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 static jalview.util.UrlConstants.EMBLEBI_STRING;
  24 import static jalview.util.UrlConstants.OLD_EMBLEBI_STRING;
  25 import static jalview.util.UrlConstants.SEQUENCE_ID;
  26 import static jalview.util.UrlConstants.SRS_STRING;
  27
  28 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
  29 import jalview.bin.Cache;
  30 import jalview.gui.Help.HelpId;
  31 import jalview.gui.StructureViewer.ViewerType;
  32 import jalview.io.JalviewFileChooser;
  33 import jalview.io.JalviewFileView;
  34 import jalview.jbgui.GPreferences;
  35 import jalview.jbgui.GSequenceLink;
  36 import jalview.schemes.ColourSchemeProperty;
  37 import jalview.util.MessageManager;
  38 import jalview.util.Platform;
  39 import jalview.ws.sifts.SiftsSettings;
  40
  41 import java.awt.BorderLayout;
  42 import java.awt.Color;
  43 import java.awt.Dimension;
  44 import java.awt.Font;
  45 import java.awt.event.ActionEvent;
  46 import java.awt.event.ActionListener;
  47 import java.awt.event.MouseEvent;
  48 import java.io.File;
  49 import java.util.ArrayList;
  50 import java.util.List;
  51 import java.util.StringTokenizer;
  52 import java.util.Vector;
  53
  54 import javax.help.HelpSetException;
  55 import javax.swing.JColorChooser;
  56 import javax.swing.JFileChooser;
  57 import javax.swing.JInternalFrame;
  58 import javax.swing.JOptionPane;
  59 import javax.swing.JPanel;
  60
  61 import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
  62
  63 /**
  64  * DOCUMENT ME!
  65  *
  66  * @author $author$
  67  * @version $Revision$
  68  */
  69 public class Preferences extends GPreferences
  70 {
  71   public static final String ENABLE_SPLIT_FRAME = "ENABLE_SPLIT_FRAME";
  72
  73   public static final String SCALE_PROTEIN_TO_CDNA = "SCALE_PROTEIN_TO_CDNA";
  74
  75   public static final String DEFAULT_COLOUR = "DEFAULT_COLOUR";
  76
  77   public static final String DEFAULT_COLOUR_PROT = "DEFAULT_COLOUR_PROT";
  78
  79   public static final String DEFAULT_COLOUR_NUC = "DEFAULT_COLOUR_NUC";
  80
  81   public static final String ADD_TEMPFACT_ANN = "ADD_TEMPFACT_ANN";
  82
  83   public static final String ADD_SS_ANN = "ADD_SS_ANN";
  84
  85   public static final String USE_RNAVIEW = "USE_RNAVIEW";
  86
  87   public static final String STRUCT_FROM_PDB = "STRUCT_FROM_PDB";
  88
  89   public static final String STRUCTURE_DISPLAY = "STRUCTURE_DISPLAY";
  90
  91   public static final String CHIMERA_PATH = "CHIMERA_PATH";
  92
  93   public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS";
  94
  95   public static final String SHOW_AUTOCALC_ABOVE = "SHOW_AUTOCALC_ABOVE";
  96
  97   private static final int MIN_FONT_SIZE = 1;
  98
  99   private static final int MAX_FONT_SIZE = 30;
 100
 101   /**
 102    * Holds name and link separated with | character. Sequence ID must be
 103    * $SEQUENCE_ID$ or $SEQUENCE_ID=/.possible | chars ./=$
 104    */
 105   public static Vector<String> sequenceURLLinks;
 106
 107   /**
 108    * Holds name and link separated with | character. Sequence IDS and Sequences
 109    * must be $SEQUENCEIDS$ or $SEQUENCEIDS=/.possible | chars ./=$ and
 110    * $SEQUENCES$ or $SEQUENCES=/.possible | chars ./=$ and separation character
 111    * for first and second token specified after a pipe character at end |,|.
 112    * (TODO: proper escape for using | to separate ids or sequences
 113    */
 114
 115   public static List<String> groupURLLinks;
 116   static
 117   {
 118     String string = Cache.getDefault("SEQUENCE_LINKS", EMBLEBI_STRING);
 119     sequenceURLLinks = new Vector<String>();
 120
 121     try
 122     {
 123       StringTokenizer st = new StringTokenizer(string, "|");
 124       while (st.hasMoreElements())
 125       {
 126         String name = st.nextToken();
 127         String url = st.nextToken();
 128         // check for '|' within a regex
 129         int rxstart = url.indexOf("$" + SEQUENCE_ID + "$");
 130         while (rxstart == -1 && url.indexOf("/=$") == -1)
 131         {
 132           url = url + "|" + st.nextToken();
 133         }
 134         sequenceURLLinks.addElement(name + "|" + url);
 135       }
 136     } catch (Exception ex)
 137     {
 138       System.out.println(ex + "\nError parsing sequence links");
 139     }
 140     {
 141       // upgrade old SRS link
 142       int srsPos = sequenceURLLinks.indexOf(SRS_STRING);
 143       if (srsPos > -1)
 144       {
 145         sequenceURLLinks.setElementAt(EMBLEBI_STRING, srsPos);
 146       }
 147       // upgrade old EMBL-EBI link
 148       int emblPos = sequenceURLLinks.indexOf(OLD_EMBLEBI_STRING);
 149       if (emblPos > -1)
 150       {
 151         sequenceURLLinks.setElementAt(EMBLEBI_STRING, emblPos);
 152       }
 153     }
 154
 155     /**
 156      * TODO: reformulate groupURL encoding so two or more can be stored in the
 157      * .properties file as '|' separated strings
 158      */
 159
 160     groupURLLinks = new ArrayList<String>();
 161   }
 162
 163   Vector<String> nameLinks, urlLinks;
 164
 165   JInternalFrame frame;
 166
 167   DasSourceBrowser dasSource;
 168
 169   private WsPreferences wsPrefs;
 170
 171   private OptionsParam promptEachTimeOpt = new OptionsParam(
 172           MessageManager.getString("label.prompt_each_time"),
 173           "Prompt each time");
 174
 175   private OptionsParam lineArtOpt = new OptionsParam(
 176           MessageManager.getString("label.lineart"), "Lineart");
 177
 178   private OptionsParam textOpt = new OptionsParam(
 179           MessageManager.getString("action.text"), "Text");
 180
 181   /**
 182    * Creates a new Preferences object.
 183    */
 184   public Preferences()
 185   {
 186     super();
 187     frame = new JInternalFrame();
 188     frame.setContentPane(this);
 189     dasSource = new DasSourceBrowser();
 190     dasTab.add(dasSource, BorderLayout.CENTER);
 191     wsPrefs = new WsPreferences();
 192     wsTab.add(wsPrefs, BorderLayout.CENTER);
 193     int width = 500, height = 450;
 194     new jalview.util.Platform();
 195     if (Platform.isAMac())
 196     {
 197       width = 570;
 198       height = 480;
 199     }
 200
 201     Desktop.addInternalFrame(frame,
 202             MessageManager.getString("label.preferences"), width, height);
 203     frame.setMinimumSize(new Dimension(width, height));
 204
 205     /*
 206      * Set Visual tab defaults
 207      */
 208     seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));
 209     rightAlign.setSelected(Cache.getDefault("RIGHT_ALIGN_IDS", false));
 210     fullScreen.setSelected(Cache.getDefault("SHOW_FULLSCREEN", false));
 211     annotations.setSelected(Cache.getDefault("SHOW_ANNOTATIONS", true));
 212
 213     conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));
 214     quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));
 215     identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));
 216     openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false));
 217     showUnconserved
 218             .setSelected(Cache.getDefault("SHOW_UNCONSERVED", false));
 219     showGroupConsensus.setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS",
 220             false));
 221     showGroupConservation.setSelected(Cache.getDefault(
 222             "SHOW_GROUP_CONSERVATION", false));
 223     showConsensHistogram.setSelected(Cache.getDefault(
 224             "SHOW_CONSENSUS_HISTOGRAM", true));
 225     showConsensLogo.setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO",
 226             false));
 227     showNpTooltip.setSelected(Cache
 228             .getDefault("SHOW_NPFEATS_TOOLTIP", true));
 229     showDbRefTooltip.setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP",
 230             true));
 231
 232     String[] fonts = java.awt.GraphicsEnvironment
 233             .getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
 234     for (int i = 0; i < fonts.length; i++)
 235     {
 236       fontNameCB.addItem(fonts[i]);
 237     }
 238
 239     for (int i = MIN_FONT_SIZE; i <= MAX_FONT_SIZE; i++)
 240     {
 241       fontSizeCB.addItem(i + "");
 242     }
 243
 244     fontStyleCB.addItem("plain");
 245     fontStyleCB.addItem("bold");
 246     fontStyleCB.addItem("italic");
 247
 248     fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
 249     fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
 250     fontStyleCB.setSelectedItem(Cache.getDefault("FONT_STYLE", Font.PLAIN
 251             + ""));
 252
 253     smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));
 254     scaleProteinToCdna.setSelected(Cache.getDefault(SCALE_PROTEIN_TO_CDNA,
 255             false));
 256
 257     idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
 258
 259     wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
 260
 261     gapSymbolCB.addItem("-");
 262     gapSymbolCB.addItem(".");
 263
 264     gapSymbolCB.setSelectedItem(Cache.getDefault("GAP_SYMBOL", "-"));
 265
 266     sortby.addItem("No sort");
 267     sortby.addItem("Id");
 268     sortby.addItem("Pairwise Identity");
 269     sortby.setSelectedItem(Cache.getDefault("SORT_ALIGNMENT", "No sort"));
 270
 271     sortAnnBy.addItem(SequenceAnnotationOrder.NONE.toString());
 272     sortAnnBy
 273             .addItem(SequenceAnnotationOrder.SEQUENCE_AND_LABEL.toString());
 274     sortAnnBy
 275             .addItem(SequenceAnnotationOrder.LABEL_AND_SEQUENCE.toString());
 276     SequenceAnnotationOrder savedSort = SequenceAnnotationOrder
 277             .valueOf(Cache.getDefault(SORT_ANNOTATIONS,
 278                     SequenceAnnotationOrder.NONE.name()));
 279     sortAnnBy.setSelectedItem(savedSort.toString());
 280
 281     sortAutocalc.addItem("Autocalculated first");
 282     sortAutocalc.addItem("Autocalculated last");
 283     final boolean showAbove = Cache.getDefault(SHOW_AUTOCALC_ABOVE, true);
 284     sortAutocalc.setSelectedItem(showAbove ? sortAutocalc.getItemAt(0)
 285             : sortAutocalc.getItemAt(1));
 286     startupCheckbox
 287             .setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
 288     startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
 289             Cache.getDefault("www.jalview.org", "http://www.jalview.org")
 290                     + "/examples/exampleFile_2_3.jar"));
 291
 292     /*
 293      * Set Colours tab defaults
 294      */
 295     for (int i = ColourSchemeProperty.FIRST_COLOUR; i <= ColourSchemeProperty.LAST_COLOUR; i++)
 296     {
 297       protColour.addItem(ColourSchemeProperty.getColourName(i));
 298       nucColour.addItem(ColourSchemeProperty.getColourName(i));
 299     }
 300     String oldProp = Cache.getDefault(DEFAULT_COLOUR, "None");
 301     String newProp = Cache.getDefault(DEFAULT_COLOUR_PROT, null);
 302     protColour.setSelectedItem(newProp != null ? newProp : oldProp);
 303     newProp = Cache.getDefault(DEFAULT_COLOUR_NUC, null);
 304     nucColour.setSelectedItem(newProp != null ? newProp : oldProp);
 305     minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN",
 306             Color.orange));
 307     maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX",
 308             Color.red));
 309
 310     /*
 311      * Set Structure tab defaults.
 312      */
 313     final boolean structSelected = Cache.getDefault(STRUCT_FROM_PDB, false);
 314     structFromPdb.setSelected(structSelected);
 315     useRnaView.setSelected(Cache.getDefault(USE_RNAVIEW, false));
 316     useRnaView.setEnabled(structSelected);
 317     addSecondaryStructure.setSelected(Cache.getDefault(ADD_SS_ANN, false));
 318     addSecondaryStructure.setEnabled(structSelected);
 319     addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, false));
 320     addTempFactor.setEnabled(structSelected);
 321     structViewer.setSelectedItem(Cache.getDefault(STRUCTURE_DISPLAY,
 322             ViewerType.JMOL.name()));
 323     chimeraPath.setText(Cache.getDefault(CHIMERA_PATH, ""));
 324     chimeraPath.addActionListener(new ActionListener()
 325     {
 326       @Override
 327       public void actionPerformed(ActionEvent e)
 328       {
 329         validateChimeraPath();
 330       }
 331     });
 332
 333     if (Cache.getDefault("MAP_WITH_SIFTS", false))
 334     {
 335       siftsMapping.setSelected(true);
 336     }
 337     else
 338     {
 339       nwMapping.setSelected(true);
 340     }
 341
 342     SiftsSettings
 343             .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
 344
 345     /*
 346      * Set Connections tab defaults
 347      */
 348     nameLinks = new Vector<String>();
 349     urlLinks = new Vector<String>();
 350     for (int i = 0; i < sequenceURLLinks.size(); i++)
 351     {
 352       String link = sequenceURLLinks.elementAt(i).toString();
 353       nameLinks.addElement(link.substring(0, link.indexOf("|")));
 354       urlLinks.addElement(link.substring(link.indexOf("|") + 1));
 355     }
 356
 357     updateLinkData();
 358
 359     useProxy.setSelected(Cache.getDefault("USE_PROXY", false));
 360     proxyServerTB.setEnabled(useProxy.isSelected());
 361     proxyPortTB.setEnabled(useProxy.isSelected());
 362     proxyServerTB.setText(Cache.getDefault("PROXY_SERVER", ""));
 363     proxyPortTB.setText(Cache.getDefault("PROXY_PORT", ""));
 364
 365     defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", ""));
 366
 367     usagestats.setSelected(Cache.getDefault("USAGESTATS", false));
 368     // note antisense here: default is true
 369     questionnaire
 370             .setSelected(Cache.getProperty("NOQUESTIONNAIRES") == null);
 371     versioncheck.setSelected(Cache.getDefault("VERSION_CHECK", true));
 372
 373     /*
 374      * Set Output tab defaults
 375      */
 376     epsRendering.addItem(promptEachTimeOpt);
 377     epsRendering.addItem(lineArtOpt);
 378     epsRendering.addItem(textOpt);
 379     String defaultEPS = Cache.getDefault("EPS_RENDERING",
 380             "Prompt each time");
 381     if (defaultEPS.equalsIgnoreCase("Text"))
 382     {
 383       epsRendering.setSelectedItem(textOpt);
 384     }
 385     else if (defaultEPS.equalsIgnoreCase("Lineart"))
 386     {
 387       epsRendering.setSelectedItem(lineArtOpt);
 388     }
 389     else
 390     {
 391       epsRendering.setSelectedItem(promptEachTimeOpt);
 392     }
 393     autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false));
 394     userIdWidth.setEnabled(!autoIdWidth.isSelected());
 395     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
 396     Integer wi = Cache.getIntegerProperty("FIGURE_USERIDWIDTH");
 397     userIdWidth.setText(wi == null ? "" : wi.toString());
 398     blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
 399     clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
 400     fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
 401     msfjv.setSelected(Cache.getDefault("MSF_JVSUFFIX", true));
 402     pfamjv.setSelected(Cache.getDefault("PFAM_JVSUFFIX", true));
 403     pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
 404     pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
 405     modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
 406     embbedBioJSON.setSelected(Cache.getDefault("EXPORT_EMBBED_BIOJSON",
 407             true));
 408
 409     /*
 410      * Set Editing tab defaults
 411      */
 412     autoCalculateConsCheck.setSelected(Cache.getDefault(
 413             "AUTO_CALC_CONSENSUS", true));
 414     padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
 415     sortByTree.setSelected(Cache.getDefault("SORT_BY_TREE", false));
 416
 417     annotations_actionPerformed(null); // update the display of the annotation
 418                                        // settings
 419   }
 420
 421   /**
 422    * Save user selections on the Preferences tabs to the Cache and write out to
 423    * file.
 424    *
 425    * @param e
 426    */
 427   @Override
 428   public void ok_actionPerformed(ActionEvent e)
 429   {
 430     if (!validateSettings())
 431     {
 432       return;
 433     }
 434
 435     /*
 436      * Save Visual settings
 437      */
 438     Cache.applicationProperties.setProperty("SHOW_JVSUFFIX",
 439             Boolean.toString(seqLimit.isSelected()));
 440     Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS",
 441             Boolean.toString(rightAlign.isSelected()));
 442     Cache.applicationProperties.setProperty("SHOW_FULLSCREEN",
 443             Boolean.toString(fullScreen.isSelected()));
 444     Cache.applicationProperties.setProperty("SHOW_OVERVIEW",
 445             Boolean.toString(openoverv.isSelected()));
 446     Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
 447             Boolean.toString(annotations.isSelected()));
 448     Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
 449             Boolean.toString(conservation.isSelected()));
 450     Cache.applicationProperties.setProperty("SHOW_QUALITY",
 451             Boolean.toString(quality.isSelected()));
 452     Cache.applicationProperties.setProperty("SHOW_IDENTITY",
 453             Boolean.toString(identity.isSelected()));
 454
 455     Cache.applicationProperties.setProperty("GAP_SYMBOL", gapSymbolCB
 456             .getSelectedItem().toString());
 457
 458     Cache.applicationProperties.setProperty("FONT_NAME", fontNameCB
 459             .getSelectedItem().toString());
 460     Cache.applicationProperties.setProperty("FONT_STYLE", fontStyleCB
 461             .getSelectedItem().toString());
 462     Cache.applicationProperties.setProperty("FONT_SIZE", fontSizeCB
 463             .getSelectedItem().toString());
 464
 465     Cache.applicationProperties.setProperty("ID_ITALICS",
 466             Boolean.toString(idItalics.isSelected()));
 467     Cache.applicationProperties.setProperty("SHOW_UNCONSERVED",
 468             Boolean.toString(showUnconserved.isSelected()));
 469     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS",
 470             Boolean.toString(showGroupConsensus.isSelected()));
 471     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION",
 472             Boolean.toString(showGroupConservation.isSelected()));
 473     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_HISTOGRAM",
 474             Boolean.toString(showConsensHistogram.isSelected()));
 475     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO",
 476             Boolean.toString(showConsensLogo.isSelected()));
 477     Cache.applicationProperties.setProperty("ANTI_ALIAS",
 478             Boolean.toString(smoothFont.isSelected()));
 479     Cache.applicationProperties.setProperty(SCALE_PROTEIN_TO_CDNA,
 480             Boolean.toString(scaleProteinToCdna.isSelected()));
 481     Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP",
 482             Boolean.toString(showNpTooltip.isSelected()));
 483     Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP",
 484             Boolean.toString(showDbRefTooltip.isSelected()));
 485
 486     Cache.applicationProperties.setProperty("WRAP_ALIGNMENT",
 487             Boolean.toString(wrap.isSelected()));
 488
 489     Cache.applicationProperties.setProperty("STARTUP_FILE",
 490             startupFileTextfield.getText());
 491     Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",
 492             Boolean.toString(startupCheckbox.isSelected()));
 493
 494     Cache.applicationProperties.setProperty("SORT_ALIGNMENT", sortby
 495             .getSelectedItem().toString());
 496
 497     // convert description of sort order to enum name for save
 498     SequenceAnnotationOrder annSortOrder = SequenceAnnotationOrder
 499             .forDescription(sortAnnBy.getSelectedItem().toString());
 500     if (annSortOrder != null)
 501     {
 502       Cache.applicationProperties.setProperty(SORT_ANNOTATIONS,
 503               annSortOrder.name());
 504     }
 505
 506     final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
 507     Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE, Boolean
 508             .valueOf(showAutocalcFirst).toString());
 509
 510     /*
 511      * Save Colours settings
 512      */
 513     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_PROT, protColour
 514             .getSelectedItem().toString());
 515     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_NUC, nucColour
 516             .getSelectedItem().toString());
 517     Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
 518             minColour.getBackground());
 519     Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
 520             maxColour.getBackground());
 521
 522     /*
 523      * Save Structure settings
 524      */
 525     Cache.applicationProperties.setProperty(ADD_TEMPFACT_ANN,
 526             Boolean.toString(addTempFactor.isSelected()));
 527     Cache.applicationProperties.setProperty(ADD_SS_ANN,
 528             Boolean.toString(addSecondaryStructure.isSelected()));
 529     Cache.applicationProperties.setProperty(USE_RNAVIEW,
 530             Boolean.toString(useRnaView.isSelected()));
 531     Cache.applicationProperties.setProperty(STRUCT_FROM_PDB,
 532             Boolean.toString(structFromPdb.isSelected()));
 533     Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY, structViewer
 534             .getSelectedItem().toString());
 535     Cache.setOrRemove(CHIMERA_PATH, chimeraPath.getText());
 536     Cache.applicationProperties.setProperty("MAP_WITH_SIFTS",
 537             Boolean.toString(siftsMapping.isSelected()));
 538     SiftsSettings.setMapWithSifts(siftsMapping.isSelected());
 539
 540     /*
 541      * Save Output settings
 542      */
 543     Cache.applicationProperties.setProperty("EPS_RENDERING",
 544             ((OptionsParam) epsRendering.getSelectedItem()).getCode());
 545
 546     /*
 547      * Save Connections settings
 548      */
 549     Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText());
 550
 551     jalview.util.BrowserLauncher.resetBrowser();
 552
 553     if (nameLinks.size() > 0)
 554     {
 555       StringBuffer links = new StringBuffer();
 556       sequenceURLLinks = new Vector<String>();
 557       for (int i = 0; i < nameLinks.size(); i++)
 558       {
 559         sequenceURLLinks.addElement(nameLinks.elementAt(i) + "|"
 560                 + urlLinks.elementAt(i));
 561         links.append(sequenceURLLinks.elementAt(i).toString());
 562         links.append("|");
 563       }
 564       // remove last "|"
 565       links.setLength(links.length() - 1);
 566       Cache.applicationProperties.setProperty("SEQUENCE_LINKS",
 567               links.toString());
 568     }
 569     else
 570     {
 571       Cache.applicationProperties.remove("SEQUENCE_LINKS");
 572     }
 573
 574     Cache.applicationProperties.setProperty("USE_PROXY",
 575             Boolean.toString(useProxy.isSelected()));
 576
 577     Cache.setOrRemove("PROXY_SERVER", proxyServerTB.getText());
 578
 579     Cache.setOrRemove("PROXY_PORT", proxyPortTB.getText());
 580
 581     if (useProxy.isSelected())
 582     {
 583       System.setProperty("http.proxyHost", proxyServerTB.getText());
 584       System.setProperty("http.proxyPort", proxyPortTB.getText());
 585     }
 586     else
 587     {
 588       System.setProperty("http.proxyHost", "");
 589       System.setProperty("http.proxyPort", "");
 590     }
 591     Cache.setProperty("VERSION_CHECK",
 592             Boolean.toString(versioncheck.isSelected()));
 593     if (Cache.getProperty("USAGESTATS") != null || usagestats.isSelected())
 594     {
 595       // default is false - we only set this if the user has actively agreed
 596       Cache.setProperty("USAGESTATS",
 597               Boolean.toString(usagestats.isSelected()));
 598     }
 599     if (!questionnaire.isSelected())
 600     {
 601       Cache.setProperty("NOQUESTIONNAIRES", "true");
 602     }
 603     else
 604     {
 605       // special - made easy to edit a property file to disable questionnaires
 606       // by just adding the given line
 607       Cache.removeProperty("NOQUESTIONNAIRES");
 608     }
 609
 610     /*
 611      * Save Output settings
 612      */
 613     Cache.applicationProperties.setProperty("BLC_JVSUFFIX",
 614             Boolean.toString(blcjv.isSelected()));
 615     Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX",
 616             Boolean.toString(clustaljv.isSelected()));
 617     Cache.applicationProperties.setProperty("FASTA_JVSUFFIX",
 618             Boolean.toString(fastajv.isSelected()));
 619     Cache.applicationProperties.setProperty("MSF_JVSUFFIX",
 620             Boolean.toString(msfjv.isSelected()));
 621     Cache.applicationProperties.setProperty("PFAM_JVSUFFIX",
 622             Boolean.toString(pfamjv.isSelected()));
 623     Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX",
 624             Boolean.toString(pileupjv.isSelected()));
 625     Cache.applicationProperties.setProperty("PIR_JVSUFFIX",
 626             Boolean.toString(pirjv.isSelected()));
 627     Cache.applicationProperties.setProperty("PIR_MODELLER",
 628             Boolean.toString(modellerOutput.isSelected()));
 629     Cache.applicationProperties.setProperty("EXPORT_EMBBED_BIOJSON",
 630             Boolean.toString(embbedBioJSON.isSelected()));
 631     jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
 632
 633     Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH",
 634             Boolean.toString(autoIdWidth.isSelected()));
 635     userIdWidth_actionPerformed();
 636     Cache.applicationProperties.setProperty("FIGURE_USERIDWIDTH",
 637             userIdWidth.getText());
 638
 639     /*
 640      * Save Editing settings
 641      */
 642     Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
 643             Boolean.toString(autoCalculateConsCheck.isSelected()));
 644     Cache.applicationProperties.setProperty("SORT_BY_TREE",
 645             Boolean.toString(sortByTree.isSelected()));
 646     Cache.applicationProperties.setProperty("PAD_GAPS",
 647             Boolean.toString(padGaps.isSelected()));
 648
 649     dasSource.saveProperties(Cache.applicationProperties);
 650     wsPrefs.updateAndRefreshWsMenuConfig(false);
 651     Cache.saveProperties();
 652     Desktop.instance.doConfigureStructurePrefs();
 653     try
 654     {
 655       frame.setClosed(true);
 656     } catch (Exception ex)
 657     {
 658     }
 659   }
 660
 661   /**
 662    * Do any necessary validation before saving settings. Return focus to the
 663    * first tab which fails validation.
 664    *
 665    * @return
 666    */
 667   private boolean validateSettings()
 668   {
 669     if (!validateStructure())
 670     {
 671       structureTab.requestFocusInWindow();
 672       return false;
 673     }
 674     return true;
 675   }
 676
 677   @Override
 678   protected boolean validateStructure()
 679   {
 680     return validateChimeraPath();
 681
 682   }
 683
 684   /**
 685    * DOCUMENT ME!
 686    */
 687   @Override
 688   public void startupFileTextfield_mouseClicked()
 689   {
 690     JalviewFileChooser chooser = new JalviewFileChooser(
 691             jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[] {
 692                 "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",
 693                 "jar" }, new String[] { "Fasta", "Clustal", "PFAM", "MSF",
 694                 "PIR", "BLC", "Jalview" },
 695             jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));
 696     chooser.setFileView(new JalviewFileView());
 697     chooser.setDialogTitle(MessageManager
 698             .getString("label.select_startup_file"));
 699
 700     int value = chooser.showOpenDialog(this);
 701
 702     if (value == JalviewFileChooser.APPROVE_OPTION)
 703     {
 704       jalview.bin.Cache.applicationProperties.setProperty(
 705               "DEFAULT_FILE_FORMAT", chooser.getSelectedFormat());
 706       startupFileTextfield.setText(chooser.getSelectedFile()
 707               .getAbsolutePath());
 708     }
 709   }
 710
 711   /**
 712    * DOCUMENT ME!
 713    *
 714    * @param e
 715    *          DOCUMENT ME!
 716    */
 717   @Override
 718   public void cancel_actionPerformed(ActionEvent e)
 719   {
 720     try
 721     {
 722       wsPrefs.updateWsMenuConfig(true);
 723       wsPrefs.refreshWs_actionPerformed(e);
 724       frame.setClosed(true);
 725     } catch (Exception ex)
 726     {
 727     }
 728   }
 729
 730   /**
 731    * DOCUMENT ME!
 732    *
 733    * @param e
 734    *          DOCUMENT ME!
 735    */
 736   @Override
 737   public void annotations_actionPerformed(ActionEvent e)
 738   {
 739     conservation.setEnabled(annotations.isSelected());
 740     quality.setEnabled(annotations.isSelected());
 741     identity.setEnabled(annotations.isSelected());
 742     showGroupConsensus.setEnabled(annotations.isSelected());
 743     showGroupConservation.setEnabled(annotations.isSelected());
 744     showConsensHistogram.setEnabled(annotations.isSelected()
 745             && (identity.isSelected() || showGroupConsensus.isSelected()));
 746     showConsensLogo.setEnabled(annotations.isSelected()
 747             && (identity.isSelected() || showGroupConsensus.isSelected()));
 748   }
 749
 750   @Override
 751   public void newLink_actionPerformed(ActionEvent e)
 752   {
 753
 754     GSequenceLink link = new GSequenceLink();
 755     boolean valid = false;
 756     while (!valid)
 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.addElement(link.getName());
 765           urlLinks.addElement(link.getURL());
 766           updateLinkData();
 767           valid = true;
 768         }
 769       }
 770       else
 771       {
 772         break;
 773       }
 774     }
 775   }
 776
 777   @Override
 778   public void editLink_actionPerformed(ActionEvent e)
 779   {
 780     GSequenceLink link = new GSequenceLink();
 781
 782     int index = linkNameList.getSelectedIndex();
 783     if (index == -1)
 784     {
 785       JOptionPane.showInternalMessageDialog(Desktop.desktop,
 786               MessageManager.getString("label.no_link_selected"),
 787               MessageManager.getString("label.no_link_selected"),
 788               JOptionPane.WARNING_MESSAGE);
 789       return;
 790     }
 791
 792     link.setName(nameLinks.elementAt(index).toString());
 793     link.setURL(urlLinks.elementAt(index).toString());
 794
 795     boolean valid = false;
 796     while (!valid)
 797     {
 798
 799       if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 800               MessageManager.getString("label.new_sequence_url_link"),
 801               JOptionPane.OK_CANCEL_OPTION, -1, null) == JOptionPane.OK_OPTION)
 802       {
 803         if (link.checkValid())
 804         {
 805           nameLinks.setElementAt(link.getName(), index);
 806           urlLinks.setElementAt(link.getURL(), index);
 807           updateLinkData();
 808           valid = true;
 809         }
 810       }
 811
 812       else
 813       {
 814         break;
 815       }
 816     }
 817   }
 818
 819   @Override
 820   public void deleteLink_actionPerformed(ActionEvent e)
 821   {
 822     int index = linkNameList.getSelectedIndex();
 823     if (index == -1)
 824     {
 825       JOptionPane.showInternalMessageDialog(Desktop.desktop,
 826               MessageManager.getString("label.no_link_selected"),
 827               MessageManager.getString("label.no_link_selected"),
 828               JOptionPane.WARNING_MESSAGE);
 829       return;
 830     }
 831     nameLinks.removeElementAt(index);
 832     urlLinks.removeElementAt(index);
 833     updateLinkData();
 834   }
 835
 836   void updateLinkData()
 837   {
 838     linkNameList.setListData(nameLinks);
 839     linkURLList.setListData(urlLinks);
 840   }
 841
 842   @Override
 843   public void defaultBrowser_mouseClicked(MouseEvent e)
 844   {
 845     JFileChooser chooser = new JFileChooser(".");
 846     chooser.setDialogTitle(MessageManager
 847             .getString("label.select_default_browser"));
 848
 849     int value = chooser.showOpenDialog(this);
 850
 851     if (value == JFileChooser.APPROVE_OPTION)
 852     {
 853       defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
 854     }
 855
 856   }
 857
 858   /*
 859    * (non-Javadoc)
 860    *
 861    * @see
 862    * jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event
 863    * .ActionEvent)
 864    */
 865   @Override
 866   protected void showunconserved_actionPerformed(ActionEvent e)
 867   {
 868     // TODO Auto-generated method stub
 869     super.showunconserved_actionPerformed(e);
 870   }
 871
 872   public static List<String> getGroupURLLinks()
 873   {
 874     return groupURLLinks;
 875   }
 876
 877   @Override
 878   public void minColour_actionPerformed(JPanel panel)
 879   {
 880     Color col = JColorChooser.showDialog(this,
 881             MessageManager.getString("label.select_colour_minimum_value"),
 882             minColour.getBackground());
 883     if (col != null)
 884     {
 885       panel.setBackground(col);
 886     }
 887     panel.repaint();
 888   }
 889
 890   @Override
 891   public void maxColour_actionPerformed(JPanel panel)
 892   {
 893     Color col = JColorChooser.showDialog(this,
 894             MessageManager.getString("label.select_colour_maximum_value"),
 895             maxColour.getBackground());
 896     if (col != null)
 897     {
 898       panel.setBackground(col);
 899     }
 900     panel.repaint();
 901   }
 902
 903   @Override
 904   protected void userIdWidth_actionPerformed()
 905   {
 906     try
 907     {
 908       String val = userIdWidth.getText().trim();
 909       if (val.length() > 0)
 910       {
 911         Integer iw = Integer.parseInt(val);
 912         if (iw.intValue() < 12)
 913         {
 914           throw new NumberFormatException();
 915         }
 916         userIdWidth.setText(iw.toString());
 917       }
 918     } catch (NumberFormatException x)
 919     {
 920       JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
 921               .getString("warn.user_defined_width_requirements"),
 922               MessageManager.getString("label.invalid_id_column_width"),
 923               JOptionPane.WARNING_MESSAGE);
 924       userIdWidth.setText("");
 925     }
 926   }
 927
 928   @Override
 929   protected void autoIdWidth_actionPerformed()
 930   {
 931     userIdWidth.setEnabled(!autoIdWidth.isSelected());
 932     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
 933   }
 934
 935   /**
 936    * Returns true if chimera path is to a valid executable, else show an error
 937    * dialog.
 938    */
 939   private boolean validateChimeraPath()
 940   {
 941     if (chimeraPath.getText().trim().length() > 0)
 942     {
 943       File f = new File(chimeraPath.getText());
 944       if (!f.canExecute())
 945       {
 946         JOptionPane.showInternalMessageDialog(Desktop.desktop,
 947                 MessageManager.getString("label.invalid_chimera_path"),
 948                 MessageManager.getString("label.invalid_name"),
 949                 JOptionPane.ERROR_MESSAGE);
 950         return false;
 951       }
 952     }
 953     return true;
 954   }
 955
 956   /**
 957    * If Chimera is selected, check it can be found on default or user-specified
 958    * path, if not show a warning/help dialog.
 959    */
 960   @Override
 961   protected void structureViewer_actionPerformed(String selectedItem)
 962   {
 963     if (!selectedItem.equals(ViewerType.CHIMERA.name()))
 964     {
 965       return;
 966     }
 967     boolean found = false;
 968
 969     /*
 970      * Try user-specified and standard paths for Chimera executable.
 971      */
 972     List<String> paths = StructureManager.getChimeraPaths();
 973     paths.add(0, chimeraPath.getText());
 974     for (String path : paths)
 975     {
 976       if (new File(path.trim()).canExecute())
 977       {
 978         found = true;
 979         break;
 980       }
 981     }
 982     if (!found)
 983     {
 984       String[] options = { "OK", "Help" };
 985       int showHelp = JOptionPane.showInternalOptionDialog(
 986               Desktop.desktop,
 987               JvSwingUtils.wrapTooltip(true,
 988                       MessageManager.getString("label.chimera_missing")),
 989               "", JOptionPane.YES_NO_OPTION, JOptionPane.WARNING_MESSAGE,
 990               null, options, options[0]);
 991       if (showHelp == JOptionPane.NO_OPTION)
 992       {
 993         try
 994         {
 995           Help.showHelpWindow(HelpId.StructureViewer);
 996         } catch (HelpSetException e)
 997         {
 998           e.printStackTrace();
 999         }
1000       }
1001     }
1002   }
1003
1004   public class OptionsParam
1005   {
1006     private String name;
1007
1008     private String code;
1009
1010     public OptionsParam(String name, String code)
1011     {
1012       this.name = name;
1013       this.code = code;
1014     }
1015
1016     public String getName()
1017     {
1018       return name;
1019     }
1020
1021     public void setName(String name)
1022     {
1023       this.name = name;
1024     }
1025
1026     public String getCode()
1027     {
1028       return code;
1029     }
1030
1031     public void setCode(String code)
1032     {
1033       this.code = code;
1034     }
1035
1036     @Override
1037     public String toString()
1038     {
1039       return name;
1040     }
1041
1042     @Override
1043     public boolean equals(Object that)
1044     {
1045       if (!(that instanceof OptionsParam))
1046       {
1047         return false;
1048       }
1049       return this.code.equalsIgnoreCase(((OptionsParam) that).code);
1050     }
1051
1052     @Override
1053     public int hashCode()
1054     {
1055       return name.hashCode() + code.hashCode();
1056     }
1057   }
1058 }