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