src/jalview/gui/Preferences.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.gui;
  22
  23 import static jalview.util.UrlConstants.EMBLEBI_STRING;
  24 import static jalview.util.UrlConstants.SEQUENCE_ID;
  25 import static jalview.util.UrlConstants.SRS_STRING;
  26
  27 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
  28 import jalview.bin.Cache;
  29 import jalview.gui.Help.HelpId;
  30 import jalview.gui.StructureViewer.ViewerType;
  31 import jalview.io.JalviewFileChooser;
  32 import jalview.io.JalviewFileView;
  33 import jalview.jbgui.GPreferences;
  34 import jalview.jbgui.GSequenceLink;
  35 import jalview.schemes.ColourSchemeProperty;
  36 import jalview.util.MessageManager;
  37 import jalview.util.Platform;
  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.StringTokenizer;
  51 import java.util.Vector;
  52
  53 import javax.help.HelpSetException;
  54 import javax.swing.JColorChooser;
  55 import javax.swing.JFileChooser;
  56 import javax.swing.JInternalFrame;
  57 import javax.swing.JOptionPane;
  58 import javax.swing.JPanel;
  59
  60 import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
  61
  62 /**
  63  * DOCUMENT ME!
  64  *
  65  * @author $author$
  66  * @version $Revision$
  67  */
  68 public class Preferences extends GPreferences
  69 {
  70   public static final String ENABLE_SPLIT_FRAME = "ENABLE_SPLIT_FRAME";
  71
  72   public static final String SCALE_PROTEIN_TO_CDNA = "SCALE_PROTEIN_TO_CDNA";
  73
  74   public static final String DEFAULT_COLOUR = "DEFAULT_COLOUR";
  75
  76   public static final String DEFAULT_COLOUR_PROT = "DEFAULT_COLOUR_PROT";
  77
  78   public static final String DEFAULT_COLOUR_NUC = "DEFAULT_COLOUR_NUC";
  79
  80   public static final String ADD_TEMPFACT_ANN = "ADD_TEMPFACT_ANN";
  81
  82   public static final String ADD_SS_ANN = "ADD_SS_ANN";
  83
  84   public static final String USE_RNAVIEW = "USE_RNAVIEW";
  85
  86   public static final String STRUCT_FROM_PDB = "STRUCT_FROM_PDB";
  87
  88   public static final String STRUCTURE_DISPLAY = "STRUCTURE_DISPLAY";
  89
  90   public static final String CHIMERA_PATH = "CHIMERA_PATH";
  91
  92   public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS";
  93
  94   public static final String SHOW_AUTOCALC_ABOVE = "SHOW_AUTOCALC_ABOVE";
  95
  96   private static final int MIN_FONT_SIZE = 1;
  97
  98   private static final int MAX_FONT_SIZE = 30;
  99
 100   /**
 101    * Holds name and link separated with | character. Sequence ID must be
 102    * $SEQUENCE_ID$ or $SEQUENCE_ID=/.possible | chars ./=$
 103    */
 104   public static Vector<String> 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 Vector<String>();
 119
 120     try
 121     {
 122       StringTokenizer st = new StringTokenizer(string, "|");
 123       while (st.hasMoreElements())
 124       {
 125         String name = st.nextToken();
 126         String url = st.nextToken();
 127         // check for '|' within a regex
 128         int rxstart = url.indexOf("$" + SEQUENCE_ID + "$");
 129         while (rxstart == -1 && url.indexOf("/=$") == -1)
 130         {
 131           url = url + "|" + st.nextToken();
 132         }
 133         sequenceURLLinks.addElement(name + "|" + url);
 134       }
 135     } catch (Exception ex)
 136     {
 137       System.out.println(ex + "\nError parsing sequence links");
 138     }
 139     {
 140       // upgrade old SRS link
 141       int srsPos = sequenceURLLinks.indexOf(SRS_STRING);
 142       if (srsPos > -1)
 143       {
 144         sequenceURLLinks.setElementAt(EMBLEBI_STRING, srsPos);
 145       }
 146     }
 147
 148     /**
 149      * TODO: reformulate groupURL encoding so two or more can be stored in the
 150      * .properties file as '|' separated strings
 151      */
 152
 153     groupURLLinks = new ArrayList<String>();
 154   }
 155
 156   Vector<String> nameLinks, urlLinks;
 157
 158   JInternalFrame frame;
 159
 160   DasSourceBrowser dasSource;
 161
 162   private WsPreferences wsPrefs;
 163
 164   private OptionsParam promptEachTimeOpt = new OptionsParam(
 165           MessageManager.getString("label.prompt_each_time"),
 166           "Prompt each time");
 167
 168   private OptionsParam lineArtOpt = new OptionsParam(
 169           MessageManager.getString("label.lineart"), "Lineart");
 170
 171   private OptionsParam textOpt = new OptionsParam(
 172           MessageManager.getString("action.text"), "Text");
 173
 174   /**
 175    * Creates a new Preferences object.
 176    */
 177   public Preferences()
 178   {
 179     super();
 180     frame = new JInternalFrame();
 181     frame.setContentPane(this);
 182     dasSource = new DasSourceBrowser();
 183     dasTab.add(dasSource, BorderLayout.CENTER);
 184     wsPrefs = new WsPreferences();
 185     wsTab.add(wsPrefs, BorderLayout.CENTER);
 186     int width = 500, height = 450;
 187     new jalview.util.Platform();
 188     if (Platform.isAMac())
 189     {
 190       width = 570;
 191       height = 480;
 192     }
 193
 194     Desktop.addInternalFrame(frame,
 195             MessageManager.getString("label.preferences"), width, height);
 196     frame.setMinimumSize(new Dimension(width, height));
 197
 198     /*
 199      * Set Visual tab defaults
 200      */
 201     seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));
 202     rightAlign.setSelected(Cache.getDefault("RIGHT_ALIGN_IDS", false));
 203     fullScreen.setSelected(Cache.getDefault("SHOW_FULLSCREEN", false));
 204     annotations.setSelected(Cache.getDefault("SHOW_ANNOTATIONS", true));
 205
 206     conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));
 207     quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));
 208     identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));
 209     openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false));
 210     showUnconserved
 211             .setSelected(Cache.getDefault("SHOW_UNCONSERVED", false));
 212     showGroupConsensus.setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS",
 213             false));
 214     showGroupConservation.setSelected(Cache.getDefault(
 215             "SHOW_GROUP_CONSERVATION", false));
 216     showConsensHistogram.setSelected(Cache.getDefault(
 217             "SHOW_CONSENSUS_HISTOGRAM", true));
 218     showConsensLogo.setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO",
 219             false));
 220     showNpTooltip.setSelected(Cache
 221             .getDefault("SHOW_NPFEATS_TOOLTIP", true));
 222     showDbRefTooltip.setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP",
 223             true));
 224
 225     String[] fonts = java.awt.GraphicsEnvironment
 226             .getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
 227     for (int i = 0; i < fonts.length; i++)
 228     {
 229       fontNameCB.addItem(fonts[i]);
 230     }
 231
 232     for (int i = MIN_FONT_SIZE; i <= MAX_FONT_SIZE; i++)
 233     {
 234       fontSizeCB.addItem(i + "");
 235     }
 236
 237     fontStyleCB.addItem("plain");
 238     fontStyleCB.addItem("bold");
 239     fontStyleCB.addItem("italic");
 240
 241     fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
 242     fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
 243     fontStyleCB.setSelectedItem(Cache.getDefault("FONT_STYLE", Font.PLAIN
 244             + ""));
 245
 246     smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));
 247     scaleProteinToCdna.setSelected(Cache.getDefault(SCALE_PROTEIN_TO_CDNA,
 248             false));
 249
 250     idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
 251
 252     wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
 253
 254     gapSymbolCB.addItem("-");
 255     gapSymbolCB.addItem(".");
 256
 257     gapSymbolCB.setSelectedItem(Cache.getDefault("GAP_SYMBOL", "-"));
 258
 259     sortby.addItem("No sort");
 260     sortby.addItem("Id");
 261     sortby.addItem("Pairwise Identity");
 262     sortby.setSelectedItem(Cache.getDefault("SORT_ALIGNMENT", "No sort"));
 263
 264     sortAnnBy.addItem(SequenceAnnotationOrder.NONE.toString());
 265     sortAnnBy
 266             .addItem(SequenceAnnotationOrder.SEQUENCE_AND_LABEL.toString());
 267     sortAnnBy
 268             .addItem(SequenceAnnotationOrder.LABEL_AND_SEQUENCE.toString());
 269     SequenceAnnotationOrder savedSort = SequenceAnnotationOrder
 270             .valueOf(Cache.getDefault(SORT_ANNOTATIONS,
 271                     SequenceAnnotationOrder.NONE.name()));
 272     sortAnnBy.setSelectedItem(savedSort.toString());
 273
 274     sortAutocalc.addItem("Autocalculated first");
 275     sortAutocalc.addItem("Autocalculated last");
 276     final boolean showAbove = Cache.getDefault(SHOW_AUTOCALC_ABOVE, true);
 277     sortAutocalc.setSelectedItem(showAbove ? sortAutocalc.getItemAt(0)
 278             : sortAutocalc.getItemAt(1));
 279     startupCheckbox
 280             .setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
 281     startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
 282             Cache.getDefault("www.jalview.org", "http://www.jalview.org")
 283                     + "/examples/exampleFile_2_3.jar"));
 284
 285     /*
 286      * Set Colours tab defaults
 287      */
 288     for (int i = ColourSchemeProperty.FIRST_COLOUR; i <= ColourSchemeProperty.LAST_COLOUR; i++)
 289     {
 290       protColour.addItem(ColourSchemeProperty.getColourName(i));
 291       nucColour.addItem(ColourSchemeProperty.getColourName(i));
 292     }
 293     String oldProp = Cache.getDefault(DEFAULT_COLOUR, "None");
 294     String newProp = Cache.getDefault(DEFAULT_COLOUR_PROT, null);
 295     protColour.setSelectedItem(newProp != null ? newProp : oldProp);
 296     newProp = Cache.getDefault(DEFAULT_COLOUR_NUC, null);
 297     nucColour.setSelectedItem(newProp != null ? newProp : oldProp);
 298     minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN",
 299             Color.orange));
 300     maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX",
 301             Color.red));
 302
 303     /*
 304      * Set Structure tab defaults.
 305      */
 306     final boolean structSelected = Cache.getDefault(STRUCT_FROM_PDB, false);
 307     structFromPdb.setSelected(structSelected);
 308     useRnaView.setSelected(Cache.getDefault(USE_RNAVIEW, false));
 309     useRnaView.setEnabled(structSelected);
 310     addSecondaryStructure.setSelected(Cache.getDefault(ADD_SS_ANN, false));
 311     addSecondaryStructure.setEnabled(structSelected);
 312     addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, false));
 313     addTempFactor.setEnabled(structSelected);
 314     structViewer.setSelectedItem(Cache.getDefault(STRUCTURE_DISPLAY,
 315             ViewerType.JMOL.name()));
 316     chimeraPath.setText(Cache.getDefault(CHIMERA_PATH, ""));
 317     chimeraPath.addActionListener(new ActionListener()
 318     {
 319       @Override
 320       public void actionPerformed(ActionEvent e)
 321       {
 322         validateChimeraPath();
 323       }
 324     });
 325
 326     if (Cache.getDefault("MAP_WITH_SIFTS", false))
 327     {
 328       siftsMapping.setSelected(true);
 329     }
 330     else
 331     {
 332       nwMapping.setSelected(true);
 333     }
 334
 335     SiftsSettings
 336             .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
 337
 338     /*
 339      * Set Connections tab defaults
 340      */
 341     nameLinks = new Vector<String>();
 342     urlLinks = new Vector<String>();
 343     for (int i = 0; i < sequenceURLLinks.size(); i++)
 344     {
 345       String link = sequenceURLLinks.elementAt(i).toString();
 346       nameLinks.addElement(link.substring(0, link.indexOf("|")));
 347       urlLinks.addElement(link.substring(link.indexOf("|") + 1));
 348     }
 349
 350     updateLinkData();
 351
 352     useProxy.setSelected(Cache.getDefault("USE_PROXY", false));
 353     proxyServerTB.setEnabled(useProxy.isSelected());
 354     proxyPortTB.setEnabled(useProxy.isSelected());
 355     proxyServerTB.setText(Cache.getDefault("PROXY_SERVER", ""));
 356     proxyPortTB.setText(Cache.getDefault("PROXY_PORT", ""));
 357
 358     defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", ""));
 359
 360     usagestats.setSelected(Cache.getDefault("USAGESTATS", false));
 361     // note antisense here: default is true
 362     questionnaire
 363             .setSelected(Cache.getProperty("NOQUESTIONNAIRES") == null);
 364     versioncheck.setSelected(Cache.getDefault("VERSION_CHECK", true));
 365
 366     /*
 367      * Set Output tab defaults
 368      */
 369     epsRendering.addItem(promptEachTimeOpt);
 370     epsRendering.addItem(lineArtOpt);
 371     epsRendering.addItem(textOpt);
 372     String defaultEPS = Cache.getDefault("EPS_RENDERING",
 373             "Prompt each time");
 374     if (defaultEPS.equalsIgnoreCase("Text"))
 375     {
 376       epsRendering.setSelectedItem(textOpt);
 377     }
 378     else if (defaultEPS.equalsIgnoreCase("Lineart"))
 379     {
 380       epsRendering.setSelectedItem(lineArtOpt);
 381     }
 382     else
 383     {
 384       epsRendering.setSelectedItem(promptEachTimeOpt);
 385     }
 386     autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false));
 387     userIdWidth.setEnabled(!autoIdWidth.isSelected());
 388     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
 389     Integer wi = Cache.getIntegerProperty("FIGURE_USERIDWIDTH");
 390     userIdWidth.setText(wi == null ? "" : wi.toString());
 391     blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
 392     clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
 393     fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
 394     msfjv.setSelected(Cache.getDefault("MSF_JVSUFFIX", true));
 395     pfamjv.setSelected(Cache.getDefault("PFAM_JVSUFFIX", true));
 396     pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
 397     pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
 398     modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
 399     embbedBioJSON.setSelected(Cache.getDefault("EXPORT_EMBBED_BIOJSON",
 400             true));
 401
 402     /*
 403      * Set Editing tab defaults
 404      */
 405     autoCalculateConsCheck.setSelected(Cache.getDefault(
 406             "AUTO_CALC_CONSENSUS", true));
 407     padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
 408     sortByTree.setSelected(Cache.getDefault("SORT_BY_TREE", false));
 409
 410     annotations_actionPerformed(null); // update the display of the annotation
 411                                        // settings
 412   }
 413
 414   /**
 415    * Save user selections on the Preferences tabs to the Cache and write out to
 416    * file.
 417    *
 418    * @param e
 419    */
 420   @Override
 421   public void ok_actionPerformed(ActionEvent e)
 422   {
 423     if (!validateSettings())
 424     {
 425       return;
 426     }
 427
 428     /*
 429      * Save Visual settings
 430      */
 431     Cache.applicationProperties.setProperty("SHOW_JVSUFFIX",
 432             Boolean.toString(seqLimit.isSelected()));
 433     Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS",
 434             Boolean.toString(rightAlign.isSelected()));
 435     Cache.applicationProperties.setProperty("SHOW_FULLSCREEN",
 436             Boolean.toString(fullScreen.isSelected()));
 437     Cache.applicationProperties.setProperty("SHOW_OVERVIEW",
 438             Boolean.toString(openoverv.isSelected()));
 439     Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
 440             Boolean.toString(annotations.isSelected()));
 441     Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
 442             Boolean.toString(conservation.isSelected()));
 443     Cache.applicationProperties.setProperty("SHOW_QUALITY",
 444             Boolean.toString(quality.isSelected()));
 445     Cache.applicationProperties.setProperty("SHOW_IDENTITY",
 446             Boolean.toString(identity.isSelected()));
 447
 448     Cache.applicationProperties.setProperty("GAP_SYMBOL", gapSymbolCB
 449             .getSelectedItem().toString());
 450
 451     Cache.applicationProperties.setProperty("FONT_NAME", fontNameCB
 452             .getSelectedItem().toString());
 453     Cache.applicationProperties.setProperty("FONT_STYLE", fontStyleCB
 454             .getSelectedItem().toString());
 455     Cache.applicationProperties.setProperty("FONT_SIZE", fontSizeCB
 456             .getSelectedItem().toString());
 457
 458     Cache.applicationProperties.setProperty("ID_ITALICS",
 459             Boolean.toString(idItalics.isSelected()));
 460     Cache.applicationProperties.setProperty("SHOW_UNCONSERVED",
 461             Boolean.toString(showUnconserved.isSelected()));
 462     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS",
 463             Boolean.toString(showGroupConsensus.isSelected()));
 464     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION",
 465             Boolean.toString(showGroupConservation.isSelected()));
 466     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_HISTOGRAM",
 467             Boolean.toString(showConsensHistogram.isSelected()));
 468     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO",
 469             Boolean.toString(showConsensLogo.isSelected()));
 470     Cache.applicationProperties.setProperty("ANTI_ALIAS",
 471             Boolean.toString(smoothFont.isSelected()));
 472     Cache.applicationProperties.setProperty(SCALE_PROTEIN_TO_CDNA,
 473             Boolean.toString(scaleProteinToCdna.isSelected()));
 474     Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP",
 475             Boolean.toString(showNpTooltip.isSelected()));
 476     Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP",
 477             Boolean.toString(showDbRefTooltip.isSelected()));
 478
 479     Cache.applicationProperties.setProperty("WRAP_ALIGNMENT",
 480             Boolean.toString(wrap.isSelected()));
 481
 482     Cache.applicationProperties.setProperty("STARTUP_FILE",
 483             startupFileTextfield.getText());
 484     Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",
 485             Boolean.toString(startupCheckbox.isSelected()));
 486
 487     Cache.applicationProperties.setProperty("SORT_ALIGNMENT", sortby
 488             .getSelectedItem().toString());
 489
 490     // convert description of sort order to enum name for save
 491     SequenceAnnotationOrder annSortOrder = SequenceAnnotationOrder
 492             .forDescription(sortAnnBy.getSelectedItem().toString());
 493     if (annSortOrder != null)
 494     {
 495       Cache.applicationProperties.setProperty(SORT_ANNOTATIONS,
 496               annSortOrder.name());
 497     }
 498
 499     final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
 500     Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE, Boolean
 501             .valueOf(showAutocalcFirst).toString());
 502
 503     /*
 504      * Save Colours settings
 505      */
 506     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_PROT, protColour
 507             .getSelectedItem().toString());
 508     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_NUC, nucColour
 509             .getSelectedItem().toString());
 510     Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
 511             minColour.getBackground());
 512     Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
 513             maxColour.getBackground());
 514
 515     /*
 516      * Save Structure settings
 517      */
 518     Cache.applicationProperties.setProperty(ADD_TEMPFACT_ANN,
 519             Boolean.toString(addTempFactor.isSelected()));
 520     Cache.applicationProperties.setProperty(ADD_SS_ANN,
 521             Boolean.toString(addSecondaryStructure.isSelected()));
 522     Cache.applicationProperties.setProperty(USE_RNAVIEW,
 523             Boolean.toString(useRnaView.isSelected()));
 524     Cache.applicationProperties.setProperty(STRUCT_FROM_PDB,
 525             Boolean.toString(structFromPdb.isSelected()));
 526     Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY, structViewer
 527             .getSelectedItem().toString());
 528     Cache.setOrRemove(CHIMERA_PATH, chimeraPath.getText());
 529     Cache.applicationProperties.setProperty("MAP_WITH_SIFTS",
 530             Boolean.toString(siftsMapping.isSelected()));
 531     SiftsSettings.setMapWithSifts(siftsMapping.isSelected());
 532
 533     /*
 534      * Save Output settings
 535      */
 536     Cache.applicationProperties.setProperty("EPS_RENDERING",
 537             ((OptionsParam) epsRendering.getSelectedItem()).getCode());
 538
 539     /*
 540      * Save Connections settings
 541      */
 542     Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText());
 543
 544     jalview.util.BrowserLauncher.resetBrowser();
 545
 546     if (nameLinks.size() > 0)
 547     {
 548       StringBuffer links = new StringBuffer();
 549       sequenceURLLinks = new Vector<String>();
 550       for (int i = 0; i < nameLinks.size(); i++)
 551       {
 552         sequenceURLLinks.addElement(nameLinks.elementAt(i) + "|"
 553                 + urlLinks.elementAt(i));
 554         links.append(sequenceURLLinks.elementAt(i).toString());
 555         links.append("|");
 556       }
 557       // remove last "|"
 558       links.setLength(links.length() - 1);
 559       Cache.applicationProperties.setProperty("SEQUENCE_LINKS",
 560               links.toString());
 561     }
 562     else
 563     {
 564       Cache.applicationProperties.remove("SEQUENCE_LINKS");
 565     }
 566
 567     Cache.applicationProperties.setProperty("USE_PROXY",
 568             Boolean.toString(useProxy.isSelected()));
 569
 570     Cache.setOrRemove("PROXY_SERVER", proxyServerTB.getText());
 571
 572     Cache.setOrRemove("PROXY_PORT", proxyPortTB.getText());
 573
 574     if (useProxy.isSelected())
 575     {
 576       System.setProperty("http.proxyHost", proxyServerTB.getText());
 577       System.setProperty("http.proxyPort", proxyPortTB.getText());
 578     }
 579     else
 580     {
 581       System.setProperty("http.proxyHost", "");
 582       System.setProperty("http.proxyPort", "");
 583     }
 584     Cache.setProperty("VERSION_CHECK",
 585             Boolean.toString(versioncheck.isSelected()));
 586     if (Cache.getProperty("USAGESTATS") != null || usagestats.isSelected())
 587     {
 588       // default is false - we only set this if the user has actively agreed
 589       Cache.setProperty("USAGESTATS",
 590               Boolean.toString(usagestats.isSelected()));
 591     }
 592     if (!questionnaire.isSelected())
 593     {
 594       Cache.setProperty("NOQUESTIONNAIRES", "true");
 595     }
 596     else
 597     {
 598       // special - made easy to edit a property file to disable questionnaires
 599       // by just adding the given line
 600       Cache.removeProperty("NOQUESTIONNAIRES");
 601     }
 602
 603     /*
 604      * Save Output settings
 605      */
 606     Cache.applicationProperties.setProperty("BLC_JVSUFFIX",
 607             Boolean.toString(blcjv.isSelected()));
 608     Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX",
 609             Boolean.toString(clustaljv.isSelected()));
 610     Cache.applicationProperties.setProperty("FASTA_JVSUFFIX",
 611             Boolean.toString(fastajv.isSelected()));
 612     Cache.applicationProperties.setProperty("MSF_JVSUFFIX",
 613             Boolean.toString(msfjv.isSelected()));
 614     Cache.applicationProperties.setProperty("PFAM_JVSUFFIX",
 615             Boolean.toString(pfamjv.isSelected()));
 616     Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX",
 617             Boolean.toString(pileupjv.isSelected()));
 618     Cache.applicationProperties.setProperty("PIR_JVSUFFIX",
 619             Boolean.toString(pirjv.isSelected()));
 620     Cache.applicationProperties.setProperty("PIR_MODELLER",
 621             Boolean.toString(modellerOutput.isSelected()));
 622     Cache.applicationProperties.setProperty("EXPORT_EMBBED_BIOJSON",
 623             Boolean.toString(embbedBioJSON.isSelected()));
 624     jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
 625
 626     Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH",
 627             Boolean.toString(autoIdWidth.isSelected()));
 628     userIdWidth_actionPerformed();
 629     Cache.applicationProperties.setProperty("FIGURE_USERIDWIDTH",
 630             userIdWidth.getText());
 631
 632     /*
 633      * Save Editing settings
 634      */
 635     Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
 636             Boolean.toString(autoCalculateConsCheck.isSelected()));
 637     Cache.applicationProperties.setProperty("SORT_BY_TREE",
 638             Boolean.toString(sortByTree.isSelected()));
 639     Cache.applicationProperties.setProperty("PAD_GAPS",
 640             Boolean.toString(padGaps.isSelected()));
 641
 642     dasSource.saveProperties(Cache.applicationProperties);
 643     wsPrefs.updateAndRefreshWsMenuConfig(false);
 644     Cache.saveProperties();
 645     Desktop.instance.doConfigureStructurePrefs();
 646     try
 647     {
 648       frame.setClosed(true);
 649     } catch (Exception ex)
 650     {
 651     }
 652   }
 653
 654   /**
 655    * Do any necessary validation before saving settings. Return focus to the
 656    * first tab which fails validation.
 657    *
 658    * @return
 659    */
 660   private boolean validateSettings()
 661   {
 662     if (!validateStructure())
 663     {
 664       structureTab.requestFocusInWindow();
 665       return false;
 666     }
 667     return true;
 668   }
 669
 670   @Override
 671   protected boolean validateStructure()
 672   {
 673     return validateChimeraPath();
 674
 675   }
 676
 677   /**
 678    * DOCUMENT ME!
 679    */
 680   @Override
 681   public void startupFileTextfield_mouseClicked()
 682   {
 683     JalviewFileChooser chooser = new JalviewFileChooser(
 684             jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[] {
 685                 "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",
 686                 "jar" }, new String[] { "Fasta", "Clustal", "PFAM", "MSF",
 687                 "PIR", "BLC", "Jalview" },
 688             jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));
 689     chooser.setFileView(new JalviewFileView());
 690     chooser.setDialogTitle(MessageManager
 691             .getString("label.select_startup_file"));
 692
 693     int value = chooser.showOpenDialog(this);
 694
 695     if (value == JalviewFileChooser.APPROVE_OPTION)
 696     {
 697       jalview.bin.Cache.applicationProperties.setProperty(
 698               "DEFAULT_FILE_FORMAT", chooser.getSelectedFormat());
 699       startupFileTextfield.setText(chooser.getSelectedFile()
 700               .getAbsolutePath());
 701     }
 702   }
 703
 704   /**
 705    * DOCUMENT ME!
 706    *
 707    * @param e
 708    *          DOCUMENT ME!
 709    */
 710   @Override
 711   public void cancel_actionPerformed(ActionEvent e)
 712   {
 713     try
 714     {
 715       wsPrefs.updateWsMenuConfig(true);
 716       wsPrefs.refreshWs_actionPerformed(e);
 717       frame.setClosed(true);
 718     } catch (Exception ex)
 719     {
 720     }
 721   }
 722
 723   /**
 724    * DOCUMENT ME!
 725    *
 726    * @param e
 727    *          DOCUMENT ME!
 728    */
 729   @Override
 730   public void annotations_actionPerformed(ActionEvent e)
 731   {
 732     conservation.setEnabled(annotations.isSelected());
 733     quality.setEnabled(annotations.isSelected());
 734     identity.setEnabled(annotations.isSelected());
 735     showGroupConsensus.setEnabled(annotations.isSelected());
 736     showGroupConservation.setEnabled(annotations.isSelected());
 737     showConsensHistogram.setEnabled(annotations.isSelected()
 738             && (identity.isSelected() || showGroupConsensus.isSelected()));
 739     showConsensLogo.setEnabled(annotations.isSelected()
 740             && (identity.isSelected() || showGroupConsensus.isSelected()));
 741   }
 742
 743   @Override
 744   public void newLink_actionPerformed(ActionEvent e)
 745   {
 746
 747     GSequenceLink link = new GSequenceLink();
 748     boolean valid = false;
 749     while (!valid)
 750     {
 751       if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 752               MessageManager.getString("label.new_sequence_url_link"),
 753               JOptionPane.OK_CANCEL_OPTION, -1, null) == JOptionPane.OK_OPTION)
 754       {
 755         if (link.checkValid())
 756         {
 757           nameLinks.addElement(link.getName());
 758           urlLinks.addElement(link.getURL());
 759           updateLinkData();
 760           valid = true;
 761         }
 762       }
 763       else
 764       {
 765         break;
 766       }
 767     }
 768   }
 769
 770   @Override
 771   public void editLink_actionPerformed(ActionEvent e)
 772   {
 773     GSequenceLink link = new GSequenceLink();
 774
 775     int index = linkNameList.getSelectedIndex();
 776     if (index == -1)
 777     {
 778       JOptionPane.showInternalMessageDialog(Desktop.desktop,
 779               MessageManager.getString("label.no_link_selected"),
 780               MessageManager.getString("label.no_link_selected"),
 781               JOptionPane.WARNING_MESSAGE);
 782       return;
 783     }
 784
 785     link.setName(nameLinks.elementAt(index).toString());
 786     link.setURL(urlLinks.elementAt(index).toString());
 787
 788     boolean valid = false;
 789     while (!valid)
 790     {
 791
 792       if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 793               MessageManager.getString("label.new_sequence_url_link"),
 794               JOptionPane.OK_CANCEL_OPTION, -1, null) == JOptionPane.OK_OPTION)
 795       {
 796         if (link.checkValid())
 797         {
 798           nameLinks.setElementAt(link.getName(), index);
 799           urlLinks.setElementAt(link.getURL(), index);
 800           updateLinkData();
 801           valid = true;
 802         }
 803       }
 804
 805       else
 806       {
 807         break;
 808       }
 809     }
 810   }
 811
 812   @Override
 813   public void deleteLink_actionPerformed(ActionEvent e)
 814   {
 815     int index = linkNameList.getSelectedIndex();
 816     if (index == -1)
 817     {
 818       JOptionPane.showInternalMessageDialog(Desktop.desktop,
 819               MessageManager.getString("label.no_link_selected"),
 820               MessageManager.getString("label.no_link_selected"),
 821               JOptionPane.WARNING_MESSAGE);
 822       return;
 823     }
 824     nameLinks.removeElementAt(index);
 825     urlLinks.removeElementAt(index);
 826     updateLinkData();
 827   }
 828
 829   void updateLinkData()
 830   {
 831     linkNameList.setListData(nameLinks);
 832     linkURLList.setListData(urlLinks);
 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 }