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 import jalview.util.Platform;
  34 import jalview.ws.sifts.SiftsSettings;
  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 import java.util.Vector;
  48
  49 import javax.help.HelpSetException;
  50 import javax.swing.JColorChooser;
  51 import javax.swing.JFileChooser;
  52 import javax.swing.JInternalFrame;
  53 import javax.swing.JOptionPane;
  54 import javax.swing.JPanel;
  55
  56 import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
  57
  58 /**
  59  * DOCUMENT ME!
  60  *
  61  * @author $author$
  62  * @version $Revision$
  63  */
  64 public class Preferences extends GPreferences
  65 {
  66   public static final String ENABLE_SPLIT_FRAME = "ENABLE_SPLIT_FRAME";
  67
  68   public static final String SCALE_PROTEIN_TO_CDNA = "SCALE_PROTEIN_TO_CDNA";
  69
  70   public static final String DEFAULT_COLOUR = "DEFAULT_COLOUR";
  71
  72   public static final String DEFAULT_COLOUR_PROT = "DEFAULT_COLOUR_PROT";
  73
  74   public static final String DEFAULT_COLOUR_NUC = "DEFAULT_COLOUR_NUC";
  75
  76   public static final String ADD_TEMPFACT_ANN = "ADD_TEMPFACT_ANN";
  77
  78   public static final String ADD_SS_ANN = "ADD_SS_ANN";
  79
  80   public static final String USE_RNAVIEW = "USE_RNAVIEW";
  81
  82   public static final String STRUCT_FROM_PDB = "STRUCT_FROM_PDB";
  83
  84   public static final String STRUCTURE_DISPLAY = "STRUCTURE_DISPLAY";
  85
  86   public static final String CHIMERA_PATH = "CHIMERA_PATH";
  87
  88   public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS";
  89
  90   public static final String SHOW_AUTOCALC_ABOVE = "SHOW_AUTOCALC_ABOVE";
  91
  92   private static final int MIN_FONT_SIZE = 1;
  93
  94   private static final int MAX_FONT_SIZE = 30;
  95
  96   /**
  97    * Holds name and link separated with | character. Sequence ID must be
  98    * $SEQUENCE_ID$ or $SEQUENCE_ID=/.possible | chars ./=$
  99    */
 100   public static Vector<String> sequenceURLLinks;
 101
 102   /**
 103    * Holds name and link separated with | character. Sequence IDS and Sequences
 104    * must be $SEQUENCEIDS$ or $SEQUENCEIDS=/.possible | chars ./=$ and
 105    * $SEQUENCES$ or $SEQUENCES=/.possible | chars ./=$ and separation character
 106    * for first and second token specified after a pipe character at end |,|.
 107    * (TODO: proper escape for using | to separate ids or sequences
 108    */
 109
 110   public static List<String> groupURLLinks;
 111   static
 112   {
 113     String string = Cache
 114             .getDefault(
 115                     "SEQUENCE_LINKS",
 116                     "EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$");
 117     sequenceURLLinks = new Vector<String>();
 118
 119     try
 120     {
 121       StringTokenizer st = new StringTokenizer(string, "|");
 122       while (st.hasMoreElements())
 123       {
 124         String name = st.nextToken();
 125         String url = st.nextToken();
 126         // check for '|' within a regex
 127         int rxstart = url.indexOf("$SEQUENCE_ID$");
 128         while (rxstart == -1 && url.indexOf("/=$") == -1)
 129         {
 130           url = url + "|" + st.nextToken();
 131         }
 132         sequenceURLLinks.addElement(name + "|" + url);
 133       }
 134     } catch (Exception ex)
 135     {
 136       System.out.println(ex + "\nError parsing sequence links");
 137     }
 138     {
 139       // upgrade old SRS link
 140       int srsPos = sequenceURLLinks
 141               .indexOf("SRS|http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$SEQUENCE_ID$]))+-view+SwissEntry");
 142       if (srsPos > -1)
 143       {
 144         sequenceURLLinks
 145                 .setElementAt(
 146                         "EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$",
 147                         srsPos);
 148       }
 149     }
 150
 151     /**
 152      * TODO: reformulate groupURL encoding so two or more can be stored in the
 153      * .properties file as '|' separated strings
 154      */
 155
 156     groupURLLinks = new ArrayList<String>();
 157   }
 158
 159   Vector<String> nameLinks, urlLinks;
 160
 161   JInternalFrame frame;
 162
 163   DasSourceBrowser dasSource;
 164
 165   private WsPreferences wsPrefs;
 166
 167   private OptionsParam promptEachTimeOpt = new OptionsParam(
 168           MessageManager.getString("label.prompt_each_time"),
 169           "Prompt each time");
 170
 171   private OptionsParam lineArtOpt = new OptionsParam(
 172           MessageManager.getString("label.lineart"), "Lineart");
 173
 174   private OptionsParam textOpt = new OptionsParam(
 175           MessageManager.getString("action.text"), "Text");
 176
 177   /**
 178    * Creates a new Preferences object.
 179    */
 180   public Preferences()
 181   {
 182     super();
 183     frame = new JInternalFrame();
 184     frame.setContentPane(this);
 185     dasSource = new DasSourceBrowser();
 186     dasTab.add(dasSource, BorderLayout.CENTER);
 187     wsPrefs = new WsPreferences();
 188     wsTab.add(wsPrefs, BorderLayout.CENTER);
 189     int width = 500, height = 450;
 190     new jalview.util.Platform();
 191     if (Platform.isAMac())
 192     {
 193       width = 570;
 194       height = 480;
 195     }
 196
 197     Desktop.addInternalFrame(frame,
 198             MessageManager.getString("label.preferences"), width, height);
 199     frame.setMinimumSize(new Dimension(width, height));
 200
 201     /*
 202      * Set Visual tab defaults
 203      */
 204     seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));
 205     rightAlign.setSelected(Cache.getDefault("RIGHT_ALIGN_IDS", false));
 206     fullScreen.setSelected(Cache.getDefault("SHOW_FULLSCREEN", false));
 207     annotations.setSelected(Cache.getDefault("SHOW_ANNOTATIONS", true));
 208
 209     conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));
 210     quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));
 211     identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));
 212     openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false));
 213     showUnconserved
 214             .setSelected(Cache.getDefault("SHOW_UNCONSERVED", false));
 215     showGroupConsensus.setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS",
 216             false));
 217     showGroupConservation.setSelected(Cache.getDefault(
 218             "SHOW_GROUP_CONSERVATION", false));
 219     showConsensHistogram.setSelected(Cache.getDefault(
 220             "SHOW_CONSENSUS_HISTOGRAM", true));
 221     showConsensLogo.setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO",
 222             false));
 223     showNpTooltip.setSelected(Cache
 224             .getDefault("SHOW_NPFEATS_TOOLTIP", true));
 225     showDbRefTooltip.setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP",
 226             true));
 227
 228     String[] fonts = java.awt.GraphicsEnvironment
 229             .getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
 230     for (int i = 0; i < fonts.length; i++)
 231     {
 232       fontNameCB.addItem(fonts[i]);
 233     }
 234
 235     for (int i = MIN_FONT_SIZE; i <= MAX_FONT_SIZE; i++)
 236     {
 237       fontSizeCB.addItem(i + "");
 238     }
 239
 240     fontStyleCB.addItem("plain");
 241     fontStyleCB.addItem("bold");
 242     fontStyleCB.addItem("italic");
 243
 244     fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
 245     fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
 246     fontStyleCB.setSelectedItem(Cache.getDefault("FONT_STYLE", Font.PLAIN
 247             + ""));
 248
 249     smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));
 250     scaleProteinToCdna.setSelected(Cache.getDefault(SCALE_PROTEIN_TO_CDNA,
 251             false));
 252
 253     idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
 254
 255     wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
 256
 257     gapSymbolCB.addItem("-");
 258     gapSymbolCB.addItem(".");
 259
 260     gapSymbolCB.setSelectedItem(Cache.getDefault("GAP_SYMBOL", "-"));
 261
 262     sortby.addItem("No sort");
 263     sortby.addItem("Id");
 264     sortby.addItem("Pairwise Identity");
 265     sortby.setSelectedItem(Cache.getDefault("SORT_ALIGNMENT", "No sort"));
 266
 267     sortAnnBy.addItem(SequenceAnnotationOrder.NONE.toString());
 268     sortAnnBy
 269             .addItem(SequenceAnnotationOrder.SEQUENCE_AND_LABEL.toString());
 270     sortAnnBy
 271             .addItem(SequenceAnnotationOrder.LABEL_AND_SEQUENCE.toString());
 272     SequenceAnnotationOrder savedSort = SequenceAnnotationOrder
 273             .valueOf(Cache.getDefault(SORT_ANNOTATIONS,
 274                     SequenceAnnotationOrder.NONE.name()));
 275     sortAnnBy.setSelectedItem(savedSort.toString());
 276
 277     sortAutocalc.addItem("Autocalculated first");
 278     sortAutocalc.addItem("Autocalculated last");
 279     final boolean showAbove = Cache.getDefault(SHOW_AUTOCALC_ABOVE, true);
 280     sortAutocalc.setSelectedItem(showAbove ? sortAutocalc.getItemAt(0)
 281             : sortAutocalc.getItemAt(1));
 282     startupCheckbox
 283             .setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
 284     startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
 285             Cache.getDefault("www.jalview.org", "http://www.jalview.org")
 286                     + "/examples/exampleFile_2_3.jar"));
 287
 288     /*
 289      * Set Colours tab defaults
 290      */
 291     for (int i = ColourSchemeProperty.FIRST_COLOUR; i <= ColourSchemeProperty.LAST_COLOUR; i++)
 292     {
 293       protColour.addItem(ColourSchemeProperty.getColourName(i));
 294       nucColour.addItem(ColourSchemeProperty.getColourName(i));
 295     }
 296     String oldProp = Cache.getDefault(DEFAULT_COLOUR, "None");
 297     String newProp = Cache.getDefault(DEFAULT_COLOUR_PROT, null);
 298     protColour.setSelectedItem(newProp != null ? newProp : oldProp);
 299     newProp = Cache.getDefault(DEFAULT_COLOUR_NUC, null);
 300     nucColour.setSelectedItem(newProp != null ? newProp : oldProp);
 301     minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN",
 302             Color.orange));
 303     maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX",
 304             Color.red));
 305
 306     /*
 307      * Set Structure tab defaults.
 308      */
 309     final boolean structSelected = Cache.getDefault(STRUCT_FROM_PDB, false);
 310     structFromPdb.setSelected(structSelected);
 311     useRnaView.setSelected(Cache.getDefault(USE_RNAVIEW, false));
 312     useRnaView.setEnabled(structSelected);
 313     addSecondaryStructure.setSelected(Cache.getDefault(ADD_SS_ANN, false));
 314     addSecondaryStructure.setEnabled(structSelected);
 315     addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, false));
 316     addTempFactor.setEnabled(structSelected);
 317     structViewer.setSelectedItem(Cache.getDefault(STRUCTURE_DISPLAY,
 318             ViewerType.JMOL.name()));
 319     chimeraPath.setText(Cache.getDefault(CHIMERA_PATH, ""));
 320     chimeraPath.addActionListener(new ActionListener()
 321     {
 322       @Override
 323       public void actionPerformed(ActionEvent e)
 324       {
 325         validateChimeraPath();
 326       }
 327     });
 328
 329     if (Cache.getDefault("MAP_WITH_SIFTS", false))
 330     {
 331       siftsMapping.setSelected(true);
 332     }
 333     else
 334     {
 335       nwMapping.setSelected(true);
 336     }
 337
 338     SiftsSettings
 339             .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
 340
 341     /*
 342      * Set Connections tab defaults
 343      */
 344     nameLinks = new Vector<String>();
 345     urlLinks = new Vector<String>();
 346     for (int i = 0; i < sequenceURLLinks.size(); i++)
 347     {
 348       String link = sequenceURLLinks.elementAt(i).toString();
 349       nameLinks.addElement(link.substring(0, link.indexOf("|")));
 350       urlLinks.addElement(link.substring(link.indexOf("|") + 1));
 351     }
 352
 353     updateLinkData();
 354
 355     useProxy.setSelected(Cache.getDefault("USE_PROXY", false));
 356     proxyServerTB.setEnabled(useProxy.isSelected());
 357     proxyPortTB.setEnabled(useProxy.isSelected());
 358     proxyServerTB.setText(Cache.getDefault("PROXY_SERVER", ""));
 359     proxyPortTB.setText(Cache.getDefault("PROXY_PORT", ""));
 360
 361     defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", ""));
 362
 363     usagestats.setSelected(Cache.getDefault("USAGESTATS", false));
 364     // note antisense here: default is true
 365     questionnaire
 366             .setSelected(Cache.getProperty("NOQUESTIONNAIRES") == null);
 367     versioncheck.setSelected(Cache.getDefault("VERSION_CHECK", true));
 368
 369     /*
 370      * Set Output tab defaults
 371      */
 372
 373     epsRendering.addItem(promptEachTimeOpt);
 374     epsRendering.addItem(lineArtOpt);
 375     epsRendering.addItem(textOpt);
 376     String defaultEPS = Cache.getDefault("EPS_RENDERING",
 377             "Prompt each time");
 378     if (defaultEPS.equalsIgnoreCase("Text"))
 379     {
 380       epsRendering.setSelectedItem(textOpt);
 381     }
 382     else if (defaultEPS.equalsIgnoreCase("Lineart"))
 383     {
 384       epsRendering.setSelectedItem(lineArtOpt);
 385     }
 386     else
 387     {
 388       epsRendering.setSelectedItem(new OptionsParam(MessageManager
 389               .getString("label.prompt_each_time"), "Prompt each time"));
 390     }
 391     autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false));
 392     userIdWidth.setEnabled(!autoIdWidth.isSelected());
 393     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
 394     Integer wi = Cache.getIntegerProperty("FIGURE_USERIDWIDTH");
 395     userIdWidth.setText(wi == null ? "" : wi.toString());
 396     blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
 397     clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
 398     fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
 399     msfjv.setSelected(Cache.getDefault("MSF_JVSUFFIX", true));
 400     pfamjv.setSelected(Cache.getDefault("PFAM_JVSUFFIX", true));
 401     pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
 402     pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
 403     modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
 404     embbedBioJSON.setSelected(Cache.getDefault("EXPORT_EMBBED_BIOJSON",
 405             true));
 406
 407     /*
 408      * Set Editing tab defaults
 409      */
 410     autoCalculateConsCheck.setSelected(Cache.getDefault(
 411             "AUTO_CALC_CONSENSUS", true));
 412     padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
 413     sortByTree.setSelected(Cache.getDefault("SORT_BY_TREE", false));
 414
 415     annotations_actionPerformed(null); // update the display of the annotation
 416                                        // settings
 417   }
 418
 419   /**
 420    * Save user selections on the Preferences tabs to the Cache and write out to
 421    * file.
 422    *
 423    * @param e
 424    */
 425   @Override
 426   public void ok_actionPerformed(ActionEvent e)
 427   {
 428     if (!validateSettings())
 429     {
 430       return;
 431     }
 432
 433     /*
 434      * Save Visual settings
 435      */
 436     Cache.applicationProperties.setProperty("SHOW_JVSUFFIX",
 437             Boolean.toString(seqLimit.isSelected()));
 438     Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS",
 439             Boolean.toString(rightAlign.isSelected()));
 440     Cache.applicationProperties.setProperty("SHOW_FULLSCREEN",
 441             Boolean.toString(fullScreen.isSelected()));
 442     Cache.applicationProperties.setProperty("SHOW_OVERVIEW",
 443             Boolean.toString(openoverv.isSelected()));
 444     Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
 445             Boolean.toString(annotations.isSelected()));
 446     Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
 447             Boolean.toString(conservation.isSelected()));
 448     Cache.applicationProperties.setProperty("SHOW_QUALITY",
 449             Boolean.toString(quality.isSelected()));
 450     Cache.applicationProperties.setProperty("SHOW_IDENTITY",
 451             Boolean.toString(identity.isSelected()));
 452
 453     Cache.applicationProperties.setProperty("GAP_SYMBOL", gapSymbolCB
 454             .getSelectedItem().toString());
 455
 456     Cache.applicationProperties.setProperty("FONT_NAME", fontNameCB
 457             .getSelectedItem().toString());
 458     Cache.applicationProperties.setProperty("FONT_STYLE", fontStyleCB
 459             .getSelectedItem().toString());
 460     Cache.applicationProperties.setProperty("FONT_SIZE", fontSizeCB
 461             .getSelectedItem().toString());
 462
 463     Cache.applicationProperties.setProperty("ID_ITALICS",
 464             Boolean.toString(idItalics.isSelected()));
 465     Cache.applicationProperties.setProperty("SHOW_UNCONSERVED",
 466             Boolean.toString(showUnconserved.isSelected()));
 467     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS",
 468             Boolean.toString(showGroupConsensus.isSelected()));
 469     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION",
 470             Boolean.toString(showGroupConservation.isSelected()));
 471     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_HISTOGRAM",
 472             Boolean.toString(showConsensHistogram.isSelected()));
 473     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO",
 474             Boolean.toString(showConsensLogo.isSelected()));
 475     Cache.applicationProperties.setProperty("ANTI_ALIAS",
 476             Boolean.toString(smoothFont.isSelected()));
 477     Cache.applicationProperties.setProperty(SCALE_PROTEIN_TO_CDNA,
 478             Boolean.toString(scaleProteinToCdna.isSelected()));
 479     Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP",
 480             Boolean.toString(showNpTooltip.isSelected()));
 481     Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP",
 482             Boolean.toString(showDbRefTooltip.isSelected()));
 483
 484     Cache.applicationProperties.setProperty("WRAP_ALIGNMENT",
 485             Boolean.toString(wrap.isSelected()));
 486
 487     Cache.applicationProperties.setProperty("STARTUP_FILE",
 488             startupFileTextfield.getText());
 489     Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",
 490             Boolean.toString(startupCheckbox.isSelected()));
 491
 492     Cache.applicationProperties.setProperty("SORT_ALIGNMENT", sortby
 493             .getSelectedItem().toString());
 494
 495     // convert description of sort order to enum name for save
 496     SequenceAnnotationOrder annSortOrder = SequenceAnnotationOrder
 497             .forDescription(sortAnnBy.getSelectedItem().toString());
 498     if (annSortOrder != null)
 499     {
 500       Cache.applicationProperties.setProperty(SORT_ANNOTATIONS,
 501               annSortOrder.name());
 502     }
 503
 504     final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
 505     Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE, Boolean
 506             .valueOf(showAutocalcFirst).toString());
 507
 508     /*
 509      * Save Colours settings
 510      */
 511     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_PROT, protColour
 512             .getSelectedItem().toString());
 513     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_NUC, nucColour
 514             .getSelectedItem().toString());
 515     Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
 516             minColour.getBackground());
 517     Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
 518             maxColour.getBackground());
 519
 520     /*
 521      * Save Structure settings
 522      */
 523     Cache.applicationProperties.setProperty(ADD_TEMPFACT_ANN,
 524             Boolean.toString(addTempFactor.isSelected()));
 525     Cache.applicationProperties.setProperty(ADD_SS_ANN,
 526             Boolean.toString(addSecondaryStructure.isSelected()));
 527     Cache.applicationProperties.setProperty(USE_RNAVIEW,
 528             Boolean.toString(useRnaView.isSelected()));
 529     Cache.applicationProperties.setProperty(STRUCT_FROM_PDB,
 530             Boolean.toString(structFromPdb.isSelected()));
 531     Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY, structViewer
 532             .getSelectedItem().toString());
 533     Cache.setOrRemove(CHIMERA_PATH, chimeraPath.getText());
 534     Cache.applicationProperties.setProperty("MAP_WITH_SIFTS",
 535             Boolean.toString(siftsMapping.isSelected()));
 536     SiftsSettings.setMapWithSifts(siftsMapping.isSelected());
 537
 538     /*
 539      * Save Output settings
 540      */
 541       Cache.applicationProperties.setProperty("EPS_RENDERING",
 542               ((OptionsParam) epsRendering.getSelectedItem()).getCode());
 543
 544     /*
 545      * Save Connections settings
 546      */
 547     Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText());
 548
 549     jalview.util.BrowserLauncher.resetBrowser();
 550
 551     if (nameLinks.size() > 0)
 552     {
 553       StringBuffer links = new StringBuffer();
 554       sequenceURLLinks = new Vector<String>();
 555       for (int i = 0; i < nameLinks.size(); i++)
 556       {
 557         sequenceURLLinks.addElement(nameLinks.elementAt(i) + "|"
 558                 + urlLinks.elementAt(i));
 559         links.append(sequenceURLLinks.elementAt(i).toString());
 560         links.append("|");
 561       }
 562       // remove last "|"
 563       links.setLength(links.length() - 1);
 564       Cache.applicationProperties.setProperty("SEQUENCE_LINKS",
 565               links.toString());
 566     }
 567     else
 568     {
 569       Cache.applicationProperties.remove("SEQUENCE_LINKS");
 570     }
 571
 572     Cache.applicationProperties.setProperty("USE_PROXY",
 573             Boolean.toString(useProxy.isSelected()));
 574
 575     Cache.setOrRemove("PROXY_SERVER", proxyServerTB.getText());
 576
 577     Cache.setOrRemove("PROXY_PORT", proxyPortTB.getText());
 578
 579     if (useProxy.isSelected())
 580     {
 581       System.setProperty("http.proxyHost", proxyServerTB.getText());
 582       System.setProperty("http.proxyPort", proxyPortTB.getText());
 583     }
 584     else
 585     {
 586       System.setProperty("http.proxyHost", "");
 587       System.setProperty("http.proxyPort", "");
 588     }
 589     Cache.setProperty("VERSION_CHECK",
 590             Boolean.toString(versioncheck.isSelected()));
 591     if (Cache.getProperty("USAGESTATS") != null || usagestats.isSelected())
 592     {
 593       // default is false - we only set this if the user has actively agreed
 594       Cache.setProperty("USAGESTATS",
 595               Boolean.toString(usagestats.isSelected()));
 596     }
 597     if (!questionnaire.isSelected())
 598     {
 599       Cache.setProperty("NOQUESTIONNAIRES", "true");
 600     }
 601     else
 602     {
 603       // special - made easy to edit a property file to disable questionnaires
 604       // by just adding the given line
 605       Cache.removeProperty("NOQUESTIONNAIRES");
 606     }
 607
 608     /*
 609      * Save Output settings
 610      */
 611     Cache.applicationProperties.setProperty("BLC_JVSUFFIX",
 612             Boolean.toString(blcjv.isSelected()));
 613     Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX",
 614             Boolean.toString(clustaljv.isSelected()));
 615     Cache.applicationProperties.setProperty("FASTA_JVSUFFIX",
 616             Boolean.toString(fastajv.isSelected()));
 617     Cache.applicationProperties.setProperty("MSF_JVSUFFIX",
 618             Boolean.toString(msfjv.isSelected()));
 619     Cache.applicationProperties.setProperty("PFAM_JVSUFFIX",
 620             Boolean.toString(pfamjv.isSelected()));
 621     Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX",
 622             Boolean.toString(pileupjv.isSelected()));
 623     Cache.applicationProperties.setProperty("PIR_JVSUFFIX",
 624             Boolean.toString(pirjv.isSelected()));
 625     Cache.applicationProperties.setProperty("PIR_MODELLER",
 626             Boolean.toString(modellerOutput.isSelected()));
 627     Cache.applicationProperties.setProperty("EXPORT_EMBBED_BIOJSON",
 628             Boolean.toString(embbedBioJSON.isSelected()));
 629     jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
 630
 631     Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH",
 632             Boolean.toString(autoIdWidth.isSelected()));
 633     userIdWidth_actionPerformed();
 634     Cache.applicationProperties.setProperty("FIGURE_USERIDWIDTH",
 635             userIdWidth.getText());
 636
 637     /*
 638      * Save Editing settings
 639      */
 640     Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
 641             Boolean.toString(autoCalculateConsCheck.isSelected()));
 642     Cache.applicationProperties.setProperty("SORT_BY_TREE",
 643             Boolean.toString(sortByTree.isSelected()));
 644     Cache.applicationProperties.setProperty("PAD_GAPS",
 645             Boolean.toString(padGaps.isSelected()));
 646
 647     dasSource.saveProperties(Cache.applicationProperties);
 648     wsPrefs.updateAndRefreshWsMenuConfig(false);
 649     Cache.saveProperties();
 650     Desktop.instance.doConfigureStructurePrefs();
 651     try
 652     {
 653       frame.setClosed(true);
 654     } catch (Exception ex)
 655     {
 656     }
 657   }
 658
 659   /**
 660    * Do any necessary validation before saving settings. Return focus to the
 661    * first tab which fails validation.
 662    *
 663    * @return
 664    */
 665   private boolean validateSettings()
 666   {
 667     if (!validateStructure())
 668     {
 669       structureTab.requestFocusInWindow();
 670       return false;
 671     }
 672     return true;
 673   }
 674
 675   @Override
 676   protected boolean validateStructure()
 677   {
 678     return validateChimeraPath();
 679
 680   }
 681
 682   /**
 683    * DOCUMENT ME!
 684    */
 685   @Override
 686   public void startupFileTextfield_mouseClicked()
 687   {
 688     JalviewFileChooser chooser = new JalviewFileChooser(
 689             jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[] {
 690                 "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",
 691                 "jar" }, new String[] { "Fasta", "Clustal", "PFAM", "MSF",
 692                 "PIR", "BLC", "Jalview" },
 693             jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));
 694     chooser.setFileView(new JalviewFileView());
 695     chooser.setDialogTitle(MessageManager
 696             .getString("label.select_startup_file"));
 697
 698     int value = chooser.showOpenDialog(this);
 699
 700     if (value == JalviewFileChooser.APPROVE_OPTION)
 701     {
 702       jalview.bin.Cache.applicationProperties.setProperty(
 703               "DEFAULT_FILE_FORMAT", chooser.getSelectedFormat());
 704       startupFileTextfield.setText(chooser.getSelectedFile()
 705               .getAbsolutePath());
 706     }
 707   }
 708
 709   /**
 710    * DOCUMENT ME!
 711    *
 712    * @param e
 713    *          DOCUMENT ME!
 714    */
 715   @Override
 716   public void cancel_actionPerformed(ActionEvent e)
 717   {
 718     try
 719     {
 720       wsPrefs.updateWsMenuConfig(true);
 721       wsPrefs.refreshWs_actionPerformed(e);
 722       frame.setClosed(true);
 723     } catch (Exception ex)
 724     {
 725     }
 726   }
 727
 728   /**
 729    * DOCUMENT ME!
 730    *
 731    * @param e
 732    *          DOCUMENT ME!
 733    */
 734   @Override
 735   public void annotations_actionPerformed(ActionEvent e)
 736   {
 737     conservation.setEnabled(annotations.isSelected());
 738     quality.setEnabled(annotations.isSelected());
 739     identity.setEnabled(annotations.isSelected());
 740     showGroupConsensus.setEnabled(annotations.isSelected());
 741     showGroupConservation.setEnabled(annotations.isSelected());
 742     showConsensHistogram.setEnabled(annotations.isSelected()
 743             && (identity.isSelected() || showGroupConsensus.isSelected()));
 744     showConsensLogo.setEnabled(annotations.isSelected()
 745             && (identity.isSelected() || showGroupConsensus.isSelected()));
 746   }
 747
 748   @Override
 749   public void newLink_actionPerformed(ActionEvent e)
 750   {
 751
 752     GSequenceLink link = new GSequenceLink();
 753     boolean valid = false;
 754     while (!valid)
 755     {
 756       if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 757               MessageManager.getString("label.new_sequence_url_link"),
 758               JOptionPane.OK_CANCEL_OPTION, -1, null) == JOptionPane.OK_OPTION)
 759       {
 760         if (link.checkValid())
 761         {
 762           nameLinks.addElement(link.getName());
 763           urlLinks.addElement(link.getURL());
 764           updateLinkData();
 765           valid = true;
 766         }
 767       }
 768       else
 769       {
 770         break;
 771       }
 772     }
 773   }
 774
 775   @Override
 776   public void editLink_actionPerformed(ActionEvent e)
 777   {
 778     GSequenceLink link = new GSequenceLink();
 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
 790     link.setName(nameLinks.elementAt(index).toString());
 791     link.setURL(urlLinks.elementAt(index).toString());
 792
 793     boolean valid = false;
 794     while (!valid)
 795     {
 796
 797       if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 798               MessageManager.getString("label.new_sequence_url_link"),
 799               JOptionPane.OK_CANCEL_OPTION, -1, null) == JOptionPane.OK_OPTION)
 800       {
 801         if (link.checkValid())
 802         {
 803           nameLinks.setElementAt(link.getName(), index);
 804           urlLinks.setElementAt(link.getURL(), index);
 805           updateLinkData();
 806           valid = true;
 807         }
 808       }
 809
 810       else
 811       {
 812         break;
 813       }
 814     }
 815   }
 816
 817   @Override
 818   public void deleteLink_actionPerformed(ActionEvent e)
 819   {
 820     int index = linkNameList.getSelectedIndex();
 821     if (index == -1)
 822     {
 823       JOptionPane.showInternalMessageDialog(Desktop.desktop,
 824               MessageManager.getString("label.no_link_selected"),
 825               MessageManager.getString("label.no_link_selected"),
 826               JOptionPane.WARNING_MESSAGE);
 827       return;
 828     }
 829     nameLinks.removeElementAt(index);
 830     urlLinks.removeElementAt(index);
 831     updateLinkData();
 832   }
 833
 834   void updateLinkData()
 835   {
 836     linkNameList.setListData(nameLinks);
 837     linkURLList.setListData(urlLinks);
 838   }
 839
 840   @Override
 841   public void defaultBrowser_mouseClicked(MouseEvent e)
 842   {
 843     JFileChooser chooser = new JFileChooser(".");
 844     chooser.setDialogTitle(MessageManager
 845             .getString("label.select_default_browser"));
 846
 847     int value = chooser.showOpenDialog(this);
 848
 849     if (value == JFileChooser.APPROVE_OPTION)
 850     {
 851       defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
 852     }
 853
 854   }
 855
 856   /*
 857    * (non-Javadoc)
 858    *
 859    * @see
 860    * jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event
 861    * .ActionEvent)
 862    */
 863   @Override
 864   protected void showunconserved_actionPerformed(ActionEvent e)
 865   {
 866     // TODO Auto-generated method stub
 867     super.showunconserved_actionPerformed(e);
 868   }
 869
 870   public static List<String> getGroupURLLinks()
 871   {
 872     return groupURLLinks;
 873   }
 874
 875   @Override
 876   public void minColour_actionPerformed(JPanel panel)
 877   {
 878     Color col = JColorChooser.showDialog(this,
 879             MessageManager.getString("label.select_colour_minimum_value"),
 880             minColour.getBackground());
 881     if (col != null)
 882     {
 883       panel.setBackground(col);
 884     }
 885     panel.repaint();
 886   }
 887
 888   @Override
 889   public void maxColour_actionPerformed(JPanel panel)
 890   {
 891     Color col = JColorChooser.showDialog(this,
 892             MessageManager.getString("label.select_colour_maximum_value"),
 893             maxColour.getBackground());
 894     if (col != null)
 895     {
 896       panel.setBackground(col);
 897     }
 898     panel.repaint();
 899   }
 900
 901   @Override
 902   protected void userIdWidth_actionPerformed()
 903   {
 904     try
 905     {
 906       String val = userIdWidth.getText().trim();
 907       if (val.length() > 0)
 908       {
 909         Integer iw = Integer.parseInt(val);
 910         if (iw.intValue() < 12)
 911         {
 912           throw new NumberFormatException();
 913         }
 914         userIdWidth.setText(iw.toString());
 915       }
 916     } catch (NumberFormatException x)
 917     {
 918       JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
 919               .getString("warn.user_defined_width_requirements"),
 920               MessageManager.getString("label.invalid_id_column_width"),
 921               JOptionPane.WARNING_MESSAGE);
 922       userIdWidth.setText("");
 923     }
 924   }
 925
 926   @Override
 927   protected void autoIdWidth_actionPerformed()
 928   {
 929     userIdWidth.setEnabled(!autoIdWidth.isSelected());
 930     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
 931   }
 932
 933   /**
 934    * Returns true if chimera path is to a valid executable, else show an error
 935    * dialog.
 936    */
 937   private boolean validateChimeraPath()
 938   {
 939     if (chimeraPath.getText().trim().length() > 0)
 940     {
 941       File f = new File(chimeraPath.getText());
 942       if (!f.canExecute())
 943       {
 944         JOptionPane.showInternalMessageDialog(Desktop.desktop,
 945                 MessageManager.getString("label.invalid_chimera_path"),
 946                 MessageManager.getString("label.invalid_name"),
 947                 JOptionPane.ERROR_MESSAGE);
 948         return false;
 949       }
 950     }
 951     return true;
 952   }
 953
 954   /**
 955    * If Chimera is selected, check it can be found on default or user-specified
 956    * path, if not show a warning/help dialog.
 957    */
 958   @Override
 959   protected void structureViewer_actionPerformed(String selectedItem)
 960   {
 961     if (!selectedItem.equals(ViewerType.CHIMERA.name()))
 962     {
 963       return;
 964     }
 965     boolean found = false;
 966
 967     /*
 968      * Try user-specified and standard paths for Chimera executable.
 969      */
 970     List<String> paths = StructureManager.getChimeraPaths();
 971     paths.add(0, chimeraPath.getText());
 972     for (String path : paths)
 973     {
 974       if (new File(path.trim()).canExecute())
 975       {
 976         found = true;
 977         break;
 978       }
 979     }
 980     if (!found)
 981     {
 982       String[] options = { "OK", "Help" };
 983       int showHelp = JOptionPane.showInternalOptionDialog(
 984               Desktop.desktop,
 985               JvSwingUtils.wrapTooltip(true,
 986                       MessageManager.getString("label.chimera_missing")),
 987               "", JOptionPane.YES_NO_OPTION, JOptionPane.WARNING_MESSAGE,
 988               null, options, options[0]);
 989       if (showHelp == JOptionPane.NO_OPTION)
 990       {
 991         try
 992         {
 993           Help.showHelpWindow(HelpId.StructureViewer);
 994         } catch (HelpSetException e)
 995         {
 996           e.printStackTrace();
 997         }
 998       }
 999     }
1000   }
1001
1002   public class OptionsParam
1003   {
1004     private String name;
1005
1006     private String code;
1007
1008     public OptionsParam(String name, String code)
1009     {
1010       this.name = name;
1011       this.code = code;
1012     }
1013
1014     public String getName()
1015     {
1016       return name;
1017     }
1018
1019     public void setName(String name)
1020     {
1021       this.name = name;
1022     }
1023
1024     public String getCode()
1025     {
1026       return code;
1027     }
1028
1029     public void setCode(String code)
1030     {
1031       this.code = code;
1032     }
1033
1034     @Override
1035     public String toString()
1036     {
1037       return name;
1038     }
1039
1040     @Override
1041     public boolean equals(Object that)
1042     {
1043       if (!(that instanceof OptionsParam))
1044       {
1045         return false;
1046       }
1047       return this.code.equalsIgnoreCase(((OptionsParam) that).code);
1048     }
1049
1050     @Override
1051     public int hashCode(){
1052       return name.hashCode() + code.hashCode();
1053     }
1054   }
1055 }