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.util.UrlProvider;
  35 import jalview.util.UrlProviderI;
  36 import jalview.ws.sifts.SiftsSettings;
  37
  38 import java.awt.BorderLayout;
  39 import java.awt.Color;
  40 import java.awt.Dimension;
  41 import java.awt.Font;
  42 import java.awt.event.ActionEvent;
  43 import java.awt.event.ActionListener;
  44 import java.awt.event.MouseEvent;
  45 import java.io.File;
  46 import java.util.ArrayList;
  47 import java.util.List;
  48 import java.util.Vector;
  49
  50 import javax.help.HelpSetException;
  51 import javax.swing.JColorChooser;
  52 import javax.swing.JFileChooser;
  53 import javax.swing.JInternalFrame;
  54 import javax.swing.JOptionPane;
  55 import javax.swing.JPanel;
  56
  57 import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
  58
  59 /**
  60  * DOCUMENT ME!
  61  *
  62  * @author $author$
  63  * @version $Revision$
  64  */
  65 public class Preferences extends GPreferences
  66 {
  67   public static final String ENABLE_SPLIT_FRAME = "ENABLE_SPLIT_FRAME";
  68
  69   public static final String SCALE_PROTEIN_TO_CDNA = "SCALE_PROTEIN_TO_CDNA";
  70
  71   public static final String DEFAULT_COLOUR = "DEFAULT_COLOUR";
  72
  73   public static final String DEFAULT_COLOUR_PROT = "DEFAULT_COLOUR_PROT";
  74
  75   public static final String DEFAULT_COLOUR_NUC = "DEFAULT_COLOUR_NUC";
  76
  77   public static final String ADD_TEMPFACT_ANN = "ADD_TEMPFACT_ANN";
  78
  79   public static final String ADD_SS_ANN = "ADD_SS_ANN";
  80
  81   public static final String USE_RNAVIEW = "USE_RNAVIEW";
  82
  83   public static final String STRUCT_FROM_PDB = "STRUCT_FROM_PDB";
  84
  85   public static final String STRUCTURE_DISPLAY = "STRUCTURE_DISPLAY";
  86
  87   public static final String CHIMERA_PATH = "CHIMERA_PATH";
  88
  89   public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS";
  90
  91   public static final String SHOW_AUTOCALC_ABOVE = "SHOW_AUTOCALC_ABOVE";
  92
  93   private static final int MIN_FONT_SIZE = 1;
  94
  95   private static final int MAX_FONT_SIZE = 30;
  96
  97   /**
  98    * Holds name and link separated with | character. Sequence ID must be
  99    * $SEQUENCE_ID$ or $SEQUENCE_ID=/.possible | chars ./=$
 100    */
 101   public static UrlProviderI sequenceUrlLinks;
 102
 103   /**
 104    * Holds name and link separated with | character. Sequence IDS and Sequences
 105    * must be $SEQUENCEIDS$ or $SEQUENCEIDS=/.possible | chars ./=$ and
 106    * $SEQUENCES$ or $SEQUENCES=/.possible | chars ./=$ and separation character
 107    * for first and second token specified after a pipe character at end |,|.
 108    * (TODO: proper escape for using | to separate ids or sequences
 109    */
 110
 111   public static List<String> groupURLLinks;
 112   static
 113   {
 114     String string = Cache.getDefault("SEQUENCE_LINKS",
 115             UrlProviderI.DEFAULT_STRING);
 116     sequenceUrlLinks = new UrlProvider(UrlProviderI.DEFAULT_LABEL, string);
 117
 118     /**
 119      * TODO: reformulate groupURL encoding so two or more can be stored in the
 120      * .properties file as '|' separated strings
 121      */
 122
 123     groupURLLinks = new ArrayList<String>();
 124   }
 125
 126   Vector<String> nameLinks, urlLinks;
 127
 128   JInternalFrame frame;
 129
 130   DasSourceBrowser dasSource;
 131
 132   private WsPreferences wsPrefs;
 133
 134   private OptionsParam promptEachTimeOpt = new OptionsParam(
 135           MessageManager.getString("label.prompt_each_time"),
 136           "Prompt each time");
 137
 138   private OptionsParam lineArtOpt = new OptionsParam(
 139           MessageManager.getString("label.lineart"), "Lineart");
 140
 141   private OptionsParam textOpt = new OptionsParam(
 142           MessageManager.getString("action.text"), "Text");
 143
 144   /**
 145    * Creates a new Preferences object.
 146    */
 147   public Preferences()
 148   {
 149     super();
 150     frame = new JInternalFrame();
 151     frame.setContentPane(this);
 152     dasSource = new DasSourceBrowser();
 153     dasTab.add(dasSource, BorderLayout.CENTER);
 154     wsPrefs = new WsPreferences();
 155     wsTab.add(wsPrefs, BorderLayout.CENTER);
 156     int width = 500, height = 450;
 157     new jalview.util.Platform();
 158     if (Platform.isAMac())
 159     {
 160       width = 570;
 161       height = 480;
 162     }
 163
 164     Desktop.addInternalFrame(frame,
 165             MessageManager.getString("label.preferences"), width, height);
 166     frame.setMinimumSize(new Dimension(width, height));
 167
 168     /*
 169      * Set Visual tab defaults
 170      */
 171     seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));
 172     rightAlign.setSelected(Cache.getDefault("RIGHT_ALIGN_IDS", false));
 173     fullScreen.setSelected(Cache.getDefault("SHOW_FULLSCREEN", false));
 174     annotations.setSelected(Cache.getDefault("SHOW_ANNOTATIONS", true));
 175
 176     conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));
 177     quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));
 178     identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));
 179     openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false));
 180     showUnconserved
 181             .setSelected(Cache.getDefault("SHOW_UNCONSERVED", false));
 182     showGroupConsensus.setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS",
 183             false));
 184     showGroupConservation.setSelected(Cache.getDefault(
 185             "SHOW_GROUP_CONSERVATION", false));
 186     showConsensHistogram.setSelected(Cache.getDefault(
 187             "SHOW_CONSENSUS_HISTOGRAM", true));
 188     showConsensLogo.setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO",
 189             false));
 190     showNpTooltip.setSelected(Cache
 191             .getDefault("SHOW_NPFEATS_TOOLTIP", true));
 192     showDbRefTooltip.setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP",
 193             true));
 194
 195     String[] fonts = java.awt.GraphicsEnvironment
 196             .getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
 197     for (int i = 0; i < fonts.length; i++)
 198     {
 199       fontNameCB.addItem(fonts[i]);
 200     }
 201
 202     for (int i = MIN_FONT_SIZE; i <= MAX_FONT_SIZE; i++)
 203     {
 204       fontSizeCB.addItem(i + "");
 205     }
 206
 207     fontStyleCB.addItem("plain");
 208     fontStyleCB.addItem("bold");
 209     fontStyleCB.addItem("italic");
 210
 211     fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
 212     fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
 213     fontStyleCB.setSelectedItem(Cache.getDefault("FONT_STYLE", Font.PLAIN
 214             + ""));
 215
 216     smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));
 217     scaleProteinToCdna.setSelected(Cache.getDefault(SCALE_PROTEIN_TO_CDNA,
 218             false));
 219
 220     idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
 221
 222     wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
 223
 224     gapSymbolCB.addItem("-");
 225     gapSymbolCB.addItem(".");
 226
 227     gapSymbolCB.setSelectedItem(Cache.getDefault("GAP_SYMBOL", "-"));
 228
 229     sortby.addItem("No sort");
 230     sortby.addItem("Id");
 231     sortby.addItem("Pairwise Identity");
 232     sortby.setSelectedItem(Cache.getDefault("SORT_ALIGNMENT", "No sort"));
 233
 234     sortAnnBy.addItem(SequenceAnnotationOrder.NONE.toString());
 235     sortAnnBy
 236             .addItem(SequenceAnnotationOrder.SEQUENCE_AND_LABEL.toString());
 237     sortAnnBy
 238             .addItem(SequenceAnnotationOrder.LABEL_AND_SEQUENCE.toString());
 239     SequenceAnnotationOrder savedSort = SequenceAnnotationOrder
 240             .valueOf(Cache.getDefault(SORT_ANNOTATIONS,
 241                     SequenceAnnotationOrder.NONE.name()));
 242     sortAnnBy.setSelectedItem(savedSort.toString());
 243
 244     sortAutocalc.addItem("Autocalculated first");
 245     sortAutocalc.addItem("Autocalculated last");
 246     final boolean showAbove = Cache.getDefault(SHOW_AUTOCALC_ABOVE, true);
 247     sortAutocalc.setSelectedItem(showAbove ? sortAutocalc.getItemAt(0)
 248             : sortAutocalc.getItemAt(1));
 249     startupCheckbox
 250             .setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
 251     startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
 252             Cache.getDefault("www.jalview.org", "http://www.jalview.org")
 253                     + "/examples/exampleFile_2_3.jar"));
 254
 255     /*
 256      * Set Colours tab defaults
 257      */
 258     for (int i = ColourSchemeProperty.FIRST_COLOUR; i <= ColourSchemeProperty.LAST_COLOUR; i++)
 259     {
 260       protColour.addItem(ColourSchemeProperty.getColourName(i));
 261       nucColour.addItem(ColourSchemeProperty.getColourName(i));
 262     }
 263     String oldProp = Cache.getDefault(DEFAULT_COLOUR, "None");
 264     String newProp = Cache.getDefault(DEFAULT_COLOUR_PROT, null);
 265     protColour.setSelectedItem(newProp != null ? newProp : oldProp);
 266     newProp = Cache.getDefault(DEFAULT_COLOUR_NUC, null);
 267     nucColour.setSelectedItem(newProp != null ? newProp : oldProp);
 268     minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN",
 269             Color.orange));
 270     maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX",
 271             Color.red));
 272
 273     /*
 274      * Set Structure tab defaults.
 275      */
 276     final boolean structSelected = Cache.getDefault(STRUCT_FROM_PDB, false);
 277     structFromPdb.setSelected(structSelected);
 278     useRnaView.setSelected(Cache.getDefault(USE_RNAVIEW, false));
 279     useRnaView.setEnabled(structSelected);
 280     addSecondaryStructure.setSelected(Cache.getDefault(ADD_SS_ANN, false));
 281     addSecondaryStructure.setEnabled(structSelected);
 282     addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, false));
 283     addTempFactor.setEnabled(structSelected);
 284     structViewer.setSelectedItem(Cache.getDefault(STRUCTURE_DISPLAY,
 285             ViewerType.JMOL.name()));
 286     chimeraPath.setText(Cache.getDefault(CHIMERA_PATH, ""));
 287     chimeraPath.addActionListener(new ActionListener()
 288     {
 289       @Override
 290       public void actionPerformed(ActionEvent e)
 291       {
 292         validateChimeraPath();
 293       }
 294     });
 295
 296     if (Cache.getDefault("MAP_WITH_SIFTS", false))
 297     {
 298       siftsMapping.setSelected(true);
 299     }
 300     else
 301     {
 302       nwMapping.setSelected(true);
 303     }
 304
 305     SiftsSettings
 306             .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
 307
 308     /*
 309      * Set Connections tab defaults
 310      */
 311     nameLinks = new Vector<String>();
 312     urlLinks = new Vector<String>();
 313
 314     resetStoredLinks();
 315     updateLinkData();
 316
 317     useProxy.setSelected(Cache.getDefault("USE_PROXY", false));
 318     proxyServerTB.setEnabled(useProxy.isSelected());
 319     proxyPortTB.setEnabled(useProxy.isSelected());
 320     proxyServerTB.setText(Cache.getDefault("PROXY_SERVER", ""));
 321     proxyPortTB.setText(Cache.getDefault("PROXY_PORT", ""));
 322
 323     defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", ""));
 324
 325     usagestats.setSelected(Cache.getDefault("USAGESTATS", false));
 326     // note antisense here: default is true
 327     questionnaire
 328             .setSelected(Cache.getProperty("NOQUESTIONNAIRES") == null);
 329     versioncheck.setSelected(Cache.getDefault("VERSION_CHECK", true));
 330
 331     /*
 332      * Set Output tab defaults
 333      */
 334     epsRendering.addItem(promptEachTimeOpt);
 335     epsRendering.addItem(lineArtOpt);
 336     epsRendering.addItem(textOpt);
 337     String defaultEPS = Cache.getDefault("EPS_RENDERING",
 338             "Prompt each time");
 339     if (defaultEPS.equalsIgnoreCase("Text"))
 340     {
 341       epsRendering.setSelectedItem(textOpt);
 342     }
 343     else if (defaultEPS.equalsIgnoreCase("Lineart"))
 344     {
 345       epsRendering.setSelectedItem(lineArtOpt);
 346     }
 347     else
 348     {
 349       epsRendering.setSelectedItem(promptEachTimeOpt);
 350     }
 351     autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false));
 352     userIdWidth.setEnabled(!autoIdWidth.isSelected());
 353     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
 354     Integer wi = Cache.getIntegerProperty("FIGURE_USERIDWIDTH");
 355     userIdWidth.setText(wi == null ? "" : wi.toString());
 356     blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
 357     clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
 358     fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
 359     msfjv.setSelected(Cache.getDefault("MSF_JVSUFFIX", true));
 360     pfamjv.setSelected(Cache.getDefault("PFAM_JVSUFFIX", true));
 361     pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
 362     pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
 363     modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
 364     embbedBioJSON.setSelected(Cache.getDefault("EXPORT_EMBBED_BIOJSON",
 365             true));
 366
 367     /*
 368      * Set Editing tab defaults
 369      */
 370     autoCalculateConsCheck.setSelected(Cache.getDefault(
 371             "AUTO_CALC_CONSENSUS", true));
 372     padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
 373     sortByTree.setSelected(Cache.getDefault("SORT_BY_TREE", false));
 374
 375     annotations_actionPerformed(null); // update the display of the annotation
 376                                        // settings
 377   }
 378
 379   /**
 380    * Save user selections on the Preferences tabs to the Cache and write out to
 381    * file.
 382    *
 383    * @param e
 384    */
 385   @Override
 386   public void ok_actionPerformed(ActionEvent e)
 387   {
 388     if (!validateSettings())
 389     {
 390       return;
 391     }
 392
 393     /*
 394      * Save Visual settings
 395      */
 396     Cache.applicationProperties.setProperty("SHOW_JVSUFFIX",
 397             Boolean.toString(seqLimit.isSelected()));
 398     Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS",
 399             Boolean.toString(rightAlign.isSelected()));
 400     Cache.applicationProperties.setProperty("SHOW_FULLSCREEN",
 401             Boolean.toString(fullScreen.isSelected()));
 402     Cache.applicationProperties.setProperty("SHOW_OVERVIEW",
 403             Boolean.toString(openoverv.isSelected()));
 404     Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
 405             Boolean.toString(annotations.isSelected()));
 406     Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
 407             Boolean.toString(conservation.isSelected()));
 408     Cache.applicationProperties.setProperty("SHOW_QUALITY",
 409             Boolean.toString(quality.isSelected()));
 410     Cache.applicationProperties.setProperty("SHOW_IDENTITY",
 411             Boolean.toString(identity.isSelected()));
 412
 413     Cache.applicationProperties.setProperty("GAP_SYMBOL", gapSymbolCB
 414             .getSelectedItem().toString());
 415
 416     Cache.applicationProperties.setProperty("FONT_NAME", fontNameCB
 417             .getSelectedItem().toString());
 418     Cache.applicationProperties.setProperty("FONT_STYLE", fontStyleCB
 419             .getSelectedItem().toString());
 420     Cache.applicationProperties.setProperty("FONT_SIZE", fontSizeCB
 421             .getSelectedItem().toString());
 422
 423     Cache.applicationProperties.setProperty("ID_ITALICS",
 424             Boolean.toString(idItalics.isSelected()));
 425     Cache.applicationProperties.setProperty("SHOW_UNCONSERVED",
 426             Boolean.toString(showUnconserved.isSelected()));
 427     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS",
 428             Boolean.toString(showGroupConsensus.isSelected()));
 429     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION",
 430             Boolean.toString(showGroupConservation.isSelected()));
 431     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_HISTOGRAM",
 432             Boolean.toString(showConsensHistogram.isSelected()));
 433     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO",
 434             Boolean.toString(showConsensLogo.isSelected()));
 435     Cache.applicationProperties.setProperty("ANTI_ALIAS",
 436             Boolean.toString(smoothFont.isSelected()));
 437     Cache.applicationProperties.setProperty(SCALE_PROTEIN_TO_CDNA,
 438             Boolean.toString(scaleProteinToCdna.isSelected()));
 439     Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP",
 440             Boolean.toString(showNpTooltip.isSelected()));
 441     Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP",
 442             Boolean.toString(showDbRefTooltip.isSelected()));
 443
 444     Cache.applicationProperties.setProperty("WRAP_ALIGNMENT",
 445             Boolean.toString(wrap.isSelected()));
 446
 447     Cache.applicationProperties.setProperty("STARTUP_FILE",
 448             startupFileTextfield.getText());
 449     Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",
 450             Boolean.toString(startupCheckbox.isSelected()));
 451
 452     Cache.applicationProperties.setProperty("SORT_ALIGNMENT", sortby
 453             .getSelectedItem().toString());
 454
 455     // convert description of sort order to enum name for save
 456     SequenceAnnotationOrder annSortOrder = SequenceAnnotationOrder
 457             .forDescription(sortAnnBy.getSelectedItem().toString());
 458     if (annSortOrder != null)
 459     {
 460       Cache.applicationProperties.setProperty(SORT_ANNOTATIONS,
 461               annSortOrder.name());
 462     }
 463
 464     final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
 465     Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE, Boolean
 466             .valueOf(showAutocalcFirst).toString());
 467
 468     /*
 469      * Save Colours settings
 470      */
 471     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_PROT, protColour
 472             .getSelectedItem().toString());
 473     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_NUC, nucColour
 474             .getSelectedItem().toString());
 475     Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
 476             minColour.getBackground());
 477     Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
 478             maxColour.getBackground());
 479
 480     /*
 481      * Save Structure settings
 482      */
 483     Cache.applicationProperties.setProperty(ADD_TEMPFACT_ANN,
 484             Boolean.toString(addTempFactor.isSelected()));
 485     Cache.applicationProperties.setProperty(ADD_SS_ANN,
 486             Boolean.toString(addSecondaryStructure.isSelected()));
 487     Cache.applicationProperties.setProperty(USE_RNAVIEW,
 488             Boolean.toString(useRnaView.isSelected()));
 489     Cache.applicationProperties.setProperty(STRUCT_FROM_PDB,
 490             Boolean.toString(structFromPdb.isSelected()));
 491     Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY, structViewer
 492             .getSelectedItem().toString());
 493     Cache.setOrRemove(CHIMERA_PATH, chimeraPath.getText());
 494     Cache.applicationProperties.setProperty("MAP_WITH_SIFTS",
 495             Boolean.toString(siftsMapping.isSelected()));
 496     SiftsSettings.setMapWithSifts(siftsMapping.isSelected());
 497
 498     /*
 499      * Save Output settings
 500      */
 501     Cache.applicationProperties.setProperty("EPS_RENDERING",
 502             ((OptionsParam) epsRendering.getSelectedItem()).getCode());
 503
 504     /*
 505      * Save Connections settings
 506      */
 507     Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText());
 508
 509     jalview.util.BrowserLauncher.resetBrowser();
 510
 511     // save user-defined and selected links
 512     String links = sequenceUrlLinks.writeUrlsAsString();
 513     if (links.isEmpty())
 514     {
 515       Cache.applicationProperties.remove("SEQUENCE_LINKS");
 516     }
 517     else
 518     {
 519       Cache.applicationProperties.setProperty("SEQUENCE_LINKS",
 520               links.toString());
 521     }
 522
 523     Cache.applicationProperties.setProperty("USE_PROXY",
 524             Boolean.toString(useProxy.isSelected()));
 525
 526     Cache.setOrRemove("PROXY_SERVER", proxyServerTB.getText());
 527
 528     Cache.setOrRemove("PROXY_PORT", proxyPortTB.getText());
 529
 530     if (useProxy.isSelected())
 531     {
 532       System.setProperty("http.proxyHost", proxyServerTB.getText());
 533       System.setProperty("http.proxyPort", proxyPortTB.getText());
 534     }
 535     else
 536     {
 537       System.setProperty("http.proxyHost", "");
 538       System.setProperty("http.proxyPort", "");
 539     }
 540     Cache.setProperty("VERSION_CHECK",
 541             Boolean.toString(versioncheck.isSelected()));
 542     if (Cache.getProperty("USAGESTATS") != null || usagestats.isSelected())
 543     {
 544       // default is false - we only set this if the user has actively agreed
 545       Cache.setProperty("USAGESTATS",
 546               Boolean.toString(usagestats.isSelected()));
 547     }
 548     if (!questionnaire.isSelected())
 549     {
 550       Cache.setProperty("NOQUESTIONNAIRES", "true");
 551     }
 552     else
 553     {
 554       // special - made easy to edit a property file to disable questionnaires
 555       // by just adding the given line
 556       Cache.removeProperty("NOQUESTIONNAIRES");
 557     }
 558
 559     /*
 560      * Save Output settings
 561      */
 562     Cache.applicationProperties.setProperty("BLC_JVSUFFIX",
 563             Boolean.toString(blcjv.isSelected()));
 564     Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX",
 565             Boolean.toString(clustaljv.isSelected()));
 566     Cache.applicationProperties.setProperty("FASTA_JVSUFFIX",
 567             Boolean.toString(fastajv.isSelected()));
 568     Cache.applicationProperties.setProperty("MSF_JVSUFFIX",
 569             Boolean.toString(msfjv.isSelected()));
 570     Cache.applicationProperties.setProperty("PFAM_JVSUFFIX",
 571             Boolean.toString(pfamjv.isSelected()));
 572     Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX",
 573             Boolean.toString(pileupjv.isSelected()));
 574     Cache.applicationProperties.setProperty("PIR_JVSUFFIX",
 575             Boolean.toString(pirjv.isSelected()));
 576     Cache.applicationProperties.setProperty("PIR_MODELLER",
 577             Boolean.toString(modellerOutput.isSelected()));
 578     Cache.applicationProperties.setProperty("EXPORT_EMBBED_BIOJSON",
 579             Boolean.toString(embbedBioJSON.isSelected()));
 580     jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
 581
 582     Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH",
 583             Boolean.toString(autoIdWidth.isSelected()));
 584     userIdWidth_actionPerformed();
 585     Cache.applicationProperties.setProperty("FIGURE_USERIDWIDTH",
 586             userIdWidth.getText());
 587
 588     /*
 589      * Save Editing settings
 590      */
 591     Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
 592             Boolean.toString(autoCalculateConsCheck.isSelected()));
 593     Cache.applicationProperties.setProperty("SORT_BY_TREE",
 594             Boolean.toString(sortByTree.isSelected()));
 595     Cache.applicationProperties.setProperty("PAD_GAPS",
 596             Boolean.toString(padGaps.isSelected()));
 597
 598     dasSource.saveProperties(Cache.applicationProperties);
 599     wsPrefs.updateAndRefreshWsMenuConfig(false);
 600     Cache.saveProperties();
 601     Desktop.instance.doConfigureStructurePrefs();
 602     try
 603     {
 604       frame.setClosed(true);
 605     } catch (Exception ex)
 606     {
 607     }
 608   }
 609
 610   /**
 611    * Do any necessary validation before saving settings. Return focus to the
 612    * first tab which fails validation.
 613    *
 614    * @return
 615    */
 616   private boolean validateSettings()
 617   {
 618     if (!validateStructure())
 619     {
 620       structureTab.requestFocusInWindow();
 621       return false;
 622     }
 623     return true;
 624   }
 625
 626   @Override
 627   protected boolean validateStructure()
 628   {
 629     return validateChimeraPath();
 630
 631   }
 632
 633   /**
 634    * DOCUMENT ME!
 635    */
 636   @Override
 637   public void startupFileTextfield_mouseClicked()
 638   {
 639     JalviewFileChooser chooser = new JalviewFileChooser(
 640             jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[] {
 641                 "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",
 642                 "jar" }, new String[] { "Fasta", "Clustal", "PFAM", "MSF",
 643                 "PIR", "BLC", "Jalview" },
 644             jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));
 645     chooser.setFileView(new JalviewFileView());
 646     chooser.setDialogTitle(MessageManager
 647             .getString("label.select_startup_file"));
 648
 649     int value = chooser.showOpenDialog(this);
 650
 651     if (value == JalviewFileChooser.APPROVE_OPTION)
 652     {
 653       jalview.bin.Cache.applicationProperties.setProperty(
 654               "DEFAULT_FILE_FORMAT", chooser.getSelectedFormat());
 655       startupFileTextfield.setText(chooser.getSelectedFile()
 656               .getAbsolutePath());
 657     }
 658   }
 659
 660   /**
 661    * DOCUMENT ME!
 662    *
 663    * @param e
 664    *          DOCUMENT ME!
 665    */
 666   @Override
 667   public void cancel_actionPerformed(ActionEvent e)
 668   {
 669     try
 670     {
 671       wsPrefs.updateWsMenuConfig(true);
 672       wsPrefs.refreshWs_actionPerformed(e);
 673       frame.setClosed(true);
 674     } catch (Exception ex)
 675     {
 676     }
 677   }
 678
 679   /**
 680    * DOCUMENT ME!
 681    *
 682    * @param e
 683    *          DOCUMENT ME!
 684    */
 685   @Override
 686   public void annotations_actionPerformed(ActionEvent e)
 687   {
 688     conservation.setEnabled(annotations.isSelected());
 689     quality.setEnabled(annotations.isSelected());
 690     identity.setEnabled(annotations.isSelected());
 691     showGroupConsensus.setEnabled(annotations.isSelected());
 692     showGroupConservation.setEnabled(annotations.isSelected());
 693     showConsensHistogram.setEnabled(annotations.isSelected()
 694             && (identity.isSelected() || showGroupConsensus.isSelected()));
 695     showConsensLogo.setEnabled(annotations.isSelected()
 696             && (identity.isSelected() || showGroupConsensus.isSelected()));
 697   }
 698
 699   @Override
 700   public void newLink_actionPerformed(ActionEvent e)
 701   {
 702
 703     GSequenceLink link = new GSequenceLink();
 704     boolean valid = false;
 705     while (!valid)
 706     {
 707       if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 708               MessageManager.getString("label.new_sequence_url_link"),
 709               JOptionPane.OK_CANCEL_OPTION, -1, null) == JOptionPane.OK_OPTION)
 710       {
 711         if (link.checkValid())
 712         {
 713           nameLinks.addElement(link.getName());
 714           urlLinks.addElement(link.getURL());
 715           if (updateLinkData())
 716           {
 717             valid = true;
 718           }
 719           else
 720           {
 721             break;
 722           }
 723         }
 724       }
 725       else
 726       {
 727         break;
 728       }
 729     }
 730   }
 731
 732   @Override
 733   public void editLink_actionPerformed(ActionEvent e)
 734   {
 735     GSequenceLink link = new GSequenceLink();
 736
 737     int index = linkNameList.getSelectedIndex();
 738     if (index == -1)
 739     {
 740       JOptionPane.showInternalMessageDialog(Desktop.desktop,
 741               MessageManager.getString("label.no_link_selected"),
 742               MessageManager.getString("label.no_link_selected"),
 743               JOptionPane.WARNING_MESSAGE);
 744       return;
 745     }
 746
 747     link.setName(nameLinks.elementAt(index).toString());
 748     link.setURL(urlLinks.elementAt(index).toString());
 749
 750     boolean valid = false;
 751     while (!valid)
 752     {
 753
 754       if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 755               MessageManager.getString("label.new_sequence_url_link"),
 756               JOptionPane.OK_CANCEL_OPTION, -1, null) == JOptionPane.OK_OPTION)
 757       {
 758         if (link.checkValid())
 759         {
 760           nameLinks.setElementAt(link.getName(), index);
 761           urlLinks.setElementAt(link.getURL(), index);
 762           if (updateLinkData())
 763           {
 764             valid = true;
 765           }
 766           else
 767           {
 768             break;
 769           }
 770         }
 771       }
 772
 773       else
 774       {
 775         break;
 776       }
 777     }
 778   }
 779
 780   @Override
 781   public void deleteLink_actionPerformed(ActionEvent e)
 782   {
 783     int index = linkNameList.getSelectedIndex();
 784     if (index == -1)
 785     {
 786       JOptionPane.showInternalMessageDialog(Desktop.desktop,
 787               MessageManager.getString("label.no_link_selected"),
 788               MessageManager.getString("label.no_link_selected"),
 789               JOptionPane.WARNING_MESSAGE);
 790       return;
 791     }
 792     nameLinks.removeElementAt(index);
 793     urlLinks.removeElementAt(index);
 794     updateLinkData();
 795   }
 796
 797   private boolean updateLinkData()
 798   {
 799     try
 800     {
 801       sequenceUrlLinks.setUrlLinks(nameLinks, urlLinks);
 802       linkNameList.setListData(nameLinks);
 803       linkURLList.setListData(urlLinks);
 804     } catch (IllegalArgumentException e)
 805     {
 806
 807       // put back the old links
 808       resetStoredLinks();
 809
 810       linkNameList.setListData(nameLinks);
 811       linkURLList.setListData(urlLinks);
 812
 813       JOptionPane.showInternalMessageDialog(Desktop.desktop,
 814               e.getMessage(), MessageManager.getString("label.link_name"),
 815               JOptionPane.WARNING_MESSAGE);
 816
 817       return false;
 818     }
 819     return true;
 820   }
 821
 822   private void resetStoredLinks()
 823   {
 824     Vector<String> nlinks = sequenceUrlLinks.getLinksForDisplay();
 825
 826     nameLinks.clear();
 827     urlLinks.clear();
 828     for (String entry : nlinks)
 829     {
 830       nameLinks.addElement(entry.split("\\|")[0]);
 831       urlLinks.addElement(entry.split("\\|")[1]);
 832     }
 833   }
 834
 835   @Override
 836   public void defaultBrowser_mouseClicked(MouseEvent e)
 837   {
 838     JFileChooser chooser = new JFileChooser(".");
 839     chooser.setDialogTitle(MessageManager
 840             .getString("label.select_default_browser"));
 841
 842     int value = chooser.showOpenDialog(this);
 843
 844     if (value == JFileChooser.APPROVE_OPTION)
 845     {
 846       defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
 847     }
 848
 849   }
 850
 851   /*
 852    * (non-Javadoc)
 853    *
 854    * @see
 855    * jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event
 856    * .ActionEvent)
 857    */
 858   @Override
 859   protected void showunconserved_actionPerformed(ActionEvent e)
 860   {
 861     // TODO Auto-generated method stub
 862     super.showunconserved_actionPerformed(e);
 863   }
 864
 865   public static List<String> getGroupURLLinks()
 866   {
 867     return groupURLLinks;
 868   }
 869
 870   @Override
 871   public void minColour_actionPerformed(JPanel panel)
 872   {
 873     Color col = JColorChooser.showDialog(this,
 874             MessageManager.getString("label.select_colour_minimum_value"),
 875             minColour.getBackground());
 876     if (col != null)
 877     {
 878       panel.setBackground(col);
 879     }
 880     panel.repaint();
 881   }
 882
 883   @Override
 884   public void maxColour_actionPerformed(JPanel panel)
 885   {
 886     Color col = JColorChooser.showDialog(this,
 887             MessageManager.getString("label.select_colour_maximum_value"),
 888             maxColour.getBackground());
 889     if (col != null)
 890     {
 891       panel.setBackground(col);
 892     }
 893     panel.repaint();
 894   }
 895
 896   @Override
 897   protected void userIdWidth_actionPerformed()
 898   {
 899     try
 900     {
 901       String val = userIdWidth.getText().trim();
 902       if (val.length() > 0)
 903       {
 904         Integer iw = Integer.parseInt(val);
 905         if (iw.intValue() < 12)
 906         {
 907           throw new NumberFormatException();
 908         }
 909         userIdWidth.setText(iw.toString());
 910       }
 911     } catch (NumberFormatException x)
 912     {
 913       JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
 914               .getString("warn.user_defined_width_requirements"),
 915               MessageManager.getString("label.invalid_id_column_width"),
 916               JOptionPane.WARNING_MESSAGE);
 917       userIdWidth.setText("");
 918     }
 919   }
 920
 921   @Override
 922   protected void autoIdWidth_actionPerformed()
 923   {
 924     userIdWidth.setEnabled(!autoIdWidth.isSelected());
 925     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
 926   }
 927
 928   /**
 929    * Returns true if chimera path is to a valid executable, else show an error
 930    * dialog.
 931    */
 932   private boolean validateChimeraPath()
 933   {
 934     if (chimeraPath.getText().trim().length() > 0)
 935     {
 936       File f = new File(chimeraPath.getText());
 937       if (!f.canExecute())
 938       {
 939         JOptionPane.showInternalMessageDialog(Desktop.desktop,
 940                 MessageManager.getString("label.invalid_chimera_path"),
 941                 MessageManager.getString("label.invalid_name"),
 942                 JOptionPane.ERROR_MESSAGE);
 943         return false;
 944       }
 945     }
 946     return true;
 947   }
 948
 949   /**
 950    * If Chimera is selected, check it can be found on default or user-specified
 951    * path, if not show a warning/help dialog.
 952    */
 953   @Override
 954   protected void structureViewer_actionPerformed(String selectedItem)
 955   {
 956     if (!selectedItem.equals(ViewerType.CHIMERA.name()))
 957     {
 958       return;
 959     }
 960     boolean found = false;
 961
 962     /*
 963      * Try user-specified and standard paths for Chimera executable.
 964      */
 965     List<String> paths = StructureManager.getChimeraPaths();
 966     paths.add(0, chimeraPath.getText());
 967     for (String path : paths)
 968     {
 969       if (new File(path.trim()).canExecute())
 970       {
 971         found = true;
 972         break;
 973       }
 974     }
 975     if (!found)
 976     {
 977       String[] options = { "OK", "Help" };
 978       int showHelp = JOptionPane.showInternalOptionDialog(
 979               Desktop.desktop,
 980               JvSwingUtils.wrapTooltip(true,
 981                       MessageManager.getString("label.chimera_missing")),
 982               "", JOptionPane.YES_NO_OPTION, JOptionPane.WARNING_MESSAGE,
 983               null, options, options[0]);
 984       if (showHelp == JOptionPane.NO_OPTION)
 985       {
 986         try
 987         {
 988           Help.showHelpWindow(HelpId.StructureViewer);
 989         } catch (HelpSetException e)
 990         {
 991           e.printStackTrace();
 992         }
 993       }
 994     }
 995   }
 996
 997   public class OptionsParam
 998   {
 999     private String name;
1000
1001     private String code;
1002
1003     public OptionsParam(String name, String code)
1004     {
1005       this.name = name;
1006       this.code = code;
1007     }
1008
1009     public String getName()
1010     {
1011       return name;
1012     }
1013
1014     public void setName(String name)
1015     {
1016       this.name = name;
1017     }
1018
1019     public String getCode()
1020     {
1021       return code;
1022     }
1023
1024     public void setCode(String code)
1025     {
1026       this.code = code;
1027     }
1028
1029     @Override
1030     public String toString()
1031     {
1032       return name;
1033     }
1034
1035     @Override
1036     public boolean equals(Object that)
1037     {
1038       if (!(that instanceof OptionsParam))
1039       {
1040         return false;
1041       }
1042       return this.code.equalsIgnoreCase(((OptionsParam) that).code);
1043     }
1044
1045     @Override
1046     public int hashCode()
1047     {
1048       return name.hashCode() + code.hashCode();
1049     }
1050   }
1051 }