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
  25 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
  26 import jalview.bin.Cache;
  27 import jalview.gui.Help.HelpId;
  28 import jalview.gui.StructureViewer.ViewerType;
  29 import jalview.io.JalviewFileChooser;
  30 import jalview.io.JalviewFileView;
  31 import jalview.jbgui.GPreferences;
  32 import jalview.jbgui.GSequenceLink;
  33 import jalview.schemes.ColourSchemeProperty;
  34 import jalview.util.MessageManager;
  35 import jalview.util.Platform;
  36 import jalview.util.UrlProvider;
  37 import jalview.util.UrlProviderI;
  38 import jalview.ws.sifts.SiftsSettings;
  39
  40 import java.awt.BorderLayout;
  41 import java.awt.Color;
  42 import java.awt.Dimension;
  43 import java.awt.Font;
  44 import java.awt.event.ActionEvent;
  45 import java.awt.event.ActionListener;
  46 import java.awt.event.MouseEvent;
  47 import java.io.File;
  48 import java.util.ArrayList;
  49 import java.util.List;
  50 import java.util.Vector;
  51
  52 import javax.help.HelpSetException;
  53 import javax.swing.JColorChooser;
  54 import javax.swing.JFileChooser;
  55 import javax.swing.JInternalFrame;
  56 import javax.swing.JOptionPane;
  57 import javax.swing.JPanel;
  58
  59 import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
  60
  61 /**
  62  * DOCUMENT ME!
  63  *
  64  * @author $author$
  65  * @version $Revision$
  66  */
  67 public class Preferences extends GPreferences
  68 {
  69   public static final String ENABLE_SPLIT_FRAME = "ENABLE_SPLIT_FRAME";
  70
  71   public static final String SCALE_PROTEIN_TO_CDNA = "SCALE_PROTEIN_TO_CDNA";
  72
  73   public static final String DEFAULT_COLOUR = "DEFAULT_COLOUR";
  74
  75   public static final String DEFAULT_COLOUR_PROT = "DEFAULT_COLOUR_PROT";
  76
  77   public static final String DEFAULT_COLOUR_NUC = "DEFAULT_COLOUR_NUC";
  78
  79   public static final String ADD_TEMPFACT_ANN = "ADD_TEMPFACT_ANN";
  80
  81   public static final String ADD_SS_ANN = "ADD_SS_ANN";
  82
  83   public static final String USE_RNAVIEW = "USE_RNAVIEW";
  84
  85   public static final String STRUCT_FROM_PDB = "STRUCT_FROM_PDB";
  86
  87   public static final String STRUCTURE_DISPLAY = "STRUCTURE_DISPLAY";
  88
  89   public static final String CHIMERA_PATH = "CHIMERA_PATH";
  90
  91   public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS";
  92
  93   public static final String SHOW_AUTOCALC_ABOVE = "SHOW_AUTOCALC_ABOVE";
  94
  95   private static final int MIN_FONT_SIZE = 1;
  96
  97   private static final int MAX_FONT_SIZE = 30;
  98
  99   /**
 100    * Holds name and link separated with | character. Sequence ID must be
 101    * $SEQUENCE_ID$ or $SEQUENCE_ID=/.possible | chars ./=$
 102    */
 103   // public static Vector<String> sequenceURLLinks;
 104   public static UrlProviderI sequenceUrlLinks;
 105
 106   /**
 107    * Holds name and link separated with | character. Sequence IDS and Sequences
 108    * must be $SEQUENCEIDS$ or $SEQUENCEIDS=/.possible | chars ./=$ and
 109    * $SEQUENCES$ or $SEQUENCES=/.possible | chars ./=$ and separation character
 110    * for first and second token specified after a pipe character at end |,|.
 111    * (TODO: proper escape for using | to separate ids or sequences
 112    */
 113
 114   public static List<String> groupURLLinks;
 115   static
 116   {
 117     String string = Cache.getDefault("SEQUENCE_LINKS", EMBLEBI_STRING);
 118     sequenceUrlLinks = new UrlProvider(EMBLEBI_STRING.split("\\|")[0],
 119             string); // TODO sort out the default string
 120     // sequenceURLLinks = new Vector<String>();
 121
 122     /*    try
 123         {
 124           StringTokenizer st = new StringTokenizer(string, "|");
 125           while (st.hasMoreElements())
 126           {
 127             String name = st.nextToken();
 128             String url = st.nextToken();
 129             // check for '|' within a regex
 130             int rxstart = url.indexOf("$" + DB_ACCESSION + "$");
 131             if (rxstart == -1)
 132             {
 133               rxstart = url.indexOf("$" + SEQUENCE_ID + "$");
 134             }
 135             while (rxstart == -1 && url.indexOf("/=$") == -1)
 136             {
 137               url = url + "|" + st.nextToken();
 138             }
 139             sequenceURLLinks.addElement(name + "|" + url);
 140           }
 141         } catch (Exception ex)
 142         {
 143           System.out.println(ex + "\nError parsing sequence links");
 144         }
 145         {
 146           // upgrade old SRS link
 147           int srsPos = sequenceURLLinks.indexOf(SRS_STRING);
 148           if (srsPos > -1)
 149           {
 150             sequenceURLLinks.setElementAt(EMBLEBI_STRING, srsPos);
 151           }
 152         }
 153     */
 154     /**
 155      * TODO: reformulate groupURL encoding so two or more can be stored in the
 156      * .properties file as '|' separated strings
 157      */
 158
 159     groupURLLinks = new ArrayList<String>();
 160   }
 161
 162   Vector<String> nameLinks, urlLinks;
 163
 164   JInternalFrame frame;
 165
 166   DasSourceBrowser dasSource;
 167
 168   private WsPreferences wsPrefs;
 169
 170   private OptionsParam promptEachTimeOpt = new OptionsParam(
 171           MessageManager.getString("label.prompt_each_time"),
 172           "Prompt each time");
 173
 174   private OptionsParam lineArtOpt = new OptionsParam(
 175           MessageManager.getString("label.lineart"), "Lineart");
 176
 177   private OptionsParam textOpt = new OptionsParam(
 178           MessageManager.getString("action.text"), "Text");
 179
 180   /**
 181    * Creates a new Preferences object.
 182    */
 183   public Preferences()
 184   {
 185     super();
 186     frame = new JInternalFrame();
 187     frame.setContentPane(this);
 188     dasSource = new DasSourceBrowser();
 189     dasTab.add(dasSource, BorderLayout.CENTER);
 190     wsPrefs = new WsPreferences();
 191     wsTab.add(wsPrefs, BorderLayout.CENTER);
 192     int width = 500, height = 450;
 193     new jalview.util.Platform();
 194     if (Platform.isAMac())
 195     {
 196       width = 570;
 197       height = 480;
 198     }
 199
 200     Desktop.addInternalFrame(frame,
 201             MessageManager.getString("label.preferences"), width, height);
 202     frame.setMinimumSize(new Dimension(width, height));
 203
 204     /*
 205      * Set Visual tab defaults
 206      */
 207     seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));
 208     rightAlign.setSelected(Cache.getDefault("RIGHT_ALIGN_IDS", false));
 209     fullScreen.setSelected(Cache.getDefault("SHOW_FULLSCREEN", false));
 210     annotations.setSelected(Cache.getDefault("SHOW_ANNOTATIONS", true));
 211
 212     conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));
 213     quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));
 214     identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));
 215     openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false));
 216     showUnconserved
 217             .setSelected(Cache.getDefault("SHOW_UNCONSERVED", false));
 218     showGroupConsensus.setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS",
 219             false));
 220     showGroupConservation.setSelected(Cache.getDefault(
 221             "SHOW_GROUP_CONSERVATION", false));
 222     showConsensHistogram.setSelected(Cache.getDefault(
 223             "SHOW_CONSENSUS_HISTOGRAM", true));
 224     showConsensLogo.setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO",
 225             false));
 226     showNpTooltip.setSelected(Cache
 227             .getDefault("SHOW_NPFEATS_TOOLTIP", true));
 228     showDbRefTooltip.setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP",
 229             true));
 230
 231     String[] fonts = java.awt.GraphicsEnvironment
 232             .getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
 233     for (int i = 0; i < fonts.length; i++)
 234     {
 235       fontNameCB.addItem(fonts[i]);
 236     }
 237
 238     for (int i = MIN_FONT_SIZE; i <= MAX_FONT_SIZE; i++)
 239     {
 240       fontSizeCB.addItem(i + "");
 241     }
 242
 243     fontStyleCB.addItem("plain");
 244     fontStyleCB.addItem("bold");
 245     fontStyleCB.addItem("italic");
 246
 247     fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
 248     fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
 249     fontStyleCB.setSelectedItem(Cache.getDefault("FONT_STYLE", Font.PLAIN
 250             + ""));
 251
 252     smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));
 253     scaleProteinToCdna.setSelected(Cache.getDefault(SCALE_PROTEIN_TO_CDNA,
 254             false));
 255
 256     idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
 257
 258     wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
 259
 260     gapSymbolCB.addItem("-");
 261     gapSymbolCB.addItem(".");
 262
 263     gapSymbolCB.setSelectedItem(Cache.getDefault("GAP_SYMBOL", "-"));
 264
 265     sortby.addItem("No sort");
 266     sortby.addItem("Id");
 267     sortby.addItem("Pairwise Identity");
 268     sortby.setSelectedItem(Cache.getDefault("SORT_ALIGNMENT", "No sort"));
 269
 270     sortAnnBy.addItem(SequenceAnnotationOrder.NONE.toString());
 271     sortAnnBy
 272             .addItem(SequenceAnnotationOrder.SEQUENCE_AND_LABEL.toString());
 273     sortAnnBy
 274             .addItem(SequenceAnnotationOrder.LABEL_AND_SEQUENCE.toString());
 275     SequenceAnnotationOrder savedSort = SequenceAnnotationOrder
 276             .valueOf(Cache.getDefault(SORT_ANNOTATIONS,
 277                     SequenceAnnotationOrder.NONE.name()));
 278     sortAnnBy.setSelectedItem(savedSort.toString());
 279
 280     sortAutocalc.addItem("Autocalculated first");
 281     sortAutocalc.addItem("Autocalculated last");
 282     final boolean showAbove = Cache.getDefault(SHOW_AUTOCALC_ABOVE, true);
 283     sortAutocalc.setSelectedItem(showAbove ? sortAutocalc.getItemAt(0)
 284             : sortAutocalc.getItemAt(1));
 285     startupCheckbox
 286             .setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
 287     startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
 288             Cache.getDefault("www.jalview.org", "http://www.jalview.org")
 289                     + "/examples/exampleFile_2_3.jar"));
 290
 291     /*
 292      * Set Colours tab defaults
 293      */
 294     for (int i = ColourSchemeProperty.FIRST_COLOUR; i <= ColourSchemeProperty.LAST_COLOUR; i++)
 295     {
 296       protColour.addItem(ColourSchemeProperty.getColourName(i));
 297       nucColour.addItem(ColourSchemeProperty.getColourName(i));
 298     }
 299     String oldProp = Cache.getDefault(DEFAULT_COLOUR, "None");
 300     String newProp = Cache.getDefault(DEFAULT_COLOUR_PROT, null);
 301     protColour.setSelectedItem(newProp != null ? newProp : oldProp);
 302     newProp = Cache.getDefault(DEFAULT_COLOUR_NUC, null);
 303     nucColour.setSelectedItem(newProp != null ? newProp : oldProp);
 304     minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN",
 305             Color.orange));
 306     maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX",
 307             Color.red));
 308
 309     /*
 310      * Set Structure tab defaults.
 311      */
 312     final boolean structSelected = Cache.getDefault(STRUCT_FROM_PDB, false);
 313     structFromPdb.setSelected(structSelected);
 314     useRnaView.setSelected(Cache.getDefault(USE_RNAVIEW, false));
 315     useRnaView.setEnabled(structSelected);
 316     addSecondaryStructure.setSelected(Cache.getDefault(ADD_SS_ANN, false));
 317     addSecondaryStructure.setEnabled(structSelected);
 318     addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, false));
 319     addTempFactor.setEnabled(structSelected);
 320     structViewer.setSelectedItem(Cache.getDefault(STRUCTURE_DISPLAY,
 321             ViewerType.JMOL.name()));
 322     chimeraPath.setText(Cache.getDefault(CHIMERA_PATH, ""));
 323     chimeraPath.addActionListener(new ActionListener()
 324     {
 325       @Override
 326       public void actionPerformed(ActionEvent e)
 327       {
 328         validateChimeraPath();
 329       }
 330     });
 331
 332     if (Cache.getDefault("MAP_WITH_SIFTS", false))
 333     {
 334       siftsMapping.setSelected(true);
 335     }
 336     else
 337     {
 338       nwMapping.setSelected(true);
 339     }
 340
 341     SiftsSettings
 342             .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
 343
 344     /*
 345      * Set Connections tab defaults
 346      */
 347     nameLinks = new Vector<String>();
 348     urlLinks = new Vector<String>();
 349     sequenceUrlLinks.getLinksForDisplay(nameLinks, urlLinks);
 350     /*    for (HashMap.Entry<String, UrlLink> entry: sequenceUrlLinks.getUrlLinks())
 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     String links = sequenceUrlLinks.writeUrlsAsString();
 554     if (links.isEmpty())
 555     {
 556       Cache.applicationProperties.remove("SEQUENCE_LINKS");
 557     }
 558     else
 559     {
 560       Cache.applicationProperties.setProperty("SEQUENCE_LINKS",
 561               links.toString());
 562     }
 563
 564     /*    if (nameLinks.size() > 0)
 565         {
 566           StringBuffer links = new StringBuffer();
 567           sequenceURLLinks = new Vector<String>();
 568           for (int i = 0; i < nameLinks.size(); i++)
 569           {
 570             sequenceURLLinks.addElement(nameLinks.elementAt(i) + "|"
 571                     + urlLinks.elementAt(i));
 572             links.append(sequenceURLLinks.elementAt(i).toString());
 573             links.append("|");
 574           }
 575           // remove last "|"
 576           links.setLength(links.length() - 1);
 577           Cache.applicationProperties.setProperty("SEQUENCE_LINKS",
 578                   links.toString());
 579         }
 580         else
 581         {
 582           Cache.applicationProperties.remove("SEQUENCE_LINKS");
 583           sequenceURLLinks.clear();
 584         }*/
 585
 586     Cache.applicationProperties.setProperty("USE_PROXY",
 587             Boolean.toString(useProxy.isSelected()));
 588
 589     Cache.setOrRemove("PROXY_SERVER", proxyServerTB.getText());
 590
 591     Cache.setOrRemove("PROXY_PORT", proxyPortTB.getText());
 592
 593     if (useProxy.isSelected())
 594     {
 595       System.setProperty("http.proxyHost", proxyServerTB.getText());
 596       System.setProperty("http.proxyPort", proxyPortTB.getText());
 597     }
 598     else
 599     {
 600       System.setProperty("http.proxyHost", "");
 601       System.setProperty("http.proxyPort", "");
 602     }
 603     Cache.setProperty("VERSION_CHECK",
 604             Boolean.toString(versioncheck.isSelected()));
 605     if (Cache.getProperty("USAGESTATS") != null || usagestats.isSelected())
 606     {
 607       // default is false - we only set this if the user has actively agreed
 608       Cache.setProperty("USAGESTATS",
 609               Boolean.toString(usagestats.isSelected()));
 610     }
 611     if (!questionnaire.isSelected())
 612     {
 613       Cache.setProperty("NOQUESTIONNAIRES", "true");
 614     }
 615     else
 616     {
 617       // special - made easy to edit a property file to disable questionnaires
 618       // by just adding the given line
 619       Cache.removeProperty("NOQUESTIONNAIRES");
 620     }
 621
 622     /*
 623      * Save Output settings
 624      */
 625     Cache.applicationProperties.setProperty("BLC_JVSUFFIX",
 626             Boolean.toString(blcjv.isSelected()));
 627     Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX",
 628             Boolean.toString(clustaljv.isSelected()));
 629     Cache.applicationProperties.setProperty("FASTA_JVSUFFIX",
 630             Boolean.toString(fastajv.isSelected()));
 631     Cache.applicationProperties.setProperty("MSF_JVSUFFIX",
 632             Boolean.toString(msfjv.isSelected()));
 633     Cache.applicationProperties.setProperty("PFAM_JVSUFFIX",
 634             Boolean.toString(pfamjv.isSelected()));
 635     Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX",
 636             Boolean.toString(pileupjv.isSelected()));
 637     Cache.applicationProperties.setProperty("PIR_JVSUFFIX",
 638             Boolean.toString(pirjv.isSelected()));
 639     Cache.applicationProperties.setProperty("PIR_MODELLER",
 640             Boolean.toString(modellerOutput.isSelected()));
 641     Cache.applicationProperties.setProperty("EXPORT_EMBBED_BIOJSON",
 642             Boolean.toString(embbedBioJSON.isSelected()));
 643     jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
 644
 645     Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH",
 646             Boolean.toString(autoIdWidth.isSelected()));
 647     userIdWidth_actionPerformed();
 648     Cache.applicationProperties.setProperty("FIGURE_USERIDWIDTH",
 649             userIdWidth.getText());
 650
 651     /*
 652      * Save Editing settings
 653      */
 654     Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
 655             Boolean.toString(autoCalculateConsCheck.isSelected()));
 656     Cache.applicationProperties.setProperty("SORT_BY_TREE",
 657             Boolean.toString(sortByTree.isSelected()));
 658     Cache.applicationProperties.setProperty("PAD_GAPS",
 659             Boolean.toString(padGaps.isSelected()));
 660
 661     dasSource.saveProperties(Cache.applicationProperties);
 662     wsPrefs.updateAndRefreshWsMenuConfig(false);
 663     Cache.saveProperties();
 664     Desktop.instance.doConfigureStructurePrefs();
 665     try
 666     {
 667       frame.setClosed(true);
 668     } catch (Exception ex)
 669     {
 670     }
 671   }
 672
 673   /**
 674    * Do any necessary validation before saving settings. Return focus to the
 675    * first tab which fails validation.
 676    *
 677    * @return
 678    */
 679   private boolean validateSettings()
 680   {
 681     if (!validateStructure())
 682     {
 683       structureTab.requestFocusInWindow();
 684       return false;
 685     }
 686     return true;
 687   }
 688
 689   @Override
 690   protected boolean validateStructure()
 691   {
 692     return validateChimeraPath();
 693
 694   }
 695
 696   /**
 697    * DOCUMENT ME!
 698    */
 699   @Override
 700   public void startupFileTextfield_mouseClicked()
 701   {
 702     JalviewFileChooser chooser = new JalviewFileChooser(
 703             jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[] {
 704                 "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",
 705                 "jar" }, new String[] { "Fasta", "Clustal", "PFAM", "MSF",
 706                 "PIR", "BLC", "Jalview" },
 707             jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));
 708     chooser.setFileView(new JalviewFileView());
 709     chooser.setDialogTitle(MessageManager
 710             .getString("label.select_startup_file"));
 711
 712     int value = chooser.showOpenDialog(this);
 713
 714     if (value == JalviewFileChooser.APPROVE_OPTION)
 715     {
 716       jalview.bin.Cache.applicationProperties.setProperty(
 717               "DEFAULT_FILE_FORMAT", chooser.getSelectedFormat());
 718       startupFileTextfield.setText(chooser.getSelectedFile()
 719               .getAbsolutePath());
 720     }
 721   }
 722
 723   /**
 724    * DOCUMENT ME!
 725    *
 726    * @param e
 727    *          DOCUMENT ME!
 728    */
 729   @Override
 730   public void cancel_actionPerformed(ActionEvent e)
 731   {
 732     try
 733     {
 734       wsPrefs.updateWsMenuConfig(true);
 735       wsPrefs.refreshWs_actionPerformed(e);
 736       frame.setClosed(true);
 737     } catch (Exception ex)
 738     {
 739     }
 740   }
 741
 742   /**
 743    * DOCUMENT ME!
 744    *
 745    * @param e
 746    *          DOCUMENT ME!
 747    */
 748   @Override
 749   public void annotations_actionPerformed(ActionEvent e)
 750   {
 751     conservation.setEnabled(annotations.isSelected());
 752     quality.setEnabled(annotations.isSelected());
 753     identity.setEnabled(annotations.isSelected());
 754     showGroupConsensus.setEnabled(annotations.isSelected());
 755     showGroupConservation.setEnabled(annotations.isSelected());
 756     showConsensHistogram.setEnabled(annotations.isSelected()
 757             && (identity.isSelected() || showGroupConsensus.isSelected()));
 758     showConsensLogo.setEnabled(annotations.isSelected()
 759             && (identity.isSelected() || showGroupConsensus.isSelected()));
 760   }
 761
 762   @Override
 763   public void newLink_actionPerformed(ActionEvent e)
 764   {
 765
 766     GSequenceLink link = new GSequenceLink();
 767     boolean valid = false;
 768     while (!valid)
 769     {
 770       if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 771               MessageManager.getString("label.new_sequence_url_link"),
 772               JOptionPane.OK_CANCEL_OPTION, -1, null) == JOptionPane.OK_OPTION)
 773       {
 774         if (link.checkValid())
 775         {
 776           nameLinks.addElement(link.getName());
 777           urlLinks.addElement(link.getURL());
 778           updateLinkData();
 779           valid = true;
 780         }
 781       }
 782       else
 783       {
 784         break;
 785       }
 786     }
 787   }
 788
 789   @Override
 790   public void editLink_actionPerformed(ActionEvent e)
 791   {
 792     GSequenceLink link = new GSequenceLink();
 793
 794     int index = linkNameList.getSelectedIndex();
 795     if (index == -1)
 796     {
 797       JOptionPane.showInternalMessageDialog(Desktop.desktop,
 798               MessageManager.getString("label.no_link_selected"),
 799               MessageManager.getString("label.no_link_selected"),
 800               JOptionPane.WARNING_MESSAGE);
 801       return;
 802     }
 803
 804     link.setName(nameLinks.elementAt(index).toString());
 805     link.setURL(urlLinks.elementAt(index).toString());
 806
 807     boolean valid = false;
 808     while (!valid)
 809     {
 810
 811       if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 812               MessageManager.getString("label.new_sequence_url_link"),
 813               JOptionPane.OK_CANCEL_OPTION, -1, null) == JOptionPane.OK_OPTION)
 814       {
 815         if (link.checkValid())
 816         {
 817           nameLinks.setElementAt(link.getName(), index);
 818           urlLinks.setElementAt(link.getURL(), index);
 819           updateLinkData();
 820           valid = true;
 821         }
 822       }
 823
 824       else
 825       {
 826         break;
 827       }
 828     }
 829   }
 830
 831   @Override
 832   public void deleteLink_actionPerformed(ActionEvent e)
 833   {
 834     int index = linkNameList.getSelectedIndex();
 835     if (index == -1)
 836     {
 837       JOptionPane.showInternalMessageDialog(Desktop.desktop,
 838               MessageManager.getString("label.no_link_selected"),
 839               MessageManager.getString("label.no_link_selected"),
 840               JOptionPane.WARNING_MESSAGE);
 841       return;
 842     }
 843     nameLinks.removeElementAt(index);
 844     urlLinks.removeElementAt(index);
 845     updateLinkData();
 846   }
 847
 848   void updateLinkData()
 849   {
 850     linkNameList.setListData(nameLinks);
 851     linkURLList.setListData(urlLinks);
 852   }
 853
 854   @Override
 855   public void defaultBrowser_mouseClicked(MouseEvent e)
 856   {
 857     JFileChooser chooser = new JFileChooser(".");
 858     chooser.setDialogTitle(MessageManager
 859             .getString("label.select_default_browser"));
 860
 861     int value = chooser.showOpenDialog(this);
 862
 863     if (value == JFileChooser.APPROVE_OPTION)
 864     {
 865       defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
 866     }
 867
 868   }
 869
 870   /*
 871    * (non-Javadoc)
 872    *
 873    * @see
 874    * jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event
 875    * .ActionEvent)
 876    */
 877   @Override
 878   protected void showunconserved_actionPerformed(ActionEvent e)
 879   {
 880     // TODO Auto-generated method stub
 881     super.showunconserved_actionPerformed(e);
 882   }
 883
 884   public static List<String> getGroupURLLinks()
 885   {
 886     return groupURLLinks;
 887   }
 888
 889   @Override
 890   public void minColour_actionPerformed(JPanel panel)
 891   {
 892     Color col = JColorChooser.showDialog(this,
 893             MessageManager.getString("label.select_colour_minimum_value"),
 894             minColour.getBackground());
 895     if (col != null)
 896     {
 897       panel.setBackground(col);
 898     }
 899     panel.repaint();
 900   }
 901
 902   @Override
 903   public void maxColour_actionPerformed(JPanel panel)
 904   {
 905     Color col = JColorChooser.showDialog(this,
 906             MessageManager.getString("label.select_colour_maximum_value"),
 907             maxColour.getBackground());
 908     if (col != null)
 909     {
 910       panel.setBackground(col);
 911     }
 912     panel.repaint();
 913   }
 914
 915   @Override
 916   protected void userIdWidth_actionPerformed()
 917   {
 918     try
 919     {
 920       String val = userIdWidth.getText().trim();
 921       if (val.length() > 0)
 922       {
 923         Integer iw = Integer.parseInt(val);
 924         if (iw.intValue() < 12)
 925         {
 926           throw new NumberFormatException();
 927         }
 928         userIdWidth.setText(iw.toString());
 929       }
 930     } catch (NumberFormatException x)
 931     {
 932       JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
 933               .getString("warn.user_defined_width_requirements"),
 934               MessageManager.getString("label.invalid_id_column_width"),
 935               JOptionPane.WARNING_MESSAGE);
 936       userIdWidth.setText("");
 937     }
 938   }
 939
 940   @Override
 941   protected void autoIdWidth_actionPerformed()
 942   {
 943     userIdWidth.setEnabled(!autoIdWidth.isSelected());
 944     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
 945   }
 946
 947   /**
 948    * Returns true if chimera path is to a valid executable, else show an error
 949    * dialog.
 950    */
 951   private boolean validateChimeraPath()
 952   {
 953     if (chimeraPath.getText().trim().length() > 0)
 954     {
 955       File f = new File(chimeraPath.getText());
 956       if (!f.canExecute())
 957       {
 958         JOptionPane.showInternalMessageDialog(Desktop.desktop,
 959                 MessageManager.getString("label.invalid_chimera_path"),
 960                 MessageManager.getString("label.invalid_name"),
 961                 JOptionPane.ERROR_MESSAGE);
 962         return false;
 963       }
 964     }
 965     return true;
 966   }
 967
 968   /**
 969    * If Chimera is selected, check it can be found on default or user-specified
 970    * path, if not show a warning/help dialog.
 971    */
 972   @Override
 973   protected void structureViewer_actionPerformed(String selectedItem)
 974   {
 975     if (!selectedItem.equals(ViewerType.CHIMERA.name()))
 976     {
 977       return;
 978     }
 979     boolean found = false;
 980
 981     /*
 982      * Try user-specified and standard paths for Chimera executable.
 983      */
 984     List<String> paths = StructureManager.getChimeraPaths();
 985     paths.add(0, chimeraPath.getText());
 986     for (String path : paths)
 987     {
 988       if (new File(path.trim()).canExecute())
 989       {
 990         found = true;
 991         break;
 992       }
 993     }
 994     if (!found)
 995     {
 996       String[] options = { "OK", "Help" };
 997       int showHelp = JOptionPane.showInternalOptionDialog(
 998               Desktop.desktop,
 999               JvSwingUtils.wrapTooltip(true,
1000                       MessageManager.getString("label.chimera_missing")),
1001               "", JOptionPane.YES_NO_OPTION, JOptionPane.WARNING_MESSAGE,
1002               null, options, options[0]);
1003       if (showHelp == JOptionPane.NO_OPTION)
1004       {
1005         try
1006         {
1007           Help.showHelpWindow(HelpId.StructureViewer);
1008         } catch (HelpSetException e)
1009         {
1010           e.printStackTrace();
1011         }
1012       }
1013     }
1014   }
1015
1016   public class OptionsParam
1017   {
1018     private String name;
1019
1020     private String code;
1021
1022     public OptionsParam(String name, String code)
1023     {
1024       this.name = name;
1025       this.code = code;
1026     }
1027
1028     public String getName()
1029     {
1030       return name;
1031     }
1032
1033     public void setName(String name)
1034     {
1035       this.name = name;
1036     }
1037
1038     public String getCode()
1039     {
1040       return code;
1041     }
1042
1043     public void setCode(String code)
1044     {
1045       this.code = code;
1046     }
1047
1048     @Override
1049     public String toString()
1050     {
1051       return name;
1052     }
1053
1054     @Override
1055     public boolean equals(Object that)
1056     {
1057       if (!(that instanceof OptionsParam))
1058       {
1059         return false;
1060       }
1061       return this.code.equalsIgnoreCase(((OptionsParam) that).code);
1062     }
1063
1064     @Override
1065     public int hashCode()
1066     {
1067       return name.hashCode() + code.hashCode();
1068     }
1069   }
1070 }