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
 363             .addItem(MessageManager.getString("label.prompt_each_time"));
 364     epsRendering.addItem(MessageManager.getString("label.lineart"));
 365     epsRendering.addItem(MessageManager.getString("action.text"));
 366     epsRendering.setSelectedItem(Cache.getDefault("EPS_RENDERING",
 367             "Prompt each time"));
 368     autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false));
 369     userIdWidth.setEnabled(!autoIdWidth.isSelected());
 370     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
 371     Integer wi = Cache.getIntegerProperty("FIGURE_USERIDWIDTH");
 372     userIdWidth.setText(wi == null ? "" : wi.toString());
 373     blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
 374     clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
 375     fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
 376     msfjv.setSelected(Cache.getDefault("MSF_JVSUFFIX", true));
 377     pfamjv.setSelected(Cache.getDefault("PFAM_JVSUFFIX", true));
 378     pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
 379     pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
 380     modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
 381     embbedBioJSON.setSelected(Cache.getDefault("EXPORT_EMBBED_BIOJSON",
 382             true));
 383
 384     /*
 385      * Set Editing tab defaults
 386      */
 387     autoCalculateConsCheck.setSelected(Cache.getDefault(
 388             "AUTO_CALC_CONSENSUS", true));
 389     padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
 390     sortByTree.setSelected(Cache.getDefault("SORT_BY_TREE", false));
 391
 392     annotations_actionPerformed(null); // update the display of the annotation
 393                                        // settings
 394   }
 395
 396   /**
 397    * Save user selections on the Preferences tabs to the Cache and write out to
 398    * file.
 399    *
 400    * @param e
 401    */
 402   @Override
 403   public void ok_actionPerformed(ActionEvent e)
 404   {
 405     if (!validateSettings())
 406     {
 407       return;
 408     }
 409
 410     /*
 411      * Save Visual settings
 412      */
 413     Cache.applicationProperties.setProperty("SHOW_JVSUFFIX",
 414             Boolean.toString(seqLimit.isSelected()));
 415     Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS",
 416             Boolean.toString(rightAlign.isSelected()));
 417     Cache.applicationProperties.setProperty("SHOW_FULLSCREEN",
 418             Boolean.toString(fullScreen.isSelected()));
 419     Cache.applicationProperties.setProperty("SHOW_OVERVIEW",
 420             Boolean.toString(openoverv.isSelected()));
 421     Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
 422             Boolean.toString(annotations.isSelected()));
 423     Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
 424             Boolean.toString(conservation.isSelected()));
 425     Cache.applicationProperties.setProperty("SHOW_QUALITY",
 426             Boolean.toString(quality.isSelected()));
 427     Cache.applicationProperties.setProperty("SHOW_IDENTITY",
 428             Boolean.toString(identity.isSelected()));
 429
 430     Cache.applicationProperties.setProperty("GAP_SYMBOL", gapSymbolCB
 431             .getSelectedItem().toString());
 432
 433     Cache.applicationProperties.setProperty("FONT_NAME", fontNameCB
 434             .getSelectedItem().toString());
 435     Cache.applicationProperties.setProperty("FONT_STYLE", fontStyleCB
 436             .getSelectedItem().toString());
 437     Cache.applicationProperties.setProperty("FONT_SIZE", fontSizeCB
 438             .getSelectedItem().toString());
 439
 440     Cache.applicationProperties.setProperty("ID_ITALICS",
 441             Boolean.toString(idItalics.isSelected()));
 442     Cache.applicationProperties.setProperty("SHOW_UNCONSERVED",
 443             Boolean.toString(showUnconserved.isSelected()));
 444     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS",
 445             Boolean.toString(showGroupConsensus.isSelected()));
 446     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION",
 447             Boolean.toString(showGroupConservation.isSelected()));
 448     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_HISTOGRAM",
 449             Boolean.toString(showConsensHistogram.isSelected()));
 450     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO",
 451             Boolean.toString(showConsensLogo.isSelected()));
 452     Cache.applicationProperties.setProperty("ANTI_ALIAS",
 453             Boolean.toString(smoothFont.isSelected()));
 454     Cache.applicationProperties.setProperty(SCALE_PROTEIN_TO_CDNA,
 455             Boolean.toString(scaleProteinToCdna.isSelected()));
 456     Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP",
 457             Boolean.toString(showNpTooltip.isSelected()));
 458     Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP",
 459             Boolean.toString(showDbRefTooltip.isSelected()));
 460
 461     Cache.applicationProperties.setProperty("WRAP_ALIGNMENT",
 462             Boolean.toString(wrap.isSelected()));
 463
 464     Cache.applicationProperties.setProperty("STARTUP_FILE",
 465             startupFileTextfield.getText());
 466     Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",
 467             Boolean.toString(startupCheckbox.isSelected()));
 468
 469     Cache.applicationProperties.setProperty("SORT_ALIGNMENT", sortby
 470             .getSelectedItem().toString());
 471
 472     // convert description of sort order to enum name for save
 473     SequenceAnnotationOrder annSortOrder = SequenceAnnotationOrder
 474             .forDescription(sortAnnBy.getSelectedItem().toString());
 475     if (annSortOrder != null)
 476     {
 477       Cache.applicationProperties.setProperty(SORT_ANNOTATIONS,
 478               annSortOrder.name());
 479     }
 480
 481     final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
 482     Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE, Boolean
 483             .valueOf(showAutocalcFirst).toString());
 484
 485     /*
 486      * Save Colours settings
 487      */
 488     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_PROT, protColour
 489             .getSelectedItem().toString());
 490     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_NUC, nucColour
 491             .getSelectedItem().toString());
 492     Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
 493             minColour.getBackground());
 494     Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
 495             maxColour.getBackground());
 496
 497     /*
 498      * Save Structure settings
 499      */
 500     Cache.applicationProperties.setProperty(ADD_TEMPFACT_ANN,
 501             Boolean.toString(addTempFactor.isSelected()));
 502     Cache.applicationProperties.setProperty(ADD_SS_ANN,
 503             Boolean.toString(addSecondaryStructure.isSelected()));
 504     Cache.applicationProperties.setProperty(USE_RNAVIEW,
 505             Boolean.toString(useRnaView.isSelected()));
 506     Cache.applicationProperties.setProperty(STRUCT_FROM_PDB,
 507             Boolean.toString(structFromPdb.isSelected()));
 508     Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY, structViewer
 509             .getSelectedItem().toString());
 510     Cache.setOrRemove(CHIMERA_PATH, chimeraPath.getText());
 511     Cache.applicationProperties.setProperty("MAP_WITH_SIFTS",
 512             Boolean.toString(siftsMapping.isSelected()));
 513     SiftsSettings.setMapWithSifts(siftsMapping.isSelected());
 514
 515     /*
 516      * Save Output settings
 517      */
 518     if (epsRendering.getSelectedItem().equals("Prompt each time"))
 519     {
 520       Cache.applicationProperties.remove("EPS_RENDERING");
 521     }
 522     else
 523     {
 524       Cache.applicationProperties.setProperty("EPS_RENDERING", epsRendering
 525               .getSelectedItem().toString());
 526     }
 527
 528     /*
 529      * Save Connections settings
 530      */
 531     Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText());
 532
 533     jalview.util.BrowserLauncher.resetBrowser();
 534
 535     if (nameLinks.size() > 0)
 536     {
 537       StringBuffer links = new StringBuffer();
 538       sequenceURLLinks = new Vector<String>();
 539       for (int i = 0; i < nameLinks.size(); i++)
 540       {
 541         sequenceURLLinks.addElement(nameLinks.elementAt(i) + "|"
 542                 + urlLinks.elementAt(i));
 543         links.append(sequenceURLLinks.elementAt(i).toString());
 544         links.append("|");
 545       }
 546       // remove last "|"
 547       links.setLength(links.length() - 1);
 548       Cache.applicationProperties.setProperty("SEQUENCE_LINKS",
 549               links.toString());
 550     }
 551     else
 552     {
 553       Cache.applicationProperties.remove("SEQUENCE_LINKS");
 554     }
 555
 556     Cache.applicationProperties.setProperty("USE_PROXY",
 557             Boolean.toString(useProxy.isSelected()));
 558
 559     Cache.setOrRemove("PROXY_SERVER", proxyServerTB.getText());
 560
 561     Cache.setOrRemove("PROXY_PORT", proxyPortTB.getText());
 562
 563     if (useProxy.isSelected())
 564     {
 565       System.setProperty("http.proxyHost", proxyServerTB.getText());
 566       System.setProperty("http.proxyPort", proxyPortTB.getText());
 567     }
 568     else
 569     {
 570       System.setProperty("http.proxyHost", "");
 571       System.setProperty("http.proxyPort", "");
 572     }
 573     Cache.setProperty("VERSION_CHECK",
 574             Boolean.toString(versioncheck.isSelected()));
 575     if (Cache.getProperty("USAGESTATS") != null || usagestats.isSelected())
 576     {
 577       // default is false - we only set this if the user has actively agreed
 578       Cache.setProperty("USAGESTATS",
 579               Boolean.toString(usagestats.isSelected()));
 580     }
 581     if (!questionnaire.isSelected())
 582     {
 583       Cache.setProperty("NOQUESTIONNAIRES", "true");
 584     }
 585     else
 586     {
 587       // special - made easy to edit a property file to disable questionnaires
 588       // by just adding the given line
 589       Cache.removeProperty("NOQUESTIONNAIRES");
 590     }
 591
 592     /*
 593      * Save Output settings
 594      */
 595     Cache.applicationProperties.setProperty("BLC_JVSUFFIX",
 596             Boolean.toString(blcjv.isSelected()));
 597     Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX",
 598             Boolean.toString(clustaljv.isSelected()));
 599     Cache.applicationProperties.setProperty("FASTA_JVSUFFIX",
 600             Boolean.toString(fastajv.isSelected()));
 601     Cache.applicationProperties.setProperty("MSF_JVSUFFIX",
 602             Boolean.toString(msfjv.isSelected()));
 603     Cache.applicationProperties.setProperty("PFAM_JVSUFFIX",
 604             Boolean.toString(pfamjv.isSelected()));
 605     Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX",
 606             Boolean.toString(pileupjv.isSelected()));
 607     Cache.applicationProperties.setProperty("PIR_JVSUFFIX",
 608             Boolean.toString(pirjv.isSelected()));
 609     Cache.applicationProperties.setProperty("PIR_MODELLER",
 610             Boolean.toString(modellerOutput.isSelected()));
 611     Cache.applicationProperties.setProperty("EXPORT_EMBBED_BIOJSON",
 612             Boolean.toString(embbedBioJSON.isSelected()));
 613     jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
 614
 615     Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH",
 616             Boolean.toString(autoIdWidth.isSelected()));
 617     userIdWidth_actionPerformed();
 618     Cache.applicationProperties.setProperty("FIGURE_USERIDWIDTH",
 619             userIdWidth.getText());
 620
 621     /*
 622      * Save Editing settings
 623      */
 624     Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
 625             Boolean.toString(autoCalculateConsCheck.isSelected()));
 626     Cache.applicationProperties.setProperty("SORT_BY_TREE",
 627             Boolean.toString(sortByTree.isSelected()));
 628     Cache.applicationProperties.setProperty("PAD_GAPS",
 629             Boolean.toString(padGaps.isSelected()));
 630
 631     dasSource.saveProperties(Cache.applicationProperties);
 632     wsPrefs.updateAndRefreshWsMenuConfig(false);
 633     Cache.saveProperties();
 634     Desktop.instance.doConfigureStructurePrefs();
 635     try
 636     {
 637       frame.setClosed(true);
 638     } catch (Exception ex)
 639     {
 640     }
 641   }
 642
 643   /**
 644    * Do any necessary validation before saving settings. Return focus to the
 645    * first tab which fails validation.
 646    *
 647    * @return
 648    */
 649   private boolean validateSettings()
 650   {
 651     if (!validateStructure())
 652     {
 653       structureTab.requestFocusInWindow();
 654       return false;
 655     }
 656     return true;
 657   }
 658
 659   @Override
 660   protected boolean validateStructure()
 661   {
 662     return validateChimeraPath();
 663
 664   }
 665
 666   /**
 667    * DOCUMENT ME!
 668    */
 669   @Override
 670   public void startupFileTextfield_mouseClicked()
 671   {
 672     JalviewFileChooser chooser = new JalviewFileChooser(
 673             jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[] {
 674                 "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",
 675                 "jar" }, new String[] { "Fasta", "Clustal", "PFAM", "MSF",
 676                 "PIR", "BLC", "Jalview" },
 677             jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));
 678     chooser.setFileView(new JalviewFileView());
 679     chooser.setDialogTitle(MessageManager
 680             .getString("label.select_startup_file"));
 681
 682     int value = chooser.showOpenDialog(this);
 683
 684     if (value == JalviewFileChooser.APPROVE_OPTION)
 685     {
 686       jalview.bin.Cache.applicationProperties.setProperty(
 687               "DEFAULT_FILE_FORMAT", chooser.getSelectedFormat());
 688       startupFileTextfield.setText(chooser.getSelectedFile()
 689               .getAbsolutePath());
 690     }
 691   }
 692
 693   /**
 694    * DOCUMENT ME!
 695    *
 696    * @param e
 697    *          DOCUMENT ME!
 698    */
 699   @Override
 700   public void cancel_actionPerformed(ActionEvent e)
 701   {
 702     try
 703     {
 704       wsPrefs.updateWsMenuConfig(true);
 705       wsPrefs.refreshWs_actionPerformed(e);
 706       frame.setClosed(true);
 707     } catch (Exception ex)
 708     {
 709     }
 710   }
 711
 712   /**
 713    * DOCUMENT ME!
 714    *
 715    * @param e
 716    *          DOCUMENT ME!
 717    */
 718   @Override
 719   public void annotations_actionPerformed(ActionEvent e)
 720   {
 721     conservation.setEnabled(annotations.isSelected());
 722     quality.setEnabled(annotations.isSelected());
 723     identity.setEnabled(annotations.isSelected());
 724     showGroupConsensus.setEnabled(annotations.isSelected());
 725     showGroupConservation.setEnabled(annotations.isSelected());
 726     showConsensHistogram.setEnabled(annotations.isSelected()
 727             && (identity.isSelected() || showGroupConsensus.isSelected()));
 728     showConsensLogo.setEnabled(annotations.isSelected()
 729             && (identity.isSelected() || showGroupConsensus.isSelected()));
 730   }
 731
 732   @Override
 733   public void newLink_actionPerformed(ActionEvent e)
 734   {
 735
 736     GSequenceLink link = new GSequenceLink();
 737     boolean valid = false;
 738     while (!valid)
 739     {
 740       if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 741               MessageManager.getString("label.new_sequence_url_link"),
 742               JOptionPane.OK_CANCEL_OPTION, -1, null) == JOptionPane.OK_OPTION)
 743       {
 744         if (link.checkValid())
 745         {
 746           nameLinks.addElement(link.getName());
 747           urlLinks.addElement(link.getURL());
 748           updateLinkData();
 749           valid = true;
 750         }
 751       }
 752       else
 753       {
 754         break;
 755       }
 756     }
 757   }
 758
 759   @Override
 760   public void editLink_actionPerformed(ActionEvent e)
 761   {
 762     GSequenceLink link = new GSequenceLink();
 763
 764     int index = linkNameList.getSelectedIndex();
 765     if (index == -1)
 766     {
 767       JOptionPane.showInternalMessageDialog(Desktop.desktop,
 768               MessageManager.getString("label.no_link_selected"),
 769               MessageManager.getString("label.no_link_selected"),
 770               JOptionPane.WARNING_MESSAGE);
 771       return;
 772     }
 773
 774     link.setName(nameLinks.elementAt(index).toString());
 775     link.setURL(urlLinks.elementAt(index).toString());
 776
 777     boolean valid = false;
 778     while (!valid)
 779     {
 780
 781       if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 782               MessageManager.getString("label.new_sequence_url_link"),
 783               JOptionPane.OK_CANCEL_OPTION, -1, null) == JOptionPane.OK_OPTION)
 784       {
 785         if (link.checkValid())
 786         {
 787           nameLinks.setElementAt(link.getName(), index);
 788           urlLinks.setElementAt(link.getURL(), index);
 789           updateLinkData();
 790           valid = true;
 791         }
 792       }
 793
 794       else
 795       {
 796         break;
 797       }
 798     }
 799   }
 800
 801   @Override
 802   public void deleteLink_actionPerformed(ActionEvent e)
 803   {
 804     int index = linkNameList.getSelectedIndex();
 805     if (index == -1)
 806     {
 807       JOptionPane.showInternalMessageDialog(Desktop.desktop,
 808               MessageManager.getString("label.no_link_selected"),
 809               MessageManager.getString("label.no_link_selected"),
 810               JOptionPane.WARNING_MESSAGE);
 811       return;
 812     }
 813     nameLinks.removeElementAt(index);
 814     urlLinks.removeElementAt(index);
 815     updateLinkData();
 816   }
 817
 818   void updateLinkData()
 819   {
 820     linkNameList.setListData(nameLinks);
 821     linkURLList.setListData(urlLinks);
 822   }
 823
 824   @Override
 825   public void defaultBrowser_mouseClicked(MouseEvent e)
 826   {
 827     JFileChooser chooser = new JFileChooser(".");
 828     chooser.setDialogTitle(MessageManager
 829             .getString("label.select_default_browser"));
 830
 831     int value = chooser.showOpenDialog(this);
 832
 833     if (value == JFileChooser.APPROVE_OPTION)
 834     {
 835       defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
 836     }
 837
 838   }
 839
 840   /*
 841    * (non-Javadoc)
 842    *
 843    * @see
 844    * jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event
 845    * .ActionEvent)
 846    */
 847   @Override
 848   protected void showunconserved_actionPerformed(ActionEvent e)
 849   {
 850     // TODO Auto-generated method stub
 851     super.showunconserved_actionPerformed(e);
 852   }
 853
 854   public static List<String> getGroupURLLinks()
 855   {
 856     return groupURLLinks;
 857   }
 858
 859   @Override
 860   public void minColour_actionPerformed(JPanel panel)
 861   {
 862     Color col = JColorChooser.showDialog(this,
 863             MessageManager.getString("label.select_colour_minimum_value"),
 864             minColour.getBackground());
 865     if (col != null)
 866     {
 867       panel.setBackground(col);
 868     }
 869     panel.repaint();
 870   }
 871
 872   @Override
 873   public void maxColour_actionPerformed(JPanel panel)
 874   {
 875     Color col = JColorChooser.showDialog(this,
 876             MessageManager.getString("label.select_colour_maximum_value"),
 877             maxColour.getBackground());
 878     if (col != null)
 879     {
 880       panel.setBackground(col);
 881     }
 882     panel.repaint();
 883   }
 884
 885   @Override
 886   protected void userIdWidth_actionPerformed()
 887   {
 888     try
 889     {
 890       String val = userIdWidth.getText().trim();
 891       if (val.length() > 0)
 892       {
 893         Integer iw = Integer.parseInt(val);
 894         if (iw.intValue() < 12)
 895         {
 896           throw new NumberFormatException();
 897         }
 898         userIdWidth.setText(iw.toString());
 899       }
 900     } catch (NumberFormatException x)
 901     {
 902       JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
 903               .getString("warn.user_defined_width_requirements"),
 904               MessageManager.getString("label.invalid_id_column_width"),
 905               JOptionPane.WARNING_MESSAGE);
 906       userIdWidth.setText("");
 907     }
 908   }
 909
 910   @Override
 911   protected void autoIdWidth_actionPerformed()
 912   {
 913     userIdWidth.setEnabled(!autoIdWidth.isSelected());
 914     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
 915   }
 916
 917   /**
 918    * Returns true if chimera path is to a valid executable, else show an error
 919    * dialog.
 920    */
 921   private boolean validateChimeraPath()
 922   {
 923     if (chimeraPath.getText().trim().length() > 0)
 924     {
 925       File f = new File(chimeraPath.getText());
 926       if (!f.canExecute())
 927       {
 928         JOptionPane.showInternalMessageDialog(Desktop.desktop,
 929                 MessageManager.getString("label.invalid_chimera_path"),
 930                 MessageManager.getString("label.invalid_name"),
 931                 JOptionPane.ERROR_MESSAGE);
 932         return false;
 933       }
 934     }
 935     return true;
 936   }
 937
 938   /**
 939    * If Chimera is selected, check it can be found on default or user-specified
 940    * path, if not show a warning/help dialog.
 941    */
 942   @Override
 943   protected void structureViewer_actionPerformed(String selectedItem)
 944   {
 945     if (!selectedItem.equals(ViewerType.CHIMERA.name()))
 946     {
 947       return;
 948     }
 949     boolean found = false;
 950
 951     /*
 952      * Try user-specified and standard paths for Chimera executable.
 953      */
 954     List<String> paths = StructureManager.getChimeraPaths();
 955     paths.add(0, chimeraPath.getText());
 956     for (String path : paths)
 957     {
 958       if (new File(path.trim()).canExecute())
 959       {
 960         found = true;
 961         break;
 962       }
 963     }
 964     if (!found)
 965     {
 966       String[] options = { "OK", "Help" };
 967       int showHelp = JOptionPane.showInternalOptionDialog(
 968               Desktop.desktop,
 969               JvSwingUtils.wrapTooltip(true,
 970                       MessageManager.getString("label.chimera_missing")),
 971               "", JOptionPane.YES_NO_OPTION, JOptionPane.WARNING_MESSAGE,
 972               null, options, options[0]);
 973       if (showHelp == JOptionPane.NO_OPTION)
 974       {
 975         try
 976         {
 977           Help.showHelpWindow(HelpId.StructureViewer);
 978         } catch (HelpSetException e)
 979         {
 980           e.printStackTrace();
 981         }
 982       }
 983     }
 984   }
 985
 986 }