!questionnaire.isSelected())
 565     {
 566       Cache.setProperty("NOQUESTIONNAIRES", "true");
 567     }
 568     else
 569     {
 570       // special - made easy to edit a property file to disable questionnaires
 571       // by just adding the given line
 572       Cache.removeProperty("NOQUESTIONNAIRES");
 573     }
 574
 575     /*
 576      * Save Output settings
 577      */
 578     Cache.applicationProperties.setProperty("BLC_JVSUFFIX",
 579             Boolean.toString(blcjv.isSelected()));
 580     Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX",
 581             Boolean.toString(clustaljv.isSelected()));
 582     Cache.applicationProperties.setProperty("FASTA_JVSUFFIX",
 583             Boolean.toString(fastajv.isSelected()));
 584     Cache.applicationProperties.setProperty("MSF_JVSUFFIX",
 585             Boolean.toString(msfjv.isSelected()));
 586     Cache.applicationProperties.setProperty("PFAM_JVSUFFIX",
 587             Boolean.toString(pfamjv.isSelected()));
 588     Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX",
 589             Boolean.toString(pileupjv.isSelected()));
 590     Cache.applicationProperties.setProperty("PIR_JVSUFFIX",
 591             Boolean.toString(pirjv.isSelected()));
 592     Cache.applicationProperties.setProperty("PIR_MODELLER",
 593             Boolean.toString(modellerOutput.isSelected()));
 594     Cache.applicationProperties.setProperty("EXPORT_EMBBED_BIOJSON",
 595             Boolean.toString(embbedBioJSON.isSelected()));
 596     jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
 597
 598     Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH",
 599             Boolean.toString(autoIdWidth.isSelected()));
 600     userIdWidth_actionPerformed();
 601     Cache.applicationProperties.setProperty("FIGURE_USERIDWIDTH",
 602             userIdWidth.getText());
 603
 604     /*
 605      * Save Editing settings
 606      */
 607     Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
 608             Boolean.toString(autoCalculateConsCheck.isSelected()));
 609     Cache.applicationProperties.setProperty("SORT_BY_TREE",
 610             Boolean.toString(sortByTree.isSelected()));
 611     Cache.applicationProperties.setProperty("PAD_GAPS",
 612             Boolean.toString(padGaps.isSelected()));
 613
 614     dasSource.saveProperties(Cache.applicationProperties);
 615     wsPrefs.updateAndRefreshWsMenuConfig(false);
 616     Cache.saveProperties();
 617     Desktop.instance.doConfigureStructurePrefs();
 618     try
 619     {
 620       frame.setClosed(true);
 621     } catch (Exception ex)
 622     {
 623     }
 624   }
 625
 626   /**
 627    * Do any necessary validation before saving settings. Return focus to the
 628    * first tab which fails validation.
 629    *
 630    * @return
 631    */
 632   private boolean validateSettings()
 633   {
 634     if (!validateStructure())
 635     {
 636       structureTab.requestFocusInWindow();
 637       return false;
 638     }
 639     return true;
 640   }
 641
 642   @Override
 643   protected boolean validateStructure()
 644   {
 645     return validateChimeraPath();
 646
 647   }
 648   /**
 649    * DOCUMENT ME!
 650    */
 651   public void startupFileTextfield_mouseClicked()
 652   {
 653     JalviewFileChooser chooser = new JalviewFileChooser(
 654             jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
 655             new String[]
 656             { "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc", "jar" },
 657             new String[]
 658             { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview" },
 659             jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));
 660     chooser.setFileView(new JalviewFileView());
 661     chooser.setDialogTitle(MessageManager.getString("label.select_startup_file"));
 662
 663     int value = chooser.showOpenDialog(this);
 664
 665     if (value == JalviewFileChooser.APPROVE_OPTION)
 666     {
 667       jalview.bin.Cache.applicationProperties.setProperty(
 668               "DEFAULT_FILE_FORMAT", chooser.getSelectedFormat());
 669       startupFileTextfield.setText(chooser.getSelectedFile()
 670               .getAbsolutePath());
 671     }
 672   }
 673
 674   /**
 675    * DOCUMENT ME!
 676    *
 677    * @param e
 678    *          DOCUMENT ME!
 679    */
 680   public void cancel_actionPerformed(ActionEvent e)
 681   {
 682     try
 683     {
 684       wsPrefs.updateWsMenuConfig(true);
 685       wsPrefs.refreshWs_actionPerformed(e);
 686       frame.setClosed(true);
 687     } catch (Exception ex)
 688     {
 689     }
 690   }
 691
 692   /**
 693    * DOCUMENT ME!
 694    *
 695    * @param e
 696    *          DOCUMENT ME!
 697    */
 698   public void annotations_actionPerformed(ActionEvent e)
 699   {
 700     conservation.setEnabled(annotations.isSelected());
 701     quality.setEnabled(annotations.isSelected());
 702     identity.setEnabled(annotations.isSelected());
 703     showGroupConsensus.setEnabled(annotations.isSelected());
 704     showGroupConservation.setEnabled(annotations.isSelected());
 705     showConsensHistogram.setEnabled(annotations.isSelected()
 706             && (identity.isSelected() || showGroupConsensus.isSelected()));
 707     showConsensLogo.setEnabled(annotations.isSelected()
 708             && (identity.isSelected() || showGroupConsensus.isSelected()));
 709   }
 710
 711   public void newLink_actionPerformed(ActionEvent e)
 712   {
 713
 714     GSequenceLink link = new GSequenceLink();
 715     boolean valid = false;
 716     while (!valid)
 717     {
 718       if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 719               MessageManager.getString("label.new_sequence_url_link"),
 720               JOptionPane.OK_CANCEL_OPTION, -1, null) == JOptionPane.OK_OPTION)
 721       {
 722         if (link.checkValid())
 723         {
 724           nameLinks.addElement(link.getName());
 725           urlLinks.addElement(link.getURL());
 726           updateLinkData();
 727           valid = true;
 728         }
 729       }
 730       else
 731       {
 732         break;
 733       }
 734     }
 735   }
 736
 737   public void editLink_actionPerformed(ActionEvent e)
 738   {
 739     GSequenceLink link = new GSequenceLink();
 740
 741     int index = linkNameList.getSelectedIndex();
 742     if (index == -1)
 743     {
 744       JOptionPane.showInternalMessageDialog(Desktop.desktop,
 745               MessageManager.getString("label.no_link_selected"),
 746               MessageManager.getString("label.no_link_selected"),
 747               JOptionPane.WARNING_MESSAGE);
 748       return;
 749     }
 750
 751     link.setName(nameLinks.elementAt(index).toString());
 752     link.setURL(urlLinks.elementAt(index).toString());
 753
 754     boolean valid = false;
 755     while (!valid)
 756     {
 757
 758       if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 759               MessageManager.getString("label.new_sequence_url_link"),
 760               JOptionPane.OK_CANCEL_OPTION, -1, null) == JOptionPane.OK_OPTION)
 761       {
 762         if (link.checkValid())
 763         {
 764           nameLinks.setElementAt(link.getName(), index);
 765           urlLinks.setElementAt(link.getURL(), index);
 766           updateLinkData();
 767           valid = true;
 768         }
 769       }
 770
 771       else
 772       {
 773         break;
 774       }
 775     }
 776   }
 777
 778   public void deleteLink_actionPerformed(ActionEvent e)
 779   {
 780     int index = linkNameList.getSelectedIndex();
 781     if (index == -1)
 782     {
 783       JOptionPane.showInternalMessageDialog(Desktop.desktop,
 784               MessageManager.getString("label.no_link_selected"),
 785               MessageManager.getString("label.no_link_selected"),
 786               JOptionPane.WARNING_MESSAGE);
 787       return;
 788     }
 789     nameLinks.removeElementAt(index);
 790     urlLinks.removeElementAt(index);
 791     updateLinkData();
 792   }
 793
 794   void updateLinkData()
 795   {
 796     linkNameList.setListData(nameLinks);
 797     linkURLList.setListData(urlLinks);
 798   }
 799
 800   public void defaultBrowser_mouseClicked(MouseEvent e)
 801   {
 802     JFileChooser chooser = new JFileChooser(".");
 803     chooser.setDialogTitle(MessageManager.getString("label.select_default_browser"));
 804
 805     int value = chooser.showOpenDialog(this);
 806
 807     if (value == JFileChooser.APPROVE_OPTION)
 808     {
 809       defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
 810     }
 811
 812   }
 813
 814   /*
 815    * (non-Javadoc)
 816    *
 817    * @see
 818    * jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event
 819    * .ActionEvent)
 820    */
 821   protected void showunconserved_actionPerformed(ActionEvent e)
 822   {
 823     // TODO Auto-generated method stub
 824     super.showunconserved_actionPerformed(e);
 825   }
 826
 827   public static Collection getGroupURLLinks()
 828   {
 829     return groupURLLinks;
 830   }
 831
 832   @Override
 833   public void minColour_actionPerformed(JPanel panel)
 834   {
 835     Color col = JColorChooser.showDialog(this,
 836             MessageManager.getString("label.select_colour_minimum_value"), minColour.getBackground());
 837     if (col != null)
 838     {
 839       panel.setBackground(col);
 840     }
 841     panel.repaint();
 842   }
 843
 844   @Override
 845   public void maxColour_actionPerformed(JPanel panel)
 846   {
 847     Color col = JColorChooser.showDialog(this,
 848             MessageManager.getString("label.select_colour_maximum_value"), maxColour.getBackground());
 849     if (col != null)
 850     {
 851       panel.setBackground(col);
 852     }
 853     panel.repaint();
 854   }
 855
 856   @Override
 857   protected void userIdWidth_actionPerformed()
 858   {
 859     try
 860     {
 861       String val = userIdWidth.getText().trim();
 862       if (val.length() > 0)
 863       {
 864         Integer iw = Integer.parseInt(val);
 865         if (iw.intValue() < 12)
 866         {
 867           throw new NumberFormatException();
 868         }
 869         userIdWidth.setText(iw.toString());
 870       }
 871     } catch (NumberFormatException x)
 872     {
 873       JOptionPane
 874               .showInternalMessageDialog(
 875                       Desktop.desktop,
 876                       MessageManager.getString("warn.user_defined_width_requirements"),
 877                       MessageManager.getString("label.invalid_id_column_width"),
 878                       JOptionPane.WARNING_MESSAGE);
 879       userIdWidth.setText("");
 880     }
 881   }
 882
 883   @Override
 884   protected void autoIdWidth_actionPerformed()
 885   {
 886     userIdWidth.setEnabled(!autoIdWidth.isSelected());
 887     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
 888   }
 889
 890   /**
 891    * Returns true if chimera path is to a valid executable, else show an error
 892    * dialog.
 893    */
 894   private boolean validateChimeraPath()
 895   {
 896     if (chimeraPath.getText().trim().length() > 0)
 897     {
 898       File f = new File(chimeraPath.getText());
 899       if (!f.canExecute())
 900       {
 901         JOptionPane.showInternalMessageDialog(Desktop.desktop,
 902                 MessageManager.getString("label.invalid_chimera_path"),
 903                 MessageManager.getString("label.invalid_name"),
 904                 JOptionPane.ERROR_MESSAGE);
 905         return false;
 906       }
 907     }
 908     return true;
 909   }
 910
 911   /**
 912    * If Chimera is selected, check it can be found on default or user-specified
 913    * path, if not show a warning/help dialog.
 914    */
 915   @Override
 916   protected void structureViewer_actionPerformed(String selectedItem)
 917   {
 918     if (!selectedItem.equals(ViewerType.CHIMERA.name()))
 919     {
 920       return;
 921     }
 922     boolean found = false;
 923
 924     /*
 925      * Try user-specified and standard paths for Chimera executable.
 926      */
 927     List<String> paths = StructureManager.getChimeraPaths();
 928     paths.add(0, chimeraPath.getText());
 929     for (String path : paths)
 930     {
 931       if (new File(path.trim()).canExecute())
 932       {
 933         found = true;
 934         break;
 935       }
 936     }
 937     if (!found)
 938     {
 939       String[] options =
 940       { "OK", "Help" };
 941       int showHelp = JOptionPane.showInternalOptionDialog(
 942               Desktop.desktop,
 943               JvSwingUtils.wrapTooltip(true,
 944                       MessageManager.getString("label.chimera_missing")),
 945               "", JOptionPane.YES_NO_OPTION,
 946               JOptionPane.WARNING_MESSAGE, null, options, options[0]);
 947       if (showHelp == JOptionPane.NO_OPTION)
 948       {
 949         try
 950         {
 951           Help.showHelpWindow(HelpId.StructureViewer);
 952         } catch (HelpSetException e)
 953         {
 954           e.printStackTrace();
 955         }
 956       }
 957     }
 958   }
 959
 960 }