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.io.PIRFile;
  30 import jalview.jbgui.GPreferences;
  31 import jalview.jbgui.GSequenceLink;
  32 import jalview.schemes.ColourSchemeProperty;
  33 import jalview.util.BrowserLauncher;
  34 import jalview.util.MessageManager;
  35 import jalview.util.Platform;
  36
  37 import java.awt.BorderLayout;
  38 import java.awt.Color;
  39 import java.awt.Dimension;
  40 import java.awt.Font;
  41 import java.awt.event.ActionEvent;
  42 import java.awt.event.ActionListener;
  43 import java.awt.event.MouseEvent;
  44 import java.io.File;
  45 import java.util.Collection;
  46 import java.util.List;
  47 import java.util.StringTokenizer;
  48 import java.util.Vector;
  49
  50 import javax.help.HelpSetException;
  51 import javax.swing.JColorChooser;
  52 import javax.swing.JFileChooser;
  53 import javax.swing.JInternalFrame;
  54 import javax.swing.JOptionPane;
  55 import javax.swing.JPanel;
  56
  57 import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
  58
  59 /**
  60  * DOCUMENT ME!
  61  *
  62  * @author $author$
  63  * @version $Revision$
  64  */
  65 public class Preferences extends GPreferences
  66 {
  67   public static final String ENABLE_SPLIT_FRAME = "ENABLE_SPLIT_FRAME";
  68
  69   public static final String SCALE_PROTEIN_TO_CDNA = "SCALE_PROTEIN_TO_CDNA";
  70
  71   public static final String DEFAULT_COLOUR = "DEFAULT_COLOUR";
  72
  73   public static final String DEFAULT_COLOUR_PROT = "DEFAULT_COLOUR_PROT";
  74
  75   public static final String DEFAULT_COLOUR_NUC = "DEFAULT_COLOUR_NUC";
  76
  77   public static final String ADD_TEMPFACT_ANN = "ADD_TEMPFACT_ANN";
  78
  79   public static final String ADD_SS_ANN = "ADD_SS_ANN";
  80
  81   public static final String USE_RNAVIEW = "USE_RNAVIEW";
  82
  83   public static final String STRUCT_FROM_PDB = "STRUCT_FROM_PDB";
  84
  85   public static final String STRUCTURE_DISPLAY = "STRUCTURE_DISPLAY";
  86
  87   public static final String CHIMERA_PATH = "CHIMERA_PATH";
  88
  89   public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS";
  90
  91   public static final String SHOW_AUTOCALC_ABOVE = "SHOW_AUTOCALC_ABOVE";
  92
  93   private static final int MIN_FONT_SIZE = 1;
  94
  95   private static final int MAX_FONT_SIZE = 30;
  96
  97   /**
  98    * Holds name and link separated with | character. Sequence ID must be
  99    * $SEQUENCE_ID$ or $SEQUENCE_ID=/.possible | chars ./=$
 100    */
 101   public static Vector sequenceURLLinks;
 102
 103   /**
 104    * Holds name and link separated with | character. Sequence IDS and Sequences
 105    * must be $SEQUENCEIDS$ or $SEQUENCEIDS=/.possible | chars ./=$ and
 106    * $SEQUENCES$ or $SEQUENCES=/.possible | chars ./=$ and separation character
 107    * for first and second token specified after a pipe character at end |,|.
 108    * (TODO: proper escape for using | to separate ids or sequences
 109    */
 110
 111   public static Vector groupURLLinks;
 112   static
 113   {
 114     String string = Cache
 115             .getDefault(
 116                     "SEQUENCE_LINKS",
 117                     "EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$");
 118     sequenceURLLinks = new Vector();
 119
 120     try
 121     {
 122       StringTokenizer st = new StringTokenizer(string, "|");
 123       while (st.hasMoreElements())
 124       {
 125         String name = st.nextToken();
 126         String url = st.nextToken();
 127         // check for '|' within a regex
 128         int rxstart = url.indexOf("$SEQUENCE_ID$");
 129         while (rxstart == -1 && url.indexOf("/=$") == -1)
 130         {
 131           url = url + "|" + st.nextToken();
 132         }
 133         sequenceURLLinks.addElement(name + "|" + url);
 134       }
 135     } catch (Exception ex)
 136     {
 137       System.out.println(ex + "\nError parsing sequence links");
 138     }
 139     {
 140       // upgrade old SRS link
 141       int srsPos = sequenceURLLinks
 142               .indexOf("SRS|http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$SEQUENCE_ID$]))+-view+SwissEntry");
 143       if (srsPos > -1)
 144       {
 145         sequenceURLLinks
 146                 .setElementAt(
 147                         "EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$",
 148                         srsPos);
 149       }
 150     }
 151
 152     /**
 153      * TODO: reformulate groupURL encoding so two or more can be stored in the
 154      * .properties file as '|' separated strings
 155      */
 156
 157     groupURLLinks = new Vector();
 158   }
 159
 160   Vector nameLinks, urlLinks;
 161
 162   JInternalFrame frame;
 163
 164   DasSourceBrowser dasSource;
 165
 166   private WsPreferences wsPrefs;
 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,
 270             true);
 271     sortAutocalc.setSelectedItem(showAbove ? sortAutocalc.getItemAt(0)
 272             : sortAutocalc.getItemAt(1));
 273     startupCheckbox
 274             .setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
 275     startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
 276             Cache.getDefault("www.jalview.org", "http://www.jalview.org")
 277                     + "/examples/exampleFile_2_3.jar"));
 278
 279     /*
 280      * Set Colours tab defaults
 281      */
 282     for (int i = ColourSchemeProperty.FIRST_COLOUR; i <= ColourSchemeProperty.LAST_COLOUR; i++)
 283     {
 284       protColour.addItem(ColourSchemeProperty.getColourName(i));
 285       nucColour.addItem(ColourSchemeProperty.getColourName(i));
 286     }
 287     String oldProp = Cache.getDefault(DEFAULT_COLOUR, "None");
 288     String newProp = Cache.getDefault(DEFAULT_COLOUR_PROT, null);
 289     protColour.setSelectedItem(newProp != null ? newProp : oldProp);
 290     newProp = Cache.getDefault(DEFAULT_COLOUR_NUC, null);
 291     nucColour.setSelectedItem(newProp != null ? newProp : oldProp);
 292     minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN",
 293             Color.orange));
 294     maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX",
 295             Color.red));
 296
 297     /*
 298      * Set Structure tab defaults.
 299      */
 300     final boolean structSelected = Cache.getDefault(STRUCT_FROM_PDB, false);
 301     structFromPdb.setSelected(structSelected);
 302     useRnaView.setSelected(Cache.getDefault(USE_RNAVIEW, false));
 303     useRnaView.setEnabled(structSelected);
 304     addSecondaryStructure
 305             .setSelected(Cache.getDefault(ADD_SS_ANN, false));
 306     addSecondaryStructure.setEnabled(structSelected);
 307     addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, false));
 308     addTempFactor.setEnabled(structSelected);
 309     structViewer.setSelectedItem(Cache.getDefault(STRUCTURE_DISPLAY,
 310             ViewerType.JMOL.name()));
 311     chimeraPath.setText(Cache.getDefault(CHIMERA_PATH, ""));
 312     chimeraPath.addActionListener(new ActionListener()
 313     {
 314       @Override
 315       public void actionPerformed(ActionEvent e)
 316       {
 317         validateChimeraPath();
 318       }
 319     });
 320
 321     /*
 322      * Set Connections tab defaults
 323      */
 324     nameLinks = new Vector();
 325     urlLinks = new Vector();
 326     for (int i = 0; i < sequenceURLLinks.size(); i++)
 327     {
 328       String link = sequenceURLLinks.elementAt(i).toString();
 329       nameLinks.addElement(link.substring(0, link.indexOf("|")));
 330       urlLinks.addElement(link.substring(link.indexOf("|") + 1));
 331     }
 332
 333     updateLinkData();
 334
 335     useProxy.setSelected(Cache.getDefault("USE_PROXY", false));
 336     proxyServerTB.setEnabled(useProxy.isSelected());
 337     proxyPortTB.setEnabled(useProxy.isSelected());
 338     proxyServerTB.setText(Cache.getDefault("PROXY_SERVER", ""));
 339     proxyPortTB.setText(Cache.getDefault("PROXY_PORT", ""));
 340
 341     defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", ""));
 342
 343     usagestats.setSelected(Cache.getDefault("USAGESTATS", false));
 344     // note antisense here: default is true
 345     questionnaire
 346             .setSelected(Cache.getProperty("NOQUESTIONNAIRES") == null);
 347     versioncheck.setSelected(Cache.getDefault("VERSION_CHECK", true));
 348
 349     /*
 350      * Set Output tab defaults
 351      */
 352     epsRendering
 353             .addItem(MessageManager.getString("label.prompt_each_time"));
 354     epsRendering.addItem(MessageManager.getString("label.lineart"));
 355     epsRendering.addItem(MessageManager.getString("action.text"));
 356     epsRendering.setSelectedItem(Cache.getDefault("EPS_RENDERING",
 357             "Prompt each time"));
 358     autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false));
 359     userIdWidth.setEnabled(autoIdWidth.isSelected());
 360     userIdWidthlabel.setEnabled(autoIdWidth.isSelected());
 361     Integer wi = Cache.getIntegerProperty("FIGURE_USERIDWIDTH");
 362     userIdWidth.setText(wi == null ? "" : wi.toString());
 363     blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
 364     clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
 365     fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
 366     msfjv.setSelected(Cache.getDefault("MSF_JVSUFFIX", true));
 367     pfamjv.setSelected(Cache.getDefault("PFAM_JVSUFFIX", true));
 368     pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
 369     pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
 370     modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
 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,
 470             Boolean.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 Vector();
 523       for (int i = 0; i < nameLinks.size(); i++)
 524       {
 525         sequenceURLLinks.addElement(nameLinks.elementAt(i) + "|"
 526                 + urlLinks.elementAt(i));
 527         links.append(sequenceURLLinks.elementAt(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("MSF_JVSUFFIX",
 586             Boolean.toString(msfjv.isSelected()));
 587     Cache.applicationProperties.setProperty("PFAM_JVSUFFIX",
 588             Boolean.toString(pfamjv.isSelected()));
 589     Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX",
 590             Boolean.toString(pileupjv.isSelected()));
 591     Cache.applicationProperties.setProperty("PIR_JVSUFFIX",
 592             Boolean.toString(pirjv.isSelected()));
 593     Cache.applicationProperties.setProperty("PIR_MODELLER",
 594             Boolean.toString(modellerOutput.isSelected()));
 595     PIRFile.useModellerOutput = modellerOutput.isSelected();
 596
 597     Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH",
 598             Boolean.toString(autoIdWidth.isSelected()));
 599     userIdWidth_actionPerformed();
 600     Cache.applicationProperties.setProperty("FIGURE_USERIDWIDTH",
 601             userIdWidth.getText());
 602
 603     /*
 604      * Save Editing settings
 605      */
 606     Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
 607             Boolean.toString(autoCalculateConsCheck.isSelected()));
 608     Cache.applicationProperties.setProperty("SORT_BY_TREE",
 609             Boolean.toString(sortByTree.isSelected()));
 610     Cache.applicationProperties.setProperty("PAD_GAPS",
 611             Boolean.toString(padGaps.isSelected()));
 612
 613     dasSource.saveProperties(Cache.applicationProperties);
 614     wsPrefs.updateAndRefreshWsMenuConfig(false);
 615     Cache.saveProperties();
 616     Desktop.instance.doConfigureStructurePrefs();
 617     try
 618     {
 619       frame.setClosed(true);
 620     } catch (Exception ex)
 621     {
 622     }
 623   }
 624
 625   /**
 626    * Do any necessary validation before saving settings. Return focus to the
 627    * first tab which fails validation.
 628    *
 629    * @return
 630    */
 631   private boolean validateSettings()
 632   {
 633     if (!validateStructure())
 634     {
 635       structureTab.requestFocusInWindow();
 636       return false;
 637     }
 638     return true;
 639   }
 640
 641   @Override
 642   protected boolean validateStructure()
 643   {
 644     return validateChimeraPath();
 645
 646   }
 647   /**
 648    * DOCUMENT ME!
 649    */
 650   public void startupFileTextfield_mouseClicked()
 651   {
 652     JalviewFileChooser chooser = new JalviewFileChooser(
 653             Cache.getProperty("LAST_DIRECTORY"),
 654             new String[]
 655             { "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc", "jar" },
 656             new String[]
 657             { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview" },
 658             Cache.getProperty("DEFAULT_FILE_FORMAT"));
 659     chooser.setFileView(new JalviewFileView());
 660     chooser.setDialogTitle(MessageManager.getString("label.select_startup_file"));
 661
 662     int value = chooser.showOpenDialog(this);
 663
 664     if (value == JalviewFileChooser.APPROVE_OPTION)
 665     {
 666       Cache.applicationProperties.setProperty(
 667               "DEFAULT_FILE_FORMAT", chooser.getSelectedFormat());
 668       startupFileTextfield.setText(chooser.getSelectedFile()
 669               .getAbsolutePath());
 670     }
 671   }
 672
 673   /**
 674    * DOCUMENT ME!
 675    *
 676    * @param e
 677    *          DOCUMENT ME!
 678    */
 679   public void cancel_actionPerformed(ActionEvent e)
 680   {
 681     try
 682     {
 683       wsPrefs.updateWsMenuConfig(true);
 684       wsPrefs.refreshWs_actionPerformed(e);
 685       frame.setClosed(true);
 686     } catch (Exception ex)
 687     {
 688     }
 689   }
 690
 691   /**
 692    * DOCUMENT ME!
 693    *
 694    * @param e
 695    *          DOCUMENT ME!
 696    */
 697   public void annotations_actionPerformed(ActionEvent e)
 698   {
 699     conservation.setEnabled(annotations.isSelected());
 700     quality.setEnabled(annotations.isSelected());
 701     identity.setEnabled(annotations.isSelected());
 702     showGroupConsensus.setEnabled(annotations.isSelected());
 703     showGroupConservation.setEnabled(annotations.isSelected());
 704     showConsensHistogram.setEnabled(annotations.isSelected()
 705             && (identity.isSelected() || showGroupConsensus.isSelected()));
 706     showConsensLogo.setEnabled(annotations.isSelected()
 707             && (identity.isSelected() || showGroupConsensus.isSelected()));
 708   }
 709
 710   public void newLink_actionPerformed(ActionEvent e)
 711   {
 712
 713     GSequenceLink link = new GSequenceLink();
 714     boolean valid = false;
 715     while (!valid)
 716     {
 717       if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 718               MessageManager.getString("label.new_sequence_url_link"),
 719               JOptionPane.OK_CANCEL_OPTION, -1, null) == JOptionPane.OK_OPTION)
 720       {
 721         if (link.checkValid())
 722         {
 723           nameLinks.addElement(link.getName());
 724           urlLinks.addElement(link.getURL());
 725           updateLinkData();
 726           valid = true;
 727         }
 728       }
 729       else
 730       {
 731         break;
 732       }
 733     }
 734   }
 735
 736   public void editLink_actionPerformed(ActionEvent e)
 737   {
 738     GSequenceLink link = new GSequenceLink();
 739
 740     int index = linkNameList.getSelectedIndex();
 741     if (index == -1)
 742     {
 743       JOptionPane.showInternalMessageDialog(Desktop.desktop,
 744               MessageManager.getString("label.no_link_selected"),
 745               MessageManager.getString("label.no_link_selected"),
 746               JOptionPane.WARNING_MESSAGE);
 747       return;
 748     }
 749
 750     link.setName(nameLinks.elementAt(index).toString());
 751     link.setURL(urlLinks.elementAt(index).toString());
 752
 753     boolean valid = false;
 754     while (!valid)
 755     {
 756
 757       if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 758               MessageManager.getString("label.new_sequence_url_link"),
 759               JOptionPane.OK_CANCEL_OPTION, -1, null) == JOptionPane.OK_OPTION)
 760       {
 761         if (link.checkValid())
 762         {
 763           nameLinks.setElementAt(link.getName(), index);
 764           urlLinks.setElementAt(link.getURL(), index);
 765           updateLinkData();
 766           valid = true;
 767         }
 768       }
 769
 770       else
 771       {
 772         break;
 773       }
 774     }
 775   }
 776
 777   public void deleteLink_actionPerformed(ActionEvent e)
 778   {
 779     int index = linkNameList.getSelectedIndex();
 780     if (index == -1)
 781     {
 782       JOptionPane.showInternalMessageDialog(Desktop.desktop,
 783               MessageManager.getString("label.no_link_selected"),
 784               MessageManager.getString("label.no_link_selected"),
 785               JOptionPane.WARNING_MESSAGE);
 786       return;
 787     }
 788     nameLinks.removeElementAt(index);
 789     urlLinks.removeElementAt(index);
 790     updateLinkData();
 791   }
 792
 793   void updateLinkData()
 794   {
 795     linkNameList.setListData(nameLinks);
 796     linkURLList.setListData(urlLinks);
 797   }
 798
 799   public void defaultBrowser_mouseClicked(MouseEvent e)
 800   {
 801     JFileChooser chooser = new JFileChooser(".");
 802     chooser.setDialogTitle(MessageManager.getString("label.select_default_browser"));
 803
 804     int value = chooser.showOpenDialog(this);
 805
 806     if (value == JFileChooser.APPROVE_OPTION)
 807     {
 808       defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
 809     }
 810
 811   }
 812
 813   /*
 814    * (non-Javadoc)
 815    *
 816    * @see
 817    * jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event
 818    * .ActionEvent)
 819    */
 820   protected void showunconserved_actionPerformed(ActionEvent e)
 821   {
 822     // TODO Auto-generated method stub
 823     super.showunconserved_actionPerformed(e);
 824   }
 825
 826   public static Collection getGroupURLLinks()
 827   {
 828     return groupURLLinks;
 829   }
 830
 831   @Override
 832   public void minColour_actionPerformed(JPanel panel)
 833   {
 834     Color col = JColorChooser.showDialog(this,
 835             MessageManager.getString("label.select_colour_minimum_value"), minColour.getBackground());
 836     if (col != null)
 837     {
 838       panel.setBackground(col);
 839     }
 840     panel.repaint();
 841   }
 842
 843   @Override
 844   public void maxColour_actionPerformed(JPanel panel)
 845   {
 846     Color col = JColorChooser.showDialog(this,
 847             MessageManager.getString("label.select_colour_maximum_value"), 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
 873               .showInternalMessageDialog(
 874                       Desktop.desktop,
 875                       MessageManager.getString("warn.user_defined_width_requirements"),
 876                       MessageManager.getString("label.invalid_id_column_width"),
 877                       JOptionPane.WARNING_MESSAGE);
 878       userIdWidth.setText("");
 879     }
 880   }
 881
 882   @Override
 883   protected void autoIdWidth_actionPerformed()
 884   {
 885     userIdWidth.setEnabled(!autoIdWidth.isSelected());
 886     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
 887   }
 888
 889   /**
 890    * Returns true if chimera path is to a valid executable, else show an error
 891    * dialog.
 892    */
 893   private boolean validateChimeraPath()
 894   {
 895     if (chimeraPath.getText().trim().length() > 0)
 896     {
 897       File f = new File(chimeraPath.getText());
 898       if (!f.canExecute())
 899       {
 900         JOptionPane.showInternalMessageDialog(Desktop.desktop,
 901                 MessageManager.getString("label.invalid_chimera_path"),
 902                 MessageManager.getString("label.invalid_name"),
 903                 JOptionPane.ERROR_MESSAGE);
 904         return false;
 905       }
 906     }
 907     return true;
 908   }
 909
 910   /**
 911    * If Chimera is selected, check it can be found on default or user-specified
 912    * path, if not show a warning/help dialog.
 913    */
 914   @Override
 915   protected void structureViewer_actionPerformed(String selectedItem)
 916   {
 917     if (!selectedItem.equals(ViewerType.CHIMERA.name()))
 918     {
 919       return;
 920     }
 921     boolean found = false;
 922
 923     /*
 924      * Try user-specified and standard paths for Chimera executable.
 925      */
 926     List<String> paths = StructureManager.getChimeraPaths();
 927     paths.add(0, chimeraPath.getText());
 928     for (String path : paths)
 929     {
 930       if (new File(path.trim()).canExecute())
 931       {
 932         found = true;
 933         break;
 934       }
 935     }
 936     if (!found)
 937     {
 938       String[] options =
 939       { "OK", "Help" };
 940       int showHelp = JOptionPane.showInternalOptionDialog(
 941               Desktop.desktop,
 942               JvSwingUtils.wrapTooltip(true,
 943                       MessageManager.getString("label.chimera_missing")),
 944               "", JOptionPane.YES_NO_OPTION,
 945               JOptionPane.WARNING_MESSAGE, null, options, options[0]);
 946       if (showHelp == JOptionPane.NO_OPTION)
 947       {
 948         try
 949         {
 950           Help.showHelpWindow(HelpId.StructureViewer);
 951         } catch (HelpSetException e)
 952         {
 953           e.printStackTrace();
 954         }
 955       }
 956     }
 957   }
 958
 959 }